@article{15254,
abstract = {We consider the problem of reliable communication over a network containing a hidden myopic adversary who can eavesdrop on some zro links, jam some zwo links, and do both on some zrw links. We provide the first information-theoretically tight characterization of the optimal rate of communication possible under all possible settings of the tuple (zro,zwo,zrw) by providing a novel coding scheme/analysis for a subset of parameter regimes. In particular, our vanishing-error schemes bypass the Network Singleton Bound (which requires a zero-error recovery criteria) in a certain parameter regime where the capacity had been heretofore open. As a direct corollary we also obtain the capacity of the corresponding problem where information-theoretic secrecy against eavesdropping is required in addition to reliable communication.},
author = {Li, Sijie and Bitar, Rawad and Jaggi, Sidharth and Zhang, Yihan},
issn = {2641-8770},
journal = {IEEE Journal on Selected Areas in Information Theory},
number = {4},
pages = {1108--1119},
publisher = {IEEE},
title = {{Network coding with myopic adversaries}},
doi = {10.1109/JSAIT.2021.3126474},
volume = {2},
year = {2021},
}
@article{15259,
abstract = {We consider words Gi1⋯Gim involving i.i.d. complex Ginibre matrices and study tracial expressions of their eigenvalues and singular values. We show that the limit distribution of the squared singular values of every word of length m is a Fuss–Catalan distribution with parameter
m+1. This generalizes previous results concerning powers of a complex Ginibre matrix and products of independent Ginibre matrices. In addition, we find other combinatorial parameters of the word that determine the second-order limits of the spectral statistics. For instance, the so-called coperiod of a word characterizes the fluctuations of the eigenvalues. We extend these results to words of general non-Hermitian matrices with i.i.d. entries under moment-matching assumptions, band matrices, and sparse matrices.
These results rely on the moments method and genus expansion, relating Gaussian matrix integrals to the counting of compact orientable surfaces of a given genus. This allows us to derive a central limit theorem for the trace of any word of complex Ginibre matrices and their conjugate transposes, where all parameters are defined topologically.},
author = {Dubach, Guillaume and Peled, Yuval},
issn = {0091-1798},
journal = {The Annals of Probability},
keywords = {Statistics, Probability and Uncertainty, Statistics and Probability},
number = {4},
pages = {1886--1916},
publisher = {Institute of Mathematical Statistics},
title = {{On words of non-Hermitian random matrices}},
doi = {10.1214/20-aop1496},
volume = {49},
year = {2021},
}
@article{15260,
abstract = {Significant advances in the synthesis and processing of colloidal nanocrystals have given scientists and engineers access to a vast library of building blocks with precisely defined size, shape, and composition. These materials have inspired exciting prospects to enable bottom-up fabrication of programmable materials with properties by design. Successfully assembling and connecting the building blocks into superstructures in which constituent nanocrystals can purposefully interact requires robust understanding of and control over a complex interplay of dynamic physicochemical processes. Fluid interfaces provide an advantageous experimental workbench to both probe and control these processes. Despite the ostensible simplicity of fabricating nanocrystal assemblies at a fluid interface, sensitivity to processing conditions and limited reproducibility have underscored the complexity of this process. In situ studies have provided mechanistic insights into the competing dynamics of key subprocesses including solvent spreading and evaporation, superlattice formation, ligand detachment kinetics, and nanocrystal attachment. Understanding how these subprocesses influence the complex choreography of self-assembly, structure transformation, and oriented attachment processes presents a rich research challenge. In this context, we present a detailed methodology for self-assembly and attachment of lead chalcogenide nanocrystals at a liquid–gas interface as a model system for the fabrication of mono- and multilayer cubic connected superlattices. We discuss key experimental parameters such as the characteristics of the building blocks and processing conditions and detailed steps from colloidal nanocrystal injection to superlattice transfer. We hope that this Methods/Protocols paper will provide guidance for future advances in the exciting path toward bringing the prospect of nanocrystal-based programmable materials to fruition.},
author = {Cimada daSilva, Jessica and Balazs, Daniel and Dunbar, Tyler A. and Hanrath, Tobias},
issn = {1520-5002},
journal = {Chemistry of Materials},
keywords = {Materials Chemistry, General Chemical Engineering, General Chemistry},
number = {24},
