@article{13201, abstract = {As a crucial nitrogen source, nitrate (NO3−) is a key nutrient for plants. Accordingly, root systems adapt to maximize NO3− availability, a developmental regulation also involving the phytohormone auxin. Nonetheless, the molecular mechanisms underlying this regulation remain poorly understood. Here, we identify low-nitrate-resistant mutant (lonr) in Arabidopsis (Arabidopsis thaliana), whose root growth fails to adapt to low-NO3− conditions. lonr2 is defective in the high-affinity NO3− transporter NRT2.1. lonr2 (nrt2.1) mutants exhibit defects in polar auxin transport, and their low-NO3−-induced root phenotype depends on the PIN7 auxin exporter activity. NRT2.1 directly associates with PIN7 and antagonizes PIN7-mediated auxin efflux depending on NO3− levels. These results reveal a mechanism by which NRT2.1 in response to NO3− limitation directly regulates auxin transport activity and, thus, root growth. This adaptive mechanism contributes to the root developmental plasticity to help plants cope with changes in NO3− availability.}, author = {Wang, Yalu and Yuan, Zhi and Wang, Jinyi and Xiao, Huixin and Wan, Lu and Li, Lanxin and Guo, Yan and Gong, Zhizhong and Friml, Jiří and Zhang, Jing}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {25}, publisher = {National Academy of Sciences}, title = {{The nitrate transporter NRT2.1 directly antagonizes PIN7-mediated auxin transport for root growth adaptation}}, doi = {10.1073/pnas.2221313120}, volume = {120}, year = {2023}, } @article{12802, abstract = {Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction.}, author = {Knaus, Lisa and Basilico, Bernadette and Malzl, Daniel and Gerykova Bujalkova, Maria and Smogavec, Mateja and Schwarz, Lena A. and Gorkiewicz, Sarah and Amberg, Nicole and Pauler, Florian and Knittl-Frank, Christian and Tassinari, Marianna and Maulide, Nuno and Rülicke, Thomas and Menche, Jörg and Hippenmeyer, Simon and Novarino, Gaia}, issn = {0092-8674}, journal = {Cell}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {9}, pages = {1950--1967.e25}, publisher = {Elsevier}, title = {{Large neutral amino acid levels tune perinatal neuronal excitability and survival}}, doi = {10.1016/j.cell.2023.02.037}, volume = {186}, year = {2023}, } @phdthesis{14697, abstract = {During my Ph.D. research, I managed a series of projects, each focused on the mechanisms underlying cell migration. My work involved an in-depth examination of the complex strategies employed by neutrophils, with a specific focus on their ability to synchronize spatial-temporal cues and optimize their gradient perception. However, it is essential to acknowledge that not all projects yielded successful results, as some ideas were discontinued and are archived for future reference within this thesis. My main project investigated how neutrophils decode spatial cues for precise navigation. Human neutrophils showcased distinct movement patterns based on source type – linear or point-like. By combining single-cell tracking in 3D environments with proxy dyes, this project linked cell behaviors to gradient changes, revealing a stronger response to semi-exponential gradients from point sources. In addition, neutrophils exhibited oscillating migration speeds, using speed minima to adjust trajectories toward sources. Experiencing continuous concentration changes, they accelerated over time and employed a "Run and Fumble" strategy, alternating between consistent runs and strategic "tumbles" for efficient navigation. The project extended to the possibility of cells amplifying perceived gradients by enclosing their immediate surroundings, pushing attractants forward for enrichment while depleting it at the cell rear. Microfluidic devices were employed, and various experimental parameters configurations were optimized. Although significant differences in migratory efficacy were detected across pore sizes and device heights, quantifying gradient manipulation effects proved challenging. The "Laser-Assisted Protein Adsorption by Photobleaching" (LAPAP) project was promising, as it allowed the printing of gradients. Initially successful with dendritic cells, we aimed to adapt it for neutrophils. Through extensive experimentation with multiple parameters, we attempted to trigger responses from neutrophils. Despite these efforts and collaboration, the project failed due to practical challenges and limitations. Facing a lack of neutrophil-like cells at IST, we initially established the SCF-HoxB8 primary murine cell line. Despite their existence, their migratory behavior was largely unexplored due to potential limitations. Through differentiation protocol refinements we enhanced their migratory capabilities, though their capacity still lagged behind human neutrophils. Despite this, the improved migration potential of these cells pointed toward their utility for in vitro murine neutrophil migration studies.}, author = {Stopp, Julian A}, isbn = {978-3-99078-038-1}, issn = {2663-337X}, pages = {226}, publisher = {Institute of Science and Technology Austria}, title = {{Neutrophils on the hunt : Migratory strategies employed by neutrophils to fulfill their effector function}}, doi = {10.15479/at:ista:14697}, year = {2023}, } @article{14360, abstract = {To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.