Interaction of atomic systems with quantum vacuum beyond electric dipole approximation

The photonic environment can significantly influence emission properties and interactions among atomic systems. In such scenarios, frequently the electric dipole approximation is assumed that is justified as long as the spatial extent of the atomic system is negligible compared to the spatial variations of the field. While this holds true for many canonical systems, it ceases to be applicable for more contemporary nanophotonic structures. To go beyond the electric dipole approximation, we propose and develop in this article an analytical framework to describe the impact of the photonic environment on emission and interaction properties of atomic systems beyond the electric dipole approximation. Particularly, we retain explicitly magnetic dipolar and electric quadrupolar contributions to the light-matter interactions. We exploit a field quantization scheme based on electromagnetic Green’s tensors, suited for dispersive materials. We obtain expressions for spontaneous emission rate, Lamb shift, multipole-multipole shift and superradiance rate, all being modified with dispersive environment. The considered influence could be substantial for suitably tailored nanostructured photonic environments, as demonstrated exemplarily

Comparison of the dietary fibre composition of old and modern durum wheat (Triticum turgidum spp. durum) genotypes

It has been suggested that intensive breeding has led to decreased contents of health-promoting components in modern wheats. We therefore compared the contents and compositions of the major dietary fibre components, arabinoxylan and β-glucan, in semolina and wholemeal flour of old and modern Italian durum wheats. No differences in total arabinoxylan content were observed but the modern varieties had higher proportions of soluble arabinoxylan in wholemeals and of β-glucan in semolina. The study therefore provides no evidence that intensive breeding has had negative effects on the contents of dietary fibre components in durum wheat. However, comparison of material grown over two years indicated that the content and composition of arabinoxylan and β-glucan were more stable in the older than in the modern genotypes. The identification of modern cultivars with high viscosity associated with a high content of β-glucan suggests that they are good sources of fibre for human health

Loss of TaIRX9b gene function in wheat decreases chain length and amount of arabinoxylan in grain but increases cross-linking

Wheat contains abundant xylan in cell walls of all tissues, but in endosperm there is an unusual form of xylan substituted only by arabinose (arabinoxylan; AX) that has long chains and low levels of feruloylation, a fraction of which is extractable in water (WE-AX). WE-AX acts as soluble dietary fibre but also gives rise to viscous extracts from grain, a detrimental trait for some non-food uses of wheat. Here we show that a glycosyl transferase family 43 wheat gene abundantly expressed in endosperm complements the Arabidopsis irx9 mutant and so name the three homoeologous genes TaIRX9b. We generated wheat lines with a constitutive knock-out of TaIRX9b by stacking loss-of-function alleles for these homeologues from a mutagenized hexaploid wheat population resulting in decreases in grain extract viscosity of 50-80%. The amount and chain length of WE-AX molecules from grain of these triple stack lines was decreased accounting for the changes in extract viscosity. Imaging of immature wheat grain sections of triple stacks showed abolition of immunolabelling in endosperm with LM11 antibody that recognises epitopes in AX, but also showed apparently normal cell size and shape in all cell types, including endosperm. We identified differentially expressed genes from endosperm of triple stacks suggesting that compensatory changes occur to maintain this endosperm cell wall integrity. Consistent with this, we observed increased ferulate dimerisation and increased cross-linking of WE-AX molecules in triple stacks. These novel wheat lines lacking functional TaIRX9b therefore provide insight into control of wheat endosperm cell walls

RNAi suppression of xylan synthase genes in wheat starchy endosperm

The xylan backbone of arabinoxylan (AX), the major cell wall polysaccharide in the wheat starchy endosperm, is synthesised by xylan synthase which is a complex of three subunits encoded by the GT43_1, GT43_2 and GT47_2 genes. RNAi knock-down of either GT43_1 or all three genes (triple lines) resulted in decreased AX measured by digestion with endoxylanase (to 33 and 34.9% of the controls) and by monosaccharide analysis (to 45.9% and 47.4% of the controls) with greater effects on the amount of water-extractable AX (to 20.6 and 19.9% of the controls). Both sets of RNAi lines also had greater decreases in the amounts of substituted oligosaccharides released by digestion of AX with endoxylanase than in fragments derived only from the xylan backbone. Although the GT43_1 and triple lines had similar effects on AX they did differ in their contents of soluble sugars (increased in triple only) and on grain size (decreased in triple only). Both sets of transgenic lines had decreased grain hardness, indicating effects on cell wall mechanics. These results, and previously published studies of RNAi suppression of GT43_2 and GT47_2 and of a triple mutant of GT43_2, are consistent with the model of xylan synthase comprising three subunits one of which (GT47_2) is responsible for catalysis with the other two subunits being required for correct functioning but indicate that separate xylan synthase complexes may be responsible for the synthesis of populations of AX which differ in their structure and solubility

Data set of enzyme fingerprinting of dietary fibre components (arabinoxylan and β-glucan) in old and modern Italian durum wheat genotypes

The data presented are related to the research article entitled “Comparison of the dietary fibre composition of old and modern durum wheat (Triticum turgidum spp. durum) genotypes” (M.A. De Santis, O. Kosik, D. Passmore, Z. Flagella, P. Shewry, A. Lovegrove) [1]. This article provides details of the structures of the major dietary fibre components, arabinoxylan and β-glucan, in semolina and wholemeal flour of old and modern Italian durum wheat genotypes grown in two seasons, determined by enzyme digestion followed by high-performance anion-exchange chromatography (enzyme fingerprinting

Comparison of the dietary fibre composition of old and modern durum wheat (Triticum turgidum spp. durum) genotypes

It has been suggested that intensive breeding has led to decreased contents of health-promoting components in modern wheats. We therefore compared the contents and compositions of the major dietary fibre components, arabinoxylan and β-glucan, in semolina and wholemeal flour of old and modern Italian durum wheats. No differences in total arabinoxylan content were observed but the modern varieties had higher proportions of soluble arabinoxylan in wholemeals and of β-glucan in semolina. The study therefore provides no evidence that intensive breeding has had negