@article{6749, abstract = {This article refers to algorithms based on finite difference schemes for computing mean and affine curvature evolutions of digital images, introduced by Alvarez and Morel [L. Alvarez, J.M. Morel, “Formalization and computational aspects of image analysis”, Acta Numerica, pp. 159, 1994]. We discuss consistency, stability and convergence. Our analysis focuses on some possible choices of the parameters, choices that generate multiple variants in the implementations. Meaningful visual examples on how the algorithms actually work are provided.}, author = {Mondelli, Marco and Ciomaga, Adina}, issn = {2105-1232}, journal = {Image Processing On Line}, pages = {127--177}, publisher = {IPOL Image Processing On Line}, title = {{Finite difference schemes for MCM and AMSS}}, doi = {10.5201/ipol.2011.cm_fds}, volume = {1}, year = {2011}, } @inproceedings{6767, abstract = {In the present paper we give a thorough analysis of two finite difference schemes for the Mean Curvature Motion and its affine variant, the Affine Morphological Scale Space, schemes introduced in the Image Processing framework. This analysis brings in a series of parameters that allow us to compute an accurate discrete evolution of curvature motions. The choice of these parameters is based on intrinsic geometric properties of the evolution equations for linear, radial and elliptical functions. In the last part we present several examples, underlining the main advantages of the algorithms (the removal of pixelization effects and JPEG artifacts) as well as their major drawbacks (absence of contrast invariance and grid dependence). A detailed explanatory report, the ANSI C implementations and an on-line demo can be found at http://www.ipol.im/.}, author = {Mondelli, Marco and Ciomaga, Adina}, booktitle = {Proceedings of the International Student Conference on Pure and Applied Mathematics}, isbn = {978-973-703-602-5}, location = {Iasi, Romania}, pages = {137--156}, publisher = {Editura Universitãtii „Alexandru Ioan Cuza” Iasi}, title = {{On finite difference schemes for curvature motions}}, doi = {10.13140/2.1.1862.4646}, year = {2011}, } @article{7076, abstract = {Iron is a ubiquitous impurity in metamict (radiation-damaged and partially amorphized) materials such as titanite (CaSiTiO5). Using 57Fe Mössbauer spectroscopy we find that iron in metamict titanite is partitioned between amorphous and crystalline regions based on valence. Trivalent iron exists in the crystalline titanite matrix whereas divalent iron exists almost exclusively in radiation-amorphized regions. We find that the relative abundances of the oxidation states correlate with the volume fraction of amorphous and crystalline regions. Our data also show that oxidation of iron proceeds along with the recrystallization of the amorphized regions. Recrystallization is confirmed to occur over the range 700 °C < T < 925 °C, and no further structural changes are observed at higher temperatures. It is surprising that our Mössbauer measurements show divalent iron to be surrounded by titanite with a high degree of short-range structural order in the amorphized regions. This observation is fundamentally different from other metamict materials such as zircon (ZrSiO4), where amorphized regions show no short-range order.}, author = {Salje, E K H and Safarik, D J and Taylor, R D and Pasternak, M P and Modic, Kimberly A and Groat, L A and Lashley, J C}, issn = {0953-8984}, journal = {Journal of Physics: Condensed Matter}, number = {10}, publisher = {IOP Publishing}, title = {{Determination of iron sites and the amount of amorphization in radiation-damaged titanite (CaSiTiO5)}}, doi = {10.1088/0953-8984/23/10/105402}, volume = {23}, year = {2011}, } @article{7077, abstract = {Pb, Te, Ag and Se, when reacted in a 1:1:x:1 (x = 1.9, 2.0, 2.01) molar ratio, form a two phase composite which consists of a phase which crystallizes in the fcc cubic PbSe structure and a phase that crystallizes in the Ag2Te structure. In this article, we demonstrate that by varying the Ag concentration, we can manipulate which variant of the Ag2Te structure stabilizes at room temperature (monoclinic α-Ag2Te or cubic β-Ag1.9Te) and can consequently manipulate the electrical and thermal transport behavior of the composite and hence the thermoelectric performance. Additionally, we show that Cu-doping results in an overall improvement in thermoelectric performance. Our results suggest that formation of composites is a viable path for achieving a phonon-glass-electron-crystal (PGEC) alloy.}, author = {Capps, J. and Ma, B. and Drye, T. and Nucklos, C. and Lindsey, S. and Rhodes, D. and Zhang, Q. and Modic, Kimberly A and Cawthorne, S. and Drymiotis, F.