@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}, } @phdthesis{20364, abstract = {Auxin is a central regulator of plant growth and development, orchestrating processes from embryogenesis to senescence through a complex network of biosynthesis, transport, and signaling pathways. In Arabidopsis thaliana, canonical nuclear auxin signaling is mediated by the TIR1/AFB receptors, which promote degradation of AUX/IAA repressors to enable ARF transcription factors-driven transcriptional reprogramming. Parallel to this well-established nuclear mechanism, auxin also triggers rapid, non-transcriptional responses. In particular, at the cell surface, most notably through ABP1 and TMKs. Despite decades of research, the integration of these pathways and their links to fundamental cellular processes remains not fully understood. In this study, we uncover a new role for TIR1/AFB signaling in rapidly activating macroautophagy during developmental reprogramming. Auxin induces autophagy via TIR1/AFB adenylate cyclase activity, linking auxin perception to cAMP production and transcriptional activation of autophagy machinery. Autophagy-deficient mutants exhibit delayed meristem differentiation, impaired lateral root progression, and reduced shoot organogenesis, demonstrating its necessity for timely developmental transitions. We also revisit the ABP1-TMK1 cell-surface auxin perception complex, providing biochemical and mass photometry evidence for auxin-dependent complex formation. We show that ABP1-TMK1 triggers an ultrafast global phosphorylation response targeting ~1000 proteins, including the auxin transporter PIN2, and Rho-of-plants (ROP) GTPases regulators. This pathway directly regulates PIN2 phosphorylation, for gravitropism and auxin dependent ROP activation. These findings establish an integrated framework in which nuclear TIR1/AFB signaling and cell-surface ABP1-TMK signaling act in parallel to synchronize gene expression, cytoplasmic remodelling, and transporter regulation, thereby ensuring robust developmental plasticity in Arabidopsis thaliana. }, author = {Giannini, Caterina}, issn = {2663-337X}, keywords = {Auxin Signaling, Plant Development}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Nuclear and cell surface auxin signaling in A. thaliana developmental transitions}}, doi = {10.15479/AT-ISTA-20364}, year = {2025}, } @unpublished{19399, abstract = {Phytohormone auxin and its directional transport mediate much of the remarkably plastic development of higher plants. Positive feedback between auxin signaling and transport is a key prerequisite for (i) self-organizing processes including vascular tissue formation and (ii) directional growth responses such as gravitropism. Here we identify a mechanism, by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface ABP1-TMK1 receptor module, auxin rapidly induces phosphorylation and thus stabilization of PIN2. Following gravistimulation, initial auxin asymmetry activates autophosphorylation of the TMK1 kinase. This induces TMK1 interaction with and phosphorylation of PIN2, stabilizing PIN2 at the lower root side, thus reinforcing asymmetric auxin flow for root bending. Upstream of TMK1 in this regulation, ABP1 acts redundantly with the root-expressed ABP1-LIKE auxin receptor ABL3. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably also for other self-organizing developmental phenomena.}, author = {Rodriguez Solovey, Lesia and Fiedler, Lukas and Zou, Minxia and Giannini, Caterina and Monzer, Aline and Vladimirtsev, Dmitrii and Randuch, Marek and Yu, Yongfan and Gelová, Zuzana and Verstraeten, Inge and Hajny, Jakub and Chen, Meng and Tan, Shutang and Hörmayer, Lukas and Li, Lanxin and Marques-Bueno, Maria Mar and Quddoos, Zainab and Molnar, Gergely and Xu, Tongda and Kulich, Ivan and Jaillais, Yvon and Friml, Jiří}, booktitle = {bioRxiv}, title = {{ABP1/ABL3-TMK1 cell-surface auxin signaling directly targets PIN2-mediated auxin fluxes for root gravitropism}}, doi = {10.1101/2022.11.30.518503}, year = {2025}, } @phdthesis{20694, abstract = {Understanding the mechanisms underlying speciation is a central aim of evolutionary biology. A persistent challenge in the field is to identify loci that contribute to reproductive isolation, while disentangling signals of selection from demography, linkage and intrinsic genomic features. Traditional population genomic approaches that rely on site-based statistics in arbitrary fixed windows face inherent limitations, as they conflate historical and contemporary processes of divergence and overlook haplotype structure. Recent advances in whole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now offer