@phdthesis{14697,
  abstract     = {During my Ph.D. research, I managed a series of projects, each focused on the
mechanisms underlying cell migration. My work involved an in-depth examination of
the complex strategies employed by neutrophils, with a specific focus on their ability to
synchronize spatial-temporal cues and optimize their gradient perception. However, it
is essential to acknowledge that not all projects yielded successful results, as some
ideas were discontinued and are archived for future reference within this thesis.
My main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source
type – linear or point-like. By combining single-cell tracking in 3D environments with
proxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger
response to semi-exponential gradients from point sources. In addition, neutrophils
exhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over
time and employed a "Run and Fumble" strategy, alternating between consistent runs
and strategic "tumbles" for efficient navigation.
The project extended to the possibility of cells amplifying perceived gradients by
enclosing their immediate surroundings, pushing attractants forward for enrichment
while depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences
in migratory efficacy were detected across pore sizes and device heights, quantifying
gradient manipulation effects proved challenging.
The "Laser-Assisted Protein Adsorption by Photobleaching" (LAPAP) project was
promising, as it allowed the printing of gradients. Initially successful with dendritic cells,
we aimed to adapt it for neutrophils. Through extensive experimentation with multiple
parameters, we attempted to trigger responses from neutrophils. Despite these efforts
and collaboration, the project failed due to practical challenges and limitations.
Facing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8
primary murine cell line. Despite their existence, their migratory behavior was largely
unexplored due to potential limitations. Through differentiation protocol refinements we
enhanced their migratory capabilities, though their capacity still lagged behind human
neutrophils. Despite this, the improved migration potential of these cells pointed toward
their utility for in vitro murine neutrophil migration studies.},
  author       = {Stopp, Julian A},
  isbn         = {978-3-99078-038-1},
  issn         = {2663-337X},
  pages        = {226},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function}},
  doi          = {10.15479/at:ista:14697},
  year         = {2023},
}

@phdthesis{12470,
  abstract     = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of 
connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is 
pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of 
nm-small synapses.
To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across 
Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular
space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse 
identification.
I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue 
architecture, neuronal in- and output-fields, down to synapse morphology.
Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy 
fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 
pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal 
connectivity with light microscopy.},
  author       = {Michalska, Julia M},
  isbn         = {978-3-99078-026-8},
  issn         = {2663-337X},
  pages        = {201},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}},
  doi          = {10.15479/at:ista:12470},
  year         = {2023},
}

@phdthesis{12491,
  abstract     = {The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. 
Despite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. 
In this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). 
To this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. 
In order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. 
High-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. 
In summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions.},
  author       = {Zens, Bettina},
  isbn         = {978-3-99078-027-5},
  issn         = {2663-337X},
  keywords     = {cryo-EM, cryo-ET, FIB milling, method development, FIBSEM, extracellular matrix, ECM, cell-derived matrices, CDMs, cell culture, high pressure freezing, HPF, structural biology, tomography, collagen},
  pages        = {187},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography}},
  doi          = {10.15479/at:ista:12491},
  year         = {2023},
}

@phdthesis{12809,
  abstract     = {Understanding the mechanisms of learning and memory formation has always been one of
the main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic
conditioning experiments to study the neural mechanisms governing behavioral adaptation.
What was not known back then was that the part of the brain that is largely responsible for
this type of associative learning is the cerebellum.
Since then, plenty of theories on cerebellar learning have emerged. Despite their differences,
one thing they all have in common is that learning relies on synaptic and intrinsic plasticity.
The goal of my PhD project was to unravel the molecular mechanisms underlying synaptic
plasticity in two synapses that have been shown to be implicated in motor learning, in an
effort to understand how learning and memory formation are processed in the cerebellum.
One of the earliest and most well-known cerebellar theories postulates that motor learning
largely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.
However, the discovery of other types of plasticity in the cerebellar circuitry, like long-term
potentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),
and plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the
popularity of the idea that multiple sites of plasticity might be involved in learning.
Still a lot remains unknown about the molecular mechanisms responsible for these types of
plasticity and whether they occur during physiological learning.
In the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid
type glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC
LTP. We have found that on the last day of adaptation there is no learning trace in form of
VGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of
PF-PC synapses. These data seem to support the view that learning is only stored in the
cerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.
Next, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We
have found behavior-induced MLI potentiation in form of release probability increase that
could be explained by the increase of VGCCs at the presynaptic side. Our results strengthen
the idea of distributed cerebellar plasticity contributing to learning and provide a novel
mechanism for release probability increase. },
  author       = {Alcarva, Catarina},
  issn         = {2663-337X},
  pages        = {115},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning}},
  doi          = {10.15479/at:ista:12809},
  year         = {2023},
}

