@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{20798, abstract = {Atom interferometers measure the relative phase shifts between coherent matter-wave paths that arise from interactions with external fields or inertial forces. Due to their exceptional phase sensitivity, atom interferometers became an essential tool for precision measurements and fundamental physics experiments, finding applications in geodesy, gravimetry, and inertial navigation. However, their measurement precision is limited by quantum projection noise, which arises from the Heisenberg uncertainty principle, preventing the measurement of atomic states with absolute precision. The generation of entanglement between the atoms offers a path to surpass this so-called standard quantum limit, thereby enhancing the interferometer’s phase sensitivity beyond classical measurement bounds. This thesis reports on the development of an atom interferometer experiment designed to realize cavity-mediated, squeezed Mach-Zehnder-type interferometry with ultra-cold 87Rb atoms. The experiment combines cavity-aided spin-squeezing with cavity-mediated Mach-Zehnder interferometry to demonstrate entanglement-enhanced phase sensitivity. The experiment is centered on a triangular optical cavity that mediates all relevant atom-light interactions. The cavity provides optical trapping, spin-squeezing, and Raman beam-splitter operations, enabling to perform interferometry on a continuously trapped atomic ensemble. The thesis elaborates on the fundamental theoretical framework, the cavity design, and the full optical setup, including the detailed configuration of the developed laser stabilization methods. Experimentally, continuous loading methods were explored, resulting in an accumulation of up to 4 × 106 atoms in the dipole trap within a cycle time of 500 ms. The AC Stark shift compensation method developed for continuous loading was further applied for in-trap cooling to 10 µK, and optical pumping for efficient atomic state preparation. Coherent state control was verified via observation of microwave-driven Rabi oscillations, and used to characterize atom-cavity coupling. These presented results establish the experimental groundwork for the future development of cavity-mediated, entanglement-enhanced Mach-Zehnder-type atom interferometry.}, author = {Wald, Sebastian}, isbn = {978-3-99078-075-6}, issn = {2663-337X}, keywords = {entanglement-enhanced atom interferometry, cavity QED, spin-squeezing, dipole trap, quantum optics}, pages = {152}, publisher = {Institute of Science and Technology Austria}, title = {{Atoms in a propagating-wave cavity for squeezed Mach-Zehnder atom interferometry}}, doi = {10.15479/AT-ISTA-20798}, year = {2025}, } @article{19498, abstract = {A dynamic interplay between fast synaptic signals and slower neuromodulatory signals controls the excitatory/inhibitory (E/I) balance within neuronal circuits. The mechanisms by which neuropeptide signaling is regulated to maintain E/I balance remain uncertain. We designed a genetic screen to isolate genes involved in the peptidergic maintenance of the E/I balance in the C. elegans motor circuit. This screen identified the C. elegans orthologs of the presynaptic phosphoprotein synapsin (snn-1) and the protein phosphatase 1 (PP1) regulatory subunit PHACTR1 (phac-1). We demonstrate that both phac-1 and snn-1 alter the motor behavior of C. elegans, and genetic interactions suggest that SNN-1 contributes to PP1-PHAC-1 holoenzyme signaling. De novo variants of human PHACTR1, associated with early-onset epilepsies [developmental and epileptic encephalopathy 70 (DEE70)], when expressed in C. elegans resulted in constitutive PP1-PHAC-1 holoenzyme activity. Unregulated PP1-PHAC-1 signaling alters the synapsin and actin cytoskeleton and increases neuropeptide release by cholinergic motor neurons, which secondarily affects the presynaptic vesicle cycle. Together, these results clarify the dominant mechanisms of action of the DEE70 alleles and suggest that altered neuropeptide release may alter E/I balance in DEE70.}, author = {Stratigi, Aikaterini and Soler-García, Miguel and Krout, Mia and Shukla, Shikha and De Bono, Mario and Richmond, Janet E. and Laurent, Patrick}, issn = {1529-2401}, journal = {Journal of Neuroscience}, number = {13}, publisher = {Society for Neuroscience}, title = {{Neuroendocrine control of synaptic transmission by PHAC-1 in C. elegans}}, doi = {10.1523/JNEUROSCI.1767-23.2024}, volume = {45}, year = {2025}, } @phdthesis{18871, abstract = {"Can we do this with a new type of computer - a quantum computer?". This famous quotation of the brilliant Richard Feynman within a conference talk on "Simulating physics with computers.” is often reverently praised as the origin of the field of quantum computing. The idea was to use quantum mechanical systems itself to simulate "Nature", which is inherently quantum mechanical. Now, 43 years later, the theoretical framework of how such a computer can operate has been developed. Two main important concepts for a potential quantum supremacy, superposition and entanglement, have been exploited to design quantum algorithms to significantly speed up certain tasks. Yet, the specific hardware implementation is still far from being certain, in fact the race between the most promising platforms such as superconducting qubits, bosonic codes, cold atoms, trapped ions, optical computing as well as spin qubits has recently intensified. If one also includes the most mature applications of quantum communication technologies, secure quantum key distribution and quantum random number generators, as part of a quantum information technology ecosystem, we are confronted with a plethora of different materials, concepts, and also operation frequencies. While superconducting qubits, bosonic codes and spin qubits work in the regime of approximately 5 GHz and are controlled by electrical fields, trapped ions, cold atoms, and optical quantum computing operate with light