@phdthesis{21360, author = {Riegler, Stefan}, issn = {2663-337X}, pages = {185}, publisher = {Institute of Science and Technology Austria}, title = {{Root system plasticity under nutrient limitation : Investigating hormonal and molecular drivers in Arabidopsis thaliana and Coffea species}}, doi = {10.15479/AT-ISTA-21360}, year = {2026}, } @misc{21363, abstract = {The data contains information on coffee differential gene expression as well as co-expression and trait correlations in two separate experiments. First, contrasting nitrogen supply, second, intra- and interspecific grafting.}, author = {Riegler, Stefan}, publisher = {Institute of Science and Technology Austria}, title = {{Thesis Data for Root System Plasticity under Nutrient Limitation: Investigating Hormonal and Molecular Drivers in Arabidopsis thaliana and Coffea species}}, doi = {10.15479/AT-ISTA-21363}, year = {2026}, } @article{20080, abstract = {Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored. Methods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation. Results: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation. Discussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction.}, author = {Gallemi, Marçal and Montesinos López, Juan C and Zarevski, Nikola and Pribyl, Jan and Skládal, Petr and Hannezo, Edouard B and Benková, Eva}, issn = {1664-462X}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Media}, title = {{Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties}}, doi = {10.3389/fpls.2025.1612366}, volume = {16}, year = {2025}, } @article{19003, abstract = {Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens. }, author = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G}, issn = {1532-298X}, journal = {The Plant Cell}, number = {4}, publisher = {Oxford University Press}, title = {{Super-resolution expansion microscopy in plant roots}}, doi = {10.1093/plcell/koaf006}, volume = {37}, year = {2025}, } @article{19594, abstract = {In this issue of Developmental Cell, Lee et al. identify a pivotal role for glutathione (GSH) in plant regeneration, a vital biological process enabling plants to regrow tissues and organs after injury. Applying single-cell RNA sequencing (scRNA-seq) and live imaging, the authors demonstrate that GSH, released upon tissue damage, accelerates cell-cycle transitions, particularly shortening the G1 phase, thereby facilitating efficient organ regeneration.}, author = {Benková, Eva}, issn = {1878-1551}, journal = {Developmental Cell}, number = {8}, pages = {1137--1139}, publisher = {Elsevier}, title = {{Unlocking plant regeneration: The role for glutathione}}, doi = {10.1016/j.devcel.2025.03.012}, volume = {60}, year = {2025}, } @phdthesis{19722, 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}, } @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}, publisher = {Cold Spring Harbor Laboratory}, title = {{TMK interacting network of receptor like kinases for auxin canalization and beyond}}, doi = {10.1101/2025.02.28.640727}, year = {2025}, } @phdthesis{20117, author = {Wang, Yiqun}, issn = {2663-337X}, pages = {108}, publisher = {Institute of Science and Technology Austria}, title = {{The role of dynamin related protein 2A in cytokinin regulated plant growth and development}}, doi = {10.15479/AT-ISTA-20117}, year = {2025}, } @article{20187, abstract = {Very long-chain fatty acids (VLCFAs), being constituents of different types of lipids, are critical factors in plant development, presumably due to their impact on the endomembrane system. The VLCFAs are synthesized in the endoplasmic reticulum by a heterotetrameric enzymatic complex including β-ketoacyl CoA reductase 1 (KCR1), whose mutant is lethal. Here, we describe the ectopic shoot meristems (esm) mutant, a viable kcr1 allele presumably affecting surface properties of the KCR1 protein. This kcr1-2 mutant shows reduced fatty acyl elongation that impacts VLCFAs. The kcr1-2 plants show severe defects during different stages of development, which all correlate with defects in polar localization and subcellular trafficking of PIN auxin transporters and resulting asymmetric auxin distribution. Detailed analysis of KCR1 expression and patterning defects in kcr1-2 suggests that KCR1 plays a role in delineating boundaries around meristematic and specialized differentiating tissues, including root and shoot meristems, initiating lateral roots, lateral root primordia, and trichomes. In these contexts, KCR1-produced VLCFAs may act in a non-cell-autonomous manner. Viable kcr1-2 represents a useful tool to study VLCFA roles in plant development and highlights VLCFAs as critical developmental factors at the interface of cell polarity and tissue development.