@phdthesis{12781,
  abstract     = {Most energy in humans is produced in form of ATP by the mitochondrial respiratory chain consisting of several protein assemblies embedded into lipid membrane (complexes I-V). Complex I is the first and the largest enzyme of the respiratory chain which is essential for energy production. It couples the transfer of two electrons from NADH to ubiquinone with proton translocation across bacterial or inner mitochondrial membrane. The coupling mechanism between electron transfer and proton translocation is one of the biggest enigma in bioenergetics and structural biology. Even though the enzyme has been studied for decades, only recent technological advances in cryo-EM allowed its extensive structural investigation. 

Complex I from E.coli appears to be of special importance because it is a perfect model system with a rich mutant library, however the structure of the entire complex was unknown. In this thesis I have resolved structures of the minimal complex I version from E. coli in different states including reduced, inhibited, under reaction turnover and several others. Extensive structural analyses of these structures and comparison to structures from other species allowed to derive general features of conformational dynamics and propose a universal coupling mechanism. The mechanism is straightforward, robust and consistent with decades of experimental data available for complex I from different species. 

Cyanobacterial NDH (cyanobacterial complex I) is a part of broad complex I superfamily and was studied as well in this thesis. It plays an important role in cyclic electron transfer (CET), during which electrons are cycled within PSI through ferredoxin and plastoquinone to generate proton gradient without NADPH production. Here, I solved structure of NDH and revealed additional state, which was not observed before. The novel “resting” state allowed to propose the mechanism of CET regulation. Moreover, conformational dynamics of NDH resembles one in complex I which suggest more broad universality of the proposed coupling mechanism.

In summary, results presented here helped to interpret decades of experimental data for complex I and contributed to fundamental mechanistic understanding of protein function.
},
  author       = {Kravchuk, Vladyslav},
  isbn         = {978-3-99078-029-9},
  issn         = {2663-337X},
  pages        = {127},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Structural and mechanistic study of bacterial complex I and its cyanobacterial ortholog}},
  doi          = {10.15479/at:ista:12781},
  year         = {2023},
}

@phdthesis{12964,
  abstract     = {Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are
established to determine cell fate and complex tissue patterns emerge to define structures such
as limbs and vascular networks. Patterns are also seen in collectively migrating groups, for
instance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through
the local interaction of individual constituents or are dictated by higher level instructions is
still an open question however there is evidence for the involvement of both types of process.
Where patterns arise spontaneously there is a long standing interest in how far the interplay
of mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation
and signaling, contributes to the behaviour. This is because many systems are able to both
chemically regulate mechanical force production and chemically sense mechanical deformation,
forming mechano-chemical feedback loops which can potentially become unstable towards
spatio and/or temporal patterning.
We work with experimental collaborators to investigate the possibility that this type of
interaction drives pattern formation in biological systems at different scales. We focus first on
tissue-level ERK-density waves observed during the wound healing response across different
systems where many previous studies have proposed that patterns depend on polarized cell
migration and arise from a mechanical flocking-like mechanism. By combining theory with
mechanical and optogenetic perturbation experiments on in vitro monolayers we instead find
evidence for mechanochemical pattern formation involving only scalar bilateral feedbacks
between ERK signaling and cell contraction. We perform further modeling and experiment
to study how this instability couples with polar cell migration in order to produce a robust
and efficient wound healing response. In a following chapter we implement ERK-density
coupling and cell migration in a 2D active vertex model to investigate the interaction of
ERK-density patterning with different tissue rheologies and find that the spatio-temporal
dynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass
transition. In a last chapter we move towards lower spatial scales in the context of subcellular
patterning of the cell cytoskeleton where we investigate the transition between phases of
spatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the
dynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton
and its activator). Experimental evidence supports an intrinsic chemical oscillator which we
encode in a reaction model and couple to a contractile active gel description of the cell cortex.
The model exhibits phases of chemical oscillations and contractile spatial patterning which
reproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However,
additional pharmacological perturbations to inhibit myosin contractility leaves the role of
contractile instability unclear. We discuss alternative hypotheses and investigate the possibility
of reaction-diffusion instability.},
  author       = {Boocock, Daniel R},
  isbn         = {978-3-99078-032-9},
  issn         = {2663-337X},
  pages        = {146},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mechanochemical pattern formation across biological scales}},
  doi          = {10.15479/at:ista:12964},
  year         = {2023},
}