the opportunity to study genealogical relationships explicitly, revealing how lineages coalesce and recombine through time. By directly analysing haplotype clustering by species or phenotype and their patterns of coalescence, ARG-based methods show promise for diagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene flow, and tracing their evolutionary history. In this thesis, I explore the utility of genealogical approaches for studying species divergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks through the structure of the ARG, using simulations and empirical data to highlight how genealogical processes generate rich and often overlooked haplotypic patterns. In chapter 3, I examine the genomic basis of a key evolutionary innovation in marine snails Littorina. These snails offer a unique opportunity to study an innovation because they include a very recent transition from egg-laying to live bearing, yet snails with the different reproductive modes are not reciprocally monophyletic. I exploited this by using topology clustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or haplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying to live-bearing involves multiple, live-bearer-specific sweeps. Chapter 4 establishes a population-scale, phased genomic resource for Antirrhinum majus, using cost-effective haplotagging, then optimizes imputation from low-coverage data against high-accuracy KASP sequencing to maximize sequence completeness with modest accuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing strategy combines molecular phasing with statistical phasing to generate phased whole genome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing costs. In chapter 5, I analyse hybridising populations from two replicate hybrid zones to find a parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape driven by variation in demographic history. While outlier genome scans of FST failed to dissect the causes of differentiation, ARG-based topology clustering revealed a reuse of colour associated haplotypes across hybrid zones. In addition to the biological insight, this chapter also presents a comparison of the latest ARG inference tools, showing that signals of Abstract viii topological clustering qualitatively agree between methods, despite differences in the tree sequences. Next, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I integrated genome-wide association studies of floral pigmentation with genealogical inference, to test for additional colour loci, and confirm the effect of previously described loci. This work demonstrates that flower colour variation is driven by a small number of large effect loci, while also hinting at the presence of a new candidate regulatory factor. Finally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of speciation around Rosea/Eluta to understand its evolutionary origins. My results show that it consists of 5 highly divergent loci, each of which is associated with flower colour. Using patterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps and a persistent localized barrier to gene flow within an otherwise permeable genome. Together, these chapters add to the increasing pool of studies using genealogical approaches to complement and extend site-based statistics to use haplotype structures in speciation research. By tracking haplotypes directly and connecting genealogical clustering to population processes, ARG-based inference promises to provide new insights into how local selective pressures, demographic history, and long-term barriers interact to shape the genomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about the benefits of using genealogical inference to learn more than what site-based statistics could tell us.}, author = {Pal, Arka}, issn = {2663-337X}, pages = {268}, publisher = {Institute of Science and Technology Austria}, title = {{Using genealogies to study the genomic basis of species divergence}}, doi = {10.15479/AT-ISTA-20694}, year = {2025}, } @article{20190, abstract = {A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.