pages = {9457--9472},
publisher = {American Chemical Society},
title = {{Fundamental processes and practical considerations of lead chalcogenide mesocrystals formed via self-assembly and directed attachment of nanocrystals at a fluid interface}},
doi = {10.1021/acs.chemmater.1c02910},
volume = {33},
year = {2021},
}
@article{15261,
abstract = {In this article, we study uniqueness of form extensions in a rather general setting. The method is based on the theory of ordered Hilbert spaces and the concept of domination of semigroups. Our main abstract result transfers uniqueness of form extension of a dominating form to that of a dominated form. This result can be applied to a multitude of examples including various magnetic Schrödinger forms on graphs and on manifolds.},
author = {Lenz, Daniel and Schmidt, Marcel and Wirth, Melchior},
issn = {1096-0783},
journal = {Journal of Functional Analysis},
keywords = {Analysis},
number = {6},
publisher = {Elsevier},
title = {{Uniqueness of form extensions and domination of semigroups}},
doi = {10.1016/j.jfa.2020.108848},
volume = {280},
year = {2021},
}
@article{15262,
abstract = {The Hunchback (Hb) transcription factor is crucial for anterior-posterior patterning of the Drosophila embryo. The maternal hb mRNA acts as a paradigm for translational regulation due to its repression in the posterior of the embryo. However, little is known about the translatability of zygotically transcribed hb mRNAs. Here, we adapt the SunTag system, developed for imaging translation at single-mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using single-molecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. Whereas the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila.},
author = {Vinter, Daisy J. and Hoppe, Caroline and Minchington, Thomas and Sutcliffe, Catherine and Ashe, Hilary L.},
issn = {1477-9129},
journal = {Development},
keywords = {Developmental Biology, Molecular Biology},
number = {18},
publisher = {The Company of Biologists},
title = {{Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo}},
doi = {10.1242/dev.196121},
volume = {148},
year = {2021},
}
@inproceedings{15263,
abstract = {We develop a new Riemannian descent algorithm that relies on momentum to improve over existing first-order methods for geodesically convex optimization. In contrast, accelerated convergence rates proved in prior work have only been shown to hold for geodesically strongly-convex objective functions. We further extend our algorithm to geodesically weakly-quasi-convex objectives. Our proofs of convergence rely on a novel estimate sequence that illustrates the dependency of the convergence rate on the curvature of the manifold. We validate our theoretical results empirically on several optimization problems defined on the sphere and on the manifold of positive definite matrices.},
author = {Alimisis, Foivos and Orvieto, Antonio and Becigneul, Gary and Lucchi, Aurelien},
booktitle = {Proceedings of the 24th International Conference on Artificial Intelligence and Statistics},
location = {San Diego, CA, United States; Virtual},
pages = {1351--1359},
publisher = {ML Research Press},
title = {{Momentum improves optimization on Riemannian manifolds}},
volume = {130},
year = {2021},
}
@article{15264,
abstract = {Signaling by the B cell antigen receptor (BCR) initiates actin remodeling. The assembly of branched actin networks that are nucleated by the Arp2/3 complex exert outward force on the plasma membrane, allowing B cells to form membrane protrusions that can scan the surface of antigen-presenting cells (APCs). The resulting Arp2/3 complex-dependent actin retrograde flow promotes the centripetal movement and progressive coalescence of BCR microclusters, which amplifies BCR signaling. Glia maturation factor γ (GMFγ) is an actin disassembly-protein that releases Arp2/3 complex-nucleated actin filaments from actin networks. By doing so, GMFγ could either oppose the actions of the Arp2/3 complex or support Arp2/3 complex-nucleated actin polymerization by contributing to the recycling of actin monomers and Arp2/3 complexes. We now show that reducing the levels of GMFγ in human B cell lines via transfection with a specific siRNA impairs the ability of B cells to spread on antigen-coated surfaces, decreases the velocity of actin retrograde flow, diminishes the coalescence of BCR microclusters into a central cluster at the B cell-APC contact site, and decreases APC-induced BCR signaling. These effects of depleting GMFγ are similar to what occurs when the Arp2/3 complex is inhibited. This suggests that GMFγ cooperates with the Arp2/3 complex to support BCR-induced actin remodeling and amplify BCR signaling at the immune synapse.},
author = {Deretic, Nikola and Bolger-Munro, Madison and Choi, Kate and Abraham, Libin and Gold, Michael R.},
issn = {2296-634X},
journal = {Frontiers in Cell and Developmental Biology},
keywords = {Cell Biology, Developmental Biology},