@phdthesis{12897,
  abstract     = {Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations.

The first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics.

We show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. 

The second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.},
  author       = {Hafner, Christian},
  isbn         = {978-3-99078-031-2},
  issn         = {2663-337X},
  pages        = {180},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models}},
  doi          = {10.15479/at:ista:12897},
  year         = {2023},
}

@phdthesis{12891,
  abstract     = {The tight spatiotemporal coordination of signaling activity determining embryo
patterning and the physical processes driving embryo morphogenesis renders
embryonic development robust, such that key developmental processes can unfold
relatively normally even outside of the full embryonic context. For instance, embryonic
stem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry
leading to germ layer formation and morphogenesis, in a very reduced environment.
This leads to questions on specific contributions of embryo-specific features, such as
the presence of extraembryonic tissues, which are inherently involved in gastrulation
in the full embryonic context. To address this, we established zebrafish embryonic
explants without the extraembryonic yolk cell, an important player as a signaling
source and for morphogenesis during gastrulation, as a model of ex vivo development.
We found that dorsal-marginal determinants are required and sufficient in these
explants to form and pattern all three germ layers. However, formation of tissues,
which require the highest Nodal-signaling levels, is variable, demonstrating a
contribution of extraembryonic tissues for reaching peak Nodal signaling levels.
Blastoderm explants also undergo gastrulation-like axis elongation. We found that this
elongation movement shows hallmarks of oriented mesendoderm cell intercalations
typically associated with dorsal tissues in the intact embryo. These are disrupted by
uniform upregulation of BMP signaling activity and concomitant explant ventralization,
suggesting that tight spatial control of BMP signaling is a prerequisite for explant
morphogenesis. This control is achieved by Nodal signaling, which is critical for
effectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal
signaling is not only directly required for mesendoderm cell fate specification and
morphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side.
Collectively, we provide insights into the capacity and organization of signaling and
morphogenetic domains to recapitulate features of zebrafish gastrulation outside of
the full embryonic context.},
  author       = {Schauer, Alexandra},
  issn         = {2663-337X},
  pages        = {190},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues}},
  doi          = {10.15479/at:ista:12891},
  year         = {2023},
}

