@article{3067, abstract = {Remarkable progress in various techniques of in vivo fluorescence microscopy has brought an urgent need for reliable markers for tracking cellular structures and processes. The goal of this manuscript is to describe unexplored effects of the FM (Fei Mao) styryl dyes, which are widely used probes that label processes of endocytosis and vesicle trafficking in eukaryotic cells. Although there are few reports on the effect of styryl dyes on membrane fluidity and the activity of mammalian receptors, FM dyes have been considered as reliable tools for tracking of plant endocytosis. Using plasma membrane-localized transporters for the plant hormone auxin in tobacco BY-2 and Arabidopsis thaliana cell suspensions, we show that routinely used concentrations of FM 4-64 and FM 5-95 trigger transient re-localization of these proteins, and FM 1-43 affects their activity. The active process of re-localization is blocked neither by inhibitors of endocytosis nor by cytoskeletal drugs. It does not occur in A. thaliana roots and depends on the degree of hydrophobicity (lipophilicity) of a particular FM dye. Our results emphasize the need for circumspection during in vivo studies of membrane proteins performed using simultaneous labelling with FM dyes.}, author = {Jelínková, Adriana and Malínská, Kateřina and Sibu Simon and Kleine-Vehn, Jürgen and Pařezová, Markéta and Pejchar, Přemysl and Kubeš, Martin and Martinec, Jan and Jirí Friml and Zažímalová, Eva and Petrášek, Jan}, journal = {Plant Journal}, number = {5}, pages = {883 -- 892}, publisher = {Wiley-Blackwell}, title = {{Probing plant membranes with FM dyes: Tracking dragging or blocking?}}, doi = {10.1111/j.1365-313X.2009.04102.x}, volume = {61}, year = {2010}, } @article{3068, abstract = {Differential distribution of the plant hormone auxin within tissues mediates a variety of developmental processes. Cellular auxin levels are determined by metabolic processes including synthesis, degradation, and (de)conjugation, as well as by auxin transport across the plasma membrane. Whereas transport of free auxins such as naturally occurring indole-3-acetic acid (IAA) is well characterized, little is known about the transport of auxin precursors and metabolites. Here, we identify amutation in the ABCG37 gene of Arabidopsis that causes the polar auxin transport inhibitor sensitive1 (pis1) phenotype manifested by hypersensitivity to auxinic compounds. ABCG37 encodes the pleiotropic drug resistance transporter that transports a range of synthetic auxinic compounds as well as the endogenous auxin precursor indole-3-butyric acid (IBA), but not free IAA. ABCG37 and its homolog ABCG36 act redundantly at outermost root plasma membranes and,unlike established IAA transporters from the PIN and ABCB families, transport IBA out of the cells. Our findings explore possible novel modes of regulating auxin homeostasis and plant development by means of directional transport of the auxin precursor IBA and presumably also other auxin metabolites.}, author = {Růžička, Kamil and Strader, Lucia C and Bailly, Aurélien and Yang, Haibing and Blakeslee, Joshua and Łangowski, Łukasz and Nejedlá, Eliška and Fujita, Hironori and Itoh, Hironori and Syōno, Kunihiko and Hejátko, Jan and Gray, William M and Martinoia, Enrico and Geisler, Markus and Bartel, Bonnie and Murphy, Angus S and Jirí Friml}, journal = {PNAS}, number = {23}, pages = {10749 -- 10753}, publisher = {National Academy of Sciences}, title = {{Arabidopsis PIS1 encodes the ABCG37 transporter of auxinic compounds including the auxin precursor indole 3 butyric acid}}, doi = {10.1073/pnas.1005878107}, volume = {107}, year = {2010}, } @article{3069, abstract = {The stem cell niche in the root meristem is critical for the development of the plant root system. The plant hormone auxin acts as a versatile trigger in many developmental processes, including the regulation of root growth, but its role in the control of the stem cell activity remains largely unclear. Here we show that local auxin levels, determined by biosynthesis and intercellular transport, mediate maintenance or differentiation of distal stem cells in the Arabidopsis thaliana roots. Genetic analysis shows that auxin acts upstream of the major regulators of the stem cell activity, the homeodomain transcription factor WOX5, and the AP-2 transcription factor PLETHORA. Auxin signaling for differentiation of distal stem cells requires the transcriptional repressor IAA17/AXR3 as well as the ARF10 and ARF16 auxin response factors. ARF10 and ARF16 activities repress the WOX5 transcription and restrict it to the quiescent center, where WOX5, in turn, is needed for the activity of PLETHORA. Our investigations reveal that long-distance auxin signals act upstream of the short-range network of transcriptional factors to mediate the differentiation of distal stem cells in roots.