@phdthesis{19993, abstract = {Ants are frequently challenged by different pathogens, which they counter with individual and collective responses. Usually, the pathogens like fungi or viruses are solitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These entomopathogenic nematodes are active parasites with an own behavior and chasing pray. In the first chapter, we investigated the basic biology of the host-pathogen relationship. We tested different ant life stages and found that adult ants display defense behaviors and are generally resistant to nematode infection, whereas brood is highly susceptible. In the case of worker pupae, we found a slight protective effect of the cocoon. When larvae are accompanied by adults, meaning a queen or a group of workers, survival is significantly enhanced. Moreover, we found that nematodes can transmit from infected cadavers to healthy worker larvae, confirming a transmissible disease in ants. Again, worker presence significantly reduces transmission risk. In the end, we were also able to disentangle the pathogen system and investigate the pathogenic effect of the bacterial and nematode components. In the second chapter, we studied the effect of multiple infections in adult queens and queen larvae. By multiple exposures in the mode of coinfection and superinfections, we wanted to assess the detrimental effect of combined fungal and nematode exposure to better understand how the pathogens interact with each other in an ant host. We found instances where combined exposure lead to higher mortality in a given time frame in both, adult queens and queen larvae. Overall entomopathogenic nematodes are a promising model to study worm infections in ants which extend our knowledge on collective disease defense.}, author = {Strahodinsky, Florian}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Social immunity in a tri-partite host-pathogen relationship}}, doi = {10.15479/AT-ISTA-19993}, year = {2025}, } @phdthesis{19722, abstract = {As root epidermal cells progress from a phase of elongation to differentiation, their cortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The hormone cytokinin, a key regulator of root development, facilitates these cytoskeletal changes. However, the molecular mechanisms underlying hormone-mediated MT reorientation during root development are still unknown. Here, we find that MT reorientation in root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell differentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s association with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end created by katanin-mediated severing at crossovers. Notably, our findings suggest that dynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning of the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets of cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1 association in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it increases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives MT reorganization during cell development by simultaneously modulating several microtubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool during this process.}, author = {Inumella, Syamala}, isbn = {978-3-99078-059-6}, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of microtubule reorganization in elongating root epidermal cells}}, doi = {10.15479/AT-ISTA-19722}, year = {2025}, } @phdthesis{20470, abstract = {Systems design has classically relied on composable systems, in which individual subsystems have defined inputs, outputs, and interactions with each other; however, attempts at designing complex systems in synthetic biology has often run in to issues of crosstalk and interference, given that these systems must function within the context of the host. In nature, mobile genetic elements are systems that have evolved to travel between hosts, and thus appear to be a good candidate with which to evaluate composability. Selecting temperate phages as a model system, I used mathematical modelling to identify sources of information that temperate phages should respond to. I found that essential proteins of temperate phages can interfere with potential hosts, indicating limitations to composability. I also designed a lysogeny reporter construct and characterize its behavior across various laboratory and environmental strains, finding differences in phage lambda lysogens, and potential interference from prophages that already exist within the environmental strains. Although the information gathered is not conclusive, it suggests that composability is not a key property of temperate phages, implying that biological systems may not be composable, and that other system design principles should be considered when designing synthetic systems.