publisher = {Frontiers Media},
title = {{The actin-disassembly protein glia maturation factor γ enhances actin remodeling and B cell antigen receptor signaling at the immune synapse}},
doi = {10.3389/fcell.2021.647063},
volume = {9},
year = {2021},
}
@article{15265,
abstract = {The highly enhanced thermoelectric figure of merit, zT ≈ 2.6 at 573 K, obtained recently in Cd-doped polycrystalline AgSbTe2 by Roychowdhury et al. ( Science 2021, 371, 722) brings it to the forefront of thermoelectric and energy materials research. Ag/Sb cationic ordering in polycrystalline AgSbTe2 was a challenging issue for a long time: their ordered arrangement in the cationic sublattice in polycrystalline samples remained elusive despite multiple theoretical predictions and experimental studies. Recently, selective cation doping has been used to enhance the Ag/Sb ordering, and cation ordered nanoscale (2–4 nm) domains were observed in polycrystalline AgSbTe2, which reduce lattice thermal conductivity. The enhanced cation ordering also delocalizes disorder-induced localized electronic states, and consequently the electronic transport enhances. In this Focus Review, we provide the details of the rational design of a high-performance thermoelectric material using the recently developed atomic order–disorder optimization strategy with AgSbTe2 as an example. Atomic disorder is ubiquitous in most thermoelectric materials, and the atomic order–disorder optimization strategy applies to a large variety of thermoelectric materials.},
author = {Ghosh, Tanmoy and Roychowdhury, Subhajit and Dutta, Moinak and Biswas, Kanishka},
issn = {2380-8195},
journal = {ACS Energy Letters},
keywords = {Materials Chemistry, Energy Engineering and Power Technology, Fuel Technology, Renewable Energy, Sustainability and the Environment, Chemistry (miscellaneous)},
number = {8},
pages = {2825--2837},
publisher = {American Chemical Society},
title = {{High-performance thermoelectric energy conversion: A tale of atomic ordering in AgSbTe2}},
doi = {10.1021/acsenergylett.1c01184},
volume = {6},
year = {2021},
}
@article{15266,
abstract = {Plant pathogens often exploit a whole range of effectors to facilitate infection. The RXLR effector AVR1 produced by the oomycete plant pathogen Phytophthora infestans suppresses host defense by targeting Sec5. Sec5 is a subunit of the exocyst, a protein complex that is important for mediating polarized exocytosis during plant development and defense against pathogens. The mechanism by which AVR1 manipulates Sec5 functioning is unknown. In this study, we analyzed the effect of AVR1 on Sec5 localization and functioning in the moss Physcomitrium patens. P. patens has four Sec5 homologs. Two (PpSec5b and PpSec5d) were found to interact with AVR1 in yeast-two-hybrid assays while none of the four showed a positive interaction with AVR1ΔT, a truncated version of AVR1. In P. patens lines carrying β-estradiol inducible AVR1 or AVR1ΔT transgenes, expression of AVR1 or AVR1ΔT caused defects in the development of caulonemal protonema cells and abnormal morphology of chloronema cells. Similar phenotypes were observed in Sec5- or Sec6-silenced P. patens lines, suggesting that both AVR1 and AVR1ΔT affect exocyst functioning in P. patens. With respect to Sec5 localization we found no differences between β-estradiol-treated and untreated transgenic AVR1 lines. Sec5 localizes at the plasma membrane in growing caulonema cells, also during pathogen attack, and its subcellular localization is the same, with or without AVR1 in the vicinity.},
author = {Overdijk, Elysa J. R. and Putker, Vera and Smits, Joep and Tang, Han and Bouwmeester, Klaas and Govers, Francine and Ketelaar, Tijs},
issn = {1932-6203},
journal = {PLoS One},
keywords = {Multidisciplinary},
number = {4},
publisher = {Public Library of Science},
title = {{Phytophthora infestans RXLR effector AVR1 disturbs the growth of Physcomitrium patens without affecting Sec5 localization}},
doi = {10.1371/journal.pone.0249637},
volume = {16},
year = {2021},
}
@article{15267,
abstract = {We study two fundamental communication primitives: broadcasting and leader election in the classical model of multi-hop radio networks with unknown topology and without collision detection mechanisms. It has been known for almost 20 years that in undirected networks with n nodes and diameter D, randomized broadcasting requires Ω(D log n/D + log2 n) rounds, assuming that uninformed nodes are not allowed to communicate (until they are informed). Only very recently, Haeupler and Wajc (PODC'2016) showed that this bound can be improved for the model with spontaneous transmissions, providing an O(D log n log log n/log D + logO(1) n)-time broadcasting algorithm. In this article, we give a new and faster algorithm that completes broadcasting in O(D log n/log D + logO(1) n) time, succeeding with high probability. This yields the first optimal O(D)-time broadcasting algorithm whenever n is polynomial in D.