}, author = {Pal, Arka and Shipilina, Daria and Le Moan, Alan and Mcnairn, Adrian J. and Grenier, Jennifer K. and Kucka, Marek and Coop, Graham and Chan, Yingguang Frank and Barton, Nicholas H and Field, David and Stankowski, Sean}, issn = {1365-294X}, journal = {Molecular Ecology}, number = {22}, publisher = {Wiley}, title = {{Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum}}, doi = {10.1111/mec.70067}, volume = {34}, year = {2025}, } @phdthesis{19271, abstract = {The medial habenula (MHb) is implicated in regulating emotional responses to aversive events. Studies in zebrafish have identified a remarkable morphological left-right asymmetry in the dorsal habenula (zebrafish equivalent of mammalian MHb)-to-interpeduncular nucleus (IPN) pathway and its left-side specific role in modulating fear responses. However, there is little evidence for structural or functional lateralization in the mammalian MHb-IPN pathway. Here, I investigated the synaptic properties of the left and right MHb afferents to the IPN in mice and addressed whether these synaptic connections selectively influence the expression of conditioned fear in mice. My findings reveal that each individual IPN neuron receives inputs from both left and right MHb. Electrophysiological recordings from the same postsynaptic IPN neurons demonstrate that the left MHb-originating synapses exhibit lower release probability and higher 𝛾-aminobutyric acid type B receptor (GABABR)-mediated potentiation compared to the right MHb-originating synapses. Interestingly, chemogenetic inhibition of cholinergic neurons in the left but not the right MHb significantly attenuated cue-dependent fear recall. Furthermore, conditional deletion of GABABR in the left MHb interfered with the recall of cued fear memory, whereas that in the right MHb neurons spared fear memory expression. Collectively, I demonstrate a functional asymmetry of the MHb in mice, revealing a predominant role for GABABR-mediated signaling in the left MHb-IPN pathway in the modulation of fear memories. These findings suggest that lateralized pathways could represent a fundamental principle in the neural regulation of emotion across species.}, author = {Önal, Hüseyin C}, issn = {2663-337X}, publisher = {Institute of Science and Technology Austria}, title = {{Asymmetrical modulation of fear expression via GABAB receptors in the mouse medial habenula}}, doi = {10.15479/AT-ISTA-19271}, year = {2025}, } @phdthesis{19478, abstract = {Auxin is one of the most important phytohormones, playing a crucial role in plant growth and development. Genetic studies in Arabidopsis have identified core components of auxin signalling and established the classical transcriptional regulation mechanism. This classical paradigm recognizes TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN SIGNALLING F-BOX (AFB) proteins as auxin receptors possessing E3 ubiquitin ligase activity. Auxin functions as a "molecular glue" enhancing TIR1/AFB-Aux/IAA (AUXIN/INDOLE-3-ACETIC ACID) inhibitor interactions, leading to Aux/IAAs’ ubiquitination and degradation. This process releases AUXIN RESPONSE FACTORs (ARFs) from repression, enabling transcriptional activation of auxin-responsive genes. Notably, the discovery of adenylate cyclase (AC) activity in TIR1/AFBs, catalysing cAMP production from ATP, presents novel transcriptional regulatory possibilities, though cAMP's mechanistic role in auxin signalling remains unclear. Beyond transcriptional regulation (slow response) a non transcriptional pathway (rapid response) mediated by AFB1 also exists, as auxin triggers rapid root growth inhibition within 30 seconds. How TIR1 and AFB1, with their distinct subcellular localizations, differentially regulate transcriptional and non-transcriptional processes remains unclear. To address these two key questions, this study conducted the following investigations. TIR1 and AFB1 display distinct subcellular localization patterns, with AFB1 specifically mediating auxin-induced rapid root growth inhibition. To examine whether subcellular localization differences contribute to functional divergence between TIR1 and AFB1, we utilized microfluidic systems combined with genetic complementation assays. Nuclear export signal-fused TIR1 failed to rescue the rapid response defects observed in afb1 mutants. In contrast, nuclear localization signal-fused AFB1 exhibited dual functional deficiencies: it neither restored the rapid response impairment in afb1 mutants nor compensated for transcriptional regulation defects in tir1 mutants which limitation stemmed from AFB1's intrinsic incapacity to assemble functional SCF complexes. These results collectively establish that the functional specialization of TIR1 and AFB1 is governed by both their subcellular compartmentalization and inherent biochemical characteristics. The mechanism by which cAMP derived from the auxin receptor TIR1/AFB modulates transcriptional regulation remains undefined. To address this, we genetically dissociated TIR1 AC activity from its E3 ubiquitin ligase function to investigate cAMP's signalling role. AC inactivating mutations preserved TIR1-mediated Aux/IAAs’ degradation but abolished ARF i dependent transcriptional activation. tir1afb2 mutants