@article{922, abstract = {We study theoretically the morphologies of biological tubes affected by various pathologies. When epithelial cells grow, the negative tension produced by their division provokes a buckling instability. Several shapes are investigated: varicose, dilated, sinuous, or sausagelike. They are all found in pathologies of tracheal, renal tubes, or arteries. The final shape depends crucially on the mechanical parameters of the tissues: Young's modulus, wall-to-lumen ratio, homeostatic pressure. We argue that since tissues must be in quasistatic mechanical equilibrium, abnormal shapes convey information as to what causes the pathology. We calculate a phase diagram of tubular instabilities which could be a helpful guide for investigating the underlying genetic regulation.}, author = {Hannezo, Edouard B and Prost, Jacques and Joanny, Jean}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Mechanical instabilities of biological tubes}}, doi = {10.1103/PhysRevLett.109.018101}, volume = {109}, year = {2012}, } @article{9451, 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}, 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{9497, abstract = {The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes.}, author = {Coleman-Derr, Devin and Zilberman, Daniel}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {10}, publisher = {Public Library of Science}, title = {{Deposition of histone variant H2A.Z within gene bodies regulates responsive genes}}, doi = {10.1371/journal.pgen.1002988}, volume = {8}, year = {2012}, } @article{9499, abstract = {EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.}, author = {Kim, Sang Yeol and Lee, Jungeun and Eshed-Williams, Leor and Zilberman, Daniel and Sung, Z. Renee}, issn = {1553-7404}, journal = {PLoS Genetics}, number = {3}, publisher = {Public Library of Science}, title = {{EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development}}, doi = {10.1371/journal.pgen.1002512}, volume = {8}, year = {2012}, } @article{9528, abstract = {Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory.}, author = {Huff, Jason T. and Zilberman, Daniel}, issn = {0959-437X}, journal = {Current Opinion in Genetics and Development}, number = {2}, pages = {132--138}, publisher = {Elsevier}, title = {{Regulation of biological accuracy, precision, and memory by plant chromatin organization}}, doi = {10.1016/j.gde.2012.01.007}, volume = {22}, year = {2012}, } @article{9535, abstract = {The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies.}, author = {Coleman-Derr, D. and Zilberman, Daniel}, issn = {1943-4456}, journal = {Cold Spring Harbor Symposia on Quantitative Biology}, pages = {147--154}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{DNA methylation, H2A.Z, and the regulation of constitutive expression}}, doi = {10.1101/sqb.2012.77.014944}, volume = {77}, year = {2012}, } @article{966, abstract = {Motivated by recent experiments on Ba3NiSb2O 9, we investigate possible quantum spin liquid ground states for spin S=1 Heisenberg models on the triangular lattice. We use variational Monte Carlo techniques to calculate the energies of microscopic spin liquid wave functions where spin is represented by three flavors of fermionic spinon operators. These energies are compared with the energies of various competing three-sublattice ordered states. Our approach shows that the antiferromagnetic Heisenberg model with biquadratic term and single-ion anisotropy does not have a low-temperature spin liquid phase. However, for an SU(3)-invariant model with sufficiently strong ring-exchange terms, we find a paired chiral quantum spin liquid with a Fermi surface of deconfined spinons that is stable against all types of ordering patterns we considered. We discuss the physics of this exotic spin liquid state in relation to the recent experiment and suggest new ways to test this scenario.}, author = {Bieri, Samuel and Maksym Serbyn and Senthil, Todadri S and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {22}, publisher = {American Physical Society}, title = {{Paired chiral spin liquid with a Fermi surface in S=1 model on the triangular lattice}}, doi = {10.1103/PhysRevB.86.224409}, volume = {86}, 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{6588, abstract = {First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.