Furthermore, our approach can be applied to design a new leader election algorithm that matches the performance of our broadcasting algorithm. Previously, all fast randomized leader election algorithms have used broadcasting as a subroutine and their complexity has been asymptotically strictly larger than the complexity of broadcasting. In particular, the fastest previously known randomized leader election algorithm of Ghaffari and Haeupler (SODA'2013) requires O(D log n/D min {log log n, log n/D} + logO(1) n)-time, succeeding with high probability. Our new algorithm again requires O(D log n/log D + logO(1) n) time, also succeeding with high probability.},
author = {Czumaj, Artur and Davies, Peter},
issn = {1557-735X},
journal = {Journal of the ACM},
keywords = {Artificial Intelligence, Hardware and Architecture, Information Systems, Control and Systems Engineering, Software},
number = {2},
publisher = {Association for Computing Machinery},
title = {{Exploiting spontaneous transmissions for broadcasting and leader election in radio networks}},
doi = {10.1145/3446383},
volume = {68},
year = {2021},
}
@article{15269,
abstract = {We study different aspects of quantum field theory at finite density using methods from quantum information theory. For simplicity we focus on massive Dirac fermions with nonzero chemical potential, and work in 1 + 1 space-time dimensions. Using the entanglement entropy on an interval, we construct an entropic c-function that is finite. Unlike what happens in Lorentz-invariant theories, this c-function exhibits a strong violation of monotonicity; it also encodes the creation of long-range entanglement from the Fermi surface. Motivated by previous works on lattice models, we next calculate numerically the Renyi entropies and find Friedel-type oscillations; these are understood in terms of a defect operator product expansion. Furthermore, we consider the mutual information as a measure of correlation functions between different regions. Using a long-distance expansion previously developed by Cardy, we argue that the mutual information detects Fermi surface correlations already at leading order in the expansion. We also analyze the relative entropy and its Renyi generalizations in order to distinguish states with different charge and/or mass. In particular, we show that states in different superselection sectors give rise to a super-extensive behavior in the relative entropy. Finally, we discuss possible extensions to interacting theories, and argue for the relevance of some of these measures for probing non-Fermi liquids.},
author = {Daguerre, Lucas and Medina Ramos, Raimel A and Solís, Mario and Torroba, Gonzalo},
issn = {1029-8479},
journal = {Journal of High Energy Physics},
keywords = {Nuclear and High Energy Physics},
number = {3},
publisher = {Springer Nature},
title = {{Aspects of quantum information in finite density field theory}},
doi = {10.1007/jhep03(2021)079},
volume = {2021},
year = {2021},
}
@article{15270,
abstract = {Various toxic compounds disrupt bacterial physiology. While bacteria harbor defense mechanisms to mitigate the toxicity, these mechanisms are often coupled to the physiological state of the cells and become ineffective when the physiology is severely disrupted.},
author = {Le, Dai and Krasnopeeva, Ekaterina and Sinjab, Faris and Pilizota, Teuta and Kim, Minsu},
issn = {2150-7511},
journal = {mBio},
keywords = {Virology, Microbiology},
number = {4},
publisher = {American Society for Microbiology},
title = {{Active efflux leads to heterogeneous dissipation of proton motive force by protonophores in bacteria}},
doi = {10.1128/mbio.00676-21},
volume = {12},
year = {2021},
}
@article{15271,