}, author = {Babic, David and Abualia, Rashed and Fiedler, Lukas and Qi, Linlin and Tellier, Frédérique and Smoljan, Adrijana and Rakusova, Hana and Valošek, Petr and Han, Huibin and Benková, Eva and Faure, Jean Denis and Friml, Jiří}, issn = {1365-313X}, journal = {Plant Journal}, number = {3}, publisher = {Wiley}, title = {{Biosynthesis of very long-chain fatty acids is required for Arabidopsis auxin-mediated embryonic and post-embryonic development}}, doi = {10.1111/tpj.70396}, volume = {123}, year = {2025}, } @phdthesis{20362, author = {Babic, David}, issn = {2663-337X}, pages = {116}, publisher = {Institute of Science and Technology Austria}, title = {{Mechanisms of auxin-mediated early embryogenesis in Arabidopsis thaliana}}, doi = {10.15479/AT-ISTA-20362}, year = {2025}, } @article{20664, abstract = {Conference travel contributes to the climate footprint of academic research. Here, we provide a quantitative estimate of the carbon emissions associated with conference attendance by analyzing travel data from participants of 10 international conferences in the field of magnetic resonance, namely EUROMAR, ENC and ICMRBS. We find that attending a EUROMAR conference produces, on average, more than 1 t CO2 eq.. For the analyzed conferences outside Europe, the corresponding value is about 2–3 times higher, on average, with intercontinental trips amounting to up to 5 t. We compare these conference-related emissions to other activities associated with research and show that conference travel is a substantial portion of the total climate footprint of a researcher in magnetic resonance. We explore several strategies to reduce these emissions, including the impact of selecting conference venues more strategically and the possibility of decentralized conferences. Through a detailed comparison of train versus air travel – accounting for both direct and infrastructure-related emissions – we demonstrate that train travel offers considerable carbon savings. These data may provide a basis for strategic choices of future conferences in the field and for individuals deciding on their conference attendance.}, author = {Kapoor, Lucky and Ruzickova, Natalia and Zivadinovic, Predrag and Leitner, Valentin and Sisak, Maria A and Mweka, Cecelia N and Dobbelaere, Jeroen A and Katsaros, Georgios and Schanda, Paul}, issn = {2699-0016}, journal = {Magnetic Resonance}, number = {2}, pages = {243--256}, publisher = {Copernicus Publications}, title = {{Quantifying the carbon footprint of conference travel: The case of NMR meetings}}, doi = {10.5194/mr-6-243-2025}, volume = {6}, year = {2025}, } @article{18596, abstract = {Hormone perception and signaling pathways have a fundamental regulatory function in the physiological processes of plants. Cytokinins, a class of plant hormones, regulate cell division and meristem maintenance. The cytokinin signaling pathway is well established in the model plant Arabidopsis thaliana. Several negative feedback mechanisms, tightly controlling cytokinin signaling output, have been described previously. In this study, we identified a new feedback mechanism executed through alternative splicing of the cytokinin receptor AHK4/CRE1. A novel splicing variant named CRE1int7 results from seventh intron retention, introducing a premature termination codon in the transcript. We showed that CRE1int7 is translated in planta into a truncated receptor lacking the C-terminal receiver domain essential for signal transduction. CRE1int7 can bind cytokinin but cannot activate the downstream cascade. We present a novel negative feedback mechanism of the cytokinin signaling pathway, facilitated by a decoy receptor that can inactivate canonical cytokinin receptors via dimerization and compete with them for ligand binding. Ensuring proper plant growth and development requires precise control of the cytokinin signaling pathway at several levels. CRE1int7 represents a so-far unknown mechanism for fine-tuning the cytokinin signaling pathway in Arabidopsis.}, author = {Králová, Michaela and Kubalová, Ivona and Hajný, Jakub and Kubiasova, Karolina and Vagaská, Karolína and Ge, Zengxiang and Gallei, Michelle C and Semerádová, Hana and Kuchařová, Anna and Hönig, Martin and Monzer, Aline and Kovačik, Martin and Friml, Jiří and Novák, Ondřej and Benková, Eva and Ikeda, Yoshihisa and Zalabák, David}, issn = {1674-2052}, journal = {Molecular Plant}, number = {12}, pages = {1850--1865}, publisher = {Elsevier}, title = {{A decoy receptor derived from alternative splicing fine-tunes cytokinin signaling in Arabidopsis}}, doi = {10.1016/j.molp.2024.11.001}, volume = {17}, year = {2024}, } @misc{14842, abstract = {Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability.}, author = {Benková, Eva}, booktitle = {Current Biology}, issn = {1879-0445}, number = {1}, pages = {R3--R5}, publisher = {Elsevier}, title = {{Eva Benkova}}, doi = {10.1016/j.cub.2023.11.039}, volume = {34}, year = {2024}, } @article{15301, abstract = {Plant morphogenesis relies exclusively on oriented cell expansion and division. Nonetheless, the mechanism(s) determining division plane orientation remain elusive. Here, we studied tissue healing after laser-assisted wounding in roots of Arabidopsis thaliana and uncovered how mechanical forces stabilize and reorient the microtubule cytoskeleton for the orientation of cell division. We identified that root tissue functions as an interconnected cell matrix, with a radial gradient of tissue extendibility causing predictable tissue deformation after wounding. This deformation causes instant redirection of expansion in the surrounding cells and reorientation of microtubule arrays, ultimately predicting cell division orientation. Microtubules are destabilized under low tension, whereas stretching of cells, either through wounding or external aspiration, immediately induces their polymerization. The higher microtubule abundance in the stretched cell parts leads to the reorientation of microtubule arrays and, ultimately, informs cell division planes. This provides a long-sought mechanism for flexible re-arrangement of cell divisions by mechanical forces for tissue reconstruction and plant architecture.