Allelic effects on starch structure and properties of six starch biosynthetic genes in a rice recombinant inbred line population

BACKGROUND: The genetic diversity of six starch biosynthetic genes (Wx, SSI, SSIIa, SBEI, SBEIIa and SBEIIb) in indica and japonica rices opens an opportunity to produce a new variety with more favourable grain starch quality. However, there is limited information about the effects of these six gene allele combinations on starch structure and properties. A recombinant inbred line population from a cross between indica and japonica varieties offers opportunities to combine specific alleles of the six genes. RESULTS: The allelic (indica vs japonica) effects of six starch biosynthetic genes on starch structure, functional properties, and abundance of granule bound proteins in rice grains were investigated in a common genetic background using a recombinant inbred line population. The indica Wx (Wxi) allele played a major role while indica SSI (SSIi), japonica SSIIa (SSIIaj) and indica SBEI (SBEIi) alleles had minor roles on the increase of amylose content. SSIIaj and japonica SBEIIb (SBEIIbj) alleles had a major and a minor role on high ratio of ∑DP ≤ 10 to ∑DP ≤ 24 fractions (RCL10/24), respectively. Both major alleles (Wxi and SSIIaj) reduced peak viscosity (PV), onset, peak and end gelatinization temperatures (GTs) of amylopectin, and increased amylose-lipid complex dissociation enthalpy compared with their counterpart-alleles, respectively. SBEIIai and SBEIIbj decreased PV, whereas SSIi and SBEIIbj decreased FV. SBEIi reduced setback viscosity and gelatinization enthalpy. RCL10/24 of chain length distribution in amylopectin is negatively correlated with PV and BD of paste property and GTs of thermal properties. We also report RILs with superior starch properties combining Wxi, SSIj, SSIIaj, SBEIi and SBEIIbj alleles. Additionally, a clear relation is drawn to starch biosynthetic gene alleles, starch structure, properties, and abundance of granule bound starch biosynthetic enzymes inside starch granules. CONCLUSIONS: Rice Wxi and SSIIaj alleles play major roles, while SSIi, SBEIi, SBEIIai and SBEIIbj alleles have minor roles in the determination of starch properties between indica and japonica rice through starch structural modification. The combination of these alleles is a key factor for starch quality improvement in rice breeding programs. RCL10/24 value is critical for starch structure and property determination.Jixun Luo was supported by CSC (Chinese Scholarship Council) and Australian National University scholarships. This work was funded by CSIRO Food Future National Research Flagship

Ongoing oroclinal bending in the Cascadia forearc and its relation to concave-outboard plate margin geometry

The concave-inboard (concave toward the overriding plate) geometry of most convergent margins is considered a natural consequence of the depression of the edge of a thin spherical cap, whereas concave-outboard margin segments commonly form around indenters on the subducting plate. At the Cascadia subduction zone, the apex of a > 500-km-long concave-outboard bend in the trench presently shows no obvious subduction of an indenter, but does coincide with the axis of an outboard-facing concavity in upper-plate rocks arched around the Olympic Peninsula in northwestern Washington State, USA. Here we synthesize paleomagnetic and structural data together with new analyses of Global Navigation Satellite System data to show that the upper plate at Cascadia has been folded from the Miocene to the present into an orocline with an axial trace that bisects the Olympic Peninsula. The processes that accommodate bending, which we suggest include (1) folding by flexural slip on the orocline limbs and (2) shortening, uplift, and escape within the core of the fold at the Olympic Mountains, have the combined result of relative motion of the forearc towards the arc at the core of the orocline, and sustained opposing rotations of the upper plate on the orocline limbs. We propose that oroclinal bending is promoted and maintained by along-strike variations in plate-boundary tractions resulting from the geometry of the plate interface at depth and suggest that these processes can contribute to the development of concave-outboard margins without the need for a subducting indenter

A high-throughput method for the detection of homoeologous gene deletions in hexaploid wheat

<p>Abstract</p> <p>Background</p> <p>Mutational inactivation of plant genes is an essential tool in gene function studies. Plants with inactivated or deleted genes may also be exploited for crop improvement if such mutations/deletions produce a desirable agronomical and/or quality phenotype. However, the use of mutational gene inactivation/deletion has been impeded in polyploid plant species by genetic redundancy, as polyploids contain multiple copies of the same genes (homoeologous genes) encoded by each of the ancestral genomes. Similar to many other crop plants, bread wheat (<it>Triticum aestivum </it>L.) is polyploid; specifically allohexaploid possessing three progenitor genomes designated as 'A', 'B', and 'D'. Recently modified TILLING protocols have been developed specifically for mutation detection in wheat. Whilst extremely powerful in detecting single nucleotide changes and small deletions, these methods are not suitable for detecting whole gene deletions. Therefore, high-throughput methods for screening of candidate homoeologous gene deletions are needed for application to wheat populations generated by the use of certain mutagenic agents (e.g. heavy ion irradiation) that frequently generate whole-gene deletions.</p> <p>Results</p> <p>To facilitate the screening for specific homoeologous gene deletions in hexaploid wheat, we have developed a TaqMan qPCR-based method that allows high-throughput detection of deletions in homoeologous copies of any gene of interest, provided that sufficient polymorphism (as little as a single nucleotide difference) amongst homoeologues exists for specific probe design. We used this method to identify deletions of individual <it>TaPFT1 </it>homoeologues, a wheat orthologue of the disease susceptibility and flowering regulatory gene <it>PFT1 </it>in Arabidopsis. This method was applied to wheat nullisomic-tetrasomic lines as well as other chromosomal deletion lines to locate the <it>TaPFT1 </it>gene to the long arm of chromosome 5. By screening of individual DNA samples from 4500 M2 mutant wheat lines generated by heavy ion irradiation, we detected multiple mutants with deletions of each <it>TaPFT1 </it>homoeologue, and confirmed these deletions using a CAPS method. We have subsequently designed, optimized, and applied this method for the screening of homoeologous deletions of three additional wheat genes putatively involved in plant disease resistance.</p> <p>Conclusions</p> <p>We have developed a method for automated, high-throughput screening to identify deletions of individual homoeologues of a wheat gene. This method is also potentially applicable to other polyploidy plants.</p