abstract = {We settle the complexity of the (∆ + 1)-coloring and (∆ + 1)-list coloring problems intheCONGESTED CLIQUEmodel by presenting a simpledeterministicalgorithm for both problemsrunning in a constant number of rounds. This matches the complexity of the recent breakthroughrandomizedconstant-round (∆ + 1)-list coloring algorithm due to Chang et al. [Proceedings of the38th ACM Symposium on Principles of Distributed Computing, 2019] and significantly improvesupon the state-of-the-artO(log ∆)-round deterministic (∆ + 1)-coloring bound of Parter [Proceed-ings of the 45th Annual International Colloquium on Automata, Languages and Programming]. Aremarkable property of our algorithm is its simplicity. Whereas the state-of-the-artrandomizedal-gorithms for this problem are based on the quite involved local coloring algorithm of Chang, Li, andPettie [Proceedings of the 50th Annual ACM SIGACT Symposium on Theory of Computing, 2018],our algorithm can be described in just a few lines. At a high level, it applies a careful derandomiza-tion of a recursive procedure which partitions the nodes and their respective palettes into separatebins. We show that afterO(1) recursion steps, the remaining uncolored subgraph within each bin haslinear size and thus can be solved locally by collecting it to a single node. This algorithm can alsobe implemented in the massively parallel computation (MPC) model provided that each machine haslinear (inn, the number of nodes in the input graph) space. We also show an extension of our algo-rithm to theMPCregime, in which machines havesublinearspace: we present the first deterministic(∆ + 1)-list coloring algorithm designed for sublinear-spaceMPC, which runs inO(log ∆ + log logn)rounds.},
author = {Czumaj, Artur and Davies, Peter and Parter, Merav},
issn = {1095-7111},
journal = {SIAM Journal on Computing},
keywords = {General Mathematics, General Computer Science},
number = {5},
pages = {1603--1626},
publisher = {Society for Industrial and Applied Mathematics},
title = {{Simple, deterministic, constant-round coloring in congested clique and MPC}},
doi = {10.1137/20m1366502},
volume = {50},
year = {2021},
}
@article{15272,
abstract = {The assembly of neuronal circuits involves the migrations of neurons from their place of birth to their final location in the nervous system, as well as the coordinated growth and patterning of axons and dendrites. In screens for genes required for patterning of the nervous system, we identified the catp-8/P5A-ATPase as an important regulator of neural patterning. P5A-ATPases are part of the P-type ATPases, a family of proteins known to serve a conserved function as transporters of ions, lipids and polyamines in unicellular eukaryotes, plants, and humans. While the function of many P-type ATPases is relatively well understood, the function of P5A-ATPases in metazoans remained elusive. We show here, that the Caenorhabditis elegans ortholog catp-8/P5A-ATPase is required for defined aspects of nervous system development. Specifically, the catp-8/P5A-ATPase serves functions in shaping the elaborately sculpted dendritic trees of somatosensory PVD neurons. Moreover, catp-8/P5A-ATPase is required for axonal guidance and repulsion at the midline, as well as embryonic and postembryonic neuronal migrations. Interestingly, not all axons at the midline require catp-8/P5A-ATPase, although the axons run in the same fascicles and navigate the same space. Similarly, not all neuronal migrations require catp-8/P5A-ATPase. A CATP-8/P5A-ATPase reporter is localized to the ER in most, if not all, tissues and catp-8/P5A-ATPase can function both cell-autonomously and non-autonomously to regulate neuronal development. Genetic analyses establish that catp-8/P5A-ATPase can function in multiple pathways, including the Menorin pathway, previously shown to control dendritic patterning in PVD, and Wnt signaling, which functions to control neuronal migrations. Lastly, we show that catp-8/P5A-ATPase is required for localizing select transmembrane proteins necessary for dendrite morphogenesis. Collectively, our studies suggest that catp-8/P5A-ATPase serves diverse, yet specific, roles in different genetic pathways and may be involved in the regulation or localization of transmembrane and secreted proteins to specific subcellular compartments.},
author = {Tang, Leo T. H. and Trivedi, Meera and Freund, Jenna and Salazar, Christopher J. and Rahman, Maisha and Ramirez, Nelson and Lee, Garrett and Wang, Yu and Grant, Barth D. and Bülow, Hannes E.},
issn = {1553-7404},
journal = {PLOS Genetics},
keywords = {Cancer Research, Genetics (clinical), Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics},
number = {7},
publisher = {Public Library of Science},