in the infrared or visible range. Consequently, a quantum frequency converter or microwave-optic transducer is required to interface the different frequency domains or establish a long-range network connection with suitable telecom fibers. In fact, the combination of different frequency regimes is also an essential part in our classical modern communication network, where computations are performed in electrical circuits and the information exchange over longer distances happens via optical fibers. However, the specific challenges specific to building a quantum computer, also apply to the development of such a quantum frequency transducer: 1) As we deal with single excitations as the carrier of information, i.e. the smallest possible quantity, the signal can easily be corrupted by other noise sources which needs to be avoided by all means. This is also the reason why microwave quantum computers operate at temperature environments close to zero temperature (< 0.1 Kelvin) to avoid corruption by thermal noise. 2) The frequency interface generally needs to preserve the phase of the signal as an essential part of the quantum state. And 3) Quantum signals cannot be copied which would be a typical strategy to account for errors in classical computers. And finally, there is a challenge specific to microwave-optic transducers: While quantum computers are operating in one specific frequency domain, microwave-optic transducers combine microwave and optical fields in one device. This results in the particular challenge that high-energy optical radiation, which is usually well-shielded from superconducting microwave quantum processors, are now an essential part of the device. The concomitant optical radiation in the operating transducer will inevitably have a detrimental effect on the superconducting microwave components. Together with the requirement of minimal background noise for quantum-limited operation as described above, v heating from the absorption of optical photons within the same device where single microwave excitations are processed forms a formidable challenge. This thesis aims to address this challenge by developing microwave-optic transducers where the impact of optical absorption on superconducting circuits in general and superconducting qubits specifically can be mitigated. In our first approach, we developed a compact device with optimized interaction strengths between the different frequency domains. This minimizes the optical powers used for transducer operation and thus the optical absorption heating. This work was - to the best of our knowledge - the first comprehensive noise study, in an integrated microwave-optic transducer. Unfortunately, we saw that the optical absorption heating added noise way above a single excitation. Consequently, a potential quantum signal would have been buried in the noise, added by the transduction. Building on this insight, we utilized a three-dimensional microwave-optic transducer instead of an integrated device. The larger heat capacity of the macroscopic device with a size of a few millimeters can absorb a larger fraction of the optical heating before it increases the temperature of the device. This allowed us to interface the transducer directly with a superconducting qubit to readout the qubit state in a novel all-optical manner. We showed that the microwave-optic transducer can be operated in a regime in which optical fields don’t harm the sensitive qubit. This is an important prerequisite for the operation of microwave-optic transducers in conjunction with microwave quantum processors and brings the integration and seamless orchestration of different frequency components in a quantum network a step closer. }, author = {Arnold, Georg M}, issn = {2663-337X}, pages = {135}, publisher = {Institute of Science and Technology Austria}, title = {{Microwave-optic interconnects for superconducting circuits}}, doi = {10.15479/at:ista:18871}, year = {2025}, } @phdthesis{19745, abstract = {Cell migration is a crucial process in animal development and maintenance. It is incredibly heterogeneous, with different cell types utilizing fundamentally distinct migration strategies. The strategies also depend on the cellular microenvironment, where cells can switch between migration modes as they encounter new environmental cues. In this thesis, we investigated how dendritic cells adapt their migration strategy when encountering geometrically, mechanically and chemically distinct environments. When dendritic cells are embedded in a homogeneous fibrous network, they migrate in a fast and directional amoeboid manner. In this migration strategy, extracellular proteolysis and integrin-mediated adhesions are dispensable. Instead, the cells use topography of the environment to propel their cell body forward. To migrate efficiently in the maze of different pore sizes, they position the nucleus ahead of the microtubule organizing center (MTOC) and use it to gauge the pores to identify the path of least resistance. Our aim was to identify whether dendritic cells adapt their migration strategy when encountering asymmetrical transitions into much denser environments with limited choice of large pores. In such invasive transitions it is unclear if the cells can cross tight pores without the use of adhesions and extracellular proteolysis and whether they maintain the nucleus in the cell front. Using various cell migration assays such as fibrous 3D collagen gels, geometrically defined microchannels with constrictions and simplistic under agarose migration assay, we provide a comprehensive characterization of invasive migration of dendritic cells. We show that during invasion the cells stall and stretch, reflecting the difficulty to translocate the bulky cell body into the dense environment. In collagen gels, we show that dendritic cells can invade without proteolysis and adhesions. Instead, they utilize contractility, which can lead to largescale collagen compressions. During invasion, the