}, author = {Wu, Bryan}, issn = {2663-337X}, pages = {102}, publisher = {Institute of Science and Technology Austria}, title = {{An examination on phages as a naturally composable system}}, doi = {10.15479/AT-ISTA-20470}, year = {2025}, } @phdthesis{20777, abstract = {A major challenge in neuroscience is deciphering how the brain orchestrates behavior in response to changes in environmental conditions. This process is characterized by several processing stages, from perception to the storage of important information. Information storage is performed by a memory system implemented through complex networks of highly interconnected neurons. The collective operational principles of neuronal networks that support formation and storage are the main topics of this thesis. To investigate the collective dynamics of the hippocampus from the perspective of the brain criticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches ¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures derived from neuronal avalanches suggested that during wakefulness the hippocampus operated further away from criticality than during sleep/rest. In addition, neural activity propagated differently in these two brain states, as indicated by different collapses of the avalanche shapes. Next, the Phenomenological Renormalization Group approach also indicated conceptually similar differences, through the scaling exponent of activity variance α, which was higher during sleep/rest than during awake. These results confirmed that the activity of the hippocampus exhibits signatures of criticality and that these signatures change with the state of the brain. Next, I found that memory retention was predicted by the scaling exponent of activity variance α. The exponent α measured during the sleep/rest session that followed learning correlated with memory retention during the subsequent unrewarded testing session. Moreover, α predicted performance even when controlled for reactivation that occurs in parallel. Second, α measured in the sleep/rest phase that preceded learning was correlated with the learning speed. I analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day variability of these distributions, during sleep/rest that followed learning, correlated with the scaling exponent of activity variance α, as well as with memory retention. These findings confirmed that variance scaling and functional heterogeneity provide behaviorally meaningful perspectives on hippocampal activity, as they are directly related to memory consolidation. I further investigated the process of memory acquisition and consolidation between the hippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards the goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals during sleep/rest that followed learning. This shift during sleep/rest was supported by the reactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and independently of the hippocampal SWRs. Both types of reactivation predicted subsequent memory retention, as well as the amount of goal-related remapping. Again, the day-to-day variability of the distribution of the cell timescales correlated with the goal-related remapping, in CA1 during the learning session and in mEC during sleep/rest. These results suggest that in spatial navigation tasks, the functional responsibilities of CA1 and mEC change between learning and sleep/rest and that their function benefits from increased functional heterogeneity among cells. }, author = {Zivadinovic, Predrag}, issn = {2663-337X}, pages = {104}, publisher = {Institute of Science and Technology Austria}, title = {{Scale-free activity as a basis for spatial learning and memory in the brain}}, doi = {10.15479/AT-ISTA-20777}, year = {2025}, } @article{19424, abstract = {Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime is strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors.}, author = {Saez Mollejo, Jaime and Jirovec, Daniel and Schell, Yona A and Kukucka, Josip and Calcaterra, Stefano and Chrastina, Daniel and Isella, Giovanni and Rimbach-Russ, Maximilian and Bosco, Stefano and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Exchange anisotropies in microwave-driven singlet-triplet qubits}}, doi = {10.1038/s41467-025-58969-y}, volume = {16}, year = {2025}, } @phdthesis{19836, abstract = {Over the past century, researchers have been fascinated by the quantum nature of the physical world, initially striving to understand its fundamental principles and consequences, and eventually progressing toward engineering systems that can control and manipulate quantum properties. Today, we stand at the dawn of the quantum technology era. While some quantum technologies follow well-defined roadmaps, others are still in the exciting and uncertain early stages of development. In the fields of quantum computing and quantum simulation, research is being conducted across a wide variety of platforms. Each of these demonstrates control over quantum properties but also faces challenges in scaling up to the level of a