title = {{The CATP-8/P5A-type ATPase functions in multiple pathways during neuronal patterning}},
doi = {10.1371/journal.pgen.1009475},
volume = {17},
year = {2021},
}
@article{15273,
abstract = {Synapses of glutamatergic mossy fibers (MFs) onto cerebellar unipolar brush cells (UBCs) generate slow excitatory (ON) or inhibitory (OFF) postsynaptic responses dependent on the complement of glutamate receptors expressed on the UBC’s large dendritic brush. Using mouse brain slice recording and computational modeling of synaptic transmission, we found that substantial glutamate is maintained in the UBC synaptic cleft, sufficient to modify spontaneous firing in OFF UBCs and tonically desensitize AMPARs of ON UBCs. The source of this ambient glutamate was spontaneous, spike-independent exocytosis from the MF terminal, and its level was dependent on activity of glutamate transporters EAAT1–2. Increasing levels of ambient glutamate shifted the polarity of evoked synaptic responses in ON UBCs and altered the phase of responses to in vivo-like synaptic activity. Unlike classical fast synapses, receptors at the UBC synapse are virtually always exposed to a significant level of glutamate, which varies in a graded manner during transmission.},
author = {Balmer, Timothy S and Borges Merjane, Carolina and Trussell, Laurence O},
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 = {{Incomplete removal of extracellular glutamate controls synaptic transmission and integration at a cerebellar synapse}},
doi = {10.7554/elife.63819},
volume = {10},
year = {2021},
}
@article{15274,
abstract = {Copper (Cu) is a redox-active micronutrient that is both essential and toxic. Its cellular homeostasis is critical for supporting cuproprotein maturation while avoiding excessive oxidative stress. The Cu importer CcoA is the prototype of the widespread CalT subfamily of the MFS-type transporters. Hence, understanding its molecular mechanism of function is significant. Here, we show that CcoA undergoes a thiol:disulfide oxidoreduction cycle, which is important for its Cu import activity.},
author = {Khalfaoui-Hassani, Bahia and Trasnea, Petru Iulian and Steimle, Stefan and Koch, Hans-Georg and Daldal, Fevzi},
issn = {2150-7511},
journal = {mBio},
keywords = {Virology, Microbiology},
number = {4},
publisher = {American Society for Microbiology},
title = {{Cysteine mutants of the major facilitator superfamily-type transporter CcoA provide insight into copper import}},
doi = {10.1128/mbio.01567-21},
volume = {12},
year = {2021},
}
@article{15275,
abstract = {In 1916, Schur introduced the Ramsey number r(3; m), which is the minimum integer n > 1 such that for any m-coloring of the edges of the complete graph Kn, there is a monochromatic copy of K3. He showed that r(3; m) ≤ O(m!), and a simple construction demonstrates that r(3; m) ≥ 2Ω(m). An old conjecture of Erdős states that r(3; m) = 2Θ(m). In this note, we prove the conjecture for m-colorings with bounded VC-dimension, that is, for m-colorings with the property that the set system induced by the neighborhoods of the vertices with respect to each color class has bounded VC-dimension.},
author = {Fox, Jacob and Pach, János and Suk, Andrew},
issn = {1439-6912},
journal = {Combinatorica},
keywords = {Computational Mathematics, Discrete Mathematics and Combinatorics},
number = {6},
pages = {803--813},
publisher = {Springer Nature},
title = {{Bounded VC-dimension implies the Schur-Erdős conjecture}},
doi = {10.1007/s00493-021-4530-9},
volume = {41},
year = {2021},
}
@article{15276,
abstract = {Biotrophic plant pathogens secrete effector proteins to manipulate the host physiology. Effectors suppress defenses and induce an environment favorable to disease development. Sequence-based prediction of effector function is impeded by their rapid evolution rate. In the maize pathogen Ustilago maydis, effector-coding genes frequently organize in clusters. Here we describe the functional characterization of the pleiades, a cluster of ten effector genes, by analyzing the micro- and macroscopic phenotype of the cluster deletion and expressing these proteins in planta. Deletion of the pleiades leads to strongly impaired virulence and accumulation of reactive oxygen species (ROS) in infected tissue. Eight of the Pleiades suppress the production of ROS upon perception of pathogen associated molecular patterns (PAMPs). Although functionally redundant, the Pleiades target different host components. The paralogs Taygeta1 and Merope1 suppress ROS production in either the cytoplasm or nucleus, respectively. Merope1 targets and promotes the auto-ubiquitination activity of RFI2, a conserved family of E3 ligases that regulates the production of PAMP-triggered ROS burst in plants.},
