@article{8030, abstract = {While the plasticity of excitatory synaptic connections in the brain has been widely studied, the plasticity of inhibitory connections is much less understood. Here, we present recent experimental and theoretical findings concerning the rules of spike timing-dependent inhibitory plasticity and their putative network function. This is a summary of a workshop at the COSYNE conference 2012.}, author = {Vogels, Tim P and Froemke, R. C. and Doyon, N. and Gilson, M. and Haas, J. S. and Liu, R. and Maffei, A. and Miller, P. and Wierenga, C. J. and Woodin, M. A. and Zenke, F. and Sprekeler, H.}, issn = {1662-5110}, journal = {Frontiers in Neural Circuits}, publisher = {Frontiers Media}, title = {{Inhibitory synaptic plasticity: Spike timing-dependence and putative network function}}, doi = {10.3389/fncir.2013.00119}, volume = {7}, year = {2013}, } @article{810, abstract = {Cryo-electron tomography combined with image processing by sub-tomogram averaging is unique in its power to resolve the structures of proteins and macromolecular complexes in situ. Limitations of the method, including the low signal to noise ratio within individual images from cryo-tomographic datasets and difficulties in determining the defocus at which the data was collected, mean that to date the very best structures obtained by sub-tomogram averaging are limited to a resolution of approximately 15. Å. Here, by optimizing data collection and defocus determination steps, we have determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5. Å. At this resolution alpha-helices can be directly and clearly visualized. These data demonstrate for the first time that high-resolution structural information can be obtained from cryo-electron tomograms using sub-tomogram averaging. Sub-tomogram averaging has the potential to allow detailed studies of unsolved and biologically relevant structures under biologically relevant conditions.}, author = {Florian Schur and Hagen, Wim J and De Marco, Alex and Briggs, John A}, journal = {Journal of Structural Biology}, number = {3}, pages = {394 -- 400}, publisher = {Academic Press}, title = {{Determination of protein structure at 8.5Å resolution using cryo-electron tomography and sub-tomogram averaging}}, doi = {10.1016/j.jsb.2013.10.015}, volume = {184}, year = {2013}, } @article{811, abstract = {Cell migration is commonly accompanied by protrusion of membrane ruffles and lamellipodia. In two-dimensional migration, protrusion of these thin sheets of cytoplasm is considered relevant to both exploration of new space and initiation of nascent adhesion to the substratum. Lamellipodium formation can be potently stimulated by Rho GTPases of the Rac subfamily, but alsoby RhoG or Cdc42. Here we describe viable fibroblast cell lines geneticallydeficient for Rac1 that lack detectable levels of Rac2 and Rac3. Rac-deficient cells were devoid of apparent lamellipodia, but these structures were restored by expression of either Rac subfamily member, but not by Cdc42 or RhoG. Cells deficient in Rac showed strong reduction in wound closure and random cell migration and a notable loss of sensitivity to a chemotactic gradient. Despite these defects, Rac-deficient cells were able to spread, formed filopodia and established focal adhesions. Spreading in these cells was achieved by the extension of filopodia followed by the advancement of cytoplasmic veils between them. The number and size of focal adhesions as well as their intensity were largely unaffected by genetic removal of Rac1. However, Rac deficiency increased the mobility of different components in focal adhesions, potentially explaining how Rac - although not essential - can contribute to focal adhesion assembly. Together, our data demonstrate that Rac signaling is essential for lamellipodium protrusion and for efficient cell migration, but not for spreading or filopodium formation. Our findings also suggest that Rac GTPases are crucial to the establishment or maintenance of polarity in chemotactic migration.