@article{2448, abstract = {Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.}, author = {Remy, Estelle and Baster, Pawel and Friml, Jirí and Duque, Paula}, journal = {Plant Signaling & Behavior}, number = {10}, publisher = {Taylor & Francis}, title = {{ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip}}, doi = {10.4161/psb.25688}, volume = {8}, year = {2013}, } @article{2449, abstract = {Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. }, author = {Nodzyński, Tomasz and Feraru, Murguel and Hirsch, Sibylle and De Rycke, Riet and Nicuales, Claudiu and Van Leene, Jelle and De Jaeger, Geert and Vanneste, Steffen and Friml, Jirí}, journal = {Molecular Plant}, number = {6}, pages = {1849 -- 1862}, publisher = {Cell Press}, title = {{Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis}}, doi = {10.1093/mp/sst044}, volume = {6}, year = {2013}, } @article{245, abstract = {For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ.}, author = {Baier, Stephan and Timothy Browning}, journal = {Journal fur die Reine und Angewandte Mathematik}, number = {680}, pages = {69 -- 151}, publisher = {Walter de Gruyter}, title = {{Inhomogeneous cubic congruences and rational points on del Pezzo surfaces}}, doi = {10.1515/crelle.2012.039}, year = {2013}, } @article{2450, abstract = {Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network}, author = {Liu, Junli and Menhi, Saher and Topping, Jennifer and Jirí Friml and Lindsey, Keith}, journal = {Frontiers in Plant Science}, number = {75}, publisher = {Frontiers Research Foundation}, title = {{Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development}}, doi = {10.3389/fpls.2013.00075}, volume = {4}, year = {2013}, } @article{2452, abstract = {Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.}, author = {Barbez, Elke and Laňková, Martina and Pařezová, Markéta and Maizel, Alexis and Zažímalová, Eva and Petrášek, Jan and Jirí Friml and Kleine-Vehn, Jürgen}, journal = {BMC Plant Biology}, number = {1}, publisher = {BioMed Central}, title = {{Single-cell-based system to monitor carrier driven cellular auxin homeostasis}}, doi = {10.1186/1471-2229-13-20}, volume = {13}, year = {2013}, } @article{2457, author = {Viaene, Tom and Delwiche, Charles and Rensing, Stefan and Friml, Jirí}, journal = {Trends in Plant Science}, number = {1}, pages = {5 -- 10}, publisher = {Cell Press}, title = {{Origin and evolution of PIN auxin transporters in the green lineage}}, doi = {10.1016/j.tplants.2012.08.009}, volume = {18}, year = {2013}, } @article{246, abstract = {Given an intersection of two quadrics X Pm1, with m > 9, the quantitative arithmetic of the set X(Q) is investigated under the assumption that the singular locus of X consists of a pair of conjugate singular points defined over Q(i).}, author = {Timothy Browning and Munshi, Ritabrata}, journal = {Compositio Mathematica}, number = {9}, pages = {1457 -- 1494}, publisher = {Cambridge University Press}, title = {{Rational points on singular intersections of quadrics}}, doi = {10.1112/S0010437X13007185}, volume = {149}, year = {2013}, } @article{2466, abstract = {We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation.}, author = {Ando, Ryoichi and Thuerey, Nils and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Highly adaptive liquid simulations on tetrahedral meshes}}, doi = {10.1145/2461912.2461982}, volume = {32}, year = {2013}, } @article{2467, abstract = {This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.}, author = {Bernstein, Gilbert and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Putting holes in holey geometry: Topology change for arbitrary surfaces}}, doi = {10.1145/2461912.2462027}, volume = {32}, year = {2013}, } @article{2468, abstract = {Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers.}, author = {Bojsen-Hansen, Morten and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Liquid surface tracking with error compensation}}, doi = {10.1145/2461912.2461991}, volume = {32}, year = {2013}, } @article{2469, abstract = {Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.}, author = {Maître, Jean-Léon and Heisenberg, Carl-Philipp J}, journal = {Current Biology}, number = {14}, pages = {R626 -- R633}, publisher = {Cell Press}, title = {{Three functions of cadherins in cell adhesion}}, doi = {10.1016/j.cub.2013.06.019}, volume = {23}, year = {2013}, } @article{247, abstract = {An improved estimate is provided for the number of Fq-rational points on a geometrically irreducible, projective, cubic hypersurface that is not equal to a cone.