@phdthesis{13984,
  abstract     = {Social insects fight disease using their individual immune systems and the cooperative
sanitary behaviors of colony members. These social defenses are well explored against
externally-infecting pathogens, but little is known about defense strategies against
internally-infecting pathogens, such as viruses. Viruses are ubiquitous and in the last decades
it has become evident that also many ant species harbor viruses. We present one of the first
studies addressing transmission dynamics and collective disease defenses against viruses in
ants on a mechanistic level. I successfully established an experimental ant host – viral
pathogen system as a model for the defense strategies used by social insects against internal
pathogen infections, as outlined in the third chapter. In particular, we studied how garden ants
(Lasius neglectus) defend themselves and their colonies against the generalist insect virus
CrPV (cricket paralysis virus). We chose microinjections of virus directly into the ants’
hemolymph because it allowed us to use a defined exposure dose. Here we show that this is a
good model system, as the virus is replicating and thus infecting the host. The ants mount a
clear individual immune response against the viral infection, which is characterized by a
specific siRNA pattern, namely siRNAs mapping against the viral genome with a peak of 21
and 22 bp long fragments. The onset of this immune response is consistent with the timeline
of viral replication that starts already within two days post injection. The disease manifests in
decreased survival over a course of two to three weeks.
Regarding group living, we find that infected ants show a strong individual immune response,
but that their course of disease is little affected by nestmate presence, as described in chapter
four. Hence, we do not find social immunity in the context of viral infections in ants.
Nestmates, however, can contract the virus. Using Drosophila S2R+ cells in culture, we
showed that 94 % of the nestmates contract active virus within four days of social contact to
an infected individual. Virus is transmitted in low doses, thus not causing disease
transmission within the colony. While virus can be transmitted during short direct contacts,
we also assume transmission from deceased ants and show that the nestmates’ immune
system gets activated after contracting a low viral dose. We find considerable potential for
indirect transmission via the nest space. Virus is shed to the nest, where it stays viable for one
week and is also picked up by other ants. Apart from that, we want to underline the potential
of ant poison as antiviral agent. We determined that ant poison successfully inactivates CrPV
in vitro. However, we found no evidence for effective poison use to sanitize the nest space.
On the other hand, local application of ant poison by oral poison uptake, which is part of the
ants prophylactic behavioral repertoire, probably contributes to keeping the gut of each
individual sanitized. We hypothesize that oral poison uptake might be the reason why we did
not find viable virus in the trophallactic fluid.
The fifth chapter encompasses preliminary data on potential social immunization. However,
our experiments do not confirm an actual survival benefit for the nestmates upon pathogen
challenge under the given experimental settings. Nevertheless, we do not want to rule out the
possibility for nestmate immunization, but rather emphasize that considering different
experimental timelines and viral doses would provide a multitude of options for follow-up
experiments.
In conclusion, we find that prophylactic individual behaviors, such as oral poison uptake,
might play a role in preventing viral disease transmission. Compared to colony defense
against external pathogens, internal pathogen infections require a stronger component of
individual physiological immunity than behavioral social immunity, yet could still lead to
collective protection.},
  author       = {Franschitz, Anna},
  isbn         = {978-3-99078-034-3},
  issn         = {2663-337X},
  pages        = {89},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Individual and social immunity against viral infections in ants}},
  doi          = {10.15479/at:ista:13984},
  year         = {2023},
}

@phdthesis{13081,
  abstract     = {During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling.  Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.},
  author       = {Bocanegra, Laura},
  issn         = {2663-337X},
  pages        = {93},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Epithelial dynamics during mouse neural tube development}},
  doi          = {10.15479/at:ista:13081},
  year         = {2023},
}

@phdthesis{14280,
  abstract     = {Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. 
A previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?
We found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. 
Following up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. 
We propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation.},
  author       = {Radler, Philipp},
  isbn         = {978-3-99078-033-6},
  issn         = {2663-337X},
  keywords     = {Cell Division, Reconstitution, FtsZ, FtsA, Divisome, E.coli},
  pages        = {156},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Spatiotemporal signaling during assembly of the bacterial divisome}},
  doi          = {10.15479/at:ista:14280},
  year         = {2023},
}