nucleus stalls at tight constrictions, leading to a transient organelle reorientation. To resolve the stalling, upregulated rear contractility is required. This contractile force is simultaneously necessary for reverting the nucleus back to the cell front after invasion and maintaining this positioning during permissive migration. A functional role of the reorientation was uncovered in the first collaboration project. A prominent central actin pool was identified around the MTOC, especially pronounced in dense and compressive environments. The actin pool was shown to generate pushing forces to dilate the space for cell translocation. These forces are only necessary in non-permissive environments, where the nucleus reorients to the cell rear, allowing the actin pool to generate space. In permissive environments where space generation is dispensable, the MTOC is located behind the nucleus and the actin cloud has reduced intensity, allowing more actin to be incorporated into the lamellipodium, speeding up migration. In the second collaboration project, we investigated the effects of distinct chemical environments on dendritic cell migration. The strikingly persistent migration of these cells was explained by their ability to modulate and even self-generate chemokine gradients. This allows the cells to migrate faster and more persistent in uniform chemokine fields compared to imposed chemokine gradients. The chemokine receptor CCR7 was identified as a crucial player in this process, both sensing the signal and internalizing the chemokine to create a sink.}, author = {Canigova, Nikola}, isbn = {978-3-99078-058-9}, issn = {2663-337X}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Adaptive strategies of dendritic cell migration in response to environmental cues}}, doi = {10.15479/AT-ISTA-19745}, 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{19431, abstract = {Gene expression is crucial for cell differentiation, development and survival of organisms. It consists of several steps, starting with transcription that is mediated by RNA polymerases. These are protein machineries transcribing and producing different types of RNAs. Although, the individual steps of transcription by RNA polymerase II (Pol II) as well as the structure of Pol II has been extensively studied, surprisingly, there is still little known about its regulation and assembly in cytoplasm. Among the proteins that are important in biogenesis of Pol II are RNA polymerase II associating proteins (RPAP) and small GPN-loop GTPases (GPN). Both of these protein groups were shown to take essential part in assembly of Pol II. The aim of this project was to deepen our knowledge in regulation of Pol II in the cytoplasm as well as the proteins involved in this process. Techniques of structural biology, biochemistry and cell biology were employed to study and characterize cytoplasmic Pol II and its interacting partners. This study shows for the first time the structure of cytoplasmic Pol II at high resolution. The structure also reveals proteins interacting with Pol II in cytoplasm, namely GDOWN1, RPAP2. Comparing the structure of cytoplasmic Pol II with transcribing Pol II revealed striking difference in clamp region that is not in closed state. Furthermore, GDOWN1 and RPAP2 make steric clashes with various transcription factors bound to Pol II during different stages of transcription. Even though GPN1 and GPN3 proteins were not resolved in the cytoplasmic Pol II structure, they are part of the complex and their interaction with Pol II was confirmed in vitro. RPAP2 stabilizes these proteins on Pol II and several experiments suggest that they interact with the clamp region. In addition, GDOWN1, RPAP2 and GPNs might keep clamp in open or partially open state. Based on these results I propose a novel model of regulation of Pol II in cytoplasm. GDOWN1, RPAP2, GPN1 and GPN3 bind to Pol II in cytoplasm and doing so they can prevent pre-mature binding of DNA or RNA and different transcription factors to Pol II in cytoplasm or before engaging in transcription nucleus. This research contributes to the current knowledge of molecular mechanisms of Pol II regulation in cytoplasm.}, author = {Hlavata, Annamaria}, isbn = {978-3-99078-055-8}, issn = {2663-337X}, pages = {83}, publisher = {Institute of Science and Technology Austria}, title = {{Regulation of Cytoplasmic RNA Polymerase II}}, doi = {10.15479/10.15479/AT-ISTA-19431}, year = {2025}, } @phdthesis{19302, abstract = {Social interaction networks of insect colonies facilitate efficient information exchange and demonstrate adaptive changes to mitigate disease transmission. While circadian rhythms influence individual behaviour, their role in shaping colony-level defences against pathogens remains unexplored. Here, we investigate whether social networks of the black garden ant, Lasius niger, exhibit circadian rhythms and how these rhythms influence disease vulnerability when colonies are exposed to a pathogen during the day or the night. We first establish baseline daily variations in activity and network dynamics in pathogen-free colonies, revealing constitutive daily fluctuations in disease susceptibility. Subsequently, we examine pathogen-induced changes in sanitary care and network dynamics by exposing foragers to a natural pathogen (Metarhizium brunneum) during either the day or the night. Individual pathogen loads were measured after a nine-hour post-exposure period to evaluate transmission outcomes. Our results demonstrate that diurnal ant colonies maintain robust circadian patterns in network properties while flexibly adapting to pathogen exposure. Ants upregulate sanitary care irrespective of exposure timing, prioritising the protection of the valuable colony centre consisting of nurses and the queen. These findings underscore the robustness and adaptability of ant colonies in balancing circadian rhythms with effective social immune responses.