@article{12192, abstract = {Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.}, author = {He, Shengbo and Vickers, Martin and Zhang, Jingyi and Feng, Xiaoqi}, issn = {2050-084X}, journal = {eLife}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine, General Neuroscience}, publisher = {eLife Sciences Publications, Ltd}, title = {{Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation}}, doi = {10.7554/elife.42530}, volume = {8}, year = {2019}, } @article{12190, abstract = {Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor.}, author = {Lawrence, Emma J. and Gao, Hongbo and Tock, Andrew J. and Lambing, Christophe and Blackwell, Alexander R. and Feng, Xiaoqi and Henderson, Ian R.}, issn = {0960-9822}, journal = {Current Biology}, keywords = {General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology}, number = {16}, pages = {2676--2686.e3}, publisher = {Elsevier BV}, title = {{Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis}}, doi = {10.1016/j.cub.2019.06.084}, volume = {29}, year = {2019}, } @inproceedings{12901, author = {Schlögl, Alois and Kiss, Janos and Elefante, Stefano}, booktitle = {AHPC19 - Austrian HPC Meeting 2019 }, location = {Grundlsee, Austria}, pages = {25}, publisher = {Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz}, title = {{Is Debian suitable for running an HPC Cluster?}}, year = {2019}, } @inproceedings{6989, abstract = {When can a polyomino piece of paper be folded into a unit cube? Prior work studied tree-like polyominoes, but polyominoes with holes remain an intriguing open problem. We present sufficient conditions for a polyomino with hole(s) to fold into a cube, and conditions under which cube folding is impossible. In particular, we show that all but five special simple holes guarantee foldability. }, author = {Aichholzer, Oswin and Akitaya, Hugo A and Cheung, Kenneth C and Demaine, Erik D and Demaine, Martin L and Fekete, Sandor P and Kleist, Linda and Kostitsyna, Irina and Löffler, Maarten and Masárová, Zuzana and Mundilova, Klara and Schmidt, Christiane}, booktitle = {Proceedings of the 31st Canadian Conference on Computational Geometry}, location = {Edmonton, Canada}, pages = {164--170}, publisher = {Canadian Conference on Computational Geometry}, title = {{Folding polyominoes with holes into a cube}}, year = {2019}, } @inproceedings{6884, abstract = {In two-player games on graphs, the players move a token through a graph to produce a finite or infinite path, which determines the qualitative winner or quantitative payoff of the game. We study bidding games in which the players bid for the right to move the token. Several bidding rules were studied previously. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the "bank" rather than the other player. Taxman bidding spans the spectrum between Richman and poorman bidding. They are parameterized by a constant tau in [0,1]: portion tau of the winning bid is paid to the other player, and portion 1-tau to the bank. While finite-duration (reachability) taxman games have been studied before, we present, for the first time, results on infinite-duration taxman games. It was previously shown that both Richman and poorman infinite-duration games with qualitative objectives reduce to reachability games, and we show a similar result here. Our most interesting results concern quantitative taxman games, namely mean-payoff games, where poorman and Richman bidding differ significantly. A central quantity in these games is the ratio between the two players' initial budgets. While in poorman mean-payoff games, the optimal payoff of a player depends on the initial ratio, in Richman bidding, the payoff depends only on the structure of the game. In both games the optimal payoffs can be found using (different) probabilistic connections with random-turn games in which in each turn, instead of bidding, a coin is tossed to determine which player moves. While the value with Richman bidding equals the value of a random-turn game with an un-biased coin, with poorman bidding, the bias in the coin is the initial ratio of the budgets. We give a complete classification of mean-payoff taxman games that is based on a probabilistic connection: the value of a taxman bidding game with parameter tau and initial ratio r, equals the value of a random-turn game that uses a coin with bias F(tau, r) = (r+tau * (1-r))/(1+tau). Thus, we show that Richman bidding is the exception; namely, for every tau <1, the value of the game depends on the initial ratio. Our proof technique simplifies and unifies the previous proof techniques for both Richman and poorman bidding. }, author = {Avni, Guy and Henzinger, Thomas A and Zikelic, Dorde}, location = {Aachen, Germany}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Bidding mechanisms in graph games}}, doi = {10.4230/LIPICS.MFCS.2019.11}, volume = {138}, year = {2019}, } @misc{9726, abstract = {A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF)}, author = {Ucar, Mehmet C and Lipowsky, Reinhard}, publisher = {American Chemical Society }, title = {{Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding}}, doi = {10.1021/acs.nanolett.9b04445.s001}, year = {2019}, } @article{6671, abstract = {In this paper we discuss three results. The first two concern general sets of positive reach: we first characterize the reach of a closed set by means of a bound on the metric distortion between the distance measured in the ambient Euclidean space and the shortest path distance measured in the set. Secondly, we prove that the intersection of a ball with radius less than the reach with the set is geodesically convex, meaning that the shortest path between any two points in the intersection lies itself in the intersection. For our third result we focus on manifolds with positive reach and give a bound on the angle between tangent spaces at two different points in terms of the reach and the distance between the two points.