@phdthesis{17336,
abstract = {This thesis deals with the study of stochastic processes and their ergodicity properties. The
variety of problems encountered calls for a set of different approaches, ranging from classical to
modern ones: a special place is held by probabilistic methods based on couplings, by functional
inequalities, and by the theory of gradient flows in the space of measures.
The material is organized as follows. Chapter 1 contains the introduction to this thesis, starting
with a general presentation of some of the relevant topics. Section 1.1 is dedicated to the
theory of gradient flows in metric spaces, and introduces the first contribution of this thesis
[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of
curvature of Markov chains, concluding with a brief description of our second contribution
[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic
processes to the theory of sampling, in particular the recent framework of score-based diffusion
models, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses
some related problems, concerning the regularization properties of the heat flow. It serves
as a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5
discusses the last contribution of this thesis, which can be found in Chapter 6. It deals with
the convergence to equilibrium of a particular stochastic model from quantitative genetics:
this is established via some functional inequalities, which we prove with probabilistic arguments
based on couplings.
},
author = {Pedrotti, Francesco},
issn = {2663-337X},
pages = {183},
publisher = {Institute of Science and Technology Austria},
title = {{Functional inequalities and convergence of stochastic processes}},
doi = {10.15479/at:ista:17336},
year = {2024},
}
@inproceedings{18897,
abstract = {Score-based generative models (SGMs) are powerful tools to sample from complex data distributions. Their underlying idea is to (i) run a forward process for time T1 by adding noise to the data, (ii) estimate its score function, and (iii) use such estimate to run a reverse process. As the reverse process is initialized with the stationary distribution of the forward one, the existing analysis paradigm requires T1→∞. This is however problematic: from a theoretical viewpoint, for a given precision of the score approximation, the convergence guarantee fails as T1 diverges; from a practical viewpoint, a large T1 increases computational costs and leads to error propagation. This paper addresses the issue by considering a version of the popular predictor-corrector scheme: after running the forward process, we first estimate the final distribution via an inexact Langevin dynamics and then revert the process. Our key technical contribution is to provide convergence guarantees which require to run the forward process only for a fixed finite time T1. Our bounds exhibit a mild logarithmic dependence on the input dimension and the subgaussian norm of the target distribution, have minimal assumptions on the data, and require only to control the L2 loss on the score approximation, which is the quantity minimized in practice.},
author = {Pedrotti, Francesco and Maas, Jan and Mondelli, Marco},
booktitle = {Transactions on Machine Learning Research},
issn = {2835-8856},
title = {{Improved convergence of score-based diffusion models via prediction-correction}},
year = {2024},
}
@unpublished{17350,
abstract = {Score-based generative models (SGMs) are powerful tools to sample from
complex data distributions. Their underlying idea is to (i) run a forward
process for time $T_1$ by adding noise to the data, (ii) estimate its score
function, and (iii) use such estimate to run a reverse process. As the reverse
process is initialized with the stationary distribution of the forward one, the
existing analysis paradigm requires $T_1\to\infty$. This is however
problematic: from a theoretical viewpoint, for a given precision of the score
approximation, the convergence guarantee fails as $T_1$ diverges; from a
practical viewpoint, a large $T_1$ increases computational costs and leads to
error propagation. This paper addresses the issue by considering a version of
the popular predictor-corrector scheme: after running the forward process, we
first estimate the final distribution via an inexact Langevin dynamics and then
revert the process. Our key technical contribution is to provide convergence
guarantees which require to run the forward process only for a fixed finite
time $T_1$. Our bounds exhibit a mild logarithmic dependence on the input
dimension and the subgaussian norm of the target distribution, have minimal
assumptions on the data, and require only to control the $L^2$ loss on the
score approximation, which is the quantity minimized in practice.},
author = {Pedrotti, Francesco and Maas, Jan and Mondelli, Marco},
booktitle = {arXiv},
title = {{Improved convergence of score-based diffusion models via prediction-correction}},
doi = {10.48550/arXiv.2305.14164},
year = {2024},
}
@misc{22776,
author = {Du, Yunlong},
publisher = {Repository},
title = {{SeRrbJ609}},
doi = {10.6084/m9.figshare.25448191},
year = {2024},
}
@article{17103,
abstract = {Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.},