}, issn = {0925-8388}, journal = {Journal of Alloys and Compounds}, number = {5}, pages = {1544--1549}, publisher = {Elsevier}, title = {{The effect of Ag concentration on the structural, electrical and thermal transport behavior of Pb:Te:Ag:Se mixtures and improvement of thermoelectric performance via Cu doping}}, doi = {10.1016/j.jallcom.2010.10.187}, volume = {509}, year = {2011}, } @article{7313, abstract = {Li-ion batteries have transformed portable electronics and will play a key role in the electrification of transport. However, the highest energy storage possible for Li-ion batteries is insufficient for the long-term needs of society, for example, extended-range electric vehicles. To go beyond the horizon of Li-ion batteries is a formidable challenge; there are few options. Here we consider two: Li–air (O2) and Li–S. The energy that can be stored in Li–air (based on aqueous or non-aqueous electrolytes) and Li–S cells is compared with Li-ion; the operation of the cells is discussed, as are the significant hurdles that will have to be overcome if such batteries are to succeed. Fundamental scientific advances in understanding the reactions occurring in the cells as well as new materials are key to overcoming these obstacles. The potential benefits of Li–air and Li–S justify the continued research effort that will be needed.}, author = {Bruce, Peter G. and Freunberger, Stefan Alexander and Hardwick, Laurence J. and Tarascon, Jean-Marie}, issn = {1476-1122}, journal = {Nature Materials}, number = {1}, pages = {19--29}, publisher = {Springer Nature}, title = {{Li–O2 and Li–S batteries with high energy storage}}, doi = {10.1038/nmat3191}, volume = {11}, year = {2011}, } @article{7314, abstract = {The electrolyte is one of the greatest challenges facing the development of the non‐aqueous Li–O2 battery. Although ether‐based electrolytes do from Li2O2 on the first discharge, it is shown by various techniques that they also decompose and that decomposition increases while Li2O2 decreases on cycling (see picture). Thus, these electrolytes are not suitable. }, author = {Freunberger, Stefan Alexander and Chen, Yuhui and Drewett, Nicholas E. and Hardwick, Laurence J. and Bardé, Fanny and Bruce, Peter G.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {37}, pages = {8609--8613}, publisher = {Wiley}, title = {{The Lithium-Oxygen battery with ether-based electrolytes}}, doi = {10.1002/anie.201102357}, volume = {50}, year = {2011}, } @article{7315, abstract = {Spectroscopic data (see picture) provide direct evidence that in non‐aqueous Li+ electrolyte, O2 is reduced to O2−, which then forms LiO2 on the electrode surface which disproportionates to Li2O2. On charging, Li2O2 decomposes directly, in a one‐step reaction to evolve O2 and does not pass through LiO2 as an intermediate. }, author = {Peng, Zhangquan and Freunberger, Stefan Alexander and Hardwick, Laurence J. and Chen, Yuhui and Giordani, Vincent and Bardé, Fanny and Novák, Petr and Graham, Duncan and Tarascon, Jean-Marie and Bruce, Peter G.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {28}, pages = {6351--6355}, publisher = {Wiley}, title = {{Oxygen reactions in a non-aqueous Li+ electrolyte}}, doi = {10.1002/anie.201100879}, volume = {50}, year = {2011}, } @article{7316, abstract = {The nonaqueous rechargeable lithium–O2 battery containing an alkyl carbonate electrolyte discharges by formation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li, CO2, and H2O at the cathode, due to electrolyte decomposition. Charging involves oxidation of C3H6(OCO2Li)2, Li2CO3, HCO2Li, CH3CO2Li accompanied by CO2 and H2O evolution. Mechanisms are proposed for the reactions on discharge and charge. The different pathways for discharge and charge are consistent with the widely observed voltage gap in Li–O2 cells. Oxidation of C3H6(OCO2Li)2 involves terminal carbonate groups leaving behind the OC3H6O moiety that reacts to form a thick gel on the Li anode. Li2CO3, HCO2Li, CH3CO2Li, and C3H6(OCO2Li)2 accumulate in the cathode on cycling correlating with capacity fading and cell failure. The latter is compounded by continuous consumption of the electrolyte on each discharge.}, author = {Freunberger, Stefan Alexander and Chen, Yuhui and Peng, Zhangquan and Griffin, John M. and Hardwick, Laurence J. and Bardé, Fanny and Novák, Petr and Bruce, Peter G.