mature technology. This thesis explores some of the fundamental properties of hole spin qubits in planar germanium. Semiconductor spin qubits are considered strong candidates for the realization of quantum processors, owing to their long relaxation and coherence times, as well as their compatibility with existing semiconductor industry infrastructure. Among these, hole spin qubits in planar germanium are particularly promising. Their advantages include a large effective mass, which eases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit interaction, which enables fast and purely electrical control. However, spin-orbit coupling also introduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip tunneling, which might cause that the quantization axes are not aligned. In this thesis, we investigate the tilt between the quantization axes of two hole spins hosted in a double quantum dot as a function of both the magnetic field direction and various electrostatic configurations, demonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove to be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the physics governing spin qubit behavior. }, author = {Saez Mollejo, Jaime}, issn = {2663-337X}, pages = {175}, publisher = {Institute of Science and Technology Austria}, title = {{Singlet-triplet qubits in planar Germanium: From exchange anisotropies to autonomous tuning }}, doi = {10.15479/AT-ISTA-19836}, year = {2025}, } @phdthesis{19906, abstract = {Flows of ordinary fluids such as water or air transition from laminar to turbulent motion as the velocity increases. This simple dependence of the flow state solely on inertia, does not apply to more complex substances such as polymericand biofluids which commonly have elastic as well as viscous properties. Here various different instabilities and turbulent states can arise at low and even vanishing inertia, while high inertia turbulence counterintuitively is suppressed and its drag strongly reduced. We here show in experiments of a viscoelastic model fluid that the phenomena observed at low and high inertia have a common origin and that the same dynamical state, elasto-inertial turbulence, persists across four orders of magnitude in Reynolds number, ranging from very low inertia, all the way to high inertia Maximum drag reduction (MDR) asymptote. We also explore the transitions from Newtonian turbulence to MDR, and specific cases of flow at high polymer concentrations, exploring the relationship between flow at these wide range of control parameters. }, author = {Suresh, Sarath S}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Turbulence in polymeric flows: A characterisation of elasto-inertial turbulence and the maximum drag reduction asymptote}}, doi = {10.15479/AT-ISTA-19906}, year = {2025}, } @phdthesis{19386, abstract = {Crustaceans are a large group of arthropods with a great diversity of species and different types of sex determination systems and reproductive modes (Subramoniam, 2017). This makes them a great model for exploring the evolution of sex chromosomes and sexual dimorphism and investigating the evolutionary mechanisms driving and maintaining the diversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a branchiopod crustacean, are well suited for such explorations, as they have both highly dimorphic traits and closely related sexual and asexual species. Although brine shrimp are known to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex chromosomes are still not well characterized at the genomic level, the sex-determination gene is unknown, and it is still unclear whether the same sex chromosomes as shared by the different species. The first part of this thesis was to characterize the Z and W chromosomes in Artemia using an array of methods, from generating multiple chromosome and contig level genome assemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer based approaches. The second part tackles the conservation of the cell type specific regulatory pathways in the female reproductive system between Artemia and Drosophila, and the expression of the Z-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show that germline cells lack dosage compensation, with a subset of cells showing evidence of extreme repression of the Z chromosome. With multiple sexual species and several asexual lineages of parthenogenetic females that produce rare males at low frequencies, Brine shrimp present the perfect opportunity to explore the transition to asexuality and shed light on the prerequisites and repercussions of the form of modified meiosis maintaining the asexual lineages. The last chapter is an investigation of the molecular pathways involved in asexual reproduction in Artemia using newly generated single nucleus RNAseq and WGS data and previously published data. }, author = {Elkrewi, Marwan N}, isbn = {9783990780534}, issn = {2663-337X}, pages = {170}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp}}, doi = {10.15479/AT-ISTA-19386}, year = {2025}, } @phdthesis{20449, abstract = {Males and females of many species differ in morphology, physiology, and behavior. In taxa with genetic sex determination, sexual differentiation arises largely from sex-biased gene expression, which varies across tissues, developmental stages, and lineages. Increasing evidence highlights chromatin configuration, which can exist in open or closed states, and can be shaped by sex-determination path ways, as a key regulatory layer of this dimorphism. Degeneration of the Y or W chromosome further contributes to sex -specific differences by altering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these imbalances, many eukaryotes have independently evolved dosage compensation mechanisms, often mediated through chromatin -level regulation. In this thesis, we investigate the evolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana and Cameraria ohridella , with a particular focus on the extent of dosage compensation following gene loss in the heterogametic sex and the potential chromatin-based mechanisms underlying this process. We further characterize sex -biased gene expression and its regulation through histone modifications. Our analyses also reveal that the A. franciscana genome is highly repetitive, with many genes containing intronic transposable elements. We find that enrichment of histonemo difications associated with constitutive heterochromatin, positively correlates with variation in gene expression levels. Collectively, these findings underscore role of chromatin regulation in shaping the evolution of sex chromosomes and sexual differentiation. }, author = {Bett, Vincent K}, issn = {2663-337X}, pages = {114}, publisher = {Institute of Science and Technology Austria}, title = {{Evolution and regulation of the Z chromosome}}, doi = {10.15479/AT-ISTA-20449}, year = {2025}, } @article{19735, abstract = {The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome.}, author = {Bett, Vincent K and Trejo Arellano, Minerva S and Vicoso, Beatriz}, issn = {1537-1719}, journal = {Molecular Biology and Evolution}, number = {5}, publisher = {Oxford University Press}, title = {{Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana}}, doi = {10.1093/molbev/msaf085}, volume = {42}, year = {2025}, } @phdthesis{20357, author = {Ruzickova, Natalia}, isbn = {978-3-99078-066-4}, issn = {2663-337X}, keywords = {gene regulation, networks, omnigenic model, pancreas, collective behaviour}, pages = {156}, publisher = {Institute of Science and Technology Austria}, title = {{Effect propagation in biological networks}}, doi = {10.15479/AT-ISTA-20357}, year = {2025}, } @phdthesis{20563, abstract = {The theory of optimal transport provides an elegant and powerful description of many evolution equations as gradient flows. The primary objective of this thesis is to adapt and extend the theory to deal with important equations that are not covered by the classical framework, specifically boundary value problems and kinetic equations. Additionally, we establish new results in periodic homogenization for discrete dynamical optimal transport and in quantization of measures. Section 1.1 serves as an invitation to the classical theory of optimal transport, including the main definitions and a selection of well-established theorems. Sections 1.2-1.5 introduce the main results of this thesis, outline the motivations, and review the current state of the art. In Chapter 2, we consider the Fokker–Planck equation on a bounded set with positive Dirichlet boundary conditions. We construct a time-discrete scheme involving a modification of the Wasserstein distance and, under weak assumptions, prove its convergence to a solution of this boundary value problem. In dimension 1, we show that this solution is a gradient flow in a suitable space of measures. Chapter 3 presents joint work with Giovanni Brigati and Jan Maas. We introduce a new theory of optimal transport to describe and study particle systems at the mesoscopic scale. We prove adapted versions of some fundamental theorems, including the Benamou–Brenier formula and the identification of absolutely continuous curves of measures. Chapter 4 presents joint work with Lorenzo Portinale. We prove convergence of dynamical transportation functionals on periodic graphs in the large-scale limit when the cost functional is asymptotically linear. Additionally, we show that discrete 1-Wasserstein distances converge to 1-Wasserstein distances constructed from crystalline norms on R d . Chapter 5 concerns optimal empirical quantization: the problem of approximating a measure by the sum of n equally weighted Dirac deltas, so as to minimize the error in the p-Wasserstein distance. Our main result is an analog of Zador’s theorem, providing asymptotic bounds for the minimal error as n tends