author = {Navarrete, Fernando and Grujic, Nenad and Stirnberg, Alexandra and Saado, Indira and Aleksza, David and Gallei, Michelle C and Adi, Hazem and Alcântara, André and Khan, Mamoona and Bindics, Janos and Trujillo, Marco and Djamei, Armin},
issn = {1553-7374},
journal = {PLOS Pathogens},
keywords = {Virology, Genetics, Molecular Biology, Immunology, Microbiology, Parasitology},
number = {6},
publisher = {Public Library of Science},
title = {{The Pleiades are a cluster of fungal effectors that inhibit host defenses}},
doi = {10.1371/journal.ppat.1009641},
volume = {17},
year = {2021},
}
@article{15277,
abstract = {Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.},
author = {Fuchs, Armin and Riegler, Stefan and Ayatollahi, Zahra and Cavallari, Nicola and Giono, Luciana E and Nimeth, Barbara A and Mutanwad, Krishna V and Schweighofer, Alois and Lucyshyn, Doris and Barta, Andrea and Petrillo, Ezequiel and Kalyna, Maria},
issn = {1362-4962},
journal = {Nucleic Acids Research},
keywords = {Genetics},
number = {2},
pages = {1133--1151},
publisher = {Oxford University Press},
title = {{Targeting alternative splicing by RNAi: From the differential impact on splice variants to triggering artificial pre-mRNA splicing}},
doi = {10.1093/nar/gkaa1260},
volume = {49},
year = {2021},
}
@article{15278,
abstract = {‘Dysbiosis’ of the adult gut microbiota, in response to challenges such as infection, altered diet, stress, and antibiotics treatment has been recently linked to pathological alteration of brain function and behavior. Moreover, gut microbiota composition constantly controls microglia maturation, as revealed by morphological observations and gene expression analysis. However, it is unclear whether microglia functional properties and crosstalk with neurons, known to shape and modulate synaptic development and function, are influenced by the gut microbiota. Here, we investigated how antibiotic-mediated alteration of the gut microbiota influences microglial and neuronal functions in adult mice hippocampus. Hippocampal microglia from adult mice treated with oral antibiotics exhibited increased microglia density, altered basal patrolling activity, and impaired process rearrangement in response to damage. Patch clamp recordings at CA3-CA1 synapses revealed that antibiotics treatment alters neuronal functions, reducing spontaneous postsynaptic glutamatergic currents and decreasing synaptic connectivity, without reducing dendritic spines density. Antibiotics treatment was unable to modulate synaptic function in CX3CR1-deficient mice, pointing to an involvement of microglia–neuron crosstalk through the CX3CL1/CX3CR1 axis in the effect of dysbiosis on neuronal functions. Together, our findings show that antibiotic alteration of gut microbiota impairs synaptic efficacy, suggesting that CX3CL1/CX3CR1 signaling supporting microglia is a major player in in the gut–brain axis, and in particular in the gut microbiota-to-neuron communication pathway.},
author = {Cordella, Federica and Sanchini, Caterina and Rosito, Maria and Ferrucci, Laura and Pediconi, Natalia and Cortese, Barbara and Guerrieri, Francesca and Pascucci, Giuseppe Rubens and Antonangeli, Fabrizio and Peruzzi, Giovanna and Giubettini, Maria and Basilico, Bernadette and Pagani, Francesca and Grimaldi, Alfonso and D’Alessandro, Giuseppina and Limatola, Cristina and Ragozzino, Davide and Di Angelantonio, Silvia},
issn = {2073-4409},
journal = {Cells},
keywords = {General Medicine},
number = {10},
publisher = {MDPI},
title = {{Antibiotics treatment modulates microglia–synapses interaction}},
doi = {10.3390/cells10102648},
volume = {10},
year = {2021},
}