@phdthesis{14422,
  abstract     = {Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of
changes in the brain throughout adulthood, regrouped under the term "plasticity". Some cells
in the brain —neurons— and specifically changes in the connections between neurons, the
synapses, were shown to be crucial for the formation, selection, and consolidation of memories
from past experiences. These ongoing changes of synapses across time are called synaptic
plasticity. Understanding how a myriad of biochemical processes operating at individual
synapses can somehow work in concert to give rise to meaningful changes in behavior is a
fascinating problem and an active area of research.
However, the experimental search for the precise plasticity mechanisms at play in the brain
is daunting, as it is difficult to control and observe synapses during learning. Theoretical
approaches have thus been the default method to probe the plasticity-behavior connection. Such
studies attempt to extract unifying principles across synapses and model all observed synaptic
changes using plasticity rules: equations that govern the evolution of synaptic strengths across
time in neuronal network models. These rules can use many relevant quantities to determine
the magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic
action potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.
However, analytical studies rely heavily on human intuition and are forced to make simplifying
assumptions about plasticity rules.
In this thesis, we aim to assist and augment human intuition in this search for plasticity rules.
We explore whether a numerical approach could automatically discover the plasticity rules
that elicit desired behaviors in large networks of interconnected neurons. This approach is
dubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make
neuronal networks learn how to solve a desired task. We first write all the potential plasticity
mechanisms to consider using a single expression with adjustable parameters. We then optimize
these plasticity parameters using evolutionary strategies or Bayesian inference on tasks known
to involve synaptic plasticity, such as familiarity detection and network stabilization.
We show that these automated approaches are powerful tools, able to complement established
analytical methods. By comprehensively screening plasticity rules at all synapse types in
realistic, spiking neuronal network models, we discover entire sets of degenerate plausible
plasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more
robust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity
rules, and provide fresh insights on synaptic plasticity in spiking network models.
},
  author       = {Confavreux, Basile J},
  issn         = {2663-337X},
  pages        = {148},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Synapseek: Meta-learning synaptic plasticity rules}},
  doi          = {10.15479/at:ista:14422},
  year         = {2023},
}

@phdthesis{14323,
  abstract     = {Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.},
  author       = {Kuzmicz-Kowalska, Katarzyna},
  issn         = {2663-337X},
  pages        = {151},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord}},
  doi          = {10.15479/at:ista:14323},
  year         = {2023},
}

@phdthesis{10759,
  abstract     = {In this Thesis, I study composite quantum impurities with variational techniques, both inspired by machine learning as well as fully analytic. I supplement this with exploration of other applications of machine learning, in particular artificial neural networks, in many-body physics. In Chapters 3 and 4, I study quasiparticle systems with variational approach. I derive a Hamiltonian describing the angulon quasiparticle in the presence of a magnetic field. I apply analytic variational treatment to this Hamiltonian. Then, I introduce a variational approach for non-additive systems, based on artificial neural networks. I exemplify this approach on the example of the polaron quasiparticle (Fröhlich Hamiltonian). In Chapter 5, I continue using artificial neural networks, albeit in a different setting. I apply artificial neural networks to detect phases from snapshots of two types physical systems. Namely, I study Monte Carlo snapshots of multilayer classical spin models as well as molecular dynamics maps of colloidal systems. The main type of networks that I use here are convolutional neural networks, known for their applicability to image data.},
  author       = {Rzadkowski, Wojciech},
  issn         = {2663-337X},
  pages        = {120},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Analytic and machine learning approaches to composite quantum impurities}},
  doi          = {10.15479/at:ista:10759},
  year         = {2022},
}

@phdthesis{10799,
  abstract     = {Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the
sake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range
of training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the
data they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.},
  author       = {Konstantinov, Nikola H},
  isbn         = {978-3-99078-015-2},
  issn         = {2663-337X},
  keywords     = {robustness, fairness, machine learning, PAC learning, adversarial learning},
  pages        = {176},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Robustness and fairness in machine learning}},
  doi          = {10.15479/at:ista:10799},
  year         = {2022},
}

@phdthesis{11128,
  abstract     = {Although we often see studies focusing on simple or even discrete traits in studies of colouration,
the variation of “appearance” phenotypes found in nature is often more complex, continuous
and high-dimensional. Therefore, we developed automated methods suitable for large datasets
of genomes and images, striving to account for their complex nature, while minimising human
bias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and
corresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with
distinctly coloured fowers to improve our understanding of the genetic nature of the fower
colour in our study system.
Firstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in
the main fower colour regulating region. We study colour- and geography-related characteristics
of the estimated haplotypes and how they connect to their relatedness. We show discrepancies
from the expected fower colour distributions given the genotype and identify particular
haplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the
double recessive recombinant and quite surprisingly, we show that haplotypes of the most
frequent parental type are much less variable than others.
Secondly, we introduce our pipeline capable of processing tens of thousands of full fower
images without human interaction and summarising each image into a set of informative scores.
We show the compatibility of these machine-measured fower colour scores with the previously
used manual scores and study impact of external efect on the resulting scores. Finally, we use
the machine-measured fower colour scores to ft and examine a phenotype cline across the
hybrid zone in Planoles using full fower images as opposed to discrete, manual scores and
compare it with the genotypic cline.},
  author       = {Matejovicova, Lenka},
  isbn         = {978-3-99078-016-9},
  issn         = {2663-337X},
  pages        = {112},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Genetic basis of flower colour as a model for adaptive evolution}},
  doi          = {10.15479/at:ista:11128},
  year         = {2022},
}