}, author = {Sitarska, Ewa and Almeida, Silvia Dias and Beckwith, Marianne Sandvold and Stopp, Julian A and Czuchnowski, Jakub and Siggel, Marc and Roessner, Rita and Tschanz, Aline and Ejsing, Christer and Schwab, Yannick and Kosinski, Jan and Sixt, Michael K and Kreshuk, Anna and Erzberger, Anna and Diz-Muñoz, Alba}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles}}, doi = {10.1038/s41467-023-41173-1}, volume = {14}, year = {2023}, } @phdthesis{12531, abstract = {All visual experiences of the vertebrates begin with light being converted into electrical signals by the eye retina. Retinal ganglion cells (RGCs) are the neurons of the innermost layer of the mammal retina, and they transmit visual information to the rest of the brain. It has been shown that RGCs vary in their morphology and genetic profiles, moreover they can be unambiguously grouped into subtypes that share the same morphological and/or molecular properties. However, in terms of RGCs function, it remains unclear how many distinct types there are and what response properties their typology relies on. Even given the recent studies that successfully classified RGCs in a patch of the retina [1] and in scotopic conditions [2], the question remains whether the found subtypes persist across the entire retina. In this work, using a novel imaging method, we show that, when sampled from a large portion of the retina, RGCs can not be clearly divided into functional subtypes. We found that in photopic conditions, which implies more prominent natural scene statistic differences across the visual field, response properties can be exhibited by cells differently depending on their location in the retina, which leads to formation of a gradient of features rather than distinct classes. This finding suggests that RGCs follow a global organization across the visual field of the animal, adapting each RGC subtype to the requirements imposed by the natural scene statistics.}, author = {Kirillova, Kseniia}, issn = {2791-4585}, pages = {46}, publisher = {Institute of Science and Technology Austria}, title = {{Panoramic functional gradients across the mouse retina}}, doi = {10.15479/at:ista:12531}, year = {2023}, } @phdthesis{14323, abstract = {Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube.}, author = {Kuzmicz-Kowalska, Katarzyna}, issn = {2663-337X}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord}}, doi = {10.15479/at:ista:14323}, year = {2023}, } @article{12837, abstract = {As developing tissues grow in size and undergo morphogenetic changes, their material properties may be altered. Such changes result from tension dynamics at cell contacts or cellular jamming. Yet, in many cases, the cellular mechanisms controlling the physical state of growing tissues are unclear. We found that at early developmental stages, the epithelium in the developing mouse spinal cord maintains both high junctional tension and high fluidity. This is achieved via a mechanism in which interkinetic nuclear movements generate cell area dynamics that drive extensive cell rearrangements. Over time, the cell proliferation rate declines, effectively solidifying the tissue. Thus, unlike well-studied jamming transitions, the solidification uncovered here resembles a glass transition that depends on the dynamical stresses generated by proliferation and differentiation. Our finding that the fluidity of developing epithelia is linked to interkinetic nuclear movements and the dynamics of growth is likely to be relevant to multiple developing tissues.}, author = {Bocanegra, Laura and Singh, Amrita and Hannezo, Edouard B and Zagórski, Marcin P and Kicheva, Anna}, issn = {1745-2481}, journal = {Nature Physics}, pages = {1050--1058}, publisher = {Springer Nature}, title = {{Cell cycle dynamics control fluidity of the developing mouse neuroepithelium}}, doi = {10.1038/s41567-023-01977-w}, volume = {19}, year = {2023}, } @phdthesis{13081, abstract = {During development, tissues undergo changes in size and shape to form functional organs. Distinct cellular processes such as cell division and cell rearrangements underlie tissue morphogenesis. Yet how the distinct processes are controlled and coordinated, and how they contribute to morphogenesis is poorly understood. In our study, we addressed these questions using the developing mouse neural tube. This epithelial organ transforms from a flat epithelial sheet to an epithelial tube while increasing in size and undergoing morpho-gen-mediated patterning. The extent and mechanism of neural progenitor rearrangement within the developing mouse neuroepithelium is unknown. To investigate this, we per-formed high resolution lineage tracing analysis to quantify the extent of epithelial rear-rangement at different stages of neural tube development. We quantitatively described the relationship between apical cell size with cell cycle dependent interkinetic nuclear migra-tions (IKNM) and performed high cellular resolution live imaging of the neuroepithelium to study the dynamics of junctional remodeling. Furthermore, developed a vertex model of the neuroepithelium to investigate the quantitative contribution of cell proliferation, cell differentiation and mechanical properties to the epithelial rearrangement dynamics and validated the model predictions through functional experiments. Our analysis revealed that at early developmental stages, the apical cell area kinetics driven by IKNM induce high lev-els of cell rearrangements in a regime of high junctional tension and contractility. After E9.5, there is a sharp decline in the extent of cell rearrangements, suggesting that the epi-thelium transitions from a fluid-like to a solid-like state. We found that this transition is regulated by the growth rate of the tissue, rather than by changes in cell-cell adhesion and contractile forces. Overall, our study provides a quantitative description of the relationship between tissue growth, cell cycle dynamics, epithelia rearrangements and the emergent tissue material properties, and novel insights on how epithelial cell dynamics influences tissue morphogenesis.