}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {20}, pages = {8040--8047}, publisher = {ACS}, title = {{Reactions in the rechargeable Lithium–O2 battery with alkyl carbonate electrolytes}}, doi = {10.1021/ja2021747}, volume = {133}, year = {2011}, } @article{7317, abstract = {Lithium-metal oxides with a high formal Li2O content, such as Li5FeO4 (5Li2O•Fe2O3) and a Li2MnO3•LiFeO2 composite ({Li2O•MnO2}•{Li2O•Fe2O3}) have been explored as electrocatalysts for primary and rechargeable Li-O2 cells. Activation occurs predominantly by Li2O removal, either electrochemically or chemically by acid-treatment. Superior electrochemical behavior is obtained if activation occurs by acid-treatment; Li2MnO3•LiFeO2 catalysts provide 2516 mAh/g (carbon) corresponding to 931 mAh/g (electrocatalyst + carbon) during the initial discharge. The reaction is reasonably reversible during the early cycles. The approach has implications for designing electrocatalysts that participate through electrochemical Li2O extraction/reformation reactions, offering exceptionally high capacities.}, author = {Trahey, L. and Johnson, C. S. and Vaughey, J. T. and Kang, S.-H. and Hardwick, L. J. and Freunberger, Stefan Alexander and Bruce, P. G. and Thackeray, M. M.}, issn = {1099-0062}, journal = {Electrochemical and Solid-State Letters}, number = {5}, publisher = {The Electrochemical Society}, title = {{Activated Lithium-Metal-Oxides as catalytic electrodes for Li–O2 cells}}, doi = {10.1149/1.3555366}, volume = {14}, year = {2011}, } @inproceedings{9943, abstract = {Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org.}, author = {Sommer, Christoph M and Straehle, Christoph and Köthe, Ullrich and Hamprecht, Fred A.}, booktitle = {2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro}, isbn = {978-1-4244-4127-3}, issn = {1945-8452}, keywords = {image segmentation, biomedical imaging, three dimensional displays, neurons, retina, observers, image color analysis}, location = {Chicago, Illinois, USA}, publisher = {Institute of Electrical and Electronics Engineers}, title = {{Ilastik: Interactive learning and segmentation toolkit}}, doi = {10.1109/isbi.2011.5872394}, year = {2011}, } @article{3086, abstract = {PIN-FORMED (PIN)-dependent auxin transport is essential for plant development and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control PIN1 localization during organ formation, but its contribution is limited. The Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3 and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy between MAB4 and MEL genes in regulation of not only organ formation but also of root gravitropism, revealing that NPH3 family proteins have a wider range of functions than previously suspected. Multiple mutants showed severe reduction in PIN abundance and PIN polar localization, leading to defective expression of an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence recovery after photo-bleaching experiments showed that mel mutations increase PIN2 internalization from the plasma membrane, but affect neither intracellular PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all MAB4 subfamily proteins show polar localization at the cell periphery in plants. The MAB4 polarity was almost identical to PIN polarity. Our results suggest that the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner at the plasma membrane, thus controlling directional auxin transport and plant development.}, author = {Furutani, Masahiko and Sakamoto, Norihito and Yoshida, Shuhei and Kajiwara, Takahito and Robert, Hélène S and Jirí Friml and Tasaka, Masao}, journal = {Development}, number = {10}, pages = {2069 -- 2078}, publisher = {Company of Biologists}, title = {{Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers}}, doi = {10.1242/dev.057745}, volume = {138}, year = {2011}, } @article{3087, abstract = {Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrinmediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type-specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.}, author = {Kitakura, Saeko and Vanneste, Steffen and Robert, Stéphanie and Löfke, Christian and Teichmann, Thomas and Tanaka, Hirokazu and Jirí Friml}, journal = {Plant Cell}, number = {5}, pages = {1920 -- 1931}, publisher = {American Society of Plant Biologists}, title = {{Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis}}, doi = {10.1105/tpc.111.083030}, volume = {23}, year = {2011}, } @article{3088, abstract = {Background: Whereas the majority of animals develop toward a predetermined body plan, plants show iterative growth and continually produce new organs and structures from actively dividing meristems. This raises an intriguing question: How are these newly developed organs patterned? In Arabidopsis embryos, radial symmetry is broken by the bisymmetric specification of the cotyledons in the apical domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results: Here we present a mutually inhibitory feedback loop