}, author = {Ding, Zhaojun and Jirí Friml}, journal = {PNAS}, number = {26}, pages = {12046 -- 12051}, publisher = {National Academy of Sciences}, title = {{Auxin regulates distal stem cell differentiation in Arabidopsis roots}}, doi = {10.1073/pnas.1000672107}, volume = {107}, year = {2010}, } @article{3070, abstract = {Division of the Arabidopsis zygote defines two fundamentally different developmental domains, the proembryo and suspensor. The resulting boundary separates domain-specific gene expression, and a signal originating from the proembryo instructs the suspensor to generate the root stem cell niche. While root induction is known to require the phytohormone auxin and the Auxin Response Factor MONOPTEROS, it has remained largely elusive how the two domains involved in this process are initially specified. Here, we show that the GATA factor HANABA TARANU (HAN) is required to position the inductive proembryo boundary. Mutations in HAN cause a coordinated apical shift of gene expression patterns, revealing that HAN regulates transcription in the basal proembryo. Key auxin transporters are affected as early as the 8 cell stage, resulting in apical redistribution of auxin. Remarkably, han embryos eventually organize a root independent of MONOPTEROS and the suspensor around a new boundary marked by the auxin maximum.}, author = {Nawy, Tal and Bayer, Martin and Mravec, Jozef and Jirí Friml and Birnbaum, Kenneth D and Lukowitz, Wolfgang}, journal = {Developmental Cell}, number = {1}, pages = {103 -- 113}, publisher = {Cell Press}, title = {{The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo}}, doi = {10.1016/j.devcel.2010.06.004}, volume = {19}, year = {2010}, } @article{3071, abstract = {Plant vacuoles are essential multifunctional organelles largely distinct from similar organelles in other eukaryotes. Embryo protein storage vacuoles and the lytic vacuoles that perform a general degradation function are the best characterized, but little is known about the biogenesis and transition between these vacuolar types. Here, we designed a fluorescent marker- based forward genetic screen in Arabidopsis thaliana and identified a protein affected trafficking2 (pat2) mutant, whose lytic vacuoles display altered morphology and accumulation of proteins. Unlike other mutants affecting the vacuole, pat2 is specifically defective in the biogenesis, identity, and function of lytic vacuoles but shows normal sorting of proteins to storage vacuoles. PAT2 encodes a putative β-subunit of adaptor protein complex 3 (AP-3) that can partially complement the corresponding yeast mutant. Manipulations of the putative AP-3 β adaptin functions suggest a plant-specific role for the evolutionarily conserved AP-3 β in mediating lytic vacuole performance and transition of storage into the lytic vacuoles independently of the main prevacuolar compartment-based trafficking route.}, author = {Feraru, Elena and Paciorek, Tomasz and Feraru, Mugurel I and Zwiewka, Marta and De Groodt, Ruth and De Rycke, Riet M and Kleine-Vehn, Jürgen and Jirí Friml}, journal = {Plant Cell}, number = {8}, pages = {2812 -- 2824}, publisher = {American Society of Plant Biologists}, title = {{The AP 3 β adaptin mediates the biogenesis and function of lytic vacuoles in Arabidopsis}}, doi = {10.1105/tpc.110.075424}, volume = {22}, year = {2010}, } @article{3072, abstract = {Development of plants and their adaptive capacity towards ever‐changing environmental conditions largely depend on the spatial distribution of the plant hormone auxin. At the cellular level, various internal and external signals are translated into specific changes in the polar, subcellular localization of auxin transporters from the PIN family thereby directing and redirecting the intercellular fluxes of auxin. The current model of polar targeting of PIN proteins towards different plasma membrane domains encompasses apolar secretion of newly synthesized PINs followed by endocytosis and recycling back to the plasma membrane in a polarized manner. In this review, we follow the subcellular march of the PINs and highlight the cellular and molecular mechanisms behind polar foraging and subcellular trafficking pathways. Also, the entry points for different signals and regulations including by auxin itself will be discussed within the context of morphological and developmental consequences of polar targeting and subcellular trafficking.