}, author = {Bocanegra, Laura}, issn = {2663-337X}, pages = {93}, publisher = {Institute of Science and Technology Austria}, title = {{Epithelial dynamics during mouse neural tube development}}, doi = {10.15479/at:ista:13081}, year = {2023}, } @phdthesis{12800, abstract = {The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. }, author = {Julseth, Mara}, issn = {2791-4585}, pages = {21}, publisher = {Institute of Science and Technology Austria}, title = {{The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone}}, doi = {10.15479/at:ista:12800}, year = {2023}, } @phdthesis{14422, abstract = {Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of changes in the brain throughout adulthood, regrouped under the term "plasticity". Some cells in the brain —neurons— and specifically changes in the connections between neurons, the synapses, were shown to be crucial for the formation, selection, and consolidation of memories from past experiences. These ongoing changes of synapses across time are called synaptic plasticity. Understanding how a myriad of biochemical processes operating at individual synapses can somehow work in concert to give rise to meaningful changes in behavior is a fascinating problem and an active area of research. However, the experimental search for the precise plasticity mechanisms at play in the brain is daunting, as it is difficult to control and observe synapses during learning. Theoretical approaches have thus been the default method to probe the plasticity-behavior connection. Such studies attempt to extract unifying principles across synapses and model all observed synaptic changes using plasticity rules: equations that govern the evolution of synaptic strengths across time in neuronal network models. These rules can use many relevant quantities to determine the magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic action potentials, the recent neuronal activity levels, the state of neighboring synapses, etc. However, analytical studies rely heavily on human intuition and are forced to make simplifying assumptions about plasticity rules. In this thesis, we aim to assist and augment human intuition in this search for plasticity rules. We explore whether a numerical approach could automatically discover the plasticity rules that elicit desired behaviors in large networks of interconnected neurons. This approach is dubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make neuronal networks learn how to solve a desired task. We first write all the potential plasticity mechanisms to consider using a single expression with adjustable parameters. We then optimize these plasticity parameters using evolutionary strategies or Bayesian inference on tasks known to involve synaptic plasticity, such as familiarity detection and network stabilization. We show that these automated approaches are powerful tools, able to complement established analytical methods. By comprehensively screening plasticity rules at all synapse types in realistic, spiking neuronal network models, we discover entire sets of degenerate plausible plasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more robust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity rules, and provide fresh insights on synaptic plasticity in spiking network models. }, author = {Confavreux, Basile J}, issn = {2663-337X}, pages = {148}, publisher = {Institute of Science and Technology Austria}, title = {{Synapseek: Meta-learning synaptic plasticity rules}}, doi = {10.15479/at:ista:14422}, year = {2023}, } @article{14656, abstract = {Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.}, author = {Nardin, Michele and Csicsvari, Jozsef L and Tkačik, Gašper and Savin, Cristina}, issn = {1529-2401}, journal = {The Journal of Neuroscience}, number = {48}, pages = {8140--8156}, publisher = {Society for Neuroscience}, title = {{The structure of hippocampal CA1 interactions optimizes spatial coding across experience}}, doi = {10.1523/JNEUROSCI.0194-23.2023}, volume = {43}, year = {2023}, } @article{14759, abstract = {Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method.