@phdthesis{20339, abstract = {This thesis investigates the interplay between algebraic and topological methods and combinatorial problems, focusing on approximate graph colourings and mass partitioning. The unifying theme throughout the dissertation is the use of continuous maps and symmetry constraints to extract combinatorial insights. We first explore approximate graph colouring problems and more generally promise constraint satisfaction problems. Using tools from equivariant topology in combination with the general theory of polymorphism of a promise constraint satisfaction problem, we establish hardness for specific types of approximations. In the second part, we address mass partitioning problems, where one seeks to divide geometric objects or measures in Euclidean space into parts of equal size using hyperplanes. Employing techniques from topological combinatorics (configuration space/test map setup and Borsuk–Ulam type theorems), we both obtain a new equipartitioning result in the and provide a fast algorithm for computing equipartitioning of point sets in 3D. }, author = {Tasinato, Gianluca}, issn = {2663-337X}, pages = {106}, publisher = {Institute of Science and Technology Austria}, title = {{Topological methods in discrete geometry and theoretical computer science: Measure partitioning and constraint satisfaction problems}}, doi = {10.15479/AT-ISTA-20339}, year = {2025}, } @article{18157, abstract = {Interest in sliding block puzzles dates back to the 15-puzzle, seemingly invented by Noyes Chapman in 1874 (see [23] for an account of the fascinating history of the puzzle). The game consists of fifteen movable square blocks numbered and arranged within a square box, leaving one empty space (see Figure 1). The task at hand is to start from a given configuration of the numbered blocks and reach the desired target configuration, where the only allowed move is to slide a numbered block into an adjacent empty space. This task seemed to be unpredictably either very easy to accomplish, or completely impossible, and the puzzle turned into a worldwide sensation in the spring of 1880. A particularly challenging instance, known as the 13-15-14 puzzle, consisted of initial and target configurations that differed by a single swap (historically this swap involved the blocks labeled 14 and 15). The craze of this puzzle was such that it consistently made newspaper headlines in 1880, with an article in the New York Times lamenting that it was “threatening our free institutions” [23, p. 9]. Various prizes were offered for anyone who could solve this challenge, beginning with a $25 set of teeth and culminating with Sam Loyd’s famous $1,000 cash prize.}, author = {Brunck, Florestan R and Kwan, Matthew Alan}, issn = {0343-6993}, journal = {Mathematical Intelligencer}, pages = {52--65}, publisher = {Springer Nature}, title = {{Books, Hallways, and social butterflies: A note on sliding block puzzles}}, doi = {10.1007/s00283-024-10358-x}, volume = {47}, year = {2025}, } @article{21007, abstract = {Currently, the best known tradeoff between approximation ratio and complexity for the Sparsest Cut problem is achieved by the algorithm in [Sherman, FOCS 2009]: it computes O(√(log n)/ε)-approximation using O(nε logO(1) n) maxflows for any ε∈[Θ(1/log n),Θ(1)]. It works by solving the SDP relaxation of [Arora-Rao-Vazirani, STOC 2004] using the Multiplicative Weights Update algorithm (MW) of [Arora-Kale, JACM 2016]. To implement one MW step, Sherman approximately solves a multicommodity flow problem using another application of MW. Nested MW steps are solved via a certain "chaining" algorithm that combines results of multiple calls to the maxflow algorithm. We present an alternative approach that avoids solving the multicommodity flow problem and instead computes "violating paths". This simplifies Sherman's algorithm by removing a need for a nested application of MW, and also allows parallelization: we show how to compute O(√(log n)/ε)-approximation via O(logO(1) n) maxflows using O(nε) processors. We also revisit Sherman's chaining algorithm, and present a simpler version together with a new analysis.}, author = {Kolmogorov, Vladimir}, issn = {1549-6333}, journal = {ACM Transactions on Algorithms}, number = {4}, pages = {1--22}, publisher = {Association for Computing Machinery}, title = {{A simpler and parallelizable O(√log n)-approximation algorithm for SPARSEST CUT}}, doi = {10.1145/3748723}, volume = {21}, year = {2025}, } @article{19026, abstract = {The back-action damping of mechanical motion by electromagnetic radiation is typically overwhelmed by internal loss channels unless demanding experimental ingredients such as superconducting resonators, high-quality optical cavities, or large magnetic fields are employed. Here we demonstrate the first room temperature, cavity-free, all-electric device where back-action damping exceeds internal loss, enabled by a mechanically compliant parallel-plate capacitor with a nanoscale plate separation and an aspect ratio exceeding 1,000. The device has 4 orders of magnitude lower insertion loss than a comparable commercial quartz crystal and achieves a position imprecision rivaling optical interferometers. With the help of a back-action isolation scheme, we observe radiative cooling of mechanical motion by a remote cryogenic load. This work provides a technologically accessible route to high-precision sensing, transduction, and signal processing.}, author = {Puglia, Denise and Odessey, Rachel H and Burns, Peter and Luhmann, Niklas and Schmid, Silvan and Higginbotham, Andrew P}, issn = {1530-6992}, journal = {Nano Letters}, number = {7}, pages = {2749--2755}, publisher = {American Chemical Society}, title = {{Room temperature, cavity-free capacitive strong coupling to mechanical motion}}, doi = {10.1021/acs.nanolett.4c05796}, volume = {25}, year = {2025}, } @article{20656, 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 prerequisite for (1) self-organizing processes, including vascular tissue formation, and (2) directional growth responses such as gravitropism. Here, we identify a mechanism by which auxin signaling directly targets PIN auxin transporters. Via the cell-surface AUXIN-BINDING PROTEIN1 (ABP1)-TRANSMEMBRANE KINASE 1 (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 3 (ABL3) auxin receptor. Such positive feedback between cell-surface auxin signaling and PIN-mediated polar auxin transport is fundamental for robust root gravitropism and presumably 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 Kulich, Ivan and Jaillais, Yvon and Friml, Jiří}, issn = {0092-8674}, journal = {Cell}, number = {22}, pages = {6138--6150.e17}, publisher = {Cell Press}, title = {{ABP1/ABL3-TMK1 cell-surface auxin signaling targets PIN2-mediated auxin fluxes for root gravitropism}}, doi = {10.1016/j.cell.2025.08.026}, volume = {188}, year = {2025}, } @unpublished{23174, abstract = {Roots must continuously adapt their growth and have evolved the ability to rapidly respond to diverse environmental and hormonal cues, including the phytohormone auxin. Auxin-induced cellular responses involve membrane depolarization, cytosolic calcium (Ca²⁺) elevation, and extracellular pH increase, but how these processes lead to rapid growth regulation remains unclear. Here, we show that cytosolic Ca²⁺ acts as a universal signal integrating diverse cues for rapid regulation of root growth. Using live imaging, microfluidics, and optogenetics in Arabidopsis, we demonstrate that a swift rise in cytosolic Ca²⁺ is the primary target of auxin signaling affecting growth inhibition. Disruption of Ca²⁺ influx abolishes these responses, whereas light-gated Ca²⁺ influx from the apoplast or endoplasmic reticulum stores inhibits growth. Multiple unrelated stimuli—including auxin, extracellular ATP, RALF peptides, and hydrogen peroxide—converge on this Ca²⁺-dependent mechanism. Cytosolic Ca²⁺ elevation thus represents a necessary and sufficient step for rapid growth inhibition, revealing a unifying principle of root signaling.}, author = {Randuch, Marek and Kulich, Ivan and Vladimirtsev, Dmitrii and Huang, Shouguang and Hedrich, Rainer and Friml, Jiří}, booktitle = {bioRxiv}, title = {{Cytosolic Ca2+ as a universal signal for rapid root growth regulation}}, doi = {10.1101/2025.10.17.683082}, year = {2025}, } @phdthesis{20485, author = {Misova, Michaela}, isbn = {978-3-99078-068-8}, issn = {2663-337X}, pages = {155}, publisher = {Institute of Science and Technology Austria}, title = {{Dissecting gap junction biology using the C. elegans nervous system}}, doi = {10.15479/AT-ISTA-20485}, year = {2025}, } @phdthesis{19557, author = {Schwarz, Lena A}, issn = {2663-337X}, pages = {124}, publisher = {Institute of Science and Technology Austria}, title = {{Mapping developmental dynamics of autism spectrum disorder mouse models at single-cell resolution}}, doi = {10.15479/AT-ISTA-19557}, 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{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{19993, abstract = {Ants are frequently challenged by different pathogens, which they counter with individual and collective responses. Usually, the pathogens like fungi or viruses are solitary and passive pathogens transmitted from host to host. Here, we use a nematobacterial pathogen complex to study worm-borne disease in black garden ants. These entomopathogenic nematodes are active parasites with an own behavior and chasing pray. In the first chapter, we investigated the basic biology of the host-pathogen relationship. We tested different ant life stages and found that adult ants display defense behaviors and are generally resistant to nematode infection, whereas brood is highly susceptible. In the case of worker pupae, we found a slight protective effect of the cocoon. When larvae are accompanied by adults, meaning a queen or a group of