@article{6351,
abstract = {A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals.
Patterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.},
author = {Marhavá, Petra and Hörmayer, Lukas and Yoshida, Saiko and Marhavy, Peter and Benková, Eva and Friml, Jiří},
issn = {10974172},
journal = {Cell},
number = {4},
pages = {957--969.e13},
publisher = {Elsevier},
title = {{Re-activation of stem cell pathways for pattern restoration in plant wound healing}},
doi = {10.1016/j.cell.2019.04.015},
volume = {177},
year = {2019},
}
@unpublished{6313,
abstract = {We prove three principal results. First we exhibit a drawing of $K_{10}$ in the plane for which there do not exist extensions of the edges to simple closed curves with any two curves intersecting at most twice. Second, we exhibit a drawing of $K_9$ that has an extension of its edges to simple closed curves such that any two curves intersect in at most two points, but no extension to simple closed curves has every two curves intersecting in exactly two points. Third, we show that every h-convex drawing (introduced by Arroyo et al, submitted) has extensions of its edges to simple closed curves such that any two curves intersect in exactly two points. Using this result, we show that} a set of three axioms of simple closed curve extensions characterizes h-convexity.},
author = {Arroyo Guevara, Alan M and Richter, Bruce and Sunohara, Matthew},
pages = {35},
title = {{Extending drawings of complete graphs into arrangements of pseudocircles}},
year = {2019},
}
@article{6262,
abstract = {Gravitropism is an adaptive response that orients plant growth parallel to the gravity vector. Asymmetric
distribution of the phytohormone auxin is a necessary prerequisite to the tropic bending both in roots and
shoots. During hypocotyl gravitropic response, the PIN3 auxin transporter polarizes within gravity-sensing
cells to redirect intercellular auxin fluxes. First gravity-induced PIN3 polarization to the bottom cell mem-
branes leads to the auxin accumulation at the lower side of the organ, initiating bending and, later, auxin
feedback-mediated repolarization restores symmetric auxin distribution to terminate bending. Here, we per-
formed a forward genetic screen to identify regulators of both PIN3 polarization events during gravitropic
response. We searched for mutants with defective PIN3 polarizations based on easy-to-score morphological
outputs of decreased or increased gravity-induced hypocotyl bending. We identified the number of
hypocotyl reduced bending (hrb) and hypocotyl hyperbending (hhb) mutants, revealing that reduced bending corre-
lated typically with defective gravity-induced PIN3 relocation whereas all analyzed hhb mutants showed
defects in the second, auxin-mediated PIN3 relocation. Next-generation sequencing-aided mutation map-
ping identified several candidate genes, including SCARECROW and ACTIN2, revealing roles of endodermis
specification and actin cytoskeleton in the respective gravity- and auxin-induced PIN polarization events.
The hypocotyl gravitropism screen thus promises to provide novel insights into mechanisms underlying cell
polarity and plant adaptive development.},
author = {Rakusová, Hana and Han, Huibin and Valošek, Petr and Friml, Jiří},
issn = {1365-313x},
journal = {The Plant Journal},
number = {6},
pages = {1048--1059},
publisher = {Wiley},
title = {{Genetic screen for factors mediating PIN polarization in gravistimulated Arabidopsis thaliana hypocotyls}},
doi = {10.1111/tpj.14301},
volume = {98},
year = {2019},
}
@phdthesis{6363,
abstract = {Distinguishing between similar experiences is achieved by the brain in a process called pattern separation. In the hippocampus, pattern separation reduces the interference of memories and increases the storage capacity by decorrelating similar inputs patterns of neuronal activity into non-overlapping output firing patterns. Winners-take-all (WTA) mechanism is a theoretical model for pattern separation in which a "winner" cell suppresses the activity of the neighboring neurons through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of feedback inhibition in which a GC inhibits other GCs but not itself through the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron connectivity was more spatially confined but less abundant than PV+interneurons–GC connectivity, leading to an asymmetrical distribution of excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the primary mechanism. This process relied on lateral inhibition, fast-signaling properties of PV+interneurons and the asymmetrical distribution of excitatory and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in vivoleads to acute deficits in discrimination between similar environments, suggesting that PV+interneuron networks are necessary for behavioral relevant computations. Our results demonstrate that PV+interneurons possess unique connectivity and fast signaling properties that confer to the dentate gyrus network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing.