author = {Jiang, Lihui and Zhang, Xiaoyan and Zhao, Yiting and Zhu, Haiyan and Fu, Qijing and Lu, Xinqi and Huang, Wuying and Yang, Xinyue and Zhou, Xuan and Wu, Lixia and Yang, Ao and He, Xie and Dong, Man and Peng, Ziai and Yang, Jing and Guo, Liwei and Wen, Jiancheng and Huang, Huichuan and Xie, Yong and Zhu, Shusheng and Li, Chengyun and He, Xiahong and Zhu, Youyong and Friml, Jiří and Du, Yunlong},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast}},
doi = {10.1038/s41467-024-47746-y},
volume = {15},
year = {2024},
}
@article{15033,
abstract = {The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.},
author = {Adamowski, Maciek and Matijevic, Ivana and Friml, Jiří},
issn = {2050-084X},
journal = {eLife},
keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
publisher = {eLife Sciences Publications},
title = {{Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery}},
doi = {10.7554/elife.68993},
volume = {13},
year = {2024},
}
@article{14826,
abstract = {The plant-signaling molecule auxin triggers fast and slow cellular responses across land plants and algae. The nuclear auxin pathway mediates gene expression and controls growth and development in land plants, but this pathway is absent from algal sister groups. Several components of rapid responses have been identified in Arabidopsis, but it is unknown if these are part of a conserved mechanism. We recently identified a fast, proteome-wide phosphorylation response to auxin. Here, we show that this response occurs across 5 land plant and algal species and converges on a core group of shared targets. We found conserved rapid physiological responses to auxin in the same species and identified rapidly accelerated fibrosarcoma (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation across species. Genetic analysis connects this kinase to both auxin-triggered protein phosphorylation and rapid cellular response, thus identifying an ancient mechanism for fast auxin responses in the green lineage.},
author = {Kuhn, Andre and Roosjen, Mark and Mutte, Sumanth and Dubey, Shiv Mani and Carrillo Carrasco, Vanessa Polet and Boeren, Sjef and Monzer, Aline and Koehorst, Jasper and Kohchi, Takayuki and Nishihama, Ryuichi and Fendrych, Matyas and Sprakel, Joris and Friml, Jiří and Weijers, Dolf},
issn = {1097-4172},
journal = {Cell},
keywords = {General Biochemistry, Genetics and Molecular Biology},
number = {1},
pages = {130--148.e17},
publisher = {Elsevier},
title = {{RAF-like protein kinases mediate a deeply conserved, rapid auxin response}},
doi = {10.1016/j.cell.2023.11.021},
volume = {187},
year = {2024},
}
@article{15319,
abstract = {Exocyst component of 70-kDa (EXO70) proteins are constituents of the exocyst complex implicated in vesicle tethering during exocytosis. MILDEW RESISTANCE LOCUS O (MLO) proteins are plant-specific calcium channels and some MLO isoforms enable fungal powdery mildew pathogenesis. We here detected an unexpected phenotypic overlap of Arabidopsis thaliana exo70H4 and mlo2 mlo6 mlo12 triple mutant plants regarding the biogenesis of leaf trichome secondary cell walls. Biochemical and Fourier transform infrared spectroscopic analyses corroborated deficiencies in the composition of trichome cell walls in these mutants. Transgenic lines expressing fluorophore-tagged EXO70H4 and MLO exhibited extensive colocalization of these proteins. Furthermore, mCherry-EXO70H4 mislocalized in trichomes of the mlo triple mutant and, vice versa, MLO6-GFP mislocalized in trichomes of the exo70H4 mutant. Expression of GFP-marked PMR4 callose synthase, a known cargo of EXO70H4-dependent exocytosis, revealed reduced cell wall delivery of GFP-PMR4 in trichomes of mlo triple mutant plants. In vivo protein–protein interaction assays in plant and yeast cells uncovered isoform-preferential interactions between EXO70.2 subfamily members and MLO proteins. Finally, exo70H4 and mlo6 mutants, when combined, showed synergistically enhanced resistance to powdery mildew attack. Taken together, our data point to an isoform-specific interplay of EXO70 and MLO proteins in the modulation of trichome cell wall biogenesis and powdery mildew susceptibility.},
author = {Huebbers, Jan W. and Caldarescu, George A. and Kubátová, Zdeňka and Sabol, Peter and Levecque, Sophie C.J. and Kuhn, Hannah and Kulich, Ivan and Reinstädler, Anja and Büttgen, Kim and Manga-Robles, Alba and Mélida, Hugo and Pauly, Markus and Panstruga, Ralph and Žárský, Viktor},
issn = {1532-298X},
journal = {Plant Cell},
number = {4},
pages = {1007--1035},
publisher = {Oxford University Press},
title = {{Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew}},
doi = {10.1093/plcell/koad319},
volume = {36},
year = {2024},
}
@article{17436,
abstract = {The auxin signaling molecule controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of the ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and DNA-binding ARF transcription factors. Although extensive qualitative understanding of the pathway and its interactions has been obtained, mostly by studying the flowering plant Arabidopsis thaliana, it remains unknown how these translate to quantitative system behavior in vivo, a problem that is confounded by the large NAP gene families in most species. Here, we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knockin fluorescent fusion proteins. Beyond revealing the dynamic native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs, MpARF1 and MpARF2, are proteasomally degraded. This auxin-independent degradation tunes ARF protein stoichiometry to favor gene activation, thereby reprogramming auxin response during the developmental progression. Thus, quantitative analysis of the entire NAP has enabled us to identify ARF degradation and the stoichiometries of activator and repressor ARFs as a potential mechanism for controlling gemma germination.},