workers, survival is significantly enhanced. Moreover, we found that nematodes can transmit from infected cadavers to healthy worker larvae, confirming a transmissible disease in ants. Again, worker presence significantly reduces transmission risk. In the end, we were also able to disentangle the pathogen system and investigate the pathogenic effect of the bacterial and nematode components. In the second chapter, we studied the effect of multiple infections in adult queens and queen larvae. By multiple exposures in the mode of coinfection and superinfections, we wanted to assess the detrimental effect of combined fungal and nematode exposure to better understand how the pathogens interact with each other in an ant host. We found instances where combined exposure lead to higher mortality in a given time frame in both, adult queens and queen larvae. Overall entomopathogenic nematodes are a promising model to study worm infections in ants which extend our knowledge on collective disease defense.}, author = {Strahodinsky, Florian}, issn = {2663-337X}, pages = {138}, publisher = {Institute of Science and Technology Austria}, title = {{Social immunity in a tri-partite host-pathogen relationship}}, doi = {10.15479/AT-ISTA-19993}, year = {2025}, } @phdthesis{19722, abstract = {As root epidermal cells progress from a phase of elongation to differentiation, their cortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The hormone cytokinin, a key regulator of root development, facilitates these cytoskeletal changes. However, the molecular mechanisms underlying hormone-mediated MT reorientation during root development are still unknown. Here, we find that MT reorientation in root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell differentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s association with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end created by katanin-mediated severing at crossovers. Notably, our findings suggest that dynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning of the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets of cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1 association in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it increases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives MT reorganization during cell development by simultaneously modulating several microtubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool during this process.}, author = {Inumella, Syamala}, isbn = {978-3-99078-059-6}, issn = {2663-337X}, pages = {113}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of microtubule reorganization in elongating root epidermal cells}}, doi = {10.15479/AT-ISTA-19722}, year = {2025}, } @phdthesis{20470, abstract = {Systems design has classically relied on composable systems, in which individual subsystems have defined inputs, outputs, and interactions with each other; however, attempts at designing complex systems in synthetic biology has often run in to issues of crosstalk and interference, given that these systems must function within the context of the host. In nature, mobile genetic elements are systems that have evolved to travel between hosts, and thus appear to be a good candidate with which to evaluate composability. Selecting temperate phages as a model system, I used mathematical modelling to identify sources of information that temperate phages should respond to. I found that essential proteins of temperate phages can interfere with potential hosts, indicating limitations to composability. I also designed a lysogeny reporter construct and characterize its behavior across various laboratory and environmental strains, finding differences in phage lambda lysogens, and potential interference from prophages that already exist within the environmental strains. Although the information gathered is not conclusive, it suggests that composability is not a key property of temperate phages, implying that biological systems may not be composable, and that other system design principles should be considered when designing synthetic systems.}, author = {Wu, Bryan}, issn = {2663-337X}, pages = {102}, publisher = {Institute of Science and Technology Austria}, title = {{An examination on phages as a naturally composable system}}, doi = {10.15479/AT-ISTA-20470}, year = {2025}, } @phdthesis{20777, abstract = {A major challenge in neuroscience is deciphering how the brain orchestrates behavior in response to changes in environmental conditions. This process is characterized by several processing stages, from perception to the storage of important information. Information storage is performed by a memory system implemented through complex networks of highly interconnected neurons. The collective operational principles of neuronal networks that support formation and storage are the main topics of this thesis. To investigate the collective dynamics of the hippocampus from the