Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis

During angiogenesis, endothelial cells compete for the tip position during angiogenesis: a phenomenon named tip cell overtaking. It is still unclear to what extent tip cell overtaking is a side effect of sprouting or to what extent a biological function. To address this question, we studied tip cell overtaking in two existing cellular Potts models of angiogenic sprouting. In these models angiogenic sprouting-like behavior emerges from a small set of plausible cell behaviors and the endothelial cells spontaneously migrate forwards and backwards within sprouts, suggesting that tip cell overtaking might occur as a side effect of sprouting. In accordance with experimental observations, in our simulations the cells' tendency to occupy the tip position can be regulated when two cell lines with different levels of Vegfr2 expression are contributing to sprouting (mosaic sprouting assay), where cell behavior is regulated by a simple VEGF-Dll4-Notch signaling network. Our modeling results suggest that tip cell overtaking occurs spontaneously due to the stochastic motion of cells during sprouting. Thus, tip cell overtaking and sprouting dynamics may be interdependent and should be studied and interpreted in combination. VEGF-Dll4-Notch can regulate the ability of cells to occupy the tip cell position, but only when cells in the simulation strongly differ in their levels of Vegfr2. We propose that VEGF-Dll4-Notch signaling might not regulate which cell ends up at the tip, but assures that the cell that randomly ends up at the tip position acquires the tip cell phenotype.Comment: 20 pages, 6 figures, 4 supplementary figure

Black spot diseases in carrot

An important problem in organic carrot production in the Netherlands is the occurrence of black spots during storage. Several different fungal pathogens cause similar symptoms, which are collectively known as black spot diseases. We identified Alternaria radicina, A. dauci and Rhexocercosporidium carotae (syn. Acrothecium carotae) as the most prevalent black spot pathogens. We developed laboratory test methods for resistance to A. radicina and R. carotae, and assessed resistance in a collection of cultivated varieties and more exotic material

Constructive plaquette compilation for the parity architecture

Parity compilation is the challenge of laying out the required constraints for the parity mapping in a local way. We present the first constructive compilation algorithm for the parity architecture using plaquettes for arbitrary higher-order optimization problems. This enables adiabatic protocols, where the plaquette layout can natively be implemented, as well as fully parallelized digital circuits. The algorithm builds a rectangular layout of plaquettes, where in each layer of the rectangle at least one constraint is added. The core idea is that each constraint, consisting of any qubits on the boundary of the rectangle and some new qubits, can be decomposed into plaquettes with a deterministic procedure using ancillas. We show how to pick a valid set of constraints and how this decomposition works. We further give ways to optimize the ancilla count and show how to implement optimization problems with additional constraints.Comment: 8 pages, 5 figure

Space Motions of the Dwarf Spheroidal Galaxies Draco and Sculptor based on HST Proper Motions with ~10-year Time Baseline

We present new proper motion (PM) measurements of the dwarf spheroidal galaxies (dSphs) Draco and Sculptor using multi-epoch images obtained with the Hubble Space Telescope ACS/WFC. Our PM results have uncertainties far lower than previous measurements, even made with the same instrument. The PM results for Draco and Sculptor are (mu_W,mu_N)_Dra = (-0.0562+/-0.0099,-0.1765+/-0.0100) mas/yr and (mu_W,mu_N)_Scl = (-0.0296+/-0.0209,-0.1358 +/-0.0214) mas/yr. The implied Galactocentric velocity vectors for Draco and Sculptor have radial and tangential components: (V_rad,V_tan)_Dra = (-88.6,161.4) +/- (4.4,5.6) km/s; and (V_rad,V_tan)_Scl = (72.6,200.2) +/- (1.3,10.8) km/s. We study the detailed orbital history of both Draco and Sculptor via numerical orbit integrations. Orbital periods of Draco and Sculptor are found to be 1-2 and 2-5 Gyrs, respectively, accounting for uncertainties in the MW mass. We also study the influence of the Large Magellanic Cloud (LMC) on the orbits of Draco and Sculptor. Overall, the inclusion of the LMC increases the scatter in the orbital results. Based on our calculations, Draco shows a rather wide range of orbital parameters depending on the MW mass and inclusion/exclusion of the LMC, but Sculptor's orbit is very well constrained with its most recent pericentric approach to the MW being 0.3-0.4 Gyr ago. Our new PMs imply that the orbital trajectories of both Draco and Sculptor are confined within the Disk of Satellites (DoS), better so than implied by earlier PM measurements, and likely rule out the possibility that these two galaxies were accreted together as part of a tightly bound group.Comment: 17 pages, 8 figures, 6 tables. Accepted for publication in Ap

Factors affecting thrips resistance in cabbage

In two field experiments in the Netherlands the development of thrips populations and thrips damage in ten cabbage varieties was monitored. Also a number of morphological, physiological en biochemical plant traits were measured. The most important factors leading to a low level of thrips dam-age were a late development of a compact head, a low dry matter content and a high amount of leaf wax

