@phdthesis{20074, abstract = {Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. In chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. In chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. In summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development.}, author = {Hübschmann, Verena}, isbn = {978-3-99078-060-2}, issn = {2663-337X}, pages = {151}, publisher = {Institute of Science and Technology Austria}, title = {{Human microglia impact neuronal development in retinal organoids}}, doi = {10.15479/AT-ISTA-20074}, year = {2025}, } @article{19372, abstract = {We consider the confined Fröhlich polaron and establish an asymptotic series for the low-energy eigenvalues in negative powers of the coupling constant. The coefficients of the series are derived through a two-fold perturbation approach, involving expansions around the electron Pekar minimizer and the excitations of the quantum field.}, author = {Brooks, Morris and Mitrouskas, David Johannes}, issn = {2690-1005}, journal = {Probability and Mathematical Physics}, number = {1}, pages = {281--325}, publisher = {Mathematical Sciences Publishers}, title = {{Asymptotic series for low-energy excitations of the Fröhlich polaron at strong coupling}}, doi = {10.2140/pmp.2025.6.281}, volume = {6}, year = {2025}, } @article{20342, abstract = {Safety and liveness stand as fundamental concepts in formal languages, playing a key role in verification. The safety-liveness classification of boolean properties characterizes whether a given property can be falsified by observing a finite prefix of an infinite computation trace (always for safety, never for liveness). In the quantitative setting, properties are arbitrary functions from infinite words to partially-ordered domains. Extending this paradigm to the quantitative domain, where properties are arbitrary functions mapping infinite words to partially-ordered domains, we introduce and study the notions of quantitative safety and liveness. First, we formally define quantitative safety and liveness, and prove that our definitions induce conservative quantitative generalizations of both the safety-progress hierarchy and the safety-liveness decomposition of boolean properties. Consequently, like their boolean counterparts, quantitative properties can be min-decomposed into safety and liveness parts, or alternatively, max-decomposed into co-safety and co-liveness parts. We further establish a connection between quantitative safety and topological continuity and provide alternative characterizations of quantitative safety and liveness in terms of their boolean analogs. Second, we instantiate our framework with the specific classes of quantitative properties expressed by automata. These quantitative automata contain finitely many states and rational-valued transition weights, and their common value functions Inf, Sup, LimInf, LimSup, LimInfAvg, LimSupAvg, and DSum map infinite words into the totally-ordered domain of real numbers. For all common value functions, we provide a procedure for deciding whether a given automaton is safe or live, we show how to construct its safety closure, and we present a min-decomposition into safe and live automata.}, author = {Boker, Udi and Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, issn = {1860-5974}, journal = {Logical Methods in Computer Science}, number = {2}, publisher = {EPI Sciences}, title = {{Safety and liveness of quantitative properties and automata}}, doi = {10.46298/lmcs-21(2:2)2025}, volume = {21}, year = {2025}, } @article{22579, abstract = {Decades of research on the Mekong River basin have vastly expanded our knowledge of key hydrological and ecological processes, in part thanks to the development of modelling tools. However, few of these models are openly available to the research community or adhere to FAIR (Findable, Accessible, Interoperable, Reusable) principles, particularly in the domain of hydrology, in turn limiting transparency, reproducibility, and broader scientific engagement. Here, we address this gap and introduce VIC-Res Mekong, an open-source hydrologicalwater management model for the Mekong River basin. The model is implemented over a spatial domain of ∼630,000 km2 and has a resolution of 0.0625 degrees. Water and energy budgets are simulated with the Variable Infiltration Capacity (VIC) model, while streamflow routing is simulated with VIC-Res, which explicitly accounts for the storage and release dynamics of reservoirs. This is of key importance for a basin like the Mekong, where the active storage capacity of dams has increased from 20 km3 to nearly 80 km3 in the past fifteen years. To this purpose, VIC-Res Mekong integrates information from a database containing reservoir storage time series (inferred from satellite images) for 129 dams that accounts for more than 90% of total storage capacity. These data support both hindcast simulations and the derivation of reservoir operating rules, enabling a flexible and realistic representation of dam operations that allows to characterize in detail dam-induced hydrological alterations.}, author = {Eldardiry, Hisham and Mahto, Shanti Shwarup and Fatichi, Simone and Galelli, Stefano}, issn = {1873-6726}, journal = {Environmental Modelling & Software}, keywords = {VIC hydrologic model, Mekong river, Large-scale hydrology, Water resources management, Reservoir operations, Remote sensing}, publisher = {Elsevier}, title = {{VIC-Res Mekong: An open-source hydrological-water management model for the Mekong River basin}}, doi = {10.1016/j.envsoft.2025.106603}, volume = {193}, year = {2025}, } @article{22586, abstract = {Extreme rainfall events that break previous records are occurring more frequently worldwide, leading to severe flooding and infrastructure damage. Conventional flood design approaches, based on extreme value analysis (EVA) of limited historical data, often fail to anticipate such unprecedented extremes. Here, we present a stochastic approach that leverages the Advanced Weather Generator (AWE-GEN) to simulate a large ensemble of 100-year hourly rainfall time series, explicitly accounting for internal climate variability. By excluding the record-breaking event year during calibration, we assess the ability of our proposed method to reproduce unseen record-breaking events. We evaluated this approach using data from 2703 rain stations across nine countries. Our results show that the stochastic approach captures record-breaking events more reliably than EVA, achieving success rates exceeding 85% for 3–12-hour durations at a 100-year return period threshold. This framework provides a more robust way for estimating rainfall extremes and supports the design of resilient infrastructure under deep uncertainty.}, author = {Chen, Mengzhu and Mahto, Shanti Shwarup and He, Xiaogang and Jun, Changhyun and Paschalis, Athanasios and Peleg, Nadav and Mascaro, Giuseppe and Fatichi, Simone}, issn = {2948-2100}, journal = {npj Natural Hazards}, publisher = {Springer Nature}, title = {{Record-breaking rainfall: a stochastic approach for its prediction}}, doi = {10.1038/s44304-025-00148-6}, volume = {2}, year = {2025}, } @article{19701, abstract = {Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.}, author = {Tkačik, Gašper and Wolde, Pieter Rein Ten}, issn = {1936-1238}, journal = {Annual Review of Biophysics}, pages = {249--274}, publisher = {Annual Reviews}, title = {{Information processing in biochemical networks}}, doi = {10.1146/annurev-biophys-060524-102720}, volume = {54}, year = {2025}, } @article{20048, abstract = {During embryonic development, cell behaviors need to be tightly regulated in time and space. Yet how the temporal and spatial regulations of cell behaviors are interconnected during embryonic development remains elusive. To address this, we turned to zebrafish gastrulation, the process whereby dynamic cell behaviors generate the three principal germ layers of the early embryo. Here, we show that Hoxb cluster genes are expressed in a temporally collinear manner at the blastoderm margin, where mesodermal and endodermal (mesendoderm) progenitor cells are specified and ingress to form mesendoderm/hypoblast. Functional analysis shows that these Hoxb genes regulate the timing of cell ingression: under- or overexpression of Hoxb genes perturb the timing of mesendoderm cell ingression and, consequently, the positioning of these cells along the forming anterior-posterior body axis after gastrulation. Finally, we found that Hoxb genes control the timing of mesendoderm ingression by regulating cellular bleb formation and cell surface fluctuations in the ingressing cells. Collectively, our findings suggest that Hoxb genes interconnect the temporal and spatial pattern of cell behaviors during zebrafish gastrulation by controlling cell surface fluctuations.}, author = {Moriyama, Yuuta and Mitsui, Toshiyuki and Heisenberg, Carl-Philipp J}, issn = {1477-9129}, journal = {Development}, number = {12}, publisher = {Company of Biologists}, title = {{Hoxb genes determine the timing of cell ingression by regulating cell surface fluctuations during zebrafish gastrulation}}, doi = {10.1242/dev.204261}, volume = {152}, year = {2025}, } @article{21343, abstract = {The large sieve is used to estimate the density of quadratic polynomials Q ∈ Z[x], such that there exists an odd degree polynomial defined over Z which has resultant ±1 with Q. Given a monic polynomial R ∈ Z[x] of odd degree, this is used to show that for almost all quadratic polynomials Q ∈ Z[x], there exists a prime p such that Q and R share a