perspective of the brain criticality hypothesis, I started by analyzing cascades of neural activity ¯ neuronal avalanches ¯ that have been characterized by the absence of a typical spatial or temporal scale. Measures derived from neuronal avalanches suggested that during wakefulness the hippocampus operated further away from criticality than during sleep/rest. In addition, neural activity propagated differently in these two brain states, as indicated by different collapses of the avalanche shapes. Next, the Phenomenological Renormalization Group approach also indicated conceptually similar differences, through the scaling exponent of activity variance α, which was higher during sleep/rest than during awake. These results confirmed that the activity of the hippocampus exhibits signatures of criticality and that these signatures change with the state of the brain. Next, I found that memory retention was predicted by the scaling exponent of activity variance α. The exponent α measured during the sleep/rest session that followed learning correlated with memory retention during the subsequent unrewarded testing session. Moreover, α predicted performance even when controlled for reactivation that occurs in parallel. Second, α measured in the sleep/rest phase that preceded learning was correlated with the learning speed. I analyzed distributions of the cells’ characteristic timescale and burstiness. The day-to-day variability of these distributions, during sleep/rest that followed learning, correlated with the scaling exponent of activity variance α, as well as with memory retention. These findings confirmed that variance scaling and functional heterogeneity provide behaviorally meaningful perspectives on hippocampal activity, as they are directly related to memory consolidation. I further investigated the process of memory acquisition and consolidation between the hippocampus CA1 and the mEC. During learning, CA1 cells shifted their firing field towards the goals, while mEC cells remained mostly stable, shifting their firing fields towards the goals during sleep/rest that followed learning. This shift during sleep/rest was supported by the reactivation process, which occurred in two ways, synchronously with CA1 (during SWRs) and independently of the hippocampal SWRs. Both types of reactivation predicted subsequent memory retention, as well as the amount of goal-related remapping. Again, the day-to-day variability of the distribution of the cell timescales correlated with the goal-related remapping, in CA1 during the learning session and in mEC during sleep/rest. These results suggest that in spatial navigation tasks, the functional responsibilities of CA1 and mEC change between learning and sleep/rest and that their function benefits from increased functional heterogeneity among cells. }, author = {Zivadinovic, Predrag}, issn = {2663-337X}, pages = {104}, publisher = {Institute of Science and Technology Austria}, title = {{Scale-free activity as a basis for spatial learning and memory in the brain}}, doi = {10.15479/AT-ISTA-20777}, year = {2025}, } @article{19424, abstract = {Hole spin qubits are rapidly emerging as the workhorse of semiconducting quantum processors because of their large spin-orbit interaction, enabling fast all-electric operations at low power. However, spin-orbit interaction also causes non-uniformities in devices, resulting in locally varying qubit energies and site-dependent anisotropies. While these anisotropies can be used to drive single-spins, if not properly harnessed, they can hinder the path toward large-scale quantum processors. Here, we report on microwave-driven singlet-triplet qubits in planar germanium and use them to investigate the anisotropy of two spins in a double quantum dot. We show two distinct operating regimes depending on the magnetic field direction. For in-plane fields, the two spins are largely anisotropic, and electrically tunable, which enables to measure all the available transitions; coherence times exceeding 3 $\mu$s are extracted. For out-of-plane fields, they have an isotropic response but preserve the substantial energy difference required to address the singlet-triplet qubit. Even in this field direction, where the qubit lifetime is strongly affected by nuclear spins, we find 400 ns coherence times. Our work adds a valuable tool to investigate and harness the anisotropy of spin qubits and can be implemented in any large-scale NxN device, facilitating the path towards scalable quantum processors.}, author = {Saez Mollejo, Jaime and Jirovec, Daniel and Schell, Yona A and Kukucka, Josip and Calcaterra, Stefano and Chrastina, Daniel and Isella, Giovanni and Rimbach-Russ, Maximilian and Bosco, Stefano and Katsaros, Georgios}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Exchange anisotropies in microwave-driven singlet-triplet qubits}}, doi = {10.1038/s41467-025-58969-y}, volume = {16}, year = {2025}, }