Optical-phonon resonances with saddle-point excitons in twisted-bilayer graphene

Twisted-bilayer graphene (tBLG) exhibits van Hove singularities in the density of states that can be tuned by changing the twisting angle $\theta$. A $\theta$-defined tBLG has been produced and characterized with optical reflectivity and resonance Raman scattering. The $\theta$-engineered optical response is shown to be consistent with persistent saddle-point excitons. Separate resonances with Stokes and anti-Stokes Raman scattering components can be achieved due to the sharpness of the two-dimensional saddle-point excitons, similar to what has been previously observed for one-dimensional carbon nanotubes. The excitation power dependence for the Stokes and anti-Stokes emissions indicate that the two processes are correlated and that they share the same phonon.Comment: 5 pages, 6 figure

A 15-year perspective of the fabry outcome survey

The Fabry Outcome Survey (FOS) is an international long-term observational registry sponsored by Shire for patients diagnosed with Fabry disease who are receiving or are candidates for therapy with agalsidase alfa (agala). Established in 2001, FOS provides long-term data on agala safety/efficacy and collects data on the natural history of Fabry disease, with the aim of improving clinical management. The FOS publications have helped establish prognostic and severity scores, defined the incidence of specific disease variants and implications for clinical management, described clinical manifestations in special populations, confirmed the high prevalence of cardiac morbidity, and demonstrated correlations between ocular changes and Fabry disease severity. These FOS data represent a rich resource with utility not only for description of natural history/therapeutic effects but also for exploratory hypothesis testing and generation of tools for diagnosis/management, with the potential to improve future patient outcomes

Simplified, Enhanced Protein Purification Using an Inducible, Autoprocessing Enzyme Tag

We introduce a new method for purifying recombinant proteins expressed in bacteria using a highly specific, inducible, self-cleaving protease tag. This tag is comprised of the Vibrio cholerae MARTX toxin cysteine protease domain (CPD), an autoprocessing enzyme that cleaves exclusively after a leucine residue within the target protein-CPD junction. Importantly, V. cholerae CPD is specifically activated by inositol hexakisphosphate (InsP6), a eukaryotic-specific small molecule that is absent from the bacterial cytosol. As a result, when His6-tagged CPD is fused to the C-terminus of target proteins and expressed in Escherichia coli, the full-length fusion protein can be purified from bacterial lysates using metal ion affinity chromatography. Subsequent addition of InsP6 to the immobilized fusion protein induces CPD-mediated cleavage at the target protein-CPD junction, releasing untagged target protein into the supernatant. This method condenses affinity chromatography and fusion tag cleavage into a single step, obviating the need for exogenous protease addition to remove the fusion tag(s) and increasing the efficiency of tag separation. Furthermore, in addition to being timesaving, versatile, and inexpensive, our results indicate that the CPD purification system can enhance the expression, integrity, and solubility of intractable proteins from diverse organisms

Grain size-dependent thermal conductivity of polycrystalline twisted bilayer graphene

We report the room temperature thermal conductivity of polycrystalline twisted bilayer graphene (tBLG) as a function of grain size measured by employing a noncontact optical technique based on micro-Raman spectroscopy. Polycrystalline tBLG sheets of different grain sizes were synthesized on copper by hot filament chemical vapor deposition. The thermal conductivity values are 1305±122, 971±73, and 657±42 Wm−1K−1 for polycrystalline tBLG with average grain sizes of 54, 21, and 8 nm, respectively. Based on these thermal conductivity values, we also estimated the grain boundary conductance, 14.43±1.21×1010Wm−2K−1, and the thermal conductivity for single crystal tBLG, 1510±103Wm−1K−1. Our results show that the relative degradation of thermal conductivity due to grain boundaries is smaller in bilayer than in monolayer graphene. Molecular dynamics simulations indicate that interlayer interactions play an important role in the heat conductivity of polycrystalline bilayer graphene. The quantitative study of the grain size dependent thermal conductivity of polycrystalline bilayer graphene is valuable in technological applications as well as for fundamental scientific understanding