}, author = {Steffen, Anika and Ladwein, Markus and Georgi Dimchev and Hein, Anke and Schwenkmezger, Lisa and Arens, Stefan and Ladwein, Kathrin I and Holleboom, J. Margit and Florian Schur and Small, John V and Schwarz, Janett and Gerhard, Ralf and Faix, Jan and Stradal, Theresia E and Brakebusch, Cord H and Rottner, Klemens}, journal = {Journal of Cell Science}, number = {20}, pages = {4572 -- 4588}, publisher = {Company of Biologists}, title = {{Rac function is crucial for cell migration but is not required for spreading and focal adhesion formation}}, doi = {10.1242/jcs.118232}, volume = {126}, year = {2013}, } @article{812, abstract = {Lamellipodia are sheet-like protrusions formed during migration or phagocytosis and comprise a network of actin filaments. Filament formation in this network is initiated by nucleation/branching through the actin-related protein 2/3 (Arp2/3) complex downstream of its activator, suppressor of cAMP receptor/WASP-family verprolin homologous (Scar/WAVE), but the relative relevance of Arp2/3-mediated branching versus actin filament elongation is unknown. Here we use instantaneous interference with Arp2/3 complex function in live fibroblasts with established lamellipodia. This allows direct examination of both the fate of elongating filaments upon instantaneous suppression of Arp2/3 complex activity and the consequences of this treatment on the dynamics of other lamellipodial regulators. We show that Arp2/3 complex is an essential organizer of treadmilling actin filament arrays but has little effect on the net rate of actin filament turnover at the cell periphery. In addition, Arp2/3 complex serves as key upstream factor for the recruitment of modulators of lamellipodia formation such as capping protein or cofilin. Arp2/3 complex is thus decisive for filament organization and geometry within the network not only by generating branches and novel filament ends, but also by directing capping or severing activities to the lamellipodium. Arp2/3 complex is also crucial to lamellipodia-based migration of keratocytes.}, author = {Koestler, Stefan A and Steffen, Anika and Maria Nemethova and Winterhoff, Moritz and Luo, Ningning and Holleboom, J. Margit and Krupp, Jessica and Jacob, Sonja and Vinzenz, Marlene and Florian Schur and Schlüter, Kai and Gunning, Peter W and Winkler, Christoph and Schmeiser, Christian and Faix, Jan and Stradal, Theresia E and Small, John V and Rottner, Klemens}, journal = {Molecular Biology of the Cell}, number = {18}, pages = {2861 -- 2875}, publisher = {American Society for Biology}, title = {{Arp2/3 complex is essential for actin network treadmilling as well as for targeting of capping protein and cofilin}}, doi = {10.1091/mbc.E12-12-0857}, volume = {24}, year = {2013}, } @article{8245, abstract = {Background: Monoclonal antibodies (mAb), such as trastuzumab are a valuable addition to breast cancer therapy. Data obtained from neoadjuvant settings revealed that antibody-dependent cell-mediated cytotoxicity (ADCC) is a major mechanism of action for the mAb trastuzumab. Conflicting results still call into question whether disease progression, prolonged treatment or concomitant chemotherapy influences ADCC and related immunological phenomena. Methods: We analyzed the activity of ADCC and antibody-dependent cell-mediated phagocytosis (ADCP) of peripheral blood mononuclear cells (PBMCs) from human epidermal growth factor receptor 2 (HER2/neu) positive breast cancer patients receiving trastuzumab therapy either in an adjuvant (n = 13) or metastatic (n = 15) setting as well as from trastuzumab treatment-naive (t-naive) HER2/neu negative patients (n = 15). PBMCs from healthy volunteers (n = 24) were used as controls. ADCC and ADCP activity was correlated with the expression of antibody binding Fc-gamma receptor (FcγR)I (CD64), FcγRII (CD32) and FcγRIII (CD16) on CD14+ (monocytes) and CD56+ (NK) cells, as well as the expression of CD107a+ (LAMP-1) on CD56+ cells and the total amount of CD4+CD25+FOXP3+ (Treg) cells. In metastatic patients, markers were correlated with progression-free survival (PFS). Results: ADCC activity was significantly down regulated in metastatic, adjuvant and t-naive patient cohorts as compared to healthy controls. Reduced ADCC activity was inversely correlated with the expression of CD107a on CD56+ cells in adjuvant patients. ADCC and ADCP activity of the patient cohorts were similar, regardless of treatment duration or additional chemotherapy. PFS in metastatic patients inversely correlated with the number of peripheral Treg cells. Conclusion: The reduction of ADCC in patients as compared to healthy controls calls for adjuvant strategies, such as immune-enhancing agents, to improve the activity of trastuzumab. However, efficacy of trastuzumab-specific ADCC and ADCP appears not to be affected by treatment duration, disease progression or concomitant chemotherapy. This finding supports the application of trastuzumab at any stage of the disease.