to infinity. }, author = {Quattrocchi, Filippo}, issn = {2663-337X}, keywords = {optimal transport, kinetic equations, boundary value problems, quantization, gradient flows, homogenization}, pages = {240}, publisher = {Institute of Science and Technology Austria}, title = {{Optimal transport methods for kinetic equations, boundary value problems, and discretization of measures}}, doi = {10.15479/AT-ISTA-20563}, year = {2025}, } @unpublished{20569, abstract = {This is the first part of a general description in terms of mass transport for time-evolving interacting particles systems, at a mesoscopic level. Beyond kinetic theory, our framework naturally applies in biology, computer vision, and engineering. The central object of our study is a new discrepancy d between two probability distributions in position and velocity states, which is reminiscent of the 2-Wasserstein distance, but of second-order nature. We construct d in two steps. First, we optimise over transport plans. The cost function is given by the minimal acceleration between two coupled states on a fixed time horizon T. Second, we further optimise over the time horizon T > 0. We prove the existence of optimal transport plans and maps, and study two time-continuous characterisations of d. One is given in terms of dynamical transport plans. The other one -- in the spirit of the Benamou--Brenier formula -- is formulated as the minimisation of an action of the acceleration field, constrained by Vlasov's equations. Equivalence of static and dynamical formulations of d holds true. While part of this result can be derived from recent, parallel developments in optimal control between measures, we give an original proof relying on two new ingredients: Galilean regularisation of Vlasov's equations and a kinetic Monge--Mather shortening principle. Finally, we establish a first-order differential calculus in the geometry induced by d, and identify solutions to Vlasov's equations with curves of measures satisfying a certain d-absolute continuity condition. One consequence is an explicit formula for the d-derivative of such curves.}, author = {Brigati, Giovanni and Maas, Jan and Quattrocchi, Filippo}, booktitle = {arXiv}, keywords = {optimal transport, kinetic theory, second-order discrepancy, Vlasov equation, Wasserstein splines.}, title = {{Kinetic Optimal Transport (OTIKIN) -- Part 1: Second-order discrepancies between probability measures}}, doi = {10.48550/arXiv.2502.15665}, year = {2025}, } @phdthesis{19533, abstract = {This thesis explores advancements in quantum remote sensing and non-equilibrium phase transitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing. In the first project, I experimentally studied photon blockade breakdown as a dissipative phase transition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic limit, we demonstrated that the observed bistability is a genuine signature of a first-order phase transition in this system. This work provides insight into non-equilibrium quantum dynamics and phase transitions in driven-dissipative open quantum systems. The second project focuses on the experimental realization of a phase-conjugate receiver for quantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy environments using entangled light. While an ideal spontaneous parametric down-conversion (SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical illumination, no such ideal receiver exists. Instead, we explore an experimental realization of a phase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a Josephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled signal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate key experimental limitations that constrain practical QI performance, contributing to the development of quantum-enhanced sensing. Additionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These methods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been essential in data acquisition, noise filtering, and correlation analysis across multiple research projects. Although not real-time, these DSP techniques significantly enhance the accuracy of quantum measurements. Overall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic limit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver for QI. These findings contribute to quantum metrology, particularly for weak signal detection and remote sensing in noisy environments. }, author = {Sett, Riya}, issn = {2663-337X}, keywords = {phase transition, open quantum system, phase diagram, cavity quantum electrodynamics, superconducting qubits, semiclassical physics, quantum optics, josephson junction, parametric converter, phase conjugation, quantum radar, quantum entanglement, correlation, quantum sensing}, pages = {109}, publisher = {Institute of Science and Technology Austria}, title = {{Quantum remote sensing and non-equilibrium phase transitions in the microwave