@phdthesis{11473,
  abstract     = {The polaron model is a basic model of quantum field theory describing a single particle
interacting with a bosonic field. It arises in many physical contexts. We are mostly concerned
with models applicable in the context of an impurity atom in a Bose-Einstein condensate as
well as the problem of electrons moving in polar crystals.
The model has a simple structure in which the interaction of the particle with the field is given
by a term linear in the field’s creation and annihilation operators. In this work, we investigate
the properties of this model by providing rigorous estimates on various energies relevant to the
problem. The estimates are obtained, for the most part, by suitable operator techniques which
constitute the principal mathematical substance of the thesis.
The first application of these techniques is to derive the polaron model rigorously from first
principles, i.e., from a full microscopic quantum-mechanical many-body problem involving an
impurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas
in the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak
interactions as a low-energy effective theory for this problem.
In the second part, we investigate rigorously the ground state of the model at fixed momentum
and for large values of the coupling constant. Qualitatively, the system is expected to display
a transition from the quasi-particle behavior at small momenta, where the dispersion relation
is parabolic and the particle moves through the medium dragging along a cloud of phonons, to
the radiative behavior at larger momenta where the polaron decelerates and emits free phonons.
At the same time, in the strong coupling regime, the bosonic field is expected to behave purely
classically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to
be asymptotically equal to the one obtained from the semiclassical counterpart of the problem,
first studied by Landau and Pekar in the 1940s. For polaron models with regularized form
factors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear
function of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove
that for a large window of momenta below the radiation threshold, the energy-momentum
relation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the
Landau–Pekar effective mass, as expected.
For the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is
of the optical type and the form factor is formally UV–singular due to the nature of the point
charge-dipole interaction, we are able to give the corresponding upper bound. In contrast to
the regular case, this requires the inclusion of the quantum fluctuations of the phonon field,
which makes the problem considerably more difficult.
The results are supplemented by studies on the absolute ground-state energy at strong coupling,
a proof of the divergence of the effective mass with the coupling constant for a wide class of
polaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model
and the application of the techniques used for its removal for the energy estimates.
},
  author       = {Mysliwy, Krzysztof},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Polarons in Bose gases and polar crystals: Some rigorous energy estimates}},
  doi          = {10.15479/at:ista:11473},
  year         = {2022},
}

@phdthesis{11626,
  abstract     = {Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.},
  author       = {Gallei, Michelle C},
  isbn         = {978-3-99078-019-0},
  issn         = {2663-337X},
  pages        = {248},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana}},
  doi          = {10.15479/at:ista:11626},
  year         = {2022},
}

@phdthesis{11777,
  abstract     = {In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications.
Our main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs.
For the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\in \mathbb{N}}$ and $(H_n)_{n\in\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$).
Via the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\mathrm{PGL}_{d+2}(\mathbb{F}_q)$ for any $\varepsilon>0$ and sufficiently large $q=q(\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense.
By improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\mathrm{PGL}_{2}(\mathbb{F}_q)$ is not tight.
In a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.},
  author       = {Wild, Pascal},
  isbn         = {978-3-99078-021-3},
  issn         = {2663-337X},
  pages        = {170},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{High-dimensional expansion and crossing numbers of simplicial complexes}},
  doi          = {10.15479/at:ista:11777},
  year         = {2022},
}

@phdthesis{11945,
  abstract     = {G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.
We validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.
Our DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.},
  author       = {Schulz, Rouven},
  issn         = {2663-337X},
  pages        = {133},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function}},
  doi          = {10.15479/at:ista:11945},
  year         = {2022},
}