@phdthesis{14510, abstract = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment control of protein regulators for vesicle maturation and release. During the early stages of endocytosis, an area of flat membrane is remodelled by proteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated vesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane, and cargo proceeds for recycling or degradation through early endosomes / Trans Golgi network. Protein machineries that mediate membrane bending and vesicle release in plants are unknown. However, studies show, that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced live microscopy approaches we investigate the TPLATE complex, a plant-specific endocytosis protein complex. We found that TPLATE is peripherally associated with clathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of plant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a role in vesicle release, shows the recruitment of the protein already at the early stages of endocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to induce membrane deformation and tubulation, suggesting its role also in membrane bending during early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle scission machinery; however, their precise role in plant CME has not been yet elucidated. Here, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution imaging of endocytic events in vivo and protein characterisation. Although DRP2s and SH3P2 arrive together during late CME and physically interact, genetic analysis using ∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest that SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our research, these observations provide new important insights into the mechanism of plant CME and show that, despite plants posses many homologues of mammalian and yeast CME components, they do not necessarily act in the same manner. }, author = {Gnyliukh, Nataliia}, isbn = {978-3-99078-037-4}, issn = {2663-337X}, keywords = {Clathrin-Mediated Endocytosis, vesicle scission, Dynamin-Related Protein 2, SH3P2, TPLATE complex, Total internal reflection fluorescence microscopy, Arabidopsis thaliana}, pages = {180}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanism of clathrin-coated vesicle formation during endocytosis in plants}}, doi = {10.15479/at:ista:14510}, 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{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{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{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{12072, abstract = {In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm form associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations. In the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or integral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points. More precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in the power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. }, author = {Shute, Alec L}, isbn = {978-3-99078-023-7}, issn = {2663-337X}, pages = {208}, publisher = {Institute of Science and Technology Austria}, title = {{Existence and density problems in Diophantine geometry: From norm forms to Campana points}}, doi = {10.15479/at:ista:12072}, year = {2022}, } @phdthesis{12368, abstract = {Metazoan development relies on the formation and remodeling of cell-cell contacts. The binding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell interaction sites have been implicated in cell-cell contact formation. Yet, how these two processes functionally interact to drive cell-cell contact expansion and strengthening remains unclear. Here, we study how primary germ layer progenitor cells from zebrafish bind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an assay system for monitoring cell-cell contact formation at high spatiotemporal resolution. We show that cell-cell contact formation represents a two-tiered process: E-cadherinmediated downregulation of the small GTPase RhoA at the forming contact leads to both depletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin network flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the contact zone, with Myosin-2 displaying higher cortical localization outside than inside of the contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin network at the contact disc, but also lead to an accumulation of both F-actin and Ecadherin at the contact rim. Eventually, this combination of actomyosin downregulation and flows at the contact contribute to the characteristic molecular organization implicated in contact formation and maintenance: depletion of cortical actomyosin at the contact disc, driving contact expansion by lowering interfacial tension at the contact, and accumulation of both E-cadherin and F-actin at the contact rim, mechanically linking the contractile cortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how adhesion signaling and cell mechanics function together to modulate the spatial organization of cell-cell contacts.