common root in Fp. Using recent work of Landesman, an application to the average size of the odd part of the class group of quadratic number fields is also given}, author = {Browning, Timothy D and Chan, Yik Tung}, issn = {2270-518X}, journal = {Journal de l'Ecole Polytechnique - Mathematiques}, pages = {1677--1691}, publisher = {Ecole Polytechnique}, title = {{Solubility of a resultant equation and applications}}, doi = {10.5802/jep.320}, volume = {12}, year = {2025}, } @article{20249, abstract = {We develop a heuristic for the density of integer points on affine cubic surfaces. Our heuristic applies to smooth surfaces defined by cubic polynomials that are log K3, but it can also be adjusted to handle singular cubic surfaces. We compare our heuristic to Heath-Brown’s prediction for sums of three cubes, as well as to asymptotic formulae in the literature around Zagier’s work on the Markoff cubic surface, and work of Baragar and Umeda on further surfaces of Markoff-type. We also test our heuristic against numerical data for several families of cubic surfaces.}, author = {Browning, Timothy D and Wilsch, Florian Alexander}, issn = {1420-9020}, journal = {Selecta Mathematica New Series}, number = {4}, publisher = {Springer Nature}, title = {{Integral points on cubic surfaces: heuristics and numerics}}, doi = {10.1007/s00029-025-01074-1}, volume = {31}, year = {2025}, } @article{20218, abstract = {Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner.}, author = {Volpe, Giorgio and Araújo, Nuno A.M. and Guix, Maria and Miodownik, Mark and Martin, Nicolas and Alvarez, Laura and Simmchen, Juliane and Leonardo, Roberto Di and Pellicciotta, Nicola and Martinet, Quentin and Palacci, Jérémie A and Ng, Wai Kit and Saxena, Dhruv and Sapienza, Riccardo and Nadine, Sara and Mano, João F. and Mahdavi, Reza and Beck Adiels, Caroline and Forth, Joe and Santangelo, Christian and Palagi, Stefano and Seok, Ji Min and Webster-Wood, Victoria A. and Wang, Shuhong and Yao, Lining and Aghakhani, Amirreza and Barois, Thomas and Kellay, Hamid and Coulais, Corentin and Van Hecke, Martin and Pierce, Christopher J. and Wang, Tianyu and Chong, Baxi and Goldman, Daniel I. and Reina, Andreagiovanni and Trianni, Vito and Volpe, Giovanni and Beckett, Richard and Nair, Sean P. and Armstrong, Rachel}, issn = {1361-648X}, journal = {Journal of Physics: Condensed Matter}, number = {33}, publisher = {IOP Publishing}, title = {{Roadmap for animate matter}}, doi = {10.1088/1361-648X/adebd3}, volume = {37}, year = {2025}, } @article{20453, abstract = {Magnetotropic susceptibility is the thermodynamic coefficient that maps the curvature of free energy with respect to an applied magnetic field orientation, providing a means to quantify the magnetic anisotropy of a crystal. In this context, non-linear magnetic torque behavior has been reported in FePS3, motivating the investigation of similar non-linear characteristics in its magnetotropic susceptibility. In this work, we derive the non-linear magnetotropic susceptibility expressions for FePS3 in both ac*-and bc*-planes using complementary approaches: by taking the first derivative of torque and through the formal calculation of the magnetotropic susceptibility. Higher-order terms in the magnetization are included, and the final equations are obtained by applying symmetry constraints imposed by the C2h point group of the material. We analyze the behavior of the resulting non-linear expressions and identify the contributions of each parameter. Our theoretical results show good agreement with preliminary, unpublished experimental data, offering meaningful guidance for ongoing and future experimental work.}, author = {Farooq, Hamza and Nauman, Muhammad}, issn = {1361-648X}, journal = {Journal of Physics: Condensed Matter}, number = {40}, publisher = {IOP Publishing}, title = {{Non-linear magnetotropic susceptibility in FePS3}}, doi = {10.1088/1361-648X/ae0913}, volume = {37}, year = {2025}, } @article{20219, abstract = {Reproduction is a fundamental biological process, with organisms reproducing sexually, asexually, and, in some cases, utilizing both modes of reproduction within the same population. Does the ability to reproduce through a combination of asexual and sexual modes offer an evolutionary advantage over relying on either mode alone? Here, we introduce an empirically driven theoretical model to examine the dynamics and interplay between sexual and asexual reproduction in stick insect populations. We analyse it using a novel phase transition approach and corroborate it using published experimental data. We find that the presence of males can either increase or decrease the overall population size. However, maintaining an optimal ratio of parthenogenetic to sexual reproduction is crucial for male resilience, effectively delaying male extinction. Conversely, extreme levels of parthenogenetic reproduction—whether too high or too low—can lead to male extinction, emphasizing the need for a balanced number of virgin females to ensure the persistence of males. Our model also explains male absence in Carausius morosus and persistence in Extatosoma tiaratum. Our findings provide valuable insights into the interplay of reproductive strategies and contribute to broader discussions on the transitions between sexual and asexual reproduction.