}, author = {Petricevic, Branka and Laengle, Johannes and Singer, Josef and Sachet, Monika and Fazekas, Judit and Steger, Guenther and Bartsch, Rupert and Jensen-Jarolim, Erika and Bergmann, Michael}, issn = {1479-5876}, journal = {Journal of Translational Medicine}, publisher = {Springer Nature}, title = {{Trastuzumab mediates antibody-dependent cell-mediated cytotoxicity and phagocytosis to the same extent in both adjuvant and metastatic HER2/neu breast cancer patients}}, doi = {10.1186/1479-5876-11-307}, volume = {11}, year = {2013}, } @article{827, abstract = {As sessile organisms, plants have to be able to adapt to a continuously changing environment. Plants that perceive some of these changes as stress signals activate signaling pathways to modulate their development and to enable them to survive. The complex responses to environmental cues are to a large extent mediated by plant hormones that together orchestrate the final plant response. The phytohormone cytokinin is involved in many plant developmental processes. Recently, it has been established that cytokinin plays an important role in stress responses, but does not act alone. Indeed, the hormonal control of plant development and stress adaptation is the outcome of a complex network of multiple synergistic and antagonistic interactions between various hormones. Here, we review the recent findings on the cytokinin function as part of this hormonal network. We focus on the importance of the crosstalk between cytokinin and other hormones, such as abscisic acid, jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development and stress adaptation. Finally, the impact of the current research in the biotechnological industry will be discussed.}, author = {O'Brien, José and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Cytokinin cross talking during biotic and abiotic stress responses}}, doi = {10.3389/fpls.2013.00451}, volume = {4}, year = {2013}, } @article{828, abstract = {The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed.}, author = {Cuesta, Candela and Wabnik, Krzysztof T and Benková, Eva}, journal = {Frontiers in Plant Science}, publisher = {Frontiers Research Foundation}, title = {{Systems approaches to study root architecture dynamics}}, doi = {10.3389/fpls.2013.00537}, volume = {4}, year = {2013}, } @article{830, abstract = {Upon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP-SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.}, author = {Galbiati, Francesca and Sinha Roy, Dola and Simonini, Sara and Cucinotta, Mara and Ceccato, Luca and Cuesta, Candela and Šimášková, Mária and Benková, Eva and Kamiuchi, Yuri and Aida, Mitsuhiro and Weijers, Dolf and Simon, Rüdiger and Masiero, Simona and Colombo, Lucia}, journal = {The Plant journal for cell and molecular biology}, number = {3}, pages = {446 -- 455}, publisher = {Wiley-Blackwell}, title = {{An integrative model of the control of ovule primordia formation}}, doi = {10.1111/tpj.12309}, volume = {76}, year = {2013}, } @article{831, abstract = {In Arabidopsis, lateral roots originate from pericycle cells deep within the primary root. New lateral root primordia (LRP) have to emerge through several overlaying tissues. Here, we report that auxin produced in new LRP is transported towards the outer tissues where it triggers cell separation by inducing both the auxin influx carrier LAX3 and cell-wall enzymes. LAX3 is expressed in just two cell files overlaying new LRP. To understand how this striking pattern of LAX3 expression is regulated, we developed a mathematical model that captures the network regulating its expression and auxin transport within realistic three-dimensional cell and tissue geometries. Our model revealed that, for the LAX3 spatial expression to be robust to natural variations in root tissue geometry, an efflux carrier is required--later identified to be PIN3. To prevent LAX3 from being transiently expressed in multiple cell files, PIN3 and LAX3 must be induced consecutively, which we later demonstrated to be the case. Our study exemplifies how mathematical models can be used to direct experiments to elucidate complex developmental processes.}, author = {Péret, Benjamin and Middleton, Alistair M and French, Andrew P and Larrieu, Antoine and Bishopp, Anthony and Njo, Maria and Wells, Darren M and Porco, Silvana and Mellor, Nathan and Band, Leah R and Casimiro, Ilda and Kleine-Vehn, Jürgen and Vanneste, Steffen and Sairanen, Ilkka and Mallet, Romain and Sandberg, Göran and Ljung, Karin and Beeckman, Tom and Eva Benková and Jirí Friml and Kramer, Eric and King, John R and De Smet, Ive and Pridmore, Tony and Owen, Markus and Bennett, Malcolm J}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Sequential induction of auxin efflux and influx carriers regulates lateral root emergence}}, doi = {10.1038/msb.2013.43}, volume = {9}, year = {2013}, } @article{8461, abstract = {Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.