@article{17677, abstract = {Peaks in two-dimensional weak lensing (WL) maps contain significant cosmological information, complementary to the WL power spectrum. This has recently been demonstrated using N-body simulations which neglect baryonic effects. Here we employ ray-tracing N-body simulations in which we manually steepen the density profile of each dark matter halo, mimicking the cooling and concentration of baryons into dark matter potential wells. We find, in agreement with previous works, that this causes a significant increase in the amplitude of the WL power spectrum on small scales (spherical harmonic index l>1,000). We then study the impact of the halo concentration increase on the peak counts, and find the following. (i) Low peaks (with convergence 0.02 < kappa_peak < 0.08), remain nearly unaffected. These peaks are created by a constellation of several halos with low masses (10^12-10^13 M_sun) and large angular offsets from the peak center (> 0.5 R_vir); as a result, they are insensitive to the central halo density profiles. These peaks contain most of the cosmological information, and thus provide an unusually sensitive and unbiased probe. (ii) The number of high peaks (with convergence kappa_peak > 0.08) is increased. However, when the baryon effects are neglected in cosmological parameter estimation, then the high peaks lead to a modest bias, comparable to that from the power spectrum on relatively large-scales (l<2000), and much smaller than the bias from the power spectrum on smaller scales (l>2,000). (iii) In the 3D parameter space (sigma_8, Omega_m, w), the biases from the high peaks and the power spectra are in different directions. This suggests the possibility of "self-calibration": the combination of peak counts and power spectrum can simultaneously constrain baryonic physics and cosmological parameters.}, author = {Yang, Xiuyuan and Kratochvil, Jan M. and Huffenberger, Kevin and Haiman, Zoltán and May, Morgan}, issn = {1550-7998}, journal = {Physical Review D}, number = {2}, publisher = {American Physical Society}, title = {{Baryon impact on weak lensing peaks and power spectrum: Low-bias statistics and self-calibration in future surveys}}, doi = {10.1103/physrevd.87.023511}, volume = {87}, year = {2013}, } @article{17683, abstract = {When a sufficiently massive satellite (or secondary) black hole is embedded in a gas disc around a (primary) supermassive black hole, it can open an empty gap in the disc. A gap-opening secondary close to the primary will leave an imprint in the broad component of the Fe Kα emission line, which varies in a unique and predictable manner. If the gap persists into the innermost disc, the effect consists of a pair of dips in the broad line which ripple blue-ward and red-ward from the line centroid energy, respectively, as the gap moves closer to the primary. This ripple effect could be unambiguously detectable and allow an electromagnetic monitoring of massive black hole mergers as they occur. As the mass ratio of the secondary to primary black hole increases to q ≳ 0.01, we expect the gap to widen, possibly clearing a central cavity in the inner disc, which shows up in the broad Fe Kα line component. If the secondary stalls at ≥ 102rg in its in-migration, due to low corotating gas mass, a detectable ripple effect occurs in the broad line component on the disc viscous time-scale as the inner disc drains and the outer disc is dammed. If the secondary maintains an accretion disc within a central cavity, due to dam bursting or leakage, a periodic ‘see-saw’ oscillation effect is exhibited in the observed line profile. Here, we demonstrate the range of ripple effect signatures potentially detectable with Astro-H and IXO/Athena, and oscillation effects potentially detectable with XMM–Newton or LOFT for a wide variety of merger and disc conditions, including gap width (or cavity size), disc inclination angle and emissivity profile, damming of the accretion flow by the secondary, and a minidisc around the satellite black hole. A systematic study of ripple effects would require a telescope effective area substantially larger than that planned for IXO/Athena. Future mission planning should take this into account. Observations of the ripple effect and periodic oscillations can be used to provide an early warning of gravitational radiation emission from the AGN. Once gravitational waves consistent with massive black hole mergers are detected, an archival search for the Fe Kα ripple effect or periodic oscillations will help in localizing their origin.