}, author = {Sartoris, Linda}, issn = {2663-337X}, pages = {85}, publisher = {Institute of Science and Technology Austria}, title = {{The effect of circadian rhythm on organisational immunity of ant colonies}}, doi = {10.15479/AT-ISTA-19302}, year = {2025}, } @phdthesis{19456, abstract = {Making decisions requires flexibly adapting to changing environments, a process that depends on accurately interpreting current contingencies and integrating them with past experience. Two brain regions are particularly critical for this process, the medial prefrontal cortex (mPFC) and the hippocampus. Using contextual information from the hippocampus, the mPFC selects relevant cognitive frameworks and suppresses irrelevant ones to guide appropriate actions. Several studies have shown that some mPFC pyramidal neurons become spatially tuned when spatial information is required to guide goal-directed behavior. However, the role of prefrontal spatial representations in learning and decision making is not well understood. This work aims to characterize the role of mPFC spatial tuning in supporting a contextual association task. Rats were trained to learn two cue–location associations on a radial arm maze over multiple days, while we simultaneously recorded from dorsal CA1 of the hippocampus and the prelimbic area of the mPFC. We describe a subset of spatially tuned hippocampal and prefrontal pyramidal neurons that “flicker” between multiple spatial representations on different trials, suggesting dynamic, context-dependent coding. This flickering may provide a substrate for how the network reorganizes in response to task demands, likely by enabling the flexible evaluation of competing representations. }, author = {Cumpelik, Andrea D}, isbn = {978-3-99078-056-5}, issn = {2663-337X}, keywords = {neuroscience, decision making, learning, cognitive flexibility, medial prefrontal cortex, hippocampus, electrophysiology}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{The role of prefrontal spatial coding in supporting a contextual association task}}, doi = {10.15479/AT-ISTA-19456}, 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{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{19763, abstract = {Pattern formation in developing organs is controlled by morphogens. These signalling molecules form concentration gradients across tissues, thereby providing positional information that instructs the pattern of cell differentiation. Morphogen gradients are highly dynamic in space and time. Many factors such as morphogen production, spreading, degradation, cellular rearrangements and others could contribute to changes in the gradient shape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear. We studied the dynamics of morphogen signalling and tissue patterning in the developing vertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor subtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are established and interpreted to ensure ordered cell specification is poorly understood. To address this question, we developed a 2D embryonic stem cell differentiation system that captures key features of dorsal neural tube development. In this system, differentiated colonies display remarkable self-organised pattern formation in response to uniformly applied BMP ligand. We established a method of differentiating the colonies using microfabricated stencils, which allowed us to control the initial size and shape of colonies without confining cell migration and colony growth. This led to highly reproducible pattern formation that facilitates quantification. Using this approach, we observed striking two-phase temporal dynamics of BMP signalling in our colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies, subsequently disappears and is re-established again in the second phase. By combining our quantitative data with a data-driven theoretical model, we uncovered a temporal relay mechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is controlled by fast tissue-autonomous negative feedback that restricts the duration of the initial response to BMP. The early BMP activity gradient moreover controls the spatial organisation of the cell type pattern: the absence of a first phase results in disordered cell type pattern. The second phase is controlled by slow positive regulation of BMP signalling by the transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the second phase of BMP signalling via positive feedback on LMX1A. Altogether, the mechanism that we uncovered ensures the coupling of sequential developmental events, making pattern formation spatially and temporally organised. Furthermore, this mechanism allows the BMP signalling pathway to be reused in different contexts – first for the establishment of the neural plate border, and subsequently for dorsal neural progenitor patterning. Our study supports a general developmental principle in which multiple morphogens interact with transcriptional networks resulting in complex spatiotemporal signalling dynamics that ultimately drive organised pattern formation.}, author = {Rus, Stefanie}, issn = {2663-337X}, pages = {129}, publisher = {Institute of Science and Technology Austria}, title = {{Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube}}, doi = {10.15479/AT-ISTA-19763}, year = {2025}, } @article{18807, abstract = {Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.}, author = {Rus, Stefanie and Brückner, David and Minchington, Thomas and Greunz, Martina and Merrin, Jack and Hannezo, Edouard B and Kicheva, Anna}, issn = {1534-5807}, journal = {Developmental Cell}, number = {4}, pages = {567--580}, publisher = {Elsevier}, title = {{Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling}}, doi = {10.1016/j.devcel.2024.10.024}, volume = {60}, 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}, } @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{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{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}, } @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}, }