}, author = {Haller, Jens D. and Schanda, Paul}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, number = {3}, pages = {263--280}, publisher = {Springer Nature}, title = {{Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin}}, doi = {10.1007/s10858-013-9787-x}, volume = {57}, year = {2013}, } @article{8462, abstract = {The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.}, author = {Rennella, E. and Cutuil, T. and Schanda, Paul and Ayala, I. and Gabel, F. and Forge, V. and Corazza, A. and Esposito, G. and Brutscher, B.}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, keywords = {Molecular Biology}, number = {15}, pages = {2722--2736}, publisher = {Elsevier}, title = {{Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure}}, doi = {10.1016/j.jmb.2013.04.028}, volume = {425}, year = {2013}, } @article{894, abstract = {Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons. Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene. Conclusions: Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.}, author = {Derelle, Romain and Kondrashov, Fyodor and Arkhipov, Vladimir and Corbel, Hélène and Frantz, Adrien and Gasparini, Julien and Jacquin, Lisa and Jacob, Gwenaël and Thibault, Sophie and Baudry, Emmanuelle}, journal = {BMC Research Notes}, number = {1}, publisher = {BioMed Central}, title = {{Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R}}, doi = {10.1186/1756-0500-6-310}, volume = {6}, year = {2013}, } @article{899, abstract = {Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype relationship, is crucial to many areas of biology. Two aspects of fitness landscapes are the focus of contemporary studies of molecular evolution. First, the local shape of the fitness landscape defined by the contribution of individual alleles to fitness that is independent of all genetic interactions. Second, the global, multidimensional fitness landscape shape determined by how interactions between alleles at different loci change each other’s fitness impact, or epistasis. In explaining the high amino-acid usage (u), we focused on the global shape of the fitness landscape, ignoring the perturbations at individual sites.}, author = {Breen, Michael S and Kemena, Carsten and Vlasov, Peter K and Notredame, Cédric and Fyodor Kondrashov}, journal = {Nature}, number = {7451}, pages = {E2 -- E3}, publisher = {Nature Publishing Group}, title = {{Breen et al. reply}}, doi = {10.1038/nature12220}, volume = {497}, year = {2013}, } @article{905, abstract = {A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka, Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the area, which together with literature data made a final list of 104 species. For several species this area is beyond the northern, north-eastern or north-western limits of their known distribution. We collected new data for 19 globally or locally threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica, American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta stelleri was judged to be 'very likely'. There was no evidence for breeding of Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels Eudromias morinellus were recorded displaying for the first time in the area, but the status of the species is unclear. The area is important for Snowy Owl Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus, White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer domesticus are more likely to be rare vagrants or migrants. An observation of a Pine Siskin Carduelis pinus is the first record for Eurasia.}, author = {Arkhipov, Vladimir Y and Noah T and Koschkar, Steffen and Fyodor Kondrashov}, journal = {Forktail}, number = {29}, pages = {25 -- 30}, publisher = {Oriental Bird Club}, title = {{Birds of Mys Shmidta, north Chukotka, Russia}}, year = {2013}, } @article{9055, abstract = {Spontaneous formation of colonies of bacteria or flocks of birds are examples of self-organization in active living matter. Here, we demonstrate a form of self-organization from nonequilibrium driving forces in a suspension of synthetic photoactivated colloidal particles. They lead to two-dimensional "living crystals," which form, break, explode, and re-form elsewhere. The dynamic assembly results from a competition between self-propulsion of particles and an attractive interaction induced respectively by osmotic and phoretic effects and activated by light. We measured a transition from normal to giant-number fluctuations. Our experiments are quantitatively described by simple numerical simulations. We show that the existence of the living crystals is intrinsically related to the out-of-equilibrium collisions of the self-propelled particles.}, author = {Palacci, Jérémie A and Sacanna, S. and Steinberg, A. P. and Pine, D. J. and Chaikin, P. M.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {6122}, pages = {936--940}, publisher = {American Association for the Advancement of Science }, title = {{Living crystals of light-activated colloidal surfers}}, doi = {10.1126/science.1230020}, volume = {339}, year = {2013}, } @article{9153, abstract = {Internal tide driven mixing plays a key role in sustaining the deep ocean stratification and meridional overturning circulation. Internal tides can be generated by topographic horizontal scales ranging from hundreds of meters to tens of kilometers. State of the art topographic products barely resolve scales smaller than ∼10 km in the deep ocean. On these scales abyssal hills dominate ocean floor roughness. The impact of abyssal hill roughness on internal‐tide generation is evaluated in this study. The conversion of M2 barotropic to baroclinic tidal energy is calculated based on linear wave theory both in real and spectral space using the Shuttle Radar Topography Mission SRTM30_PLUS bathymetric product at 1/120° resolution with and without the addition of synthetic abyssal hill roughness. Internal tide generation by abyssal hills integrates to 0.1 TW globally or 0.03 TW when the energy flux is empirically corrected for supercritical slope (i.e., ∼10% of the energy flux due to larger topographic scales resolved in standard products in both cases). The abyssal hill driven energy conversion is dominated by mid‐ocean ridges, where abyssal hill roughness is large. Focusing on two regions located over the Mid‐Atlantic Ridge and the East Pacific Rise, it is shown that regionally linear theory predicts an increase of the energy flux due to abyssal hills of up to 100% or 60% when an empirical correction for supercritical slopes is attempted. Therefore, abyssal hills, unresolved in state of the art topographic products, can have a strong impact on internal tide generation, especially over mid‐ocean ridges.}, author = {Melet, Angélique and Nikurashin, Maxim and Muller, Caroline J and Falahat, S. and Nycander, Jonas and Timko, Patrick G. and Arbic, Brian K. and Goff, John A.}, issn = {2169-9275}, journal = {Journal of Geophysical Research: Oceans}, number = {11}, pages = {6303--6318}, publisher = {American Geophysical Union}, title = {{Internal tide generation by abyssal hills using analytical theory}}, doi = {10.1002/2013jc009212}, volume = {118}, year = {2013}, } @article{9154, abstract = {In this study the response of tropical precipitation extremes to warming in organized convection is examined using a cloud-resolving model. Vertical shear is imposed to organize the convection into squall lines. Earlier studies show that in disorganized convection, the fractional increase of precipitation extremes is similar to that of surface water vapor, which is substantially smaller than the increase in column water vapor. It has been suggested that organized convection could lead to stronger amplifications. Regardless of the strength of the shear, amplifications of precipitation extremes in the cloud-resolving simulations are comparable to those of surface water vapor and are substantially less than increases in column water vapor. The results without shear and with critical shear, for which the squall lines are perpendicular to the shear, are surprisingly similar with a fractional rate of increase of precipitation extremes slightly smaller than that of surface water vapor. Interestingly, the dependence on shear is nonmonotonic, and stronger supercritical shear yields larger rates, close to or slightly larger than surface humidity. A scaling is used to evaluate the thermodynamic and dynamic contributions to precipitation extreme changes. To first order, they are dominated by the thermodynamic component, which has the same magnitude for all shears, close to the change in surface water vapor. The dynamic contribution plays a secondary role and tends to weaken extremes without shear and with critical shear, while it strengthens extremes with supercritical shear. These different dynamic contributions for different shears are due to different responses of convective mass fluxes in individual updrafts to warming.}, author = {Muller, Caroline J}, issn = {0894-8755}, journal = {Journal of Climate}, keywords = {Atmospheric Science}, number = {14}, pages = {5028--5043}, publisher = {American Meteorological Society}, title = {{Impact of convective organization on the response of tropical precipitation extremes to warming}}, doi = {10.1175/jcli-d-12-00655.1}, volume = {26}, year = {2013}, } @article{9167, abstract = {We introduce a self-propelled colloidal hematite docker that can be steered to a small particle cargo many times its size, dock, transport the cargo to a remote location, and then release it. The self-propulsion and docking are reversible and activated by visible light. The docker can be steered either by a weak uniform magnetic field or by nanoscale tracks in a textured substrate. The light-activated motion and docking originate from osmotic/phoretic particle transport in a concentration gradient of fuel, hydrogen peroxide, induced by the photocatalytic activity of the hematite. The docking mechanism is versatile and can be applied to various materials and shapes. The hematite dockers are simple single-component particles and are synthesized in bulk quantities. This system opens up new possibilities for designing complex micrometer-size factories as well as new biomimetic systems.}, author = {Palacci, Jérémie A and Sacanna, Stefano and Vatchinsky, Adrian and Chaikin, Paul M. and Pine, David J.}, issn = {15205126}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {43}, pages = {15978--15981}, publisher = {American Chemical Society}, title = {{Photoactivated colloidal dockers for cargo transportation}}, doi = {10.1021/ja406090s}, volume = {135}, year = {2013}, } @article{921, abstract = {Recent experiments have shown that spreading epithelial sheets exhibit a long-range coordination of motility forces that leads to a buildup of tension in the tissue, which may enhance cell division and the speed of wound healing. Furthermore, the edges of these epithelial sheets commonly show finger-like protrusions whereas the bulk often displays spontaneous swirls of motile cells. To explain these experimental observations, we propose a simple flocking-type mechanism, in which cells tend to align their motility forceswith their velocity. Implementing this idea in amechanical tissue simulation, the proposed model gives rise to efficient spreading and can explain the experimentally observed long-range alignment of motility forces in highly disordered patterns, as well as the buildup of tensile stress throughout the tissue. Our model also qualitatively reproduces the dependence of swirl size and swirl velocity on cell density reported in experiments and exhibits an undulation instability at the edge of the spreading tissue commonly observed in vivo. Finally, we study the dependence of colony spreading speed on important physical and biological parameters and derive simple scaling relations that show that coordination of motility forces leads to an improvement of the wound healing process for realistic tissue parameters.}, author = {Basan, Markus and Elgeti, Jens and Hannezo, Edouard B and Rappel, Wouter and Levine, Herbert}, journal = {PNAS}, number = {7}, pages = {2452 -- 2459}, publisher = {National Academy of Sciences}, title = {{Alignment of cellular motility forces with tissue flow as a mechanism for efficient wound healing}}, doi = {10.1073/pnas.1219937110}, volume = {110}, year = {2013}, } @article{9459, abstract = {Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromatic sequences preferentially require DDM1 for DNA methylation and that this preference depends on linker histone H1. RdDM is instead inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together, DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin to allow stable silencing of transposable elements in cooperation with the RdDM pathway.}, author = {Zemach, Assaf and Kim, M. Yvonne and Hsieh, Ping-Hung and Coleman-Derr, Devin and Eshed-Williams, Leor and Thao, Ka and Harmer, Stacey L. and Zilberman, Daniel}, issn = {1097-4172}, journal = {Cell}, number = {1}, pages = {193--205}, publisher = {Elsevier}, title = {{The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin}}, doi = {10.1016/j.cell.2013.02.033}, volume = {153}, year = {2013}, }