between auxin and cytokinin that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin toward a central domain. High auxin promotes transcription of the cytokinin signaling inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response domain specifies the differentiation of protoxylem in a bisymmetric pattern. In embryonic roots, cytokinin is required to translate a bisymmetric auxin response in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions: Our results present an interactive feedback loop between hormonal signaling and transport by which small biases in hormonal input are propagated into distinct signaling domains to specify the vascular pattern in the root meristem. It is an intriguing possibility that such a mechanism could transform radial patterns and allow continuous vascular connections between other newly emerging organs.}, author = {Bishopp, Anthony and Help, Hanna and El-Showk, Sedeer and Weijers, Dolf and Scheres, Ben and Jirí Friml and Eva Benková and Mähönen, Ari Pekka and Helariutta, Ykä}, journal = {Current Biology}, number = {11}, pages = {917 -- 926}, publisher = {Cell Press}, title = {{A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots}}, doi = {10.1016/j.cub.2011.04.017}, volume = {21}, year = {2011}, } @article{3089, abstract = {The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca 2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and Ca 2+ are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca 2+ signaling-related stimuli could influence auxin-mediated development.}, author = {Zhang, Jing and Vanneste, Steffen and Brewer, Philip B and Michniewicz, Marta and Peter Grones and Kleine-Vehn, Jürgen and Löfke, Christian and Teichmann, Thomas and Bielach, Agnieszka and Cannoot, Bernard and Hoyerová, Klára and Xu Chen and Xue, Hong-Wei and Eva Benková and Zažímalová, Eva and Jirí Friml}, journal = {Developmental Cell}, number = {6}, pages = {855 -- 866}, publisher = {Cell Press}, title = {{Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity}}, doi = {10.1016/j.devcel.2011.05.013}, volume = {20}, year = {2011}, } @article{3090, abstract = {The polarized transport of the phytohormone auxin [1], which is crucial for the regulation of different stages of plant development [2, 3], depends on the asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers [4, 5]. The PIN polar localization results from clathrin-mediated endocytosis (CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis genome encodes two groups of dynamin-related proteins (DRPs) that show homology to mammalian dynamin - a protein required for fission of endocytic vesicles during CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence complementation (BiFC), and Förster resonance energy transfer (FRET) that members of the DRP1 group closely associate with PIN proteins at the cell plate. Localization and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1 function in correct PIN distribution and in auxin-mediated development. We propose that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins and the associated CME machinery from the cell plate membranes during cytokinesis is an important mechanism for proper polar PIN positioning in interphase cells.}, author = {Mravec, Jozef and Petrášek, Jan and Li, Na and Boeren, Sjef and Karlova, Rumyana and Kitakura, Saeko and Pařezová, Markéta and Naramoto, Satoshi and Nodzyński, Thomasz and Dhonukshe, Pankaj and Bednarek, Sebastian Y and Zažímalová, Eva and De Vries, Sacco and Jirí Friml}, journal = {Current Biology}, number = {12}, pages = {1055 -- 1060}, publisher = {Cell Press}, title = {{Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis}}, doi = {10.1016/j.cub.2011.05.018}, volume = {21}, year = {2011}, } @article{3091, author = {Sauer, Michael and Friml, Jirí}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Fleeting hormone cues get stabilized for plant organogenesis}}, doi = {10.1038/msb.2011.45}, volume = {7}, year = {2011}, } @article{3092, abstract = {The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting.}, author = {Wabnik, Krzysztof T and Govaerts, Willy and Friml, Jirí and Kleine Vehn, Jürgen}, journal = {Molecular BioSystems}, number = {8}, pages = {2352 -- 2359}, publisher = {Royal Society of Chemistry}, title = {{Feedback models for polarized auxin transport: An emerging trend}}, doi = {10.1039/c1mb05109a}, volume = {7}, year = {2011}, } @article{3093, abstract = { Plants take up iron from the soil using the IRON-REGULATED TRANSPORTER 1 (IRT1) high-affinity iron transporter at the root surface. Sophisticated regulatory mechanisms allow plants to tightly control the levels of IRT1, ensuring optimal absorption of essential but toxic iron. Here, we demonstrate that overexpression of Arabidopsis thaliana IRT1 leads to constitutive IRT1 protein accumulation, metal overload, and oxidative stress. IRT1 is unexpectedly found in trans-Golgi network/early endosomes of root hair cells, and its levels and localization are unaffected by iron nutrition. Using pharmacological approaches, we show that IRT1 cycles to the plasma membrane to perform iron and metal uptake at the cell surface and is sent to the vacuole for proper turnover. We also prove that IRT1 is monoubiquitinated on several cytosol-exposed residues in vivo and that mutation of two putative monoubiquitination target residues in IRT1 triggers stabilization at the plasma membrane and leads to extreme lethality. Together, these data suggest a model in which monoubiquitin-dependent internalization/sorting and turnover keep the plasma membrane pool of IRT1 low to ensure proper iron uptake and to prevent metal toxicity. More generally, our work demonstrates the existence of monoubiquitin-dependent trafficking to lytic vacuoles in plants and points to proteasome-independent turnover of plasma membrane proteins.}, author = {Barberon, Marie and Zelazny, Enric and Robert, Stéphanie and Conéjéro, Geneviève and Curie, Cathy and Jirí Friml and Vert, Grégory}, journal = {PNAS}, number = {32}, pages = {E450 -- E458}, publisher = {National Academy of Sciences}, title = {{Monoubiquitin dependent endocytosis of the Iron Regulated Transporter 1 IRT1 transporter controls iron uptake in plants}}, doi = {10.1073/pnas.1100659108}, volume = {108}, year = {2011}, } @article{3094, abstract = {Summary Gravitropism aligns plant growth with gravity. It involves gravity perception and the asymmetric distribution of the phytohormone auxin. Here we provide insights into the mechanism for hypocotyl gravitropic growth. We show that the Arabidopsis thaliana PIN3 auxin transporter is required for the asymmetric auxin distribution for the gravitropic response. Gravistimulation polarizes PIN3 to the bottom side of hypocotyl endodermal cells, which correlates with an increased auxin response at the lower hypocotyl side. Both PIN3 polarization and hypocotyl bending require the activity of the trafficking regulator GNOM and the protein kinase PINOID. Our data suggest that gravity-induced PIN3 polarization diverts the auxin flow to mediate the asymmetric distribution of auxin for gravitropic shoot bending.}, author = {Rakusová, Hana and Gallego-Bartolomé, Javier and Vanstraelen, Marleen and Robert, Hélène S and Alabadí, David and Blázquez, Miguel A and Eva Benková and Jirí Friml}, journal = {Plant Journal}, number = {5}, pages = {817 -- 826}, publisher = {Wiley-Blackwell}, title = {{Polarization of PIN3 dependent auxin transport for hypocotyl gravitropic response in Arabidopsis thaliana}}, doi = {10.1111/j.1365-313X.2011.04636.x}, volume = {67}, year = {2011}, } @article{3095, abstract = {Root system architecture depends on lateral root (LR) initiation that takes place in a relatively narrow developmental window (DW). Here, we analyzed the role of auxin gradients established along the parent root in defining this DW for LR initiation. Correlations between auxin distribution and response, and spatiotemporal control of LR initiation were analyzed in Arabidopsis thaliana and tomato (Solanum lycopersicum). In both Arabidopsis and tomato roots, a well defined zone, where auxin content and response are minimal, demarcates the position of a DW for founder cell specification and LR initiation. We show that in the zone of auxin minimum pericycle cells have highest probability to become founder cells and that auxin perception via the TIR1/AFB pathway, and polar auxin transport, are essential for the establishment of this zone. Altogether, this study reveals that the same morphogen-like molecule, auxin, can act simultaneously as a morphogenetic trigger of LR founder cell identity and as a gradient-dependent signal defining positioning of the founder cell specification. This auxin minimum zone might represent an important control mechanism ensuring the LR initiation steadiness and the acropetal LR initiation pattern. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.}, author = {Dubrovsky, Joseph G and Napsucialy-Mendivil, Selene and Duclercq, Jérôme and Cheng, Yan and Shishkova, Svetlana O and Ivanchenko, Maria G and Jirí Friml and Murphy, Angus S and Eva Benková}, journal = {New Phytologist}, number = {4}, pages = {970 -- 983}, publisher = {Wiley-Blackwell}, title = {{Auxin minimum defines a developmental window for lateral root initiation}}, doi = { 10.1111/j.1469-8137.2011.03757.x}, volume = {191}, year = {2011}, }