author = {Das, Shubhajit and De Roij, Martijn and Bellows, Simon and Alvarez, Melissa Dipp and Mutte, Sumanth and Kohlen, Wouter and Farcot, Etienne and Weijers, Dolf and Borst, Jan Willem},
issn = {2590-3462},
journal = {Plant Communications},
number = {11},
publisher = {Elsevier},
title = {{Quantitative imaging reveals the role of MpARF proteasomal degradation during gemma germination}},
doi = {10.1016/j.xplc.2024.101039},
volume = {5},
year = {2024},
}
@article{18465,
abstract = {The phytohormone auxin is polarly transported in plants by PIN-FORMED (PIN) transporters and controls virtually all growth and developmental processes. Canonical PINs possess a long, largely disordered cytosolic loop. Auxin transport by canonical PINs is activated by loop phosphorylation by certain kinases. The structure of the PIN transmembrane domains was recently determined, their transport properties remained poorly characterized, and the role of the loop in the transport process was unclear. Here, we determined the quantitative kinetic parameters of auxin transport mediated by Arabidopsis PINs to mathematically model auxin distribution in roots and to test these predictions in vivo. Using chimeras between transmembrane and loop domains of different PINs, we demonstrate a strong correlation between transport parameters and physiological output, indicating that the loop domain is not only required to activate PIN-mediated auxin transport, but it has an additional role in the transport process by a currently unknown mechanism.},
author = {Janacek, DP and Kolb, M and Schulz, L and Mergner, J and Kuster, B and Glanc, Matous and Friml, Jiří and Ten Tusscher, K and Schwechheimer, C and Hammes, UZ},
issn = {1878-1551},
journal = {Developmental Cell},
number = {14},
pages = {S1534--5807(24)00569--0},
publisher = {Elsevier},
title = {{Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport}},
doi = {10.1016/j.devcel.2024.09.020},
volume = {59},
year = {2024},
}
@article{18582,
abstract = {Identification of PIN exporters for auxin, the major coordinative signal in plants, some 25 years ago, signifies a landmark in our understanding of plant-specific mechanisms underlying development and adaptation. Auxin is directionally transported throughout the plant body; a unique feature already envisioned by Darwin and solidified by PINs’ discovery and characterization. The PIN-based auxin distribution network with its complex regulations of PIN expression, localization and activity turned out to underlie a remarkable multitude of developmental processes and represents means to integrate endogenous and environmental signals. Given the recent anniversary, we here summarize past and current developments in this exciting field.},
author = {Luschnig, Christian and Friml, Jiří},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Over 25 years of decrypting PIN-mediated plant development}},
doi = {10.1038/s41467-024-54240-y},
volume = {15},
year = {2024},
}
@article{15251,
abstract = {Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In Arabidopsis thaliana, ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.},
author = {Ying, Wei and Wang, Yaowei and Wei, Hong and Luo, Yongming and Ma, Qian and Zhu, Heyuan and Janssens, Hilde and Vukašinović, Nemanja and Kvasnica, Miroslav and Winne, Johan M. and Gao, Yongxiang and Tan, Shutang and Friml, Jiří and Liu, Xin and Russinova, Eugenia and Sun, Linfeng},
issn = {1095-9203},
journal = {Science},
number = {6689},
pages = {eadj4591},
publisher = {American Association for the Advancement of Science},
title = {{Structure and function of the Arabidopsis ABC transporter ABCB19 in brassinosteroid export}},
doi = {10.1126/science.adj4591},
volume = {383},
year = {2024},
}
@article{17377,
abstract = {Lateral root (LR) formation, that is vital for plant development, is one of many auxin-modulated processes, but the underlying regulatory mechanism is not yet fully known. Recently,
González-García et al. discovered the BiAux compound and showed that it is involved in LR development via regulating specific auxin coreceptors.},
author = {Wójcikowska, Barbara and Friml, Jiří and Mazur, Ewa},
issn = {1360-1385},
journal = {Trends in Plant Science},
number = {12},
pages = {1279--1281},
publisher = {Elsevier},
title = {{BiAux, a newly discovered compound triggering auxin signaling}},
doi = {10.1016/j.tplants.2024.07.008},
volume = {29},
year = {2024},
}
@inbook{15361,
abstract = {Bimolecular fluorescence complementation (BiFC) is a powerful tool for studying protein-protein interactions in living cells. By fusing interacting proteins to fluorescent protein fragments, BiFC allows visualization of spatial localization patterns of protein complexes. This method has been adapted to a variety of expression systems in different organisms and is widely used to study protein interactions in plant cells. The Agrobacterium-mediated transient expression protocol for BiFC assays in Nicotiana benthamiana (N. benthamiana) leaf cells is widely used, but in this chapter, a method for BiFC assay using Arabidopsis thaliana protoplasts is presented.},
