@article{2970, abstract = {Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms.}, author = {Kicheva, Anna and Bollenbach, Mark Tobias and Wartlick, Ortrud and Julicher, Frank and Gonzalez Gaitan, Marcos}, journal = {Current Opinion in Genetics & Development}, number = {6}, pages = {527 -- 532}, publisher = {Elsevier}, title = {{Investigating the principles of morphogen gradient formation: from tissues to cells}}, doi = {10.1016/j.gde.2012.08.004}, volume = {22}, year = {2012}, } @inproceedings{2971, abstract = {We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. }, author = {Zankl, Georg and Haxhimusa, Yll and Ion, Adrian}, location = {Graz, Austria}, pages = {11 -- 20}, publisher = {Springer}, title = {{Interactive labeling of image segmentation hierarchies}}, doi = {10.1007/978-3-642-32717-9_2}, volume = {7476}, year = {2012}, } @article{3105, abstract = {Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli.}, author = {Whitford, Ryan and Fernandez, Ana and Tejos, Ricardo and Pérez, Amparo Cuéllar and Kleine-Vehn, Jürgen and Vanneste, Steffen and Drozdzecki, Andrzej and Leitner, Johannes and Abas, Lindy and Aerts, Maarten and Hoogewijs, Kurt and Pawel Baster and De Groodt, Ruth and Lin, Yao-Cheng and Storme, Véronique and Van de Peer, Yves and Beeckman, Tom and Madder, Annemieke and Devreese, Bart and Luschnig, Christian and Jirí Friml and Hilson, Pierre}, journal = {Developmental Cell}, number = {3}, pages = {678 -- 685}, publisher = {Cell Press}, title = {{GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses}}, doi = {10.1016/j.devcel.2012.02.002}, volume = {22}, year = {2012}, } @article{3109, abstract = {Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane.}, author = {Irani, Niloufer G and Di Rubbo, Simone and Mylle, Evelien and Van Den Begin, Jos and Schneider-Pizoń, Joanna and Hniliková, Jaroslava and Šíša, Miroslav and Buyst, Dieter and Vilarrasa-Blasi, Josep and Szatmári, Anna-Maria and Van Damme, Daniël and Mishev, Kiril and Codreanu, Mirela-Corina and Kohout, Ladislav and Strnad, Miroslav and Caño-Delgado, Ana I and Jirí Friml and Madder, Annemieke and Russinova, Eugenia}, journal = {Nature Chemical Biology}, number = {6}, pages = {583 -- 589}, publisher = {Nature Publishing Group}, title = {{Fluorescent castasterone reveals BRI1 signaling from the plasma membrane}}, doi = {10.1038/nchembio.958}, volume = {8}, year = {2012}, } @article{3104, abstract = { Gradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.}, author = {Grunewald, Wim and De Smet, Ive and Lewis, Daniel R and Löfke, Christian and Jansen, Leentje and Goeminne, Geert and Vanden Bossche, Robin and Karimi, Mansour and De Rybel, Bert and Vanholme, Bartel and Teichmann, Thomas and Boerjan, Wout and Van Montagu, Marc C and Gheysen, Godelieve and Muday, Gloria K and Jirí Friml and Beeckman, Tom}, journal = {PNAS}, number = {5}, pages = {1554 -- 1559}, publisher = {National Academy of Sciences}, title = {{Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis}}, doi = {10.1073/pnas.1121134109}, volume = {109}, year = {2012}, } @article{3108, abstract = {The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes.}, author = {Barbez, Elke and Kubeš, Martin and Rolčík, Jakub and Béziat, Chloe and Pěnčík, Aleš and Wang, Bangjun and Rosquete, Michel Ruiz and Zhu, Jinsheng and Dobrev, Petre I and Lee, Yuree and Zašímalová, Eva and Petrášek, Jan and Geisler, Markus and Jirí Friml and Kleine-Vehn, Jürgen}, journal = {Nature}, number = {7396}, pages = {119 -- 122}, publisher = {Nature Publishing Group}, title = {{A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants}}, doi = {10.1038/nature11001}, volume = {485}, year = {2012}, } @article{3106, abstract = {Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis.}, author = {Nagawa, Shingo and Xu, Tongda and Lin, Deshu and Dhonukshe, Pankaj and Zhang, Xingxing and Jirí Friml and Scheres, Ben and Fu, Ying and Yang, Zhenbiao}, journal = {PLoS Biology}, number = {4}, publisher = {Public Library of Science}, title = {{ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis}}, doi = {10.1371/journal.pbio.1001299}, volume = {10}, year = {2012}, } @misc{3107, author = {Vanneste, Steffen and Friml, Jirí}, booktitle = {Nature Chemical Biology}, number = {5}, pages = {415 -- 416}, publisher = {Nature Publishing Group}, title = {{Plant signaling: Deconstructing auxin sensing}}, doi = {10.1038/nchembio.943}, volume = {8}, year = {2012}, } @inproceedings{3119, abstract = {We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water. }, author = {Raveendran, Karthik and Thuerey, Nils and Wojtan, Christopher J and Turk, Greg}, booktitle = {Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation}, location = {Aire-la-Ville, Switzerland}, pages = {255 -- 264}, publisher = {ACM}, title = {{Controlling liquids using meshes}}, year = {2012}, } @article{3118, abstract = {We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.