Whole genome profiling to generate a core physical map of the gene rich part of the sugarcane genome : [W778]

The sugarcane genome poses challenges that have not been addressed in any prior genome sequencing project. The main difficulties reside in its high polyploidy (2n ~ 12x ~ 120), and its high level of heterozygosity which makes an assembly of the whole genome very challenging through classical shotgun approaches. Previous studies demonstrated that sugarcane hom(e)ologous chromosomes share a very high level of microcolinearity among themselves and show good micro-colinearity with sorghum. These findings suggested that sequencing a minimum tiling path (MTP) of BACs representing the gene-rich part of the monoploid genome could represent a very-useful sugarcane reference sequence. Sorghum could provide a good template to select this core set of sugarcane BACs. In the present study, we exploited the Whole Genome Profiling (WGP) technology of Keygene to analyze a set of 20,736 BACs from cultivar R570, representing an approximate 2=- fold coverage of the monoploid genome of sugarcane. The WGP technology generates short sequence tags from the terminal ends of restriction fragments from pooled BACs, allowing the development of highly accurate sequence-based physical maps. Sequence tags were obtained for 18,787 sugarcane BACs that were assembled into 3,903 contigs with an average of 3.4 BACs per contig. An average of 37.2 sequence tags per BAC was generated which allowed the anchoring of more than 11,000 of the profiled R570 BACs on the sorghum sequence. A core subset (MTP) of these BACs will now be selected and sequenced to generate a reference sequence of the gene-rich part of the sugarcane genome. (Texte intégral

Topographical coloured plasmonic coins

The use of metal nanostructures for colourization has attracted a great deal of interest with the recent developments in plasmonics. However, the current top-down colourization methods based on plasmonic concepts are tedious and time consuming, and thus unviable for large-scale industrial applications. Here we show a bottom-up approach where, upon picosecond laser exposure, a full colour palette independent of viewing angle can be created on noble metals. We show that colours are related to a single laser processing parameter, the total accumulated fluence, which makes this process suitable for high throughput industrial applications. Statistical image analyses of the laser irradiated surfaces reveal various distributions of nanoparticle sizes which control colour. Quantitative comparisons between experiments and large-scale finite-difference time-domain computations, demonstrate that colours are produced by selective absorption phenomena in heterogeneous nanoclusters. Plasmonic cluster resonances are thus found to play the key role in colour formation.Comment: 9 pages, 5 figure

Report on the 1st SPARC Stratospheric Network for the Assessment of Predictability (SNAP). April 24-26 April 2013, Reading, UK

Stratospheric Network for the Assessment of Predictability (SNAP), 24-26 April 2013, Reading, UKThe first SPARC Stratospheric Network for the Assessment of Predictability (SPARC-SNAP) workshop was organized in the Department of Meteorology, University of Reading, UK, from 24 to 26 April 2013. This was a joint workshop with 3rd SPARC Dynamical Variability (SPARC-DynVar) (Manzini et al., this issue) workshop 22-24 April with the 24th April as a joint day. The joint workshop was well attended and had around 100 participants (http://www.met.reading.ac.uk/~pn904784/DynVar_SNAP_Workshop/participant.html) from 16 countries in Europe, Asia, Africa, Australia, North America, and South America (Participants figure). In the SNAP part of workshop (including the joint day) there were two keynote address, nine invited talks, six contributory talks and 24 posters.The authors are grateful to the Natural Environment Research Council and WCRP-SPARC for their financial support

Sub-100 nm gold nanomatryoshkas improve photo-thermal therapy efficacy in large and highly aggressive triple negative breast tumors

There is an unmet need for efficient near-infrared photothermal transducers for the treatment of highly aggressive cancers and large tumors where the penetration of light can be substantially reduced, and the intra-tumoral nanoparticle transport is restricted due to the presence of hypoxic or necrotic regions. We report the performance advantages obtained by sub 100 nm gold nanomatryushkas, comprising concentric gold–silica–gold layers compared to conventional ~ 150 nm silica core gold nanoshells for photothermal therapy of triple negative breast cancer. We demonstrate that a 33% reduction in silica–core–gold-shell nanoparticle size, while retaining near-infrared plasmon resonance, and keeping the nanoparticle surface charge constant, results in a four to five fold tumor accumulation of nanoparticles following equal dose of injected gold for both sizes. The survival time of mice bearing large (> 1000 mm3) and highly aggressive triple negative breast tumors is doubled for the nanomatryushka treatment group under identical photo-thermal therapy conditions. The higher absorption cross-section of a nanomatryoshka results in a higher efficiency of photonic to thermal energy conversion and coupled with 4–5 × accumulation within large tumors results in superior therapy efficacy

Examining the predictability of the Stratospheric Sudden Warming of January 2013 using multiple NWP systems

The first multi-model study to estimate the predictability of a boreal Sudden Stratospheric Warming (SSW) is performed using five NWP systems. During the 2012-2013 boreal winter, anomalous upward propagating planetary wave activity was observed towards the end of December, which followed by a rapid deceleration of the westerly circulation around 2 January 2013, and on 7 January 2013 the zonal mean zonal wind at 60°N and 10 hPa reversed to easterly. This stratospheric dynamical activity was followed by an equatorward shift of the tropospheric jet stream and by a high pressure anomaly over the North Atlantic, which resulted in severe cold conditions in the UK and Northern Europe. In most of the five models, the SSW event was predicted 10 days in advance. However, only some ensemble members in most of the models predicted weakening of westerly wind when the models were initialized 15 days in advance of the SSW. Further dynamical analysis of the SSW shows that this event was characterized by the anomalous planetary wave-1 amplification followed by the anomalous wave-2 amplification in the stratosphere, which resulted in a split vortex occurring between 6 January 2013 and 8 January 2013. The models have some success in reproducing wave-1 activity when initialized 15 days in advance, they but generally failed to produce the wave-2 activity during the final days of the event. Detailed analysis shows that models have reasonably good skill in forecasting tropospheric blocking features that stimulate wave-2 amplification in the troposphere, but they have limited skill in reproducing wave-2 amplification in the stratosphere

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde

Inclusive search for same-sign dilepton signatures in pp collisions at root s=7 TeV with the ATLAS detector

An inclusive search is presented for new physics in events with two isolated leptons (e or mu) having the same electric charge. The data are selected from events collected from p p collisions at root s = 7 TeV by the ATLAS detector and correspond to an integrated luminosity of 34 pb(-1). The spectra in dilepton invariant mass, missing transverse momentum and jet multiplicity are presented and compared to Standard Model predictions. In this event sample, no evidence is found for contributions beyond those of the Standard Model. Limits are set on the cross-section in a fiducial region for new sources of same-sign high-mass dilepton events in the ee, e mu and mu mu channels. Four models predicting same-sign dilepton signals are constrained: two descriptions of Majorana neutrinos, a cascade topology similar to supersymmetry or universal extra dimensions, and fourth generation d-type quarks. Assuming a new physics scale of 1 TeV, Majorana neutrinos produced by an effective operator V with masses below 460 GeV are excluded at 95% confidence level. A lower limit of 290 GeV is set at 95% confidence level on the mass of fourth generation d-type quarks