@article{10387, abstract = {We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {18}, publisher = {American Physical Society}, title = {{Mechanism of membrane tube formation induced by adhesive nanocomponents}}, doi = {10.1103/physrevlett.109.188101}, volume = {109}, year = {2012}, } @article{10388, abstract = {Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {11}, publisher = {American Physical Society}, title = {{Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles}}, doi = {10.1103/physrevlett.108.118101}, volume = {108}, year = {2012}, } @article{1056, abstract = {We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation.}, author = {Mark, Manfred and Haller, Elmar and Lauber, Katharina and Danzl, Johann G and Janisch, Alexander and Büchler, Hans and Daley, Andrew and Nägerl, Hanns}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions}}, doi = {10.1103/PhysRevLett.108.215302}, volume = {108}, year = {2012}, } @article{12198, abstract = {The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.}, author = {Ibarra, Christian A. and Feng, Xiaoqi and Schoft, Vera K. and Hsieh, Tzung-Fu and Uzawa, Rie and Rodrigues, Jessica A. and Zemach, Assaf and Chumak, Nina and Machlicova, Adriana and Nishimura, Toshiro and Rojas, Denisse and Fischer, Robert L. and Tamaru, Hisashi and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6100}, pages = {1360--1364}, publisher = {American Association for the Advancement of Science}, title = {{Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes}}, doi = {10.1126/science.1224839}, volume = {337}, year = {2012}, } @article{12644, abstract = {In the Dry Andes of central Chile, summer water resources originate mostly from snowmelt and ice melt. We use the physically based, spatially distributed hydrological model TOPKAPI to study the exchange between glaciers and climate in the upper Aconcagua River Basin during the summer season and identify the model parameters that are robust and transferable and those that are more dependent on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature index approach for snow and ice melting. We suggest a calibration procedure that allows calibration of parameters in three steps by separating parameters governing distinct processes. We evaluate the parameters' transferability in time and in space by applying the model at two spatial scales. TOPKAPI's ability to simulate the relevant processes is tested against meteorological, ablation, and glacier runoff data measured on Juncal Norte Glacier during two glacier ablation seasons. The model was applied successfully to the climatic setting of the Dry Andes once its parameters were recalibrated. We found a clear distinction between parameters that are stable in time and those that need recalibration. The parameters of the melt model are transferable from one season to the other, while the parameters governing the extrapolation of meteorological input data and the routing of glacier meltwater need recalibration from one season to the other. Sensitivity analysis revealed that the model is most sensitive to the temperature lapse rate governing the extrapolation of air temperature from point measurements to the glacier scale and to the melt parameter that multiplies the shortwave radiation balance.}, author = {Ragettli, S. and Pellicciotti, Francesca}, issn = {0043-1397}, journal = {Water Resources Research}, number = {3}, publisher = {American Geophysical Union}, title = {{Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters}}, doi = {10.1029/2011wr010559}, volume = {48}, year = {2012}, } @article{12646, abstract = {Assessment of water resources from remote mountainous catchments plays a crucial role for the development of rural areas in or in the vicinity of mountain ranges. The scarcity of data, however, prevents the application of standard approaches that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain range is a crucial area in terms of water resources, but our understanding of the response of its high-elevation catchments to a changing climate is hindered by lack of hydro-meteorological and cryospheric data. Hydrological modeling is challenging here because internal inconsistencies—such as an underestimation of precipitation input that can be compensated for by an overestimation of meltwater—might be hidden due to the complexity of feedback mechanisms that govern melt and runoff generation in such basins. Data scarcity adds to this difficulty by preventing the application of systematic calibration procedures that would allow identification of the parameter set that could guarantee internal consistency in the simulation of the single hydrological components. In this work, we use simulations from the Hunza River Basin in the Karakoram region obtained with the hydrological model TOPKAPI to quantify the predictive power of discharge and snow-cover data sets, as well as the combination of both. We also show that short-term measurements of meteorological variables such as radiative fluxes, wind speed, relative humidity, and air temperature from glacio-meteorological experiments are crucial for a correct parameterization of surface melt processes. They enable detailed simulations of the energy fluxes governing glacier–atmosphere interaction and the resulting ablation through energy-balance modeling. These simulations are used to derive calibrated parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate that such parameters are stable in space and time in similar climatic regions, thus reducing the number of parameters requiring calibration.}, author = {Pellicciotti, Francesca and Buergi, Cyrill and Immerzeel, Walter Willem and Konz, Markus and Shrestha, Arun B.