}, author = {Grunewald, Wim and Friml, Jirí}, journal = {EMBO Journal}, number = {16}, pages = {2700 -- 2714}, publisher = {Wiley-Blackwell}, title = {{The march of the PINs: Developmental plasticity by dynamic polar targeting in plant cells}}, doi = {10.1038/emboj.2010.181}, volume = {29}, year = {2010}, } @article{3073, abstract = {Polar membrane cargo delivery is crucial for establishing cell polarity and for directional transport processes. In plants, polar trafficking mediates the dynamic asymmetric distribution of PIN FORMED (PIN) carriers, which drive polar cell-to-cell transport of the hormone auxin, thereby generating auxin maxima and minima that control development. The Arabidopsis PINOID (PID) protein kinase instructs apical PIN localization by phosphorylating PINs. Here, we identified the PID homologs WAG1 and WAG2 as new PIN polarity regulators. We show that the AGC3 kinases PID, WAG1 and WAG2, and not other plant AGC kinases, instruct recruitment of PINs into the apical recycling pathway by phosphorylating the middle serine in three conserved TPRXS(N/S) motifs within the PIN central hydrophilic loop. Our results put forward a model by which apolarly localized PID, WAG1 and WAG2 phosphorylate PINs at the plasma membrane after default non-polar PIN secretion, and trigger endocytosis-dependent apical PIN recycling. This phosphorylation-triggered apical PIN recycling competes with ARF-GEF GNOM-dependent basal recycling to promote apical PIN localization. In planta, expression domains of PID, WAG1 and WAG2 correlate with apical localization of PINs in those cell types, indicating the importance of these kinases for apical PIN localization. Our data show that by directing polar PIN localization and PIN-mediated polar auxin transport, the three AGC3 kinases redundantly regulate cotyledon development, root meristem size and gravitropic response, indicating their involvement in both programmed and adaptive plant development.}, author = {Dhonukshe, Pankaj and Huang, Fang and Galván Ampudia, Carlos and Mähönen, Ari and Kleine Vehn, Jürgen and Xu, Jian and Quint, Ab and Prasad, Kalika and Friml, Jiřĺ and Scheres, Ben and Offringa, Remko}, journal = {Development}, number = {19}, pages = {3245 -- 3255}, publisher = {Company of Biologists}, title = {{Plasma membrane-bound AGC3 kinases phosphorylate PIN auxin carriers at TPRXS(N/S) motifs to direct apical PIN recycling}}, doi = {10.1242/dev.052456}, volume = {137}, year = {2010}, } @article{3074, abstract = {Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root.}, author = {Ge, Lei and Peer, Wendy A and Robert, Stéphanie and Swarup, Ranjan and Ye, Songqing and Prigge, Michael J and Cohen, Jerry D and Jirí Friml and Murphy, Angus S and Tang, Ding and Estelle, Mark A}, journal = {Plant Cell}, number = {6}, pages = {1749 -- 1761}, publisher = {American Society of Plant Biologists}, title = {{Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar auxin transport}}, doi = {10.1105/tpc.110.074195}, volume = {22}, year = {2010}, } @article{3075, abstract = { Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.}, author = {Robert, Stéphanie and Kleine-Vehn, Jürgen and Barbez, Elke and Sauer, Michael and Paciorek, Tomasz and Pawel Baster and Vanneste, Steffen and Zhang, Jing and Sibu Simon and Čovanová, Milada and Hayashi, Kenichiro and Dhonukshe, Pankaj and Yang, Zhenbiao and Bednarek, Sebastian Y and Jones, Alan M and Luschnig, Christian and Aniento, Fernando and Zažímalová, Eva and Jirí Friml}, journal = {Cell}, number = {1}, pages = {111 -- 121}, publisher = {Cell Press}, title = {{ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis}}, doi = {10.1016/j.cell.2010.09.027}, volume = {143}, year = {2010}, } @article{3076, abstract = {Auxin is a multifunctional hormone essential for plant development and pattern formation. A nuclear auxin-signaling system controlling auxin-induced gene expression is well established, but cytoplasmic auxin signaling, as in its coordination of cell polarization, is unexplored. We found a cytoplasmic auxin-signaling mechanism that modulates the interdigitated growth of Arabidopsis leaf epidermal pavement cells (PCs), which develop interdigitated lobes and indentations to form a puzzle-piece shape in a two-dimensional plane. PC interdigitation is compromised in leaves deficient in either auxin biosynthesis or its export mediated by PINFORMED 1 localized at the lobe tip. Auxin coordinately activates two Rho GTPases, ROP2 and ROP6, which promote the formation of complementary lobes and indentations, respectively. Activation of these ROPs by auxin occurs within 30 s and depends on AUXIN-BINDING PROTEIN 1. These findings reveal Rho GTPase-based auxin-signaling mechanisms, which modulate the spatial coordination of cell expansion across a field of cells.}, author = {Xu, Tongda and Wen, Mingzhang and Nagawa, Shingo and Fu, Ying and Chen, Jin-Gui and Wu, Ming-Jing and Perrot-Rechenmann, Catherine and Jirí Friml and Jones, Alan M and Yang, Zhenbiao}, journal = {Cell}, number = {1}, pages = {99 -- 110}, publisher = {Cell Press}, title = {{Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation in Arabidopsis}}, doi = {10.1016/j.cell.2010.09.003}, volume = {143}, year = {2010}, } @article{3077, author = {Friml, Jirí and Jones, Angharad}, journal = {Plant Physiology}, number = {2}, pages = {458 -- 462}, publisher = {American Society of Plant Biologists}, title = {{Endoplasmic reticulum: The rising compartment in auxin biology}}, doi = {10.1104/pp.110.161380}, volume = {154}, year = {2010}, } @inbook{3078, abstract = {Rapid advances in the field of plant biology, especially in plant cell biology, have created the need for methods that allow the localization of proteins in situ at subcellular resolution. Although in many cases recombinant proteins with fluorescent proteins can fulfill this task, antibody-based immunological detection of proteins is a complementary technique, which avoids the risk of inducing side effects by a fusion protein, such as misexpression, mistargeting, altered stability, or toxicity. Moreover, recombinant protein techniques are applicable only to a rather limited set of model plants. The immunolocalization protocols presented here can be used to display protein localization patterns in different tissues of various plant species. This chapter describes a whole mount immunolocalization protocol, which has been extensively used in Arabidopsis roots and some above-ground tissues, and that also works in other species. Additionally, for bulky or hard tissue types, a variation of this protocol for paraffin-embedded sections is given.}, author = {Sauer, Michael and Jirí Friml}, booktitle = {Plant Developmental Biology}, editor = {Hennig, Lars and Köhler, Claudia}, pages = {253 -- 263}, publisher = {Humana Press}, title = {{Immunolocalization of proteins in plants }}, doi = {10.1007/978-1-60761-765-5_17}, volume = {655}, year = {2010}, } @article{3079, abstract = {Plant development is exceptionally flexible as manifested by its potential for organogenesis and regeneration, which are processes involving rearrangements of tissue polarities. Fundamental questions concern how individual cells can polarize in a coordinated manner to integrate into the multicellular context. In canalization models, the signaling molecule auxin acts as a polarizing cue, and feedback on the intercellular auxin flow is key for synchronized polarity rearrangements. We provide a novel mechanistic framework for canalization, based on up-to-date experimental data and minimal, biologically plausible assumptions. Our model combines the intracellular auxin signaling for expression of PINFORMED (PIN) auxin transporters and the theoretical postulation of extracellular auxin signaling for modulation of PIN subcellular dynamics. Computer simulations faithfully and robustly recapitulated the experimentally observed patterns of tissue polarity and asymmetric auxin distribution during formation and regeneration of vascular systems and during the competitive regulation of shoot branching by apical dominance. Additionally, our model generated new predictions that could be experimentally validated, highlighting a mechanistically conceivable explanation for the PIN polarization and canalization of the auxin flow in plants.}, author = {Krzysztof Wabnik and Kleine-Vehn, Jürgen and Balla, Jozef and Sauer, Michael and Naramoto, Satoshi and Reinöhl, Vilém and Merks, Roeland M and Govaerts, Willy J and Jirí Friml}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling}}, doi = {10.1038/msb.2010.103}, volume = {6}, year = {2010}, } @article{3080, abstract = {Auxin is an essential plant-specific regulator of patterning processes that also controls directional growth of roots and shoots. In response to gravity stimulation, the PIN3 auxin transporter polarizes to the bottomside of gravity-sensing root cells, presumably redirecting the auxin flux toward the lower side of the root and triggering gravitropic bending. By combining live-cell imaging techniques with pharmacological and genetic approaches, we demonstrate that PIN3 polarization does not require secretion of de novo synthesized proteins or protein degradation, but instead involves rapid, transient stimulation of PIN endocytosis, presumably via a clathrin-dependent pathway. Moreover, gravity-induced PIN3 polarization requires the activity of the guanine nucleotide exchange factors for ARF GTPases (ARF-GEF) GNOM-dependent polar-targeting path-ways and might involve endosome-based PIN3 translocation from one cell side to another. Our data suggest that gravity perception acts at several instances of PIN3 trafficking, ultimately leading to the polarization of PIN3, which presumably aligns auxin fluxes with gravity vector and mediates downstream root gravitropic response.}, author = {Kleine-Vehn, Jürgen and Ding, Zhaojun and Jones, Angharad R and Tasaka, Masao and Morita, Miyo T and Jirí Friml}, journal = {PNAS}, number = {51}, pages = {22344 -- 22349}, publisher = {National Academy of Sciences}, title = {{Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells}}, doi = {10.1073/pnas.1013145107}, volume = {107}, year = {2010}, } @article{3081, abstract = {Endocytosis is crucial for various cellular functions and development of multicellular organisms. In mammals and yeast, ADP-ribosylation factor (ARF) GTPases, key components of vesicle formation, and their regulators ARF-guanine nucleotide exchange factors (GEFs) and ARF-GTPase-activating protein (GAPs) mediate endocytosis. A similar role has not been established in plants,mainly because of the lack of the canonical ARF and ARF-GEF components that are involved in endocytosis in other eukaryotes. In this study, we revealed a regulatory mechanism of endocytosis in plants based on ARF GTPase activity.Weidentified that ARF-GEFGNOMand ARF-GAP VASCULAR NETWORK DEFECTIVE 3 (VAN3), both of which are involved in polar auxin transport-dependent morphogenesis, localize at the plasma membranes as well as in intracellular structures. Variable angle epifluorescence microscopy revealed that GNOM and VAN3 localize to partially overlapping discrete foci at the plasmamembranes that are regularly associated with the endocytic vesicle coat clathrin. Genetic studies revealed that GNOM and VAN3 activities are required for endocytosis and internalization of plasma membrane proteins, including PIN-FORMED auxin transporters. These findings identified ARF GTPase-based regulatory mechanisms for endocytosis in plants. GNOMand VAN3 previously were proposed to function solely at the recycling endosomes and trans-Golgi networks, respectively. Therefore our findings uncovered an additional cellular function of these prominent developmental regulators.}, author = {Naramoto, Satoshi and Kleine-Vehn, Jürgen and Robert, Stéphanie and Fujimoto, Masaru and Dainobu, Tomoko and Paciorek, Tomasz and Ueda, Takashi and Nakano, Akihiko and Van Montagu, Marc C and Fukuda, Hiroo and Jirí Friml}, journal = {PNAS}, number = {50}, pages = {21890 -- 21895}, publisher = {National Academy of Sciences}, title = {{ADP ribosylation factor machinery mediates endocytosis in plant cells}}, doi = {10.1073/pnas.1016260107}, volume = {107}, year = {2010}, } @article{3146, abstract = {Coordinated migration of newly born neurons to their prospective target laminae is a prerequisite for neural circuit assembly in the developing brain. The evolutionarily conserved LIS1/NDEL1 complex is essential for neuronal migration in the mammalian cerebral cortex. The cytoplasmic nature of LIS1 and NDEL1 proteins suggest that they regulate neuronal migration cell autonomously. Here, we extend mosaic analysis with double markers (MADM) to mouse chromosome 11 where Lis1, Ndel1, and 14-3-3e{open} (encoding a LIS1/NDEL1 signaling partner) are located. Analyses of sparse and uniquely labeled mutant cells in mosaic animals reveal distinct cell-autonomous functions for these three genes. Lis1 regulates neuronal migration efficiency in a dose-dependent manner, while Ndel1 is essential for a specific, previously uncharacterized, late step of neuronal migration: entry into the target lamina. Comparisons with previous genetic perturbations of Lis1 and Ndel1 also suggest a surprising degree of cell-nonautonomous function for these proteins in regulating neuronal migration.