}, author = {Boissonnat, Jean-Daniel and Lieutier, André and Wintraecken, Mathijs}, issn = {2367-1734}, journal = {Journal of Applied and Computational Topology}, number = {1-2}, pages = {29–58}, publisher = {Springer Nature}, title = {{The reach, metric distortion, geodesic convexity and the variation of tangent spaces}}, doi = {10.1007/s41468-019-00029-8}, volume = {3}, year = {2019}, } @article{301, abstract = {A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.}, author = {Gerencser, Mate and Gyöngy, István}, journal = {Stochastic Processes and their Applications}, number = {3}, pages = {995--1012}, publisher = {Elsevier}, title = {{A Feynman–Kac formula for stochastic Dirichlet problems}}, doi = {10.1016/j.spa.2018.04.003}, volume = {129}, year = {2019}, } @article{80, abstract = {We consider an interacting, dilute Bose gas trapped in a harmonic potential at a positive temperature. The system is analyzed in a combination of a thermodynamic and a Gross–Pitaevskii (GP) limit where the trap frequency ω, the temperature T, and the particle number N are related by N∼ (T/ ω) 3→ ∞ while the scattering length is so small that the interaction energy per particle around the center of the trap is of the same order of magnitude as the spectral gap in the trap. We prove that the difference between the canonical free energy of the interacting gas and the one of the noninteracting system can be obtained by minimizing the GP energy functional. We also prove Bose–Einstein condensation in the following sense: The one-particle density matrix of any approximate minimizer of the canonical free energy functional is to leading order given by that of the noninteracting gas but with the free condensate wavefunction replaced by the GP minimizer.}, author = {Deuchert, Andreas and Seiringer, Robert and Yngvason, Jakob}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {723--776}, publisher = {Springer}, title = {{Bose–Einstein condensation in a dilute, trapped gas at positive temperature}}, doi = {10.1007/s00220-018-3239-0}, volume = {368}, year = {2019}, } @article{5911, abstract = {Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.}, author = {Faria, Rui and Johannesson, Kerstin and Butlin, Roger K. and Westram, Anja M}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {3}, pages = {239--248}, publisher = {Elsevier}, title = {{Evolving inversions}}, doi = {10.1016/j.tree.2018.12.005}, volume = {34}, year = {2019}, } @article{439, abstract = {We count points over a finite field on wild character varieties,of Riemann surfaces for singularities with regular semisimple leading term. The new feature in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras. Our result leads to the conjecture that the mixed Hodge polynomials of these character varieties agree with previously conjectured perverse Hodge polynomials of certain twisted parabolic Higgs moduli spaces, indicating the possibility of a P = W conjecture for a suitable wild Hitchin system.}, author = {Hausel, Tamas and Mereb, Martin and Wong, Michael}, issn = {1435-9855}, journal = {Journal of the European Mathematical Society}, number = {10}, pages = {2995--3052}, publisher = {European Mathematical Society}, title = {{Arithmetic and representation theory of wild character varieties}}, doi = {10.4171/JEMS/896}, volume = {21}, year = {2019}, } @article{105, abstract = {Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.}, author = {Marsh, Ashley and Novarino, Gaia and Lockhart, Paul and Leventer, Richard}, journal = {European Journal of Human Genetics}, pages = {161--166}, publisher = {Springer Nature}, title = {{CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63}}, doi = {10.1038/s41431-018-0231-2}, volume = {27}, year = {2019}, } @article{65, abstract = {We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.}, author = {Dareiotis, Konstantinos and Gerencser, Mate and Gess, Benjamin}, journal = {Journal of Differential Equations}, number = {6}, pages = {3732--3763}, publisher = {Elsevier}, title = {{Entropy solutions for stochastic porous media equations}}, doi = {10.1016/j.jde.2018.09.012}, volume = {266}, year = {2019}, } @article{5907, abstract = {Microalgae of the genus Chlorella vulgaris are candidates for the production of lipids for biofuel production. Besides that, Chlorella vulgaris is marketed as protein and vitamin rich food additive. Its potential as a novel expression system for recombinant proteins inspired us to study its asparagine-linked oligosaccharides (N-glycans) by mass spectrometry, chromatography and gas chromatography. Oligomannosidic N-glycans with up to nine mannoses were the structures found in culture collection strains as well as several commercial products. These glycans co-eluted with plant N-glycans in the highly shape selective porous graphitic carbon chromatography. Thus, Chlorella vulgaris generates oligomannosidic N-glycans of the structural type known from land plants and animals. In fact, Man5 (Man5GlcNAc2) served as substrate for GlcNAc-transferase I and a trace of an endogenous structure with terminal GlcNAc was seen. The unusual more linear Man5 structure recently found on glycoproteins of Chlamydomonas reinhardtii occurred - if at all - in traces only. Notably, a majority of the oligomannosidic glycans was multiply O-methylated with 3-O-methyl and 3,6-di-O-methyl mannoses at the non-reducing termini. This modification has so far been neither found on plant nor vertebrate N-glycans. It’s possible immunogenicity raises concerns as to the use of C. vulgaris for production of pharmaceutical glycoproteins.}, author = {Mócsai, Réka and Figl, Rudolf and Troschl, Clemens and Strasser, Richard and Svehla, Elisabeth and Windwarder, Markus and Thader, Andreas and Altmann, Friedrich}, journal = {Scientific Reports}, number = {1}, publisher = {Nature Publishing Group}, title = {{N-glycans of the microalga Chlorella vulgaris are of the oligomannosidic type but highly methylated}}, doi = {10.1038/s41598-018-36884-1}, volume = {9}, year = {2019}, } @article{5908, abstract = {The interorganelle communication mediated by membrane contact sites (MCSs) is an evolutionary hallmark of eukaryotic cells. MCS connections enable the nonvesicular exchange of information between organelles and allow them to coordinate responses to changing cellular environments. In plants, the importance of MCS components in the responses to environmental stress has been widely established, but the molecular mechanisms regulating interorganelle connectivity during stress still remain opaque. In this report, we use the model plant Arabidopsis thaliana to show that ionic stress increases endoplasmic reticulum (ER)–plasma membrane (PM) connectivity by promoting the cortical expansion of synaptotagmin 1 (SYT1)-enriched ER–PM contact sites (S-EPCSs). We define differential roles for the cortical cytoskeleton in the regulation of S-EPCS dynamics and ER–PM connectivity, and we identify the accumulation of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] at the PM as a molecular signal associated with the ER–PM connectivity changes. Our study highlights the functional conservation of EPCS components and PM phosphoinositides as modulators of ER–PM connectivity in eukaryotes, and uncovers unique aspects of the spatiotemporal regulation of ER–PM connectivity in plants.}, author = {Lee, Eunkyoung and Vanneste, Steffen and Pérez-Sancho, Jessica and Benitez-Fuente, Francisco and Strelau, Matthew and Macho, Alberto P. and Botella, Miguel A. and Friml, Jiří and Rosado, Abel}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {4}, pages = {1420--1429}, publisher = {National Academy of Sciences}, title = {{Ionic stress enhances ER–PM connectivity via phosphoinositide-associated SYT1 contact site expansion in Arabidopsis}}, doi = {10.1073/pnas.1818099116}, volume = {116}, year = {2019}, } @article{5680, abstract = {Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.}, author = {Andalo, Christophe and Burrus, Monique and Paute, Sandrine and Lauzeral, Christine and Field, David}, issn = {23818115}, journal = {Botany Letters}, number = {1}, pages = {80--92}, publisher = {Taylor and Francis}, title = {{Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone}}, doi = {10.1080/23818107.2018.1545142}, volume = {166}, year = {2019}, } @article{5790, abstract = {The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.}, author = {Chaplick, Steven and Fulek, Radoslav and Klavík, Pavel}, issn = {03649024}, journal = {Journal of Graph Theory}, number = {4}, pages = {365--394}, publisher = {Wiley}, title = {{Extending partial representations of circle graphs}}, doi = {10.1002/jgt.22436}, volume = {91}, year = {2019}, } @article{405, abstract = {We investigate the quantum Jensen divergences from the viewpoint of joint convexity. It turns out that the set of the functions which generate jointly convex quantum Jensen divergences on positive matrices coincides with the Matrix Entropy Class which has been introduced by Chen and Tropp quite recently.}, author = {Virosztek, Daniel}, journal = {Linear Algebra and Its Applications}, pages = {67--78}, publisher = {Elsevier}, title = {{Jointly convex quantum Jensen divergences}}, doi = {10.1016/j.laa.2018.03.002}, volume = {576}, year = {2019}, } @article{175, abstract = {An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.}, author = {Browning, Timothy D and Loughran, Daniel}, issn = {10886850}, journal = {Transactions of the American Mathematical Society}, number = {8}, pages = {5757--5785}, publisher = {American Mathematical Society}, title = {{Sieving rational points on varieties}}, doi = {10.1090/tran/7514}, volume = {371}, year = {2019}, } @article{319, abstract = {We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition.}, author = {Gerencser, Mate and Hairer, Martin}, issn = {14322064}, journal = {Probability Theory and Related Fields}, number = {3-4}, pages = {697–758}, publisher = {Springer}, title = {{Singular SPDEs in domains with boundaries}}, doi = {10.1007/s00440-018-0841-1}, volume = {173}, year = {2019}, }