}, issn = {1994-7151}, journal = {Mountain Research and Development}, number = {1}, pages = {39--50}, publisher = {International Mountain Society}, title = {{Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies}}, doi = {10.1659/mrd-journal-d-11-00092.1}, volume = {32}, year = {2012}, } @article{12647, abstract = {Accurate quantification of the spatial distribution of precipitation in mountain regions is crucial for assessments of water resources and for the understanding of high-altitude hydrology, yet it is one of the largest unknowns due to the lack of high-altitude observations. The Hunza basin in Pakistan contains very large glacier systems, which, given the melt, cannot persist unless precipitation (snow input) is much higher than what is observed at the meteorological stations, mostly located in mountain valleys. Several studies, therefore, suggest strong positive vertical precipitation lapse rates; in the present study, we quantify this lapse rate by using glaciers as a proxy. We assume a neutral mass balance for the glaciers for the period from 2001 to 2003, and we inversely model the precipitation lapse by balancing the total accumulation in the catchment area and the ablation over the glacier area for the 50 largest glacier systems in the Hunza basin in the Karakoram. Our results reveal a vertical precipitation lapse rate that equals 0.21 ± 0.12% m−1, with a maximum precipitation at an elevation of 5500 masl. We showed that the total annual basin precipitation (828 mm) is 260% higher than what is estimated based on interpolated observations (319 mm); this has major consequences for hydrological modeling and water resource assessments in general. Our results were validated by using previously published studies on individual glaciers as well as the water balance of the Hunza basin. The approach is more widely applicable in mountain ranges where precipitation measurements at high altitude are lacking.}, author = {Immerzeel, Walter Willem and Pellicciotti, Francesca and Shrestha, Arun B.}, issn = {1994-7151}, journal = {Mountain Research and Development}, keywords = {General Environmental Science, Development, Environmental Chemistry}, number = {1}, pages = {30--38}, publisher = {International Mountain Society}, title = {{Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin}}, doi = {10.1659/mrd-journal-d-11-00097.1}, volume = {32}, year = {2012}, } @article{12648, abstract = {Distributed glacier melt models generally assume that the glacier surface consists of bare exposed ice and snow. In reality, many glaciers are wholly or partially covered in layers of debris that tend to suppress ablation rates. In this paper, an existing physically based point model for the ablation of debris-covered ice is incorporated in a distributed melt model and applied to Haut Glacier d'Arolla, Switzerland, which has three large patches of debris cover on its surface. The model is based on a 10 m resolution digital elevation model (DEM) of the area; each glacier pixel in the DEM is defined as either bare or debris-covered ice, and may be covered in snow that must be melted off before ice ablation is assumed to occur. Each debris-covered pixel is assigned a debris thickness value using probability distributions based on over 1000 manual thickness measurements. Locally observed meteorological data are used to run energy balance calculations in every pixel, using an approach suitable for snow, bare ice or debris-covered ice as appropriate. The use of the debris model significantly reduces the total ablation in the debris-covered areas, however the precise reduction is sensitive to the temperature extrapolation used in the model distribution because air near the debris surface tends to be slightly warmer than over bare ice. Overall results suggest that the debris patches, which cover 10% of the glacierized area, reduce total runoff from the glacierized part of the basin by up to 7%.}, author = {Reid, T. D. and Carenzo, M. and Pellicciotti, Francesca and Brock, B. W.}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D18}, publisher = {American Geophysical Union}, title = {{Including debris cover effects in a distributed model of glacier ablation}}, doi = {10.1029/2012jd017795}, volume = {117}, year = {2012}, } @misc{9755, abstract = {Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”).}, author = {Konrad, Matthias and Vyleta, Meghan and Theis, Fabian and Stock, Miriam and Klatt, Martina and Drescher, Verena and Marr, Carsten and Ugelvig, Line V and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies}}, doi = {10.5061/dryad.sv37s}, year = {2012}, } @misc{9757, abstract = {To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies.}, author = {Tragust, Simon and Mitteregger, Barbara and Barone, Vanessa and Konrad, Matthias and Ugelvig, Line V and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison}}, doi = {10.5061/dryad.61649}, year = {2012}, } @misc{9758, abstract = {We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction.}, author = {Aeschbacher, Simon and Futschik, Andreas and Beaumont, Mark}, publisher = {Dryad}, title = {{Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates}}, doi = {10.5061/dryad.274b1}, year = {2012}, } @article{347, abstract = {A synthetic route for producing Cu 2ZnGeSe 4 nanocrystals with narrow size distributions and controlled composition is presented. These nanocrystals were used to produce densely packed nanomaterials by hot-pressing. From the characterization of the thermoelectric properties of these nanomaterials, Cu 2ZnGeSe 4 is demonstrated to show excellent thermoelectric properties. A very preliminary adjustment of the nanocrystal composition has already resulted in a figure of merit of up to 0.55 at 450°C. }, author = {Ibáñez, Maria and Zamani, Reza and Lalonde, Aaron and Cadavid, Doris and Li, Wenhua and Shavel, Alexey and Arbiol, Jordi and Morante, Joan and Gorsse, Stéphane and Snyder, G Jeffrey and Cabot, Andreu}, journal = {Journal of the American Chemical Society}, number = {9}, pages = {4060 -- 4063}, publisher = {ACS}, title = {{Cu 2ZnGeSe 4 nanocrystals: Synthesis and thermoelectric properties}}, doi = {10.1021/ja211952z}, volume = {134}, year = {2012}, } @article{3846, abstract = {We summarize classical and recent results about two-player games played on graphs with ω-regular objectives. These games have applications in the verification and synthesis of reactive systems. Important distinctions are whether a graph game is turn-based or concurrent; deterministic or stochastic; zero-sum or not. We cluster known results and open problems according to these classifications.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {Journal of Computer and System Sciences}, number = {2}, pages = {394 -- 413}, publisher = {Elsevier}, title = {{A survey of stochastic ω regular games}}, doi = {10.1016/j.jcss.2011.05.002}, volume = {78}, year = {2012}, } @article{387, abstract = {In this Letter we present detailed study of the density of states near defects in Bi 2Se 3. In particular, we present data on the commonly found triangular defects in this system. While we do not find any measurable quasiparticle scattering interference effects, we do find localized resonances, which can be well fitted by theory once the potential is taken to be extended to properly account for the observed defects. The data together with the fits confirm that while the local density of states around the Dirac point of the electronic spectrum at the surface is significantly disrupted near the impurity by the creation of low-energy resonance state, the Dirac point is not locally destroyed. We discuss our results in terms of the expected protected surface state of topological insulators. © 2012 American Physical Society.}, author = {Alpichshev, Zhanybek and Biswas, Rudro and Balatsky, Alexander and Analytis, James and Chu, Jiunhaw and Fisher, Ian and Kapitulnik, Aharon}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{STM imaging of impurity resonances on Bi 2Se 3}}, doi = {10.1103/PhysRevLett.108.206402}, volume = {108}, year = {2012}, } @article{2454, abstract = {Within a multicellular tissue cells may coordinately form a singular or multiple polar axes, but it is unclear whether a common mechanism governs different types of polar axis formation. The phosphorylation status of PIN proteins, which is directly affected by the PINOID (PID) protein kinase and the PP2A protein phosphatase, is known to regulate the apical-basal polarity of PIN localization in bipolar cells of roots and shoot apices. Here, we provide evidence that the phosphorylation status-mediated PIN polarity switch is widely used to modulate cellular processes in Arabidopsis including multipolar pavement cells (PC) with interdigitated lobes and indentations. The degree of PC interdigitation was greatly reduced either when the FYPP1 gene, which encodes a PP2A called phytochrome-associated serine/threonine protein phosphatase, was knocked out or when the PID gene was overexpressed (35S:PID). These genetic modifications caused PIN1 localization to switch from lobe to indentation regions. The PP2A and PID mediated switching of PIN1 localization is strikingly similar to their regulation of the apical-basal polarity switch of PIN proteins in other cells. Our findings suggest a common mechanism for the regulation of PIN1 polarity formation, a fundamental cellular process that is crucial for pattern formation both at the tissue/organ and cellular levels.}, author = {Hongjiang Li and Lin, Deshu and Dhonukshe, Pankaj B and Nagawa, Shingo and Chen, Dandan and Jirí Friml and Scheres, Ben and Guo, Hongwei and Yang, Zhenbiao}, journal = {Cell Research}, number = {6}, pages = {970 -- 978}, publisher = {Nature Publishing Group}, title = {{Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis}}, doi = {10.1038/cr.2011.49}, volume = {21}, year = {2011}, } @article{2961, abstract = {Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).}, author = {Malaspinas, Anna-Sapfo and Caroline Uhler}, journal = {Journal of Algebraic Statistics}, number = {1}, pages = {36 -- 53}, publisher = {Public Knowledge Project}, title = {{Detecting epistasis via Markov bases}}, doi = {http://dx.doi.org/10.18409/jas.v2i1.27}, volume = {2}, 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{3100, abstract = {In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.}, author = {Vanneste, Steffen and Coppens, Frederik and Lee, EunKyoung and Donner, Tyler J and Xie, Zidian and Van Isterdael, Gert and Dhondt, Stijn and De Winter, Freya and De Rybel, Bert and Vuylsteke, Marnik and De Veylder, Lieven and Jirí Friml and Inzé, Dirk and Grotewold, Erich and Scarpella, Enrico and Sack, Fred and Beemster, Gerrit T and Beeckman, Tom}, journal = {EMBO Journal}, number = {16}, pages = {3430 -- 3441}, publisher = {Wiley-Blackwell}, title = {{Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis }}, doi = {10.1038/emboj.2011.240}, volume = {30}, year = {2011}, } @article{3101, abstract = {Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved}, author = {Zwiewka, Marta and Feraru, Elena and Möller, Barbara and Hwang, Inhwan and Feraru, Mugurel I and Kleine-Vehn, Jürgen and Weijers, Dolf and Jirí Friml}, journal = {Cell Research}, number = {12}, pages = {1711 -- 1722}, publisher = {Nature Publishing Group}, title = {{The AP 3 adaptor complex is required for vacuolar function in Arabidopsis}}, doi = {10.1038/cr.2011.99}, volume = {21}, year = {2011}, }