author = {Jayasree, Aswathy and Salava, Hymavathi and Nodzynski, Tomasz and Sravankumar, Thula},
booktitle = {Plant Functional Genomics},
editor = {Maghuly, Fatemeh},
isbn = {9781071637777},
issn = {1940-6029},
pages = {305--313},
publisher = {Springer Nature},
title = {{Protein-Protein Interactions Visualized by Bimolecular Fluorescence Complementation in Arabidopsis thaliana Protoplasts from Leaf}},
doi = {10.1007/978-1-0716-3778-4_21},
volume = {2787},
year = {2024},
}
@article{18311,
abstract = {Local wound signaling in plants informs the surrounding tissues about an injury and initiates the regeneration process. In a recent paper published in Cell, Yang and colleagues show the involvement of a single Pep family member from tomato in wound signaling and how exogenous application of this regeneration factor enhances transformation efficiency in crops.},
author = {Hörmayer, Lukas and Friml, Jiří},
issn = {1748-7838},
journal = {Cell Research},
pages = {761--762},
publisher = {Springer Nature},
title = {{Feeling the danger: Local wound signaling in plants}},
doi = {10.1038/s41422-024-01035-x},
volume = {34},
year = {2024},
}
@article{15257,
abstract = {Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.},
author = {Kulich, Ivan and Schmid, Julia and Teplova, Anastasiia and Qi, Linlin and Friml, Jiří},
issn = {2050-084X},
journal = {eLife},
keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience},
publisher = {eLife Sciences Publications},
title = {{Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism}},
doi = {10.7554/elife.91523},
volume = {12},
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{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},
}
@article{15381,
abstract = {Cholecystokinin-expressing interneurons (CCKIs) are hypothesized to shape pyramidal cell-firing patterns and regulate network oscillations and related network state transitions. To directly probe their role in the CA1 region, we silenced their activity using optogenetic and chemogenetic tools in mice. Opto-tagged CCKIs revealed a heterogeneous population, and their optogenetic silencing triggered wide disinhibitory network changes affecting both pyramidal cells and other interneurons. CCKI silencing enhanced pyramidal cell burst firing and altered the temporal coding of place cells: theta phase precession was disrupted, whereas sequence reactivation was enhanced. Chemogenetic CCKI silencing did not alter the acquisition of spatial reference memories on the Morris water maze but enhanced the recall of contextual fear memories and enabled selective recall when similar environments were tested. This work suggests the key involvement of CCKIs in the control of place-cell temporal coding and the formation of contextual memories.},
author = {Rangel Guerrero, Dámaris K and Balueva, Kira and Barayeu, Uladzislau and Baracskay, Peter and Gridchyn, Igor and Nardin, Michele and Roth, Chiara N and Wulff, Peer and Csicsvari, Jozsef L},
issn = {1097-4199},
journal = {Neuron},
number = {12},
pages = {2045--2061.e10},
publisher = {Cell Press},
title = {{Hippocampal cholecystokinin-expressing interneurons regulate temporal coding and contextual learning}},
doi = {10.1016/j.neuron.2024.03.019},
volume = {112},
year = {2024},
}
@article{17477,
abstract = {Trapped-ion systems are a leading platform for quantum information processing, but they are currently limited to 1D and 2D arrays, which imposes restrictions on both their scalability and their range of applications. Here, we propose a path to overcome this limitation by demonstrating that Penning traps can be used to realize remarkably clean bilayer crystals, wherein hundreds of ions self-organize into two well-defined layers. These bilayer crystals are made possible by the inclusion of an anharmonic trapping potential, which is readily implementable with current technology. We study the normal modes of this system and discover salient differences compared to the modes of single-plane crystals. The bilayer geometry and the unique properties of the normal modes open new opportunities—in particular, in quantum sensing and quantum simulation—that are not straightforward in single-plane crystals. Furthermore, we illustrate that it may be possible to extend the ideas presented here to realize multilayer crystals with more than two layers. Our work increases the dimensionality of trapped-ion systems by efficiently utilizing all three spatial dimensions, and it lays the foundation for a new generation of quantum information processing experiments with multilayer 3D crystals of trapped ions.},
author = {Hawaldar, Samarth and Shahi, Prakriti and Carter, Allison L. and Rey, Ana Maria and Bollinger, John J. and Shankar, Athreya},
issn = {2160-3308},
journal = {Physical Review X},
number = {3},
publisher = {American Physical Society},
title = {{Bilayer crystals of trapped ions for quantum information processing}},
doi = {10.1103/PhysRevX.14.031030},
volume = {14},
year = {2024},
}