}, author = {Pausinger, Florian}, issn = {1812-9471}, journal = {Journal of Mathematical Physics, Analysis, Geometry}, number = {1}, pages = {63--78}, publisher = {B. Verkin Institute for Low Temperature Physics and Engineering}, title = {{Elementary solutions of the Bernstein problem on two intervals}}, volume = {8}, year = {2012}, } @inproceedings{6746, abstract = {This paper proposes a novel cooperative approach for two-hop amplify-and-forward (A&F) relaying that exploits both the signal forwarded by the relay and the one directly transmitted by the source in impulse-radio ultra-wideband (IR-UWB) systems. Specifically, we focus on a non-coherent setup employing a double-differential encoding scheme at the source node and a single differential demodulation at the relay and destination. The log-likelihood ratio based decision rule is derived at the destination node. A semi-analytical power allocation strategy is presented by evaluating a closed-form expression for the effective signal to noise ratio (SNR) at the destination, which is maximized by exhaustive search. Numerical simulations show that the proposed system outperforms both the direct transmission with single differential encoding and the non-cooperative multi-hop approach in different scenarios.}, author = {Mondelli, Marco and Zhou, Qi and Ma, Xiaoli and Lottici, Vincenzo}, booktitle = {2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)}, issn = {1520-6149}, location = {Kyoto, Japan}, pages = {2905--2908}, publisher = {IEEE}, title = {{A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems}}, doi = {10.1109/icassp.2012.6288524}, year = {2012}, } @article{7074, abstract = {The Seebeck coefficients, electrical resistivities, total thermal conductivities, and magnetization are reported for temperatures between 5 and 350 K for n-type Bi0.88Sb0.12 nano-composite alloys made by Ho-doping at the 0, 1, and 3 % atomic levels. The alloys were prepared using a dc hot-pressing method, and are shown to be single phase for both Ho contents with grain sizes on the average of 900 nm. We find the parent compound has a maximum of ZT = 0.28 at 231 K, while doping 1 % Ho increases the maximum ZT to 0.31 at 221 K and the 3 % doped sample suppresses the maximum ZT = 0.24 at a temperature of 260 K.}, author = {Lukas, K. C. and Joshi, G. and Modic, Kimberly A and Ren, Z. F. and Opeil, C. P.}, issn = {1573-4803}, journal = {Journal of Materials Science}, number = {15}, pages = {5729--5734}, publisher = {Springer Nature}, title = {{Thermoelectric properties of Ho-doped Bi0.88Sb0.12}}, doi = {10.1007/s10853-012-6463-6}, volume = {47}, year = {2012}, } @article{7308, abstract = {Carbon has been used widely as the basis of porous cathodes for nonaqueous Li–O2 cells. However, the stability of carbon and the effect of carbon on electrolyte decomposition in such cells are complex and depend on the hydrophobicity/hydrophilicity of the carbon surface. Analyzing carbon cathodes, cycled in Li–O2 cells between 2 and 4 V, using acid treatment and Fenton’s reagent, and combined with differential electrochemical mass spectrometry and FTIR, demonstrates the following: Carbon is relatively stable below 3.5 V (vs Li/Li+) on discharge or charge, especially so for hydrophobic carbon, but is unstable on charging above 3.5 V (in the presence of Li2O2), oxidatively decomposing to form Li2CO3. Direct chemical reaction with Li2O2 accounts for only a small proportion of the total carbon decomposition on cycling. Carbon promotes electrolyte decomposition during discharge and charge in a Li–O2 cell, giving rise to Li2CO3 and Li carboxylates (DMSO and tetraglyme electrolytes). The Li2CO3 and Li carboxylates present at the end of discharge and those that form on charge result in polarization on the subsequent charge. Li2CO3 (derived from carbon and from the electrolyte) as well as the Li carboxylates (derived from the electrolyte) decompose and form on charging. Oxidation of Li2CO3 on charging to ∼4 V is incomplete; Li2CO3 accumulates on cycling resulting in electrode passivation and capacity fading. Hydrophilic carbon is less stable and more catalytically active toward electrolyte decomposition than carbon with a hydrophobic surface. If the Li–O2 cell could be charged at or below 3.5 V, then carbon may be relatively stable, however, its ability to promote electrolyte decomposition, presenting problems for its use in a practical Li–O2 battery. The results emphasize that stable cycling of Li2O2 at the cathode in a Li–O2 cell depends on the synergy between electrolyte and electrode; the stability of the electrode and the electrolyte cannot be considered in isolation.