}, author = {Wald, Sebastian and Diorico, Fritz R and Hosten, Onur}, issn = {2155-3165}, journal = {Applied Optics}, keywords = {Atomic and Molecular Physics, and Optics, Engineering (miscellaneous), Electrical and Electronic Engineering}, number = {1}, pages = {1--7}, publisher = {Optica Publishing Group}, title = {{Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone}}, doi = {10.1364/ao.474118}, volume = {62}, year = {2023}, } @article{13200, abstract = {Recent quantum technologies have established precise quantum control of various microscopic systems using electromagnetic waves. Interfaces based on cryogenic cavity electro-optic systems are particularly promising, due to the direct interaction between microwave and optical fields in the quantum regime. Quantum optical control of superconducting microwave circuits has been precluded so far due to the weak electro-optical coupling as well as quasi-particles induced by the pump laser. Here we report the coherent control of a superconducting microwave cavity using laser pulses in a multimode electro-optical device at millikelvin temperature with near-unity cooperativity. Both the stationary and instantaneous responses of the microwave and optical modes comply with the coherent electro-optical interaction, and reveal only minuscule amount of excess back-action with an unanticipated time delay. Our demonstration enables wide ranges of applications beyond quantum transductions, from squeezing and quantum non-demolition measurements of microwave fields, to entanglement generation and hybrid quantum networks.}, author = {Qiu, Liu and Sahu, Rishabh and Hease, William J and Arnold, Georg M and Fink, Johannes M}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Nature Research}, title = {{Coherent optical control of a superconducting microwave cavity via electro-optical dynamical back-action}}, doi = {10.1038/s41467-023-39493-3}, volume = {14}, year = {2023}, } @unpublished{18953, abstract = {The rapid development of superconducting quantum hardware is expected to run into significant I/O restrictions due to the need for large-scale error correction in a cryogenic environment. Classical data centers rely on fiber-optic interconnects to remove similar networking bottlenecks and to allow for reconfigurable, software-defined infrastructures. In the same spirit, ultra-cold electro-optic links have been proposed and used to generate qubit control signals, or to replace cryogenic readout electronics. So far, the latter suffered from either low efficiency, low bandwidth and the need for additional microwave drives, or breaking of Cooper pairs and qubit states. In this work we realize electro-optic microwave photonics at millikelvin temperatures to implement a radio-over-fiber qubit readout that does not require any active or passive cryogenic microwave equipment. We demonstrate all-optical single-shot-readout by means of the Jaynes-Cummings nonlinearity in a circulator-free readout scheme. Importantly, we do not observe any direct radiation impact on the qubit state as verified with high-fidelity quantum-non-demolition measurements despite the absence of shielding elements. This compatibility between superconducting circuits and telecom wavelength light is not only a prerequisite to establish modular quantum networks, it is also relevant for multiplexed readout of superconducting photon detectors and classical superconducting logic. Moreover, this experiment showcases the potential of electro-optic radiometry in harsh environments - an electronics-free sensing principle that extends into the THz regime with applications in radio astronomy, planetary missions and earth observation.}, author = {Arnold, Georg M and Werner, Thomas and Sahu, Rishabh and Kapoor, Lucky and Qiu, Liu and Fink, Johannes M}, booktitle = {arXiv}, title = {{All-optical single-shot readout of a superconducting qubit}}, doi = {10.48550/ARXIV.2310.16817}, year = {2023}, } @article{14274, abstract = {Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.}, author = {Alanko, Jonna H and Ucar, Mehmet C and Canigova, Nikola and Stopp, Julian A and Schwarz, Jan and Merrin, Jack and Hannezo, Edouard B and Sixt, Michael K}, issn = {2470-9468}, journal = {Science Immunology}, keywords = {General Medicine, Immunology}, number = {87}, publisher = {American Association for the Advancement of Science}, title = {{CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration}}, doi = {10.1126/sciimmunol.adc9584}, volume = {8}, year = {2023}, } @phdthesis{14226, abstract = {We introduce the notion of a Faustian interchange in a 1-parameter family of smooth functions to generalize the medial axis to critical points of index larger than 0. We construct and implement a general purpose algorithm for approximating such generalized medial axes.}, author = {Stephenson, Elizabeth R}, issn = {2791-4585}, pages = {43}, publisher = {Institute of Science and Technology Austria}, title = {{Generalizing medial axes with homology switches}}, doi = {10.15479/at:ista:14226}, year = {2023}, } @phdthesis{14510, abstract = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment control of protein regulators for vesicle maturation and release. During the early stages of endocytosis, an area of flat membrane is remodelled by proteins to create a spherical vesicle against intracellular forces. After the Clathrin-coated vesicle (CCV) is fully formed, scission machinery releases it from the plasma membrane, and cargo proceeds for recycling or degradation through early endosomes / Trans Golgi network. Protein machineries that mediate membrane bending and vesicle release in plants are unknown. However, studies show, that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against highturgor pressure compared to other model systems. First, by using biochemical and advanced live microscopy approaches we investigate the TPLATE complex, a plant-specific endocytosis protein complex. We found that TPLATE is peripherally associated with clathrin-coated vesicles and localises at the rim of endocytosis events. Next, our study of plant Dynamin-related protein 1C (DRP1C), which was hypothesised previously to play a role in