}, author = {Arslan, Feyza N}, isbn = {978-3-99078-025-1 }, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Remodeling of E-cadherin-mediated contacts via cortical flows}}, doi = {10.15479/at:ista:12153}, 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{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{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}, } @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{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{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{12390, abstract = {The scope of this thesis is to study quantum systems exhibiting a continuous symmetry that is broken on the level of the corresponding effective theory. In particular we are going to investigate translation-invariant Bose gases in the mean field limit, effectively described by the Hartree functional, and the Fröhlich Polaron in the regime of strong coupling, effectively described by the Pekar functional. The latter is a model describing the interaction between a charged particle and the optical modes of a polar crystal. Regarding the former, we assume in addition that the particles in the gas are unconfined, and typically we will consider particles that are subject to an attractive interaction. In both cases the ground state energy of the Hamiltonian is not a proper eigenvalue due to the underlying translation-invariance, while on the contrary there exists a whole invariant orbit of minimizers for the corresponding effective functionals. Both, the absence of proper eigenstates and the broken symmetry of the effective theory, make the study significantly more involved and it is the content of this thesis to develop a frameworks which allows for a systematic way to circumvent these issues. It is a well-established result that the ground state energy of Bose gases in the mean field limit, as well as the ground state energy of the Fröhlich Polaron in the regime of strong coupling, is to leading order given by the minimal energy of the corresponding effective theory. As part of this thesis we identify the sub-leading term in the expansion of the ground state energy, which can be interpreted as the quantum correction to the classical energy, since the effective theories under consideration can be seen as classical counterparts. We are further going to establish an asymptotic expression for the energy-momentum relation of the Fröhlich Polaron in the strong coupling limit. In the regime of suitably small momenta, this asymptotic expression agrees with the energy-momentum relation of a free particle having an effectively increased mass, and we find that this effectively increased mass agrees with the conjectured value in the physics literature. In addition we will discuss two unrelated papers written by the author during his stay at ISTA in the appendix. The first one concerns the realization of anyons, which are quasi-particles acquiring a non-trivial phase under the exchange of two particles, as molecular impurities. The second one provides a classification of those vector fields defined on a given manifold that can be written as the gradient of a given functional with respect to a suitable metric, provided that some mild smoothness assumptions hold. This classification is subsequently used to identify those quantum Markov semigroups that can be written as a gradient flow of the relative entropy. }, author = {Brooks, Morris}, issn = {2663-337X}, pages = {196}, publisher = {Institute of Science and Technology Austria}, title = {{Translation-invariant quantum systems with effectively broken symmetry}}, doi = {10.15479/at:ista:12390}, year = {2022}, } @phdthesis{12358, abstract = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and visual complexity. The small-scale interactions of yarns colliding with and pulling on each other result in drastically different large-scale stretching and bending behavior, introducing anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this complexity and match the quality of real fabric, it may be too computationally expensive for large fabrics. On the other hand, continuum-based approaches do not need to discretize the cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis, we discuss three methods to try and bridge the gap between small-scale and large-scale yarn mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively fitting yarn parameters to physical measurements of real fabric. To start, we present a method for animating yarn-level cloth effects using a thin-shell solver. We first use a large number of periodic yarn-level simulations to build a model of the potential energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of full yarn-level simulation. While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching at negligible cost. Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth, based on the mechanical response of fabrics in the real world. We compile a database from physical tests of several knitted fabrics used in the textile industry spanning diverse physical properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized shell models to speed up computation and adding some small-but-necessary extensions to yarn-level models used in computer graphics. }, author = {Sperl, Georg}, isbn = {978-3-99078-020-6}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}}, doi = {10.15479/at:ista:12103}, year = {2022}, } @phdthesis{11196, abstract = {One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). In addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level. }, author = {Kim, Olena}, issn = {2663-337X}, pages = {132}, publisher = {Institute of Science and Technology Austria}, title = {{Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses}}, doi = {10.15479/at:ista:11196}, year = {2022}, } @phdthesis{10727, abstract = {Social insects are a common model to study disease dynamics in social animals. Even though pathogens should thrive in social insect colonies as the hosts engage in frequent social interactions, are closely related and live in a pathogen-rich environment, disease outbreaks are rare. This is because social insects have evolved mechanisms to keep pathogens at bay – and fight disease as a collective. Social insect colonies are often viewed as “superorganisms” with division of labor between reproductive “germ-like” queens and males and “somatic” workers, which together form an interdependent reproductive unit that parallels a multicellular body. Superorganisms possess a “social immune system” that comprises of collective disease defenses performed by the workers - summarized as “social immunity”. In social groups immunization (reduced susceptibility to a parasite upon secondary exposure to the same parasite) can e.g. be triggered