}, author = {McKernan, B. and Ford, K. E. S. and Kocsis, B. and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {1468--1482}, publisher = {Oxford University Press}, title = {{Ripple effects and oscillations in the broad Fe Kα line as a probe of massive black hole mergers}}, doi = {10.1093/mnras/stt567}, volume = {432}, year = {2013}, } @article{17684, abstract = {We have performed cosmo-hydro simulations using the RAMSES code to study atomic cooling (ACHs) haloes at z=10 with masses 5E7Msun<~M<~2E9Msun. We assume primordial gas and H2-cooling and prior star-formation have been suppressed. We analysed 19 haloes (gas and DM) at a resolution of ~10 (proper) pc, selected from a total volume of ~2E3 (comoving) Mpc3. This is the largest statistical hydro-sim. study of ACHs at z>10 to date. We examine the morphology, angular momentum (AM), thermodynamic, and turbulence of these haloes, in order to assess the prevalence of disks and supermassive black holes (SMBHs). We find no correlation between either the magnitude or the direction of the AM of the gas and its parent DM halo. Only 3 haloes form rotationally supported cores. Two of the most massive haloes form massive, compact overdense blobs. These blobs have an accretion rate ~0.5 Msun/yr (at a distance of 100 pc), and are possible sites of SMBH formation. Our results suggest that the degree of rotational support and the fate of the gas in a halo is determined by its large-scale environment and merger history. In particular, the two haloes forming blobs are located at knots of the cosmic web, cooled early on, and experienced many mergers. The gas in these haloes is lumpy and highly turbulent, with Mach N. >~ 5. In contrast, the haloes forming rotationally supported cores are relatively more isolated, located midway along filaments, cooled more recently, and underwent fewer mergers. Thus, the gas in these haloes is less lumpy and less turbulent (Mach <~ 4), and could retain most of its AM. The remaining 14 haloes have intermediate properties. If verified in a larger sample of haloes and with additional physics, our results will have implications for observations of the highest-redshift galaxies and quasars with JWST.}, author = {Prieto, Joaquin and Jimenez, Raul and Haiman, Zoltán}, issn = {1365-2966}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {3}, pages = {2301--2325}, publisher = {Oxford University Press}, title = {{Gas infall into atomic cooling haloes: On the formation of protogalactic discs and supermassive black holes at z > 10}}, doi = {10.1093/mnras/stt1730}, volume = {436}, year = {2013}, } @article{17704, abstract = {We compare the efficiency of moments and Minkowski functionals (MFs) in constraining the subset of cosmological parameters (Omega_m,w,sigma_8) using simulated weak lensing convergence maps. We study an analytic perturbative expansion of the MFs in terms of the moments of the convergence field and of its spatial derivatives. We show that this perturbation series breaks down on smoothing scales below 5', while it shows a good degree of convergence on larger scales (15'). Most of the cosmological distinguishing power is lost when the maps are smoothed on these larger scales. We also show that, on scales comparable to 1', where the perturbation series does not converge, cosmological constraints obtained from the MFs are approximately 1.5-2 times better than the ones obtained from the first few moments of the convergence distribution --- provided that the latter include spatial information, either from moments of gradients, or by combining multiple smoothing scales. Including either a set of these moments or the MFs can significantly tighten constraints on cosmological parameters, compared to the conventional method of using the power spectrum alone.}, author = {Petri, Andrea and Haiman, Zoltán and Hui, Lam and May, Morgan and Kratochvil, Jan M.}, issn = {1550-7998}, journal = {Physical Review D}, number = {12}, publisher = {American Physical Society}, title = {{Cosmology with Minkowski functionals and moments of the weak lensing convergence field}}, doi = {10.1103/physrevd.88.123002}, volume = {88}, year = {2013}, } @article{7745, abstract = {The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among individuals from high‐density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where individuals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex‐, age‐ and environment‐specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.}, author = {Robinson, Matthew Richard and Santure, Anna W. and DeCauwer, Isabelle and Sheldon, Ben C. and Slate, Jon}, issn = {0962-1083}, journal = {Molecular Ecology}, number = {15}, pages = {3963--3980}, publisher = {Wiley}, title = {{Partitioning of genetic variation across the genome using multimarker methods in a wild bird population}}, doi = {10.1111/mec.12375}, volume = {22}, year = {2013}, } @article{7746, abstract = {Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade‐off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker‐based approaches – chromosome partitioning, quantitative trait locus (QTL) mapping and a genome‐wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome‐wide significant QTL, and no individual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.