}, author = {Timothy Browning}, journal = {Canadian Mathematical Bulletin}, number = {3}, pages = {500 -- 502}, publisher = {Unknown}, title = {{The Lang-Weil estimate for cubic hypersurfaces}}, doi = {10.4153/CMB-2011-177-4}, volume = {56}, year = {2013}, } @article{2470, abstract = {Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.}, author = {Čovanová, Milada and Sauer, Michael and Rychtář, Jan and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells}}, doi = {10.1371/journal.pone.0070050}, volume = {8}, year = {2013}, } @article{2471, abstract = {The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.}, author = {Sanchez Romero, Inmaculada and Ariza, Antonio and Wilson, Keith and Skjøt, Michael and Vind, Jesper and De Maria, Leonardo and Skov, Lars and Sánchez Ruiz, Jose}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Mechanism of protein kinetic stabilization by engineered disulfide crosslinks}}, doi = {10.1371/journal.pone.0070013}, volume = {8}, year = {2013}, } @article{2472, abstract = {Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.}, author = {Cazzonelli, Christopher and Vanstraelen, Marleen and Simon, Sibu and Yin, Kuide and Carron Arthur, Ashley and Nisar, Nazia and Tarle, Gauri and Cuttriss, Abby and Searle, Iain and Benková, Eva and Mathesius, Ulrike and Masle, Josette and Friml, Jirí and Pogson, Barry}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development}}, doi = {10.1371/journal.pone.0070069}, volume = {8}, year = {2013}, } @article{2473, abstract = {When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift, . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis.}, author = {Barton, Nicholas H and Etheridge, Alison and Kelleher, Jerome and Véber, Amandine}, journal = {Theoretical Population Biology}, number = {8}, pages = {75 -- 89}, publisher = {Elsevier}, title = {{Genetic hitch-hiking in spatially extended populations}}, doi = {10.1016/j.tpb.2012.12.001}, volume = {87}, year = {2013}, } @article{2478, abstract = {Despite the pivotal functions of the NMDA receptor (NMDAR) for neural circuit development and synaptic plasticity, the molecular mechanisms underlying the dynamics of NMDAR trafficking are poorly understood. The cell adhesion molecule neuroligin-1 (NL1) modifies NMDAR-dependent synaptic transmission and synaptic plasticity, but it is unclear whether NL1 controls synaptic accumulation or function of the receptors. Here, we provide evidence that NL1 regulates the abundance of NMDARs at postsynaptic sites. This function relies on extracellular, NL1 isoform-specific sequences that facilitate biochemical interactions between NL1 and the NMDAR GluN1 subunit. Our work uncovers NL1 isoform-specific cisinteractions with ionotropic glutamate receptors as a key mechanism for controlling synaptic properties.}, author = {Budreck, Elaine C and Kwon, Oh-Bin and Jung, Jung-Hoon and Baudouin, Stéphane J and Thommen, Albert and Kim, Hye-Sun and Fukazawa, Yugo and Harumi Harada and Tabuchi, Katsuhiko and Ryuichi Shigemoto and Scheiffele, Peter and Kim, Joung-Hun}, journal = {PNAS}, number = {2}, pages = {725 -- 730}, publisher = {National Academy of Sciences}, title = {{Neuroligin-1 controls synaptic abundance of NMDA-type glutamate receptors through extracellular coupling}}, doi = {10.1073/pnas.1214718110}, volume = {110}, year = {2013}, } @article{250, abstract = {Châtelet surfaces provide a rich source of geometrically rational surfaces that do not always satisfy the Hasse principle. Restricting attention to a special class of Châtelet surfaces, we investigate the frequency that such counter-examples arise over the rational numbers.}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Proceedings of the London Mathematical Society}, number = {4}, pages = {1030 -- 1078}, publisher = {Oxford University Press}, title = {{Density of Châtelet surfaces failing the Hasse principle}}, doi = {10.1112/plms/pdt060}, volume = {108}, year = {2013}, } @article{251, abstract = {We study the density of varieties in a certain family which do not satisfy the Hasse principle. This work relies on results recently obtained by Colliot-Thélène [3].}, author = {de la Bretèche, Régis and Timothy Browning}, journal = {Journal de Theorie des Nombres de Bordeaux}, number = {1}, pages = {25 -- 44}, publisher = {Universite de Bordeaux I}, title = {{Counter examples to the Hasse principle among certain coflasque tori}}, doi = {10.5802/jtnb.857}, volume = {26}, year = {2013}, } @article{2516, abstract = {We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes.}, author = {Lampert, Christoph and Nickisch, Hannes and Harmeling, Stefan}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {3}, pages = {453 -- 465}, publisher = {IEEE}, title = {{Attribute-based classification for zero-shot learning of object categories}}, doi = {10.1109/TPAMI.2013.140}, volume = {36}, year = {2013}, }