}, author = {Ayalon, Oran and Rajendran, Harikrishnan}, issn = {1742-5662}, journal = {Journal of the Royal Society Interface}, number = {229}, publisher = {Royal Society}, title = {{Interplay of asexual and sexual reproduction in bifunctional insects}}, doi = {10.1098/rsif.2025.0202}, volume = {22}, year = {2025}, } @unpublished{19762, abstract = {The cerebral cortex must contain the appropriate numbers of neurons in each layer to acquire its proper functional organization. Accordingly, neurogenesis requires precise regulation along development. Cortical neurons are made either directly by Radial Glia Cells (RGCs) that self- consume, or indirectly from RGCs via Intermediate Progenitor Cells (IPCs) and largely preserving the RGC pool. According to the standing model of cortical development, Direct Neurogenesis predominates at early stages of development, and progressively shifts to Indirect Neurogenesis, which predominates at late stages. However, neurogenesis at early stages should be compatible with RGC amplification, and neurogenesis at late stages needs to involve RGC consumption, which seems in conflict with the standing model. Here we studied the modes of neurogenesis along cortical development using multiple approaches, including birthdating, live imaging and MADM clone labeling. Contrary to the established dogma, our data show that Indirect Neurogenesis clearly predominates at early developmental stages, gradually shifting to Direct Neurogenesis at late stages. These findings challenge the current model of cortical neurogenesis, and prompt a re-evaluation of previous and ongoing work about the genetic and molecular mechanisms regulating this process.}, author = {Cárdenas, Adrián and Çelik, Irem and Espinós, Alexandre and Streicher, Carmen and López-González, Lara and del-Valle-Anton, Lucia and Fernández, Virginia and Amin, Salma and Negri, Enrico and Ortuño, Eduardo Fernández and Hippenmeyer, Simon and Borrell, Víctor}, booktitle = {bioRxiv}, title = {{Early indirect neurogenesis transitions to late direct neurogenesis in mouse cerebral cortex development}}, doi = {10.1101/2025.05.22.655488}, year = {2025}, } @unpublished{19717, abstract = {Radial glial progenitors (RGPs) generate all projection neurons (PNs) in the cerebral cortex through incompletely understood processes. Herein, we combine Mosaic Analysis with Double Markers (MADM)-based clonal analysis at embryonic days 12.5 and 13.5 with early postnatal callosal tracing to reveal a lineage progression that challenges the inside-outside model of cortical development and the conventional view of an invariable sequence of asymmetric neurogenic divisions. Our data demonstrate that early multipotent RGPs generate all extra-telencephalic (ET) and intra-telencephalic (IT) PNs across all layers through parallel sublineages and the random specification, during the earliest neurogenic divisions, of fate-restricted daughter RGPs. While the neuronal production of the parental multipotent RGPs consists of small ET-PN or IT-PN outputs, fate-restricted RGPs produce larger translaminar outputs spanning deep and upper layers of only IT-PNs, the predominant mammalian PN subtype. We further show that the emergence of IT-PN fate-restricted RGPs also leads to quantitatively and temporally stereotyped neurogenesis population-wise.}, author = {Varela-Martínez, I and Villalba Requena, Ana and Garcia-Marqués, J. and Hippenmeyer, Simon and Nieto, M.}, booktitle = {bioRxiv}, title = {{Early emergence of projection-subtype fate-restricted radial glial progenitors orchestrates neocortical neurogenesis}}, doi = {10.1101/2025.05.07.652665}, year = {2025}, } @unpublished{19674, abstract = {When examined through the lens of their residual streams, a puzzling property emerges in transformer networks: residual contributions (e.g., attention heads) sometimes specialize in specific tasks or input attributes. In this paper, we analyze this phenomenon in vision transformers, focusing on the spectral geometry of residuals, and explore its implications for modality alignment in vision-language models. First, we link it to the intrinsically low-dimensional structure of visual head representations, zooming into their principal components and showing that they encode specialized roles across a wide variety of input data distributions. Then, we analyze the effect of head specialization in multimodal models, focusing on how improved alignment between text and specialized heads impacts zero-shot classification performance. This specialization-performance link consistently holds across diverse pre-training data, network sizes, and objectives, demonstrating a powerful new mechanism for boosting zero-shot classification through targeted alignment. Ultimately, we translate these insights into actionable terms by introducing ResiDual, a technique for spectral alignment of the residual stream. Much like panning for gold, it lets the noise from irrelevant unit principal components (i.e., attributes) wash away to amplify task-relevant ones. Remarkably, this dual perspective on modality alignment yields fine-tuning level performance on different data distributions while modelling an extremely interpretable and parameter-efficient transformation, as we extensively show on 70 pre-trained network-dataset combinations (7 models, 10 datasets).}, author = {Basile, Lorenzo and Maiorca, Valentino and Bortolussi, Luca and Rodolà, Emanuele and Locatello, Francesco}, booktitle = {arXiv}, title = {{ResiDual transformer alignment with spectral decomposition}}, doi = {10.48550/arXiv.2411.00246}, year = {2025}, } @phdthesis{20167, author = {Schön, Hanna}, isbn = {978-3-99078-061-9}, issn = {2663-337X}, pages = {171}, publisher = {Institute of Science and Technology Austria}, title = {{The ER complex SUTU-7/MACO-1 regulates the fate of mRNAs encoding GPCRs}}, doi = {10.15479/AT-ISTA-20167}, year = {2025}, } @article{20538, abstract = {In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins.}, author = {Knödlstorfer, Sonja and Toscano, Giorgia and Ptaszek, Aleksandra L. and Kontaxis, Georg and Napoli, Federico and Schneider, Jakob and Maier, Katharina and Kapitonova, Anna and Lichtenecker, Roman J. and Schanda, Paul and Konrat, Robert}, issn = {1089-8638}, journal = {Journal of Molecular Biology}, number = {23}, publisher = {Elsevier}, title = {{A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0}}, doi = {10.1016/j.jmb.2025.169465}, volume = {437}, year = {2025}, } @article{20258, abstract = {The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR.}, author = {Rohden, Darja and Napoli, Federico and Kapitonova, Anna and Tatman, Benjamin and Lichtenecker, Roman J. and Schanda, Paul}, issn = {1089-8638}, journal = {Journal of Molecular Biology}, number = {23}, publisher = {Elsevier}, title = {{Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme}}, doi = {10.1016/j.jmb.2025.169379}, volume = {437}, year = {2025}, } @misc{19956, abstract = {The specific introduction of 1H-13C or 1H-15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a 13C-1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected arginine MAS NMR approaches to probe arginine dynamics. In experiments on crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR}, author = {Schanda, Paul}, publisher = {Institute of Science and Technology Austria}, title = {{Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme}}, doi = {10.15479/AT-ISTA-19956}, year = {2025}, } @unpublished{19398, abstract = {Receptor-like kinases (RLKs), particularly the Transmembrane Kinase (TMK) family, play essential roles in signaling and development, with TMKs being key components of auxin perception and downstream phosphorylation events. While TMKs’ involvement in auxin canalization, a process essential for vasculature formation and regeneration, has been established, nonetheless, the additional signaling and regulatory partners remain poorly understood. In this study, we identify and characterize seven leucine-rich repeat RLKs (TINT1–TINT7) as novel interactors of TMK1, revealing their diverse evolutionary, structural, and functional characteristics. Our results show that TINTs interact with TMK1 and highlight their roles in regulating various developmental processes. Majority of TINTs contributes, together with TMK1, to auxin canalization, with TINT5 linking TMK1 to other canalization component CAMEL. Beyond canalization, we also establish the role of TINT-TMK1 interactions in processes such as stomatal movement and the hypocotyl’s gravitropic response. These findings suggest that TINTs, through their interaction with TMK1, are integral components of various signaling networks, contributing to both auxin canalization and broader plant development.}, author = {Monzer, Aline and Mazur, Ewa and Rodriguez Solovey, Lesia and Gallei, Michelle C and Zou, Minxia and Smejkal, Michael and Cervenova, Ema and Friml, Jiří}, booktitle = {bioRxiv}, title = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}}, doi = {10.1101/2025.02.28.640727}, year = {2025}, }