}, author = {Santure, Anna W. and De Cauwer, Isabelle and Robinson, Matthew Richard and Poissant, Jocelyn and Sheldon, Ben C. and Slate, Jon}, issn = {0962-1083}, journal = {Molecular Ecology}, number = {15}, pages = {3949--3962}, publisher = {Wiley}, title = {{Genomic dissection of variation in clutch size and egg mass in a wild great tit (Parus major) population}}, doi = {10.1111/mec.12376}, volume = {22}, year = {2013}, } @article{7747, abstract = {Acquisition and allocation of resources are central to life‐history theory. However, empirical work typically focuses only on allocation despite the fact that relationships between fitness components may be governed by differences in the ability of individuals to acquire resources across environments. Here, we outline a statistical framework to partition the genetic basis of multivariate plasticity into independent axes of genetic variation, and quantify for the first time, the extent to which specific traits drive multitrait genotype–environment interactions. Our framework generalises to analyses of plasticity, growth and ageing. We apply this approach to a unique, large‐scale, multivariate study of acquisition, allocation and plasticity in the life history of the cricket, Gryllus firmus. We demonstrate that resource acquisition and allocation are genetically correlated, and that plasticity in trade‐offs between allocation to components of fitness is 90% dependent on genetic variance for total resource acquisition. These results suggest that genotype–environment effects for resource acquisition can maintain variation in life‐history components that are typically observed in the wild.}, author = {Robinson, Matthew Richard and Beckerman, Andrew P.}, issn = {1461-023X}, journal = {Ecology Letters}, number = {3}, pages = {281--290}, publisher = {Wiley}, title = {{Quantifying multivariate plasticity: Genetic variation in resource acquisition drives plasticity in resource allocation to components of life history}}, doi = {10.1111/ele.12047}, volume = {16}, year = {2013}, } @article{7774, abstract = {In 2005, Wyart et al. [Europhys. Lett., 2005, 72, 486] showed that the low frequency vibrational properties of jammed amorphous sphere packings can be understood in terms of a length scale, called l*, that diverges as the system becomes marginally unstable. Despite the tremendous success of this theory, it has been difficult to connect the counting argument that defines l* to other length scales that diverge near the jamming transition. We present an alternate derivation of l* based on the onset of rigidity. This phenomenological approach reveals the physical mechanism underlying the length scale and is relevant to a range of systems for which the original argument breaks down. It also allows us to present the first direct numerical measurement of l*.}, author = {Goodrich, Carl Peter and Ellenbroek, Wouter G. and Liu, Andrea J.}, issn = {1744-683X}, journal = {Soft Matter}, number = {46}, publisher = {Royal Society of Chemistry}, title = {{Stability of jammed packings I: The rigidity length scale}}, doi = {10.1039/c3sm51095f}, volume = {9}, year = {2013}, } @article{7775, abstract = {As a function of packing fraction at zero temperature and applied stress, an amorphous packing of spheres exhibits a jamming transition where the system is sensitive to boundary conditions even in the thermodynamic limit. Upon further compression, the system should become insensitive to boundary conditions provided it is sufficiently large. Here we explore the linear response to a large class of boundary perturbations in 2 and 3 dimensions. We consider each finite packing with periodic-boundary conditions as the basis of an infinite square or cubic lattice and study properties of vibrational modes at arbitrary wave vector. We find that the stability of such modes can be understood in terms of a competition between plane waves and the anomalous vibrational modes associated with the jamming transition; infinitesimal boundary perturbations become irrelevant for systems that are larger than a length scale that characterizes the transverse excitations. This previously identified length diverges at the jamming transition.}, author = {Schoenholz, Samuel S. and Goodrich, Carl Peter and Kogan, Oleg and Liu, Andrea J. and Nagel, Sidney R.}, issn = {1744-683X}, journal = {Soft Matter}, number = {46}, publisher = {Royal Society of Chemistry}, title = {{Stability of jammed packings II: The transverse length scale}}, doi = {10.1039/c3sm51096d}, volume = {9}, year = {2013}, } @article{7785, abstract = {Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation.}, author = {Joo, William J. and Sweeney, Lora Beatrice Jaeger and Liang, Liang and Luo, Liqun}, issn = {0896-6273}, journal = {Neuron}, number = {4}, pages = {673--686}, publisher = {Elsevier}, title = {{Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting}}, doi = {10.1016/j.neuron.2013.03.022}, volume = {78}, year = {2013}, } @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}, }