expressing AC-deficient TIR1 variants failed to restore transcriptional responses. Crucially, compartmentalized cAMP accumulation within Aux/IAA - ARF complexes vicinity triggered auxin signalling independently of both auxin perception and Aux/IAAs’ degradation, confirming its secondary messenger identity. Further mechanistic analysis demonstrated cAMP directly interact with ARF. cAMP directly promotes ARF dissociation from Aux/IAA repressors and enhances ARF homodimerization. Genetic complementation assays revealed that ARF mutants lacking conserved cAMP-binding motifs exhibited partial functional recovery, providing direct evidence for cAMP-ARF physical interaction during signal propagation. These findings collectively challenge the established model of auxin signalling and define a novel TIR1-cAMP-ARF regulatory axis, substantially advancing our comprehension of auxin-mediated physiological regulation. }, author = {Chen, Huihuang}, issn = {2663-337X}, pages = {118}, publisher = {Institute of Science and Technology Austria}, title = {{The cAMP second messenger in auxin signalling}}, doi = {10.15479/AT-ISTA-19478}, year = {2025}, } @phdthesis{20467, abstract = {Prostaglandins play a central role in the inflammatory response. Prostaglandins are synthesized in a rate-limiting manner by the enzyme cyclooxygenase (Cox), which exists in two isoforms: the Cox-2 and Cox-1 isoforms. Traditionally, Cox-1 is thought to mediate homeostatic functions due to its constitutive expression due to its constitutive expression, whereas Cox-2 is temporary induced in response to inflammatory stimuli and is associated with the inflammatory response. Interestingly, in the central nervous system, Cox-1 is predominantly expressed in microglia. As the resident immune cells of the brain, microglia play a key role in inflammation. Cox-1 expressing microglia are increased in neurodegenerative diseases, and both global knockout of Cox-1 and selective Cox-1 inhibition has been shown to ameliorate inflammatory effects in neurodegenerative diseases. However, direct evidence elucidating how microglial Cox-1 expression influences their response to insults remains limited and warrants further investigation. First, I utilize the optic nerve crush (ONC) model to study the microglial response to injury and inflammation, confirming a reactive microglial response in both the crushed and uninjured contralateral retina using CD68 expression and morphological analysis. While previous studies reported retinal ganglion cell (RGC) loss in the contralateral eye, I did not observe this, suggesting that unilateral ONC induces microglial activation in the contralateral eye without RGC degeneration. To explore the role of Cox-1 in this response, I generated a mouse model with microglia-specific deletion of Cox-1. After ONC, these mice exhibited an attenuated microglial response in both the ipsilateral and contralateral retinas, as well as in visual processing areas of the brain. Notably, Cox-2 does not show any expression after ONC in both wild-type and Cox-1 knockout mice Additionally, Cox-1KO mice show a reduction in phagocytic cups and a reduction in microglia proliferation after ONC. However, due to reproducibility problems of the observed phenotype, even after the generation of two new mouse models, I cannot draw any definitive conclusions based on the data. Next, due to the ambiguity of the mouse model, I explored an alternative route to investigate functional consequences of Cox-1 in microglia. I generated a COX1 knock-out human induced pluripotent cell (hIPSC) line using CRISPR/Cas9. These cells are were differentiated in microglia-like cells and integrated in dissociated retinal organoids according to protocols developed in our lab. In response to LPS and POLY(I:C) stimulation, the release and expression of cytokines and chemokines was decreased in COX1 knockout cells. However, the prostaglandin PGE2 was not increased in microglia-like cells in both control and COX1 knockout cells. Overall, the results from the COX1 knock-out microglia-like cells suggests that COX1 expression in microglia play a role in neuroinflammation by affecting the release of inflammatory cytokines and chemokines. Hereby further challenging that the dogma of the Cox-1 isoform involved in housekeeping functions and the Cox-2 isoform involved in inflammation applies for the central nervous system. }, author = {Miteva, Florianne E}, issn = {2663-337X}, pages = {99}, publisher = {Institute of Science and Technology Austria}, title = {{The role of cyclooxygenase 1 on microglial response to inflammatory stressors}}, doi = {10.15479/AT-ISTA-20467}, year = {2025}, }