},
author = {Espinoza Martinez, Claudia M},
isbn = {978-3-99078-000-8},
issn = {2663-337X},
pages = {140},
publisher = {IST Austria},
title = {{Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits}},
doi = {10.15479/AT:ISTA:6363},
year = {2019},
}
@article{6419,
abstract = {Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.},
author = {Pokusaeva, Victoria and Usmanova, Dinara R. and Putintseva, Ekaterina V. and Espinar, Lorena and Sarkisyan, Karen and Mishin, Alexander S. and Bogatyreva, Natalya S. and Ivankov, Dmitry and Akopyan, Arseniy and Avvakumov, Sergey and Povolotskaya, Inna S. and Filion, Guillaume J. and Carey, Lucas B. and Kondrashov, Fyodor},
issn = {15537404},
journal = {PLoS Genetics},
number = {4},
publisher = {Public Library of Science},
title = {{An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape}},
doi = {10.1371/journal.pgen.1008079},
volume = {15},
year = {2019},
}
@misc{6060,
author = {Vicoso, Beatriz},
publisher = {IST Austria},
title = {{Supplementary data for "Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). }},
doi = {10.15479/AT:ISTA:6060},
year = {2019},
}
@phdthesis{6546,
abstract = {Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation.
Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify
a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate
a program governing migration steps important for both development and cancer metastasis.
},
author = {Valosková, Katarina},
issn = {2663-337X},
pages = {141},
publisher = {IST Austria},
title = {{The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration}},
doi = {10.15479/AT:ISTA:6546},
year = {2019},
}
@inproceedings{6565,
abstract = {In this paper, we address the problem of synthesizing periodic switching controllers for stabilizing a family of linear systems. Our broad approach consists of constructing a finite game graph based on the family of linear systems such that every winning strategy on the game graph corresponds to a stabilizing switching controller for the family of linear systems. The construction of a (finite) game graph, the synthesis of a winning strategy and the extraction of a stabilizing controller are all computationally feasible. We illustrate our method on an example.},
author = {Kundu, Atreyee and Garcia Soto, Miriam and Prabhakar, Pavithra},
booktitle = {5th Indian Control Conference Proceedings},
isbn = {978-153866246-5},
location = {Delhi, India},
publisher = {IEEE},
title = {{Formal synthesis of stabilizing controllers for periodically controlled linear switched systems}},
doi = {10.1109/INDIANCC.2019.8715598},
year = {2019},
}
@article{6596,
abstract = {It is well known that many problems in image recovery, signal processing, and machine learning can be modeled as finding zeros of the sum of maximal monotone and Lipschitz continuous monotone operators. Many papers have studied forward-backward splitting methods for finding zeros of the sum of two monotone operators in Hilbert spaces. Most of the proposed splitting methods in the literature have been proposed for the sum of maximal monotone and inverse-strongly monotone operators in Hilbert spaces. In this paper, we consider splitting methods for finding zeros of the sum of maximal monotone operators and Lipschitz continuous monotone operators in Banach spaces. We obtain weak and strong convergence results for the zeros of the sum of maximal monotone and Lipschitz continuous monotone operators in Banach spaces. Many already studied problems in the literature can be considered as special cases of this paper.},
author = {Shehu, Yekini},
issn = {1420-9012},
journal = {Results in Mathematics},
number = {4},
publisher = {Springer},
title = {{Convergence results of forward-backward algorithms for sum of monotone operators in Banach spaces}},
doi = {10.1007/s00025-019-1061-4},
volume = {74},
year = {2019},
}
@article{6609,
abstract = {Mechanical systems facilitate the development of a hybrid quantum technology comprising electrical, optical, atomic and acoustic degrees of freedom1, and entanglement is essential to realize quantum-enabled devices. Continuous-variable entangled fields—known as Einstein–Podolsky–Rosen (EPR) states—are spatially separated two-mode squeezed states that can be used for quantum teleportation and quantum communication2. In the optical domain, EPR states are typically generated using nondegenerate optical amplifiers3, and at microwave frequencies Josephson circuits can serve as a nonlinear medium4,5,6. An outstanding goal is to deterministically generate and distribute entangled states with a mechanical oscillator, which requires a carefully arranged balance between excitation, cooling and dissipation in an ultralow noise environment. Here we observe stationary emission of path-entangled microwave radiation from a parametrically driven 30-micrometre-long silicon nanostring oscillator, squeezing the joint field operators of two thermal modes by 3.40 decibels below the vacuum level. The motion of this micromechanical system correlates up to 50 photons per second per hertz, giving rise to a quantum discord that is robust with respect to microwave noise7. Such generalized quantum correlations of separable states are important for quantum-enhanced detection8 and provide direct evidence of the non-classical nature of the mechanical oscillator without directly measuring its state9. This noninvasive measurement scheme allows to infer information about otherwise inaccessible objects, with potential implications for sensing, open-system dynamics and fundamental tests of quantum gravity. In the future, similar on-chip devices could be used to entangle subsystems on very different energy scales, such as microwave and optical photons.},
author = {Barzanjeh, Shabir and Redchenko, Elena and Peruzzo, Matilda and Wulf, Matthias and Lewis, Dylan and Arnold, Georg M and Fink, Johannes M},
journal = {Nature},
pages = {480--483},
publisher = {Nature Publishing Group},
title = {{Stationary entangled radiation from micromechanical motion}},
doi = {10.1038/s41586-019-1320-2},
volume = {570},
year = {2019},
}