2D association and integrative omics analysis in rice provides systems biology view in trait analysis.

The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs. Interaction effect is demonstrated as a 2D association. Based on this linear mixed model, we developed a pipeline, namely PATOWAS. PATOWAS can be used to study transcriptome-wide and metabolome-wide associations in addition to genome-wide associations. Our case analysis with real rice recombinant inbred lines (RILs) at three omics levels demonstrates that 2D association mapping and integrative omics are able to provide a systems biology view into the analyzed traits, leading toward an answer about how genes, transcripts, proteins, and metabolites work together to produce an observable phenotype

Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner

<p>Abstract</p> <p>Background</p> <p>Allotetraploid white clover (<it>Trifolium repens </it>L.) is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover.</p> <p>Results</p> <p>Genomic libraries containing simple sequence repeat (SSR) sequences were constructed using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) procedure and phpSSRMiner was used to develop the microsatellite markers. SSR motifs were isolated using two biotin-labeled probes, (CA)₁₇and (ATG)₁₂. The sequences of 6,816 clones were assembled into 1,698 contigs, 32% of which represented novel sequences based on BLASTN searches. Approximately 32%, 28%, and 16% of these SSRs contained hexa-, tri-, and di-nucleotide repeats, respectively. The most frequent motifs were the CA and ATG complementary repeats and the associated compound sequences. Primer pairs were designed for 859 SSR loci based on sequences from these genomic libraries and from GenBank white clover nucleotide sequences. A total of 191 SSR primers developed from the two libraries were tested for polymorphism in individual clones from the parental genotypes GA43 ('Durana'), 'SRVR' and six F₁progeny from a mapping population. Ninety two percent produced amplicons and 66% of these were polymorphic.</p> <p>Conclusion</p> <p>The combined approach of identifying SSR-enriched fragments by FIASCO coupled with the primer design and <it>in silico </it>amplification using phpSSRMiner represents an efficient and low cost pipeline for the large-scale development of microsatellite markers in plants.</p> <p>The approach described here could be readily adapted and utilized in other non-related species with none or limited genomic resources.</p

A Novel Method for Defining the Leeward Edge of the Planar Jet in Crossflow

To avoid the complexity of the edge definition by the half width, a new approach to defining the leeward edge of the planar jet in crossflow is introduced in this paper. Particle Image Velocimetry (PIV) experiments were performed to measure different flow regimes within the single jet and the dual jets configurations in crossflow. Based on the experimental data acquired, a series of velocity profiles were extracted from the flow field. In each profile, a velocity threshold was given to distinguish the regions sheltered and the regions not sheltered by the planar jet. The boundary of these regions was accordingly recognized as the leeward edge. Furthermore, fitting of the edge was carried out using a second order polynomial so as to enable a mathematical expression of the leeward edge. An application of the proposed approach towards the flow induced noise reduction using a planar jet is also discussed in this paper. In addition, the PIV frame assembly algorithm used in this study is reported

Ionization structure and Fe Kα\alpha energy for irradiated accretion disks

We study the radial ionization structure at the surface of an X-ray illuminated accretion disk. We plot the expected iron K$\alpha$ line energy as a function of the Eddington ratio and of the distance of the emitting matter from the central source, for a non-rotating and a maximally-rotating black hole. We compare the predicted disk line energies with those measured in an archival sample of active galactic nuclei observed with {\it Chandra}, {\it XMM-Newton} and {\it Suzaku}, and discuss whether the line energies are consistent with the radial distances inferred from reverberation studies. We also suggest using rapidly-variable iron K$\alpha$ lines to estimate the viscosity parameter of an accretion disk. There is a forbidden region in the line energy versus Eddington ratio plane, at low Eddington ratios, where an accretion disk cannot produce highly-ionized iron K$\alpha$ lines. If such emission is observed in low-Eddington-ratio sources, it is either coming from a highly-ionized outflow, or is a blue-shifted component from fast-moving neutral matter.Comment: 5 pages, 2 figures, accepted by MNRA

Fabrication and characterization of dual function nanoscale pH-scanning ion conductance microscopy (SICM) probes for high resolution pH mapping

The easy fabrication and use of nanoscale dual function pH-scanning ion conductance microscopy (SICM) probes is reported. These probes incorporate an iridium oxide coated carbon electrode for pH measurement and an SICM barrel for distance control, enabling simultaneous pH and topography mapping. These pH-SICM probes were fabricated rapidly from laser pulled theta quartz pipets, with the pH electrode prepared by in situ carbon filling of one of the barrels by the pyrolytic decomposition of butane, followed by electrodeposition of a thin layer of hydrous iridium oxide. The other barrel was filled with an electrolyte solution and Ag/AgCl electrode as part of a conductance cell for SICM. The fabricated probes, with pH and SICM sensing elements typically on the 100 nm scale, were characterized by scanning electron microscopy, energy-dispersive X-ray spectroscopy, and various electrochemical measurements. They showed a linear super-Nernstian pH response over a range of pH (pH 2–10). The capability of the pH-SICM probe was demonstrated by detecting both pH and topographical changes during the dissolution of a calcite microcrystal in aqueous solution. This system illustrates the quantitative nature of pH-SICM imaging, because the dissolution process changes the crystal height and interfacial pH (compared to bulk), and each is sensitive to the rate. Both measurements reveal similar dissolution rates, which are in agreement with previously reported literature values measured by classical bulk methods

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology

Pairing symmetry and properties of iron-based high temperature superconductors

Pairing symmetry is important to indentify the pairing mechanism. The analysis becomes particularly timely and important for the newly discovered iron-based multi-orbital superconductors. From group theory point of view we classified all pairing matrices (in the orbital space) that carry irreducible representations of the system. The quasiparticle gap falls into three categories: full, nodal and gapless. The nodal-gap states show conventional Volovik effect even for on-site pairing. The gapless states are odd in orbital space, have a negative superfluid density and are therefore unstable. In connection to experiments we proposed possible pairing states and implications for the pairing mechanism.Comment: 4 pages, 1 table, 2 figures, polished versio