}, author = {Ottakam Thotiyl, Muhammed M. and Freunberger, Stefan Alexander and Peng, Zhangquan and Bruce, Peter G.}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {1}, pages = {494--500}, publisher = {ACS}, title = {{The carbon electrode in nonaqueous Li–O2 cells}}, doi = {10.1021/ja310258x}, volume = {135}, year = {2012}, } @article{7309, abstract = {Energy‐storage technologies, including electrical double‐layer capacitors and rechargeable batteries, have attracted significant attention for applications in portable electronic devices, electric vehicles, bulk electricity storage at power stations, and “load leveling” of renewable sources, such as solar energy and wind power. Transforming lithium batteries and electric double‐layer capacitors requires a step change in the science underpinning these devices, including the discovery of new materials, new electrochemistry, and an increased understanding of the processes on which the devices depend. The Review will consider some of the current scientific issues underpinning lithium batteries and electric double‐layer capacitors.}, author = {Choi, Nam-Soon and Chen, Zonghai and Freunberger, Stefan Alexander and Ji, Xiulei and Sun, Yang-Kook and Amine, Khalil and Yushin, Gleb and Nazar, Linda F. and Cho, Jaephil and Bruce, Peter G.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {40}, pages = {9994--10024}, publisher = {Wiley}, title = {{Challenges facing Lithium batteries and electrical double-layer capacitors}}, doi = {10.1002/anie.201201429}, volume = {51}, year = {2012}, } @article{7310, abstract = {The rechargeable nonaqueous lithium-air (Li-O2) battery is receiving a great deal of interest because, theoretically, its specific energy far exceeds the best that can be achieved with lithium-ion cells. Operation of the rechargeable Li-O2 battery depends critically on repeated and highly reversible formation/decomposition of lithium peroxide (Li2O2) at the cathode upon cycling. Here, we show that this process is possible with the use of a dimethyl sulfoxide electrolyte and a porous gold electrode (95% capacity retention from cycles 1 to 100), whereas previously only partial Li2O2 formation/decomposition and limited cycling could occur. Furthermore, we present data indicating that the kinetics of Li2O2 oxidation on charge is approximately 10 times faster than on carbon electrodes.}, author = {Peng, Z. and Freunberger, Stefan Alexander and Chen, Y. and Bruce, P. G.}, issn = {0036-8075}, journal = {Science}, number = {6094}, pages = {563--566}, publisher = {AAAS}, title = {{A reversible and higher-rate Li-O2 battery}}, doi = {10.1126/science.1223985}, volume = {337}, year = {2012}, } @article{7311, abstract = {Stability of the electrolyte toward reduced oxygen species generated at the cathode is a crucial challenge for the rechargeable nonaqueous Li–O2 battery. Here, we investigate dimethylformamide as the basis of an electrolyte. Although reactions at the O2 cathode on the first discharge–charge cycle are dominated by reversible Li2O2 formation/decomposition, there is also electrolyte decomposition, which increases on cycling. The products of decomposition at the cathode on discharge are Li2O2, Li2CO3, HCO2Li, CH3CO2Li, NO, H2O, and CO2. Li2CO3 accumulates in the electrode with cycling. The stability of dimethylformamide toward reduced oxygen species is insufficient for its use in the rechargeable nonaqueous Li–O2 battery.}, author = {Chen, Yuhui and Freunberger, Stefan Alexander and Peng, Zhangquan and Bardé, Fanny and Bruce, Peter G.}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {18}, pages = {7952--7957}, publisher = {ACS}, title = {{Li–O2 battery with a dimethylformamide electrolyte}}, doi = {10.1021/ja302178w}, volume = {134}, 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{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{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}, }