by social interactions (“social immunization”). Social immunization can be caused by (i) asymptomatic low-level infections that are acquired during caregiving to a contagious individual that can give an immune boost, which can induce protection upon later encounter with the same pathogen (active immunization) or (ii) by transfer of immune effectors between individuals (passive immunization). In the second chapter, I built up on a study that I co-authored that found that low-level infections can not only be protective, but also be costly and make the host more susceptible to detrimental superinfections after contact to a very dissimilar pathogen. I here now tested different degrees of phylogenetically-distant fungal strains of M. brunneum and M. robertsii in L. neglectus and can describe the occurrence of cross-protection of social immunization if the first and second pathogen are from the same level. Interestingly, low-level infections only provided protection when the first strain was less virulent than the second strain and elicited higher immune gene expression. In the third and fourth chapters, I expanded on the role of social immunity in sexual selection, a so far unstudied field. I used the fungus Metarhizium robertsii and the ant Cardiocondyla obscurior as a model, as in this species mating occurs in the presence of workers and can be studied under laboratory conditions. Before males mate with virgin queens in the nest they engage in fierce combat over the access to their mating partners. First, I focused on male-male competition in the third chapter and found that fighting with a contagious male is costly as it can lead to contamination of the rival, but that workers can decrease the risk of disease contraction by performing sanitary care. In the fourth chapter, I studied the effect of fungal infection on survival and mating success of sexuals (freshly emerged queens and males) and found that worker-performed sanitary care can buffer the negative effect that a pathogenic contagion would have on sexuals by spore removal from the exposed individuals. When social immunity was prevented and queens could contract spores from their mating partner, very low dosages led to negative consequences: their lifespan was reduced and they produced fewer offspring with poor immunocompetence compared to healthy queens. Interestingly, cohabitation with a late-stage infected male where no spore transfer was possible had a positive effect on offspring immunity – male offspring of mothers that apparently perceived an infected partner in their vicinity reacted more sensitively to fungal challenge than male offspring without paternal pathogen history.}, author = {Metzler, Sina}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Pathogen-mediated sexual selection and immunization in ant colonies}}, doi = {10.15479/AT:ISTA:10727}, year = {2022}, } @phdthesis{11879, abstract = {As the overall global mean surface temperature is increasing due to climate change, plant adaptation to those stressful conditions is of utmost importance for their survival. Plants are sessile organisms, thus to compensate for their lack of mobility, they evolved a variety of mechanisms enabling them to flexibly adjust their physiological, growth and developmental processes to fluctuating temperatures and to survive in harsh environments. While these unique adaptation abilities provide an important evolutionary advantage, overall modulation of plant growth and developmental program due to non-optimal temperature negatively affects biomass production, crop productivity or sensitivity to pathogens. Thus, understanding molecular processes underlying plant adaptation to increased temperature can provide important resources for breeding strategies to ensure sufficient agricultural food production. An increase in ambient temperature by a few degrees leads to profound changes in organ growth including enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and cotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin, one of the best-studied growth hormones, plays an essential role in this process by direct activation of transcriptional and non-transcriptional processes resulting in elongation growth (Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature (hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key components of the polar auxin transport (PAT) machinery, which controls the amount and direction of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence, PIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT through either chemical or genetic means dramatically affecting the adaptive responses to hAT. Intriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether and how PINs at the level of expression adapt to fluctuation in temperature is scarcely understood. With genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN auxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via adjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we identified three Zinc-Finger (ZF) transcription factors as novel molecular components of the thermo-regulatory network, which through negative regulation of PIN transcription adjust the transport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the negative feedback loop attenuating the activity of the thermo-sensing pathway to restrain exaggerated growth and developmental responses to hAT.