}, author = {Bojsen-Hansen, Morten and Li, Hao and Wojtan, Christopher J}, journal = {ACM Transactions on Graphics}, number = {4}, publisher = {ACM}, title = {{Tracking surfaces with evolving topology}}, doi = {10.1145/2185520.2185549}, volume = {31}, year = {2012}, } @article{3122, abstract = {Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. }, author = {Field, David and Barrett, Spencer}, journal = {Molecular Ecology}, number = {15}, pages = {3640 -- 3643}, publisher = {Wiley-Blackwell}, title = {{Disassortative mating and the maintenance of sexual polymorphism in painted maple}}, doi = {10.1111/j.1365-294X.2012.05643.x}, volume = {21}, year = {2012}, } @article{3121, abstract = {Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type.}, author = {Williams, Courtney and Chen, Wenyan and Lee, Chia and Yaeger, Daniel and Vyleta, Nicholas and Smith, Stephen}, journal = {Nature Neuroscience}, number = {9}, pages = {1195 -- 1197}, publisher = {Nature Publishing Group}, title = {{Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA}}, doi = {10.1038/nn.3162}, volume = {15}, year = {2012}, } @article{3120, abstract = {We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.}, author = {Brown, Gavin and Kerber, Michael and Reid, Miles}, journal = {Compositio Mathematica}, number = {4}, pages = {1171 -- 1194}, publisher = {Cambridge University Press}, title = {{Fano 3 folds in codimension 4 Tom and Jerry Part I}}, doi = {10.1112/S0010437X11007226}, volume = {148}, year = {2012}, } @article{3117, abstract = {We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.}, author = {Kolmogorov, Vladimir}, journal = {Discrete Applied Mathematics}, number = {15}, pages = {2246 -- 2258}, publisher = {Elsevier}, title = {{Minimizing a sum of submodular functions}}, doi = {10.1016/j.dam.2012.05.025}, volume = {160}, year = {2012}, } @article{3131, abstract = {In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.}, author = {Weissman, Daniel and Barton, Nicholas H}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Limits to the rate of adaptive substitution in sexual populations}}, doi = {10.1371/journal.pgen.1002740}, volume = {8}, year = {2012}, } @article{3130, abstract = {Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.}, author = {Bergmiller, Tobias and Ackermann, Martin and Silander, Olin}, journal = {PLoS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{Patterns of evolutionary conservation of essential genes correlate with their compensability}}, doi = {10.1371/journal.pgen.1002803}, volume = {8}, year = {2012}, } @inproceedings{3136, abstract = {Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag.}, author = {Guet, Calin C and Gupta, Ashutosh and Henzinger, Thomas A and Mateescu, Maria and Sezgin, Ali}, location = {Berkeley, CA, USA}, pages = {294 -- 309}, publisher = {Springer}, title = {{Delayed continuous time Markov chains for genetic regulatory circuits}}, doi = {10.1007/978-3-642-31424-7_24}, volume = {7358 }, year = {2012}, } @inproceedings{3135, abstract = {We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. }, author = {Brázdil, Brázdil and Chatterjee, Krishnendu and Kučera, Antonín and Novotny, Petr}, location = {Berkeley, CA, USA}, pages = {23 -- 38}, publisher = {Springer}, title = {{Efficient controller synthesis for consumption games with multiple resource types}}, doi = {10.1007/978-3-642-31424-7_8}, volume = {7358}, year = {2012}, } @inproceedings{3133, abstract = {This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. }, author = {Edelsbrunner, Herbert and Kerber, Michael}, booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry }, location = {Chapel Hill, NC, USA}, pages = {249 -- 258}, publisher = {ACM}, title = {{Alexander duality for functions: The persistent behavior of land and water and shore}}, doi = {10.1145/2261250.2261287}, year = {2012}, } @inproceedings{3134, abstract = {It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. }, author = {Edelsbrunner, Herbert and Fasy, Brittany and Rote, Günter}, booktitle = {Proceedings of the twenty-eighth annual symposium on Computational geometry }, location = {Chapel Hill, NC, USA}, pages = {91 -- 100}, publisher = {ACM}, title = {{Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions}}, doi = {10.1145/2261250.2261265}, year = {2012}, }