}, author = {Hörmayer, Lukas and Montesinos López, Juan C and Trozzi, N and Spona, Leonhard and Yoshida, Saiko and Marhavá, Petra and Caballero Mancebo, Silvia and Benková, Eva and Heisenberg, Carl-Philipp J and Dagdas, Y and Majda, M and Friml, Jiří}, issn = {1878-1551}, journal = {Developmental Cell}, number = {10}, pages = {1333--1344.e4}, publisher = {Elsevier}, title = {{Mechanical forces in plant tissue matrix orient cell divisions via microtubule stabilization}}, doi = {10.1016/j.devcel.2024.03.009}, volume = {59}, year = {2024}, } @article{18063, abstract = {The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.}, author = {Peng, Yakun and Ji, Kangkang and Mao, Yanbo and Wang, Yiqun and Korbei, Barbara and Luschnig, Christian and Shen, Jinbo and Benková, Eva and Friml, Jiří and Tan, Shutang}, issn = {2399-3642}, journal = {Communications Biology}, publisher = {Springer Nature}, title = {{Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis}}, doi = {10.1038/s42003-024-06747-9}, volume = {7}, year = {2024}, } @unpublished{18689, abstract = {Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.}, author = {Gallei, Michelle C and Truckenbrodt, Sven M and Kreuzinger, Caroline and Inumella, Syamala and Vistunou, Vitali and Sommer, Christoph M and Tavakoli, Mojtaba and Agudelo Duenas, Nathalie and Vorlaufer, Jakob and Jahr, Wiebke and Randuch, Marek and Johnson, Alexander J and Benková, Eva and Friml, Jiří and Danzl, Johann G}, booktitle = {bioRxiv}, title = {{Super-resolution expansion microscopy in plant roots}}, doi = {10.1101/2024.02.21.581330}, year = {2024}, } @article{14082, abstract = {Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision.}, author = {Higashi, Tomohito and Stephenson, Rachel E. and Schwayer, Cornelia and Huljev, Karla and Higashi, Atsuko Y. and Heisenberg, Carl-Philipp J and Chiba, Hideki and Miller, Ann L.}, issn = {1477-9137}, journal = {Journal of Cell Science}, number = {15}, publisher = {The Company of Biologists}, title = {{ZnUMBA - a live imaging method to detect local barrier breaches}}, doi = {10.1242/jcs.260668}, volume = {136}, year = {2023}, } @article{13214, abstract = {Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.}, author = {Abualia, R and Riegler, Stefan and Benková, Eva}, issn = {2073-4409}, journal = {Cells}, number = {12}, publisher = {MDPI}, title = {{Nitrate, auxin and cytokinin - a trio to tango}}, doi = {10.3390/cells12121613}, volume = {12}, year = {2023}, } @article{18942, abstract = {Photosynthesis is among the first processes negatively affected by environmental cues and its performance directly determines plant cell fitness and ultimately crop yield. Primarily sites of photosynthesis, chloroplasts are unique sites also for the biosynthesis of precursors of the growth regulator auxin and for sensing environmental stress, but their role in intracellular auxin homeostasis, vital for plant growth and survival in changing environments, remains poorly understood. Here, we identified two ATP-binding cassette (ABC) subfamily B transporters, ABCB28 and ABCB29, which export auxin across the chloroplast envelope to the cytosol in a concerted action in vivo. Moreover, we provide evidence for an auxin biosynthesis pathway in Arabidopsis thaliana chloroplasts. The overexpression of ABCB28 and ABCB29 influenced stomatal regulation and resulted in significantly improved water use efficiency and survival rates during salt and drought stresses. Our results suggest that chloroplast auxin production and transport contribute to stomata regulation for conserving water upon salt stress. ABCB28 and ABCB29 integrate photosynthesis and auxin signals and as such hold great potential to improve the adaptation potential of crops to environmental cues.}, author = {Tamizhselvan, Prashanth and Madhavan, Sharmila and Constan-Aguilar, Christian and Elrefaay, Eman Ryad and Liu, Jie and Pěnčík, Aleš and Novák, Ondřej and Cairó, Albert and Hrtyan, Mónika and Geisler, Markus and Tognetti, Vanesa Beatriz}, issn = {2223-7747}, journal = {Plants}, number = {1}, publisher = {MDPI}, title = {{Chloroplast auxin efflux mediated by ABCB28 and ABCB29 fine-tunes salt and drought stress responses in Arabidopsis}}, doi = {10.3390/plants13010007}, volume = {13}, year = {2023}, } @article{11734, abstract = {Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.}, author = {Abualia, Rashed and Ötvös, Krisztina and Novák, Ondřej and Bouguyon, Eleonore and Domanegg, Kevin and Krapp, Anne and Nacry, Philip and Gojon, Alain and Lacombe, Benoit and Benková, Eva}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {31}, publisher = {National Academy of Sciences}, title = {{Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses}}, doi = {10.1073/pnas.2122460119}, volume = {119}, year = {2022}, }