regime}}, doi = {10.15479/AT-ISTA-19533}, year = {2025}, } @article{19280, abstract = {Recent advancements in superconducting circuits have enabled the experimental study of collective behavior of precisely controlled intermediate-scale ensembles of qubits. In this work, we demonstrate an atomic frequency comb formed by individual artificial atoms strongly coupled to a single resonator mode. We observe periodic microwave pulses that originate from a single coherent excitation dynamically interacting with the multiqubit ensemble. We show that this revival dynamics emerges as a consequence of the constructive and periodic rephasing of the five superconducting qubits forming the vacuum Rabi split comb. In the future, similar devices could be used as a memory with in situ tunable storage time or as an on-chip periodic pulse generator with nonclassical photon statistics.}, author = {Redchenko, Elena and Zens, M. and Zemlicka, Martin and Peruzzo, Matilda and Hassani, Farid and Sett, Riya and Zielinski, Przemyslaw D and Dhar, H. S. and Krimer, D. O. and Rotter, S. and Fink, Johannes M}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {6}, publisher = {American Physical Society}, title = {{Observation of collapse and revival in a superconducting atomic frequency comb}}, doi = {10.1103/PhysRevLett.134.063601}, volume = {134}, year = {2025}, } @phdthesis{20212, abstract = {Cortical development has been studied for many decades and with each passing year, we learn more about the processes that govern the tightly regulated developmental program. Up until recently, the field has struggled to gain reliable access to progenitors at the single-cell level, limiting the resolution at which we can study cortical development in vivo. Therefore, much of the data we have on mammalian cortical development is at the cell population level. The subsequent pages of this thesis describe novel elements of cortical development in mice; acquired using a candidate gene approach in conjunction with Mosaic Analysis with Double Markers (MADM) to achieve single cell resolution. In this thesis, I briefly provide an overview of the state of the field, describe the methodology used to quantify morphological characteristics of neurons and glia, and delve into the role of Phosphatase and tensin homologue on chromosome ten (Pten) in neurogenesis and gliogenesis in the developing mouse cortex. By using MADM to generate genetic mosaics, in which only a small fraction of cells are mutated, to study population-level changes, we can bypass the early postnatal lethality reported in Pten conditional knockouts (cKOs) using Emx1-Cre. We used Emx1-CreERT2 to induce clonal deletion of Pten, and quantify RGP neurogenic output at the single progenitor level. Pten-mutant neuron populations within the mosaics were significantly expanded. In the latter parts of this thesis, we describe how Pten deletion leads to an increase in the abundance of astrocytes. We availed ourselves of the flexibility offered by the MADM system to generate Pten mosaics within a series of distinct knockout tissues to test for the interactions between Pten and a battery of genes involved in distinct pro-gliogenic signaling pathways. Our survey of Pten’s interactions with genes in key signaling pathways reveals that ERK1/2 are the critical effectors downstream of EGFR signaling essential for gliogenesis. Altogether, our results demonstrate that Pten plays critical and distinct roles throughout cortical RGP lineage progression. }, author = {Miranda, Osvaldo}, isbn = {978-3-99078-063-3}, issn = {2663-337X}, keywords = {Pten, mtor, cortical development, MADM, Mapk}, pages = {119}, publisher = {Institute of Science and Technology Austria}, title = {{Unraveling the role of Pten in cortical stem cell lineage progression using MADM}}, doi = {10.15479/AT-ISTA-20212}, year = {2025}, } @phdthesis{20117, abstract = {Auxin is essential for many aspects of plant growth and development, from embryogenesis to organ senescence. Polar auxin transport leads to local auxin maxima and gradients, which are important for regulating various plant development process, including embryogenesis, organogenesis and vascular tissue formation. The polar auxin transport is mediated by auxin influx carrier AUX1/LAX proteins and efflux carrier PIN proteins. The regulation of PIN proteins is a key convergence of crosstalk between auxin and other hormones, such as cytokinin. Cytokinin promotes the degradation of PIN1 in Arabidopsis roots, preferentially the dephosphorylated PIN1, and the process is independent of transcription and translation (Marhavý et al., 2011; Marhavý et al., 2014). The internalization of PIN proteins from plasma membrane is controlled by clathrin-mediated endocytosis (Dhonukshe et al., 2007; Kitakura et al., 2011). However, whether cytokinin affects the PIN1 degradation through regulating the phosphorylation of PIN1 or