@article{9014, abstract = {In this Letter, we explore experimentally the phase behavior of a dense active suspension of self-propelled colloids. In addition to a solidlike and gaslike phase observed for high and low densities, a novel cluster phase is reported at intermediate densities. This takes the form of a stationary assembly of dense aggregates—resulting from a permanent dynamical merging and separation of active colloids—whose average size grows with activity as a linear function of the self-propelling velocity. While different possible scenarios can be considered to account for these observations—such as a generic velocity weakening instability recently put forward—we show that the experimental results are reproduced mathematically by a chemotactic aggregation mechanism, originally introduced to account for bacterial aggregation and accounting here for diffusiophoretic chemical interaction between colloidal swimmers.}, author = {Theurkauff, I. and Cottin-Bizonne, C. and Palacci, Jérémie A and Ybert, C. and Bocquet, L.}, issn = {10797114}, journal = {Physical Review Letters}, number = {26}, publisher = {American Physical Society }, title = {{Dynamic clustering in active colloidal suspensions with chemical signaling}}, doi = {10.1103/physrevlett.108.268303}, volume = {108}, year = {2012}, } @article{91, abstract = {We demonstrate how to appropriately estimate the zero-frequency (static) hyperpolarizability of an organic molecule from its charge distribution, and we explore applications of these estimates for identifying and evaluating new organic nonlinear optical (NLO) materials. First, we calculate hyperpolarizabilities from Hartree-Fock-derived charge distributions and find order-of-magnitude agreement with experimental values. We show that these simple arithmetic calculations will enable systematic searches for new organic NLO molecules. Second, we derive hyperpolarizabilities from crystallographic data using a multipolar charge-density analysis and find good agreement with empirical calculations. This demonstrates an experimental determination of the full static hyperpolarizability tensor in a solid-state sample. }, author = {Higginbotham, Andrew P and Cole, Jacqueline and Blood Forsythe, Martin and Hickstein, Daniel}, journal = {Journal of Applied Physics}, number = {3}, publisher = {American Institute of Physics}, title = {{Identifying and evaluating organic nonlinear optical materials via molecular moments}}, doi = {10.1063/1.3678593}, volume = {111}, year = {2012}, } @article{9142, abstract = {In models of radiative–convective equilibrium it is known that convection can spontaneously aggregate into one single localized moist region if the domain is large enough. The large changes in the mean climate state and radiative fluxes accompanying this self-aggregation raise questions as to what simulations at lower resolutions with parameterized convection, in similar homogeneous geometries, should be expected to produce to be considered successful in mimicking a cloud-resolving model. The authors investigate this self-aggregation in a nonrotating, three-dimensional cloud-resolving model on a square domain without large-scale forcing. It is found that self-aggregation is sensitive not only to the domain size, but also to the horizontal resolution. With horizontally homogeneous initial conditions, convective aggregation only occurs on domains larger than about 200km and with resolutions coarser than about 2km in the model examined. The system exhibits hysteresis, so that with aggregated initial conditions, convection remains aggregated even at our finest resolution, 500m, as long as the domain is greater than 200–300km. The sensitivity of self-aggregation to resolution and domain size in this model is due to the sensitivity of the distribution of low clouds to these two parameters. Indeed, the mechanism responsible for the aggregation of convection is the dynamical response to the longwave radiative cooling from low clouds. Strong longwave cooling near cloud top in dry regions forces downward motion, which by continuity generates inflow near cloud top and near-surface outflow from dry regions. This circulation results in the net export of moist static energy from regions with low moist static energy, yielding a positive feedback.}, author = {Muller, Caroline J and Held, Isaac M.}, issn = {0022-4928}, journal = {Journal of the Atmospheric Sciences}, keywords = {Atmospheric Science}, number = {8}, pages = {2551--2565}, publisher = {American Meteorological Society}, title = {{Detailed investigation of the self-aggregation of convection in cloud-resolving simulations}}, doi = {10.1175/jas-d-11-0257.1}, volume = {69}, 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{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{3242, 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 Tragust, Simon and Klatt, Martina and Drescher, Verena and Marr, Carsten and Ugelvig, Line V and Cremer, Sylvia}, journal = {PLoS Biology}, number = {4}, publisher = {Public Library of Science}, title = {{Social transfer of pathogenic fungus promotes active immunisation in ant colonies}}, doi = {10.1371/journal.pbio.1001300}, volume = {10}, 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{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}, } @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}, } @article{8504, abstract = {In this paper we present a surprising example of a Cr unimodal map of an interval f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’ of critical points is necessary for the Martens–de Melo–van Strien theorem [M. Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional dynamics. Acta Math.168(3–4) (1992), 273–318] to hold.}, author = {Kaloshin, Vadim and KOZLOVSKI, O. S.}, issn = {0143-3857}, journal = {Ergodic Theory and Dynamical Systems}, keywords = {Applied Mathematics, General Mathematics}, number = {1}, pages = {159--165}, publisher = {Cambridge University Press}, title = {{A Cr unimodal map with an arbitrary fast growth of the number of periodic points}}, doi = {10.1017/s0143385710000817}, volume = {32}, year = {2012}, }