}, author = {Artner, Christina}, isbn = {978-3-99078-022-0}, issn = {2663-337X}, keywords = {high ambient temperature, auxin, PINs, Zinc-Finger proteins, thermomorphogenesis, stress}, pages = {128}, publisher = {Institute of Science and Technology Austria}, title = {{Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature}}, doi = {10.15479/at:ista:11879}, year = {2022}, } @phdthesis{12364, abstract = {Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders characterized by behavioral symptoms such as problems in social communication and interaction, as well as repetitive, restricted behaviors and interests. These disorders show a high degree of heritability and hundreds of risk genes have been identifed using high throughput sequencing technologies. This genetic heterogeneity has hampered eforts in understanding the pathogenesis of ASD but at the same time given rise to the concept of convergent mechanisms. Previous studies have identifed that risk genes for ASD broadly converge onto specifc functional categories with transcriptional regulation being one of the biggest groups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory consequences of some of them in the context of neurodevelopment. First, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead to perturbations of gene regulatory programs in early cell fate specifcation. In addition, adult animals display abnormal learning behavior which is mirrored at the transcriptional level by altered activity dependent regulation of postsynaptic gene expression. Lastly, we link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR complex. Second, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral organoids we demonstrate profound changes in the developmental trajectories of both inhibitory and excitatory neurons using single cell RNA-sequencing. While the former were generated earlier in CHD8+/- organoids, the generation of the latter was shifted to later times in favor of a prolonged progenitor expansion phase and ultimately increased organoid size. Finally, by modeling heterozygous mutations for four ASD associated chromatin modifers, ASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of regulatory convergence across three of those genes. We observe a shift from dorsal cortical excitatory neuron fates towards partially ventralized cell types resembling cells from the lateral ganglionic eminence. As this project is still ongoing at the time of writing, future experiments will aim at elucidating the regulatory mechanisms underlying this shift with the aim of linking these three ASD risk genes through biological convergence.}, author = {Dotter, Christoph}, issn = {2663-337X}, pages = {152}, publisher = {Institute of Science and Technology Austria}, title = {{Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder}}, doi = {10.15479/at:ista:12094}, year = {2022}, } @phdthesis{11393, abstract = {AMPA receptors (AMPARs) mediate fast excitatory neurotransmission and their role is implicated in complex processes such as learning and memory and various neurological diseases. These receptors are composed of different subunits and the subunit composition can affect channel properties, receptor trafficking and interaction with other associated proteins. Using the high sensitivity SDS-digested freeze-fracture replica labeling (SDS-FRL) for electron microscopy I investigated the number, density, and localization of AMPAR subunits, GluA1, GluA2, GluA3, and GluA1-3 (panAMPA) in pyramidal cells in the CA1 area of mouse hippocampus. I have found that the immunogold labeling for all of these subunits in the postsynaptic sites was highest in stratum radiatum and lowest in stratum lacunosummoleculare. The labeling density for the all subunits in the extrasynaptic sites showed a gradual increase from the pyramidal cell soma towards the distal part of stratum radiatum. The densities of extrasynaptic GluA1, GluA2 and panAMPA labeling reached 10-15% of synaptic densities, while the ratio of extrasynaptic labeling for GluA3 was significantly lower compared than those for other subunits. The labeling patterns for GluA1, GluA2 and GluA1-3 are similar and their densities were higher in the periphery than center of synapses. In contrast, the GluA3- containing receptors were more centrally localized compared to the GluA1- and GluA2- containing receptors. The hippocampus plays a central role in learning and memory. Contextual learning has been shown to require the delivery of AMPA receptors to CA1 synapses in the dorsal hippocampus. However, proximodistal heterogeneity of this plasticity and particular contribution of different AMPA receptor subunits are not fully understood. By combining inhibitory avoidance task, a hippocampus-dependent contextual fear-learning paradigm, with SDS-FRL, I have revealed an increase in synaptic density specific to GluA1-containing AMPA receptors in the CA1 area. The intrasynaptic distribution of GluA1 also changed from the periphery to center-preferred pattern. Furthermore, this synaptic plasticity was evident selectively in stratum radiatum but not stratum oriens, and in the CA1 subregion proximal but not distal to CA2. These findings further contribute to our understanding of how specific hippocampal subregions and AMPA receptor subunits are involved in physiological learning. Although the immunolabeling results above shed light on subunit-specific plasticity in AMPAR distribution, no tools to visualize and study the subunit composition at the single channel level in situ have been available. Electron microscopy with conventional immunogold labeling approaches has limitations in the single channel analysis because of the large size of antibodies and steric hindrance hampering multiple subunit labeling of single channels. I managed to develop a new chemical labeling system using a short peptide tag and small synthetic probes, which form specific covalent bond with a cysteine residue in the tag fused to proteins of interest (reactive tag system). I additionally made substantial progress into adapting this system for AMPA receptor subunits.}, author = {Jevtic, Marijo}, issn = {2663-337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{Contextual fear learning induced changes in AMPA receptor subtypes along the proximodistal axis in dorsal hippocampus}}, doi = {10.15479/at:ista:11393}, year = {2022}, }