trafficking components is unknown. Here, we demonstrate that dynamin related protein DRP2s are required for the cytokinin regulated trafficking of PIN1 and PIN2 in Arabidopsis root epidermal cells. Despite the reported redundancy of DRP2A and DRP2B in gametophyte development, we found that CK-mediated PIN1 degradation and –induced PIN2 membrane localization is affected in drp2a or drp2b single mutants. Interestingly, we found that cytokinin regulates the recruitment of DRP2A—but not DRP2B—to clathrin-coated pits, and affects the stability and plasma membrane localization of DRP2A. Furthermore, we studied the involvement of cytokinin receptors in the regulation of cytokinin on DRP2A. Additionally, the assembly and disassembly cycle of dynamin is mediated by its dephosphorylation and phosphotylation cycle; thus, we investigated the role of DRP2A phosphorylation in its cytokinin-regulated assembly and in cytokinin-regulated PIN trafficking. Altogether, we found that cytokinin regulated PIN trafficking in Arabidopsis root epidermal cells involves modulation of the phosphorylation of endocytosis accessory protein DRP2A. }, author = {Wang, Yiqun}, issn = {2663-337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{The role of dynamin related protein 2A in cytokinin regulated plant growth and development}}, doi = {10.15479/AT-ISTA-20117}, year = {2025}, } @article{20187, abstract = {Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.}, author = {Babic, David and Abualia, Rashed and Fiedler, Lukas and Qi, Linlin and Tellier, Frédérique and Smoljan, Adrijana and Rakusova, Hana and Valošek, Petr and Han, Huibin and Benková, Eva and Faure, Jean Denis and Friml, Jiří}, issn = {1365-313X}, journal = {Plant Journal}, number = {3}, publisher = {Wiley}, title = {{Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development}}, doi = {10.1111/tpj.70396}, volume = {123}, year = {2025}, } @phdthesis{20362, abstract = {Arabidopsis embryo has long served as a model system for understanding how plant body patterning and axis establishment arise. Previous work established that auxin flows, directed by polar transport and reinforced by local biosynthesis, underpin axes formation, while recent studies suggest that maternal tissue, membrane composition and surface receptor signaling add further regulatory layers. In this thesis, we dissect the layers of auxin-mediated processes which guide plant embryonic and post-embryonic development. We review methodological advances that allow the embryo to be imaged and studied. These tools offer exciting venues for future addressing of outstanding research questions. Furthermore, we dissect the contribution of maternal auxin for early embryo patterning. Targeted auxin scavenging in the integuments lowers the hormone reaching the proembryo, destabilizes PIN7 in the suspensor and weakens the initial apical maximum. The resulting deficit dampens downstream embryonic auxin biosynthesis, as well as auxin flow towards the root pole, indicating that maternally provided auxin controls auxin flows in the embryos on a larger scale than previously understood. Intriguingly, we uncover a prolonged maternal effect mediated by the receptor-like kinases TMK1 and TMK4. Reciprocal crosses and transgene analyses hint that these genes could be preferentially maternally-derived in both embryos and seedlings. Loss of maternal TMK activity arrests embryos, affects seedling development and persists into adult growth, suggesting that maternal effect could shape development beyond fertilization and early embryogenesis. Finally, we describe the role of very-long-chain fatty acids and membrane composition on PIN proteins and their auxin-induced relocalization. Disruption in this lipid metabolism triggers widespread patterning errors. Together, these results reposition early plant patterning as a hierarchical cascade that begins with maternal auxin, gets amplified by auxin transport and biosynthesis, potentially modulated by maternal receptor signaling and could ultimately be gated by the biophysical properties of the membrane. By integrating auxin supply, genetic imprinting and lipid-dependent trafficking into a single narrative, this thesis helps shifting the approach of viewing the embryo as an autonomous unit to regarding it as a dynamic system, continuously sculpted by its maternal context.}, author = {Babic, David}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana}}, doi = {10.15479/AT-ISTA-20362}, year = {2025}, } @unpublished{21427, abstract = {While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.}, author = {Dunajova, Zuzana and Tasciyan, Saren and Majek, Juraj and Merrin, Jack and Sahai, Erik and Sixt, Michael K and Hannezo, Edouard B}, booktitle = {bioRxiv}, title = {{Substrate heterogeneity promotes cancer cell dissemination through interface roughening}}, doi = {10.1101/2025.05.20.655037}, year = {2025}, }