}, author = {Simon Hippenmeyer and Youn, Yong H and Moon, Hyang M and Miyamichi, Kazunari and Zong, Hui and Wynshaw-Boris, Anthony and Luo, Liqun}, journal = {Neuron}, number = {4}, pages = {695 -- 709}, publisher = {Elsevier}, title = {{Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration}}, doi = {10.1016/j.neuron.2010.09.027}, volume = {68}, year = {2010}, } @article{3153, abstract = {Human immune cells have to penetrate an endothelial barrier during their beneficial pursuit of infection and their destructive infiltration of tissues in autoimmune diseases. This transmigration requires Rap1 GTPase to activate integrin affinity. We define a new model system for this process by demonstrating, with live imaging and genetics, that during embryonic development Drosophila melanogaster immune cells penetrate an epithelial, Drosophila E-cadherin (DE-cadherin)-based tissue barrier. A mutant in RhoL, a GTPase homologue that is specifically expressed in haemocytes, blocks this invasive step but not other aspects of guided migration. RhoL mediates integrin adhesion caused by Drosophila Rap1 overexpression and moves Rap1 away from a concentration in the cytoplasm to the leading edge during invasive migration. These findings indicate that a programmed migratory step during Drosophila development bears striking molecular similarities to vertebrate immune cell transmigration during inflammation, and identify RhoL as a new regulator of invasion, adhesion and Rap1 localization. Our work establishes the utility of Drosophila for identifying novel components of immune cell transmigration and for understanding the in vivo interplay of immune cells with the barriers they penetrate.}, author = {Daria Siekhaus and Haesemeyer, Martin and Moffitt, Olivia and Lehmann, Ruth}, journal = {Nature Cell Biology}, number = {6}, pages = {605 -- 610}, publisher = {Nature Publishing Group}, title = {{RhoL controls invasion and Rap1 localization during immune cell transmigration in Drosophila}}, volume = {12}, year = {2010}, } @inproceedings{3201, abstract = {The problem of cosegmentation consists of segmenting the same object (or objects of the same class) in two or more distinct images. Recently a number of different models have been proposed for this problem. However, no comparison of such models and corresponding optimization techniques has been done so far. We analyze three existing models: the L1 norm model of Rother et al. [1], the L2 norm model of Mukherjee et al. [2] and the "reward" model of Hochbaum and Singh [3]. We also study a new model, which is a straightforward extension of the Boykov-Jolly model for single image segmentation [4]. In terms of optimization, we use a Dual Decomposition (DD) technique in addition to optimization methods in [1,2]. Experiments show a significant improvement of DD over published methods. Our main conclusion, however, is that the new model is the best overall because it: (i) has fewest parameters; (ii) is most robust in practice, and (iii) can be optimized well with an efficient EM-style procedure.}, author = {Vicente, Sara and Vladimir Kolmogorov and Rother, Carsten}, pages = {465 -- 479}, publisher = {Springer}, title = {{Cosegmentation revisited: Models and optimization}}, doi = {10.1007/978-3-642-15552-9_34}, volume = {6312}, year = {2010}, } @article{3202, abstract = {We consider the following problem: given an undirected weighted graph G = (V,E,c) with nonnegative weights, minimize function c(δ(Π))- λ|Π| for all values of parameter λ. Here Π is a partition of the set of nodes, the first term is the cost of edges whose endpoints belong to different components of the partition, and |Π| is the number of components. The current best known algorithm for this problem has complexity O(|V| 2) maximum flow computations. We improve it to |V| parametric maximum flow computations. We observe that the complexity can be improved further for families of graphs which admit a good separator, e.g. for planar graphs.}, author = {Vladimir Kolmogorov}, journal = {Algorithmica}, number = {4}, pages = {394 -- 412}, publisher = {Springer}, title = {{A faster algorithm for computing the principal sequence of partitions of a graph}}, doi = {10.1007/s00453-008-9177-z}, volume = {56}, year = {2010}, } @inproceedings{3233, abstract = {We present a general parallel-repetition theorem with an efficient reduction. As a corollary of this theorem we establish that parallel repetition reduces the soundness error at an exponential rate in any public-coin argument, and more generally, any argument where the verifier's messages, but not necessarily its decision to accept or reject, can be efficiently simulated with noticeable probability.}, author = {Håstad, Johan and Pass, Rafael and Wikström, Douglas and Krzysztof Pietrzak}, pages = {1 -- 18}, publisher = {Springer}, title = {{An efficient parallel repetition theorem}}, doi = {10.1007/978-3-642-11799-2_1}, volume = {5978}, year = {2010}, }