vesicle release, shows the recruitment of the protein already at the early stages of endocytosis. Moreover, DRP1C assembles into organised ring-like structures and is able to induce membrane deformation and tubulation, suggesting its role also in membrane bending during early CME. Based on the data from mammalian and yeast systems, plant DynaminRelated Proteins 2 and SH3P2 protein are strong candidates to be part of the plant vesicle scission machinery; however, their precise role in plant CME has not been yet elucidated. Here, we characterised DRP2s and SH3P2 roles in CME by combining high-resolution imaging of endocytic events in vivo and protein characterisation. Although DRP2s and SH3P2 arrive together during late CME and physically interact, genetic analysis using ∆sh3p1,2,3 mutant and complementation with non-DRP2-interacting SH3P2 variants suggest that SH3P2 does not directly recruit DRP2s to the site of endocytosis. Summarising our research, these observations provide new important insights into the mechanism of plant CME and show that, despite plants posses many homologues of mammalian and yeast CME components, they do not necessarily act in the same manner. }, author = {Gnyliukh, Nataliia}, isbn = {978-3-99078-037-4}, issn = {2663-337X}, keywords = {Clathrin-Mediated Endocytosis, vesicle scission, Dynamin-Related Protein 2, SH3P2, TPLATE complex, Total internal reflection fluorescence microscopy, Arabidopsis thaliana}, pages = {180}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanism of clathrin-coated vesicle formation during endocytosis in plants}}, doi = {10.15479/at:ista:14510}, year = {2023}, } @unpublished{14591, abstract = {Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.}, author = {Gnyliukh, Nataliia and Johnson, Alexander J and Nagel, Marie-Kristin and Monzer, Aline and Hlavata, Annamaria and Isono, Erika and Loose, Martin and Friml, Jiří}, booktitle = {bioRxiv}, title = {{Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants}}, doi = {10.1101/2023.10.09.561523}, year = {2023}, } @phdthesis{12470, abstract = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of nm-small synapses. To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse identification. I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue architecture, neuronal in- and output-fields, down to synapse morphology. Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal connectivity with light microscopy.}, author = {Michalska, Julia M}, isbn = {978-3-99078-026-8}, issn = {2663-337X}, pages = {201}, publisher = {Institute of Science and Technology Austria}, title = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}}, doi = {10.15479/at:ista:12470}, year = {2023}, } @phdthesis{14622, abstract = {This Ph.D. thesis presents a detailed investigation into Variational Quantum Algorithms (VQAs), a promising class of quantum algorithms that are well suited for near-term quantum computation due to their moderate hardware requirements and resilience to noise. Our primary focus lies on two particular types of VQAs: the Quantum Approximate Optimization Algorithm (QAOA), used for solving binary optimization problems, and the Variational Quantum Eigensolver (VQE), utilized for finding ground states of quantum many-body systems. In the first part of the thesis, we examine the issue of effective parameter initialization for the QAOA. The work demonstrates that random initialization of the QAOA often leads to convergence in local minima with sub-optimal performance. To mitigate this issue, we propose an initialization of QAOA parameters based on the Trotterized Quantum Annealing (TQA). We show that TQA initialization leads to the same performance as the best of an exponentially scaling number of random initializations. The second study introduces Transition States (TS), stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with increasing number of circuit layers. In the third section, we extend the QAOA to qudit systems, which are higher-dimensional generalizations of qubits. This chapter provides theoretical insights and practical strategies for leveraging the increased computational power of qudits in the context of quantum optimization algorithms and suggests a quantum circuit for implementing the algorithm on an ion trap quantum computer. Finally, we propose an algorithm to avoid “barren plateaus”, regions in parameter space with vanishing gradients that obstruct efficient parameter optimization. This novel approach relies on defining a notion of weak barren plateaus based on the entropies of local reduced density matrices and showcases how these can be efficiently quantified using shadow tomography. To illustrate the approach we employ the strategy in the VQE and show that it allows to successfully avoid barren plateaus in the initialization and throughout the optimization. Taken together, this thesis greatly enhances our understanding of parameter initialization and optimization in VQAs, expands the scope of QAOA to higher-dimensional quantum systems, and presents a method to address the challenge of barren plateaus using the VQE. These insights are instrumental in advancing the field of near-term quantum computation.}, author = {Sack, Stefan}, issn = {2663-337X}, pages = {142}, publisher = {Institute of Science and Technology Austria}, title = {{Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems}}, doi = {10.15479/at:ista:14622}, year = {2023}, }