FitTetra 2.0-improved genotype calling for tetraploids with multiple population and parental data support

BackgroundGenetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.ResultsOur upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.ConclusionOur updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.</p

Genomics-based discrimination of 2n gamete formation mechanisms in polyploids: a case study in nonaploid Diospyros kaki ‘Akiou’

Unreduced gametes (2n gametes), possessing double the haploid genome, whatever ploidy that happens to be, are a common source of ploidy variation in plant populations. First and second division restitution (FDR and SDR) are the dominant mechanisms of 2n gamete production; all else being equal, FDR gametes have a higher degree of heterozygosity, thus they are advantageous in breeding. The discrimination of these mechanisms from the consequence of hybridization is challenging, especially in higher polyploids, and usually requires information on centromere location. In this study, we propose a genotyping-based strategy to uncover the mechanisms of 2n gamete formation in progeny that has a higher ploidy than its parents. Simulation of 2n gamete production revealed that FDR and SDR pathways can be discriminated based on allele transmission patterns alone without information on centromere location. We applied this strategy to study the formation mechanism of a nonaploid Diospyros kaki ‘Akiou', which was bred via hybridization between D. kaki hexaploid cultivars. The result demonstrated that ‘Akiou' was derived from the fertilization of a normal female gamete by a 2n male gamete and that this 2n gamete was produced through FDR. Consequently, the distinct duplex transmission pattern in the FDR gamete enabled us to infer the genomic characteristics of polyploid persimmon. The method could be tested only for the plant being polypoid, which allows for the ability to discriminate causes of 2n gamete formation using allele dosage in progeny, and will be useful in future studies of polyploid genomics

Genotypic variation in genome-wide transcription profiles induced by insect feeding: Brassica oleracea – Pieris rapae interactions

<p>Abstract</p> <p>Background</p> <p>Transcriptional profiling after herbivore attack reveals, at the molecular level, how plants respond to this type of biotic stress. Comparing herbivore-induced transcriptional responses of plants with different phenotypes provides insight into plant defense mechanisms. Here, we compare the global gene expression patterns induced by <it>Pieris rapae </it>caterpillar attack in two white cabbage (<it>Brassica oleracea </it>var. <it>capitata</it>) cultivars. The two cultivars are shown to differ in their level of direct defense against caterpillar feeding. Because <it>Brassica </it>full genome microarrays are not yet available, 70-mer oligonucleotide microarrays based on the <it>Arabidopsis thaliana </it>genome were used for this non-model plant.</p> <p>Results</p> <p>The transcriptional responses of the two cultivars differed in timing as characterized by changes in their expression pattern after 24, 48 and 72 hours of caterpillar feeding. In addition, they also differed qualitatively. Surprisingly, of all genes induced at any time point, only one third was induced in both cultivars. Analyses of transcriptional responses after jasmonate treatment revealed that the difference in timing did not hold for the response to this phytohormone. Additionally, comparisons between <it>Pieris rapae</it>- and jasmonate-induced transcriptional responses showed that <it>Pieris rapae </it>induced more jasmonate-independent than jasmonate-dependent genes.</p> <p>Conclusion</p> <p>The present study clearly shows that global transcriptional responses in two cultivars of the same plant species in response to insect feeding can differ dramatically. Several of these differences involve genes that are known to have an impact on <it>Pieris rapae </it>performance and probably underlie different mechanisms of direct defense, present in the cultivars.</p

Natural supramolecular protein assemblies

Supramolecular protein assemblies are an emerging area within the chemical sciences, which combine the topological structures of the field of supramolecular chemistry and the state-of-the-art chemical biology approaches to unravel the formation and function of protein assemblies. Recent chemical and biological studies on natural multimeric protein structures, including fibers, rings, tubes, catenanes, knots, and cages, have shown that the quaternary structures of proteins are a prerequisite for their highly specific biological functions. In this review, we illustrate that a striking structural diversity of protein assemblies is present in nature. Furthermore, we describe structure–function relationship studies for selected classes of protein architectures, and we highlight the techniques that enable the characterisation of supramolecular protein structures

A Young Stellar Cluster in the Nucleus of NGC 4449

We have obtained 1-2 A resolution optical Echellette spectra of the nuclear star cluster in the nearby starburst galaxy NGC 4449. The light is clearly dominated by a very young (6-10 Myr) population of stars. For our age dating, we have used recent population synthesis models to interpret the observed equivalent width of stellar absorption features such as the HI Balmer series and the CaII triplet around 8500 A. We also compare the observed spectrum of the nuclear cluster to synthesized spectra of simple stellar populations of varying ages. All these approaches yield a consistent cluster age. Metallicity estimates based on the relative intensities of various ionization lines yield no evidence for significant enrichment in the center of this low mass galaxy: the metallicity of the nuclear cluster is about one fourth of the solar value, in agreement with independent estimates for the disk material of NGC 4449.Comment: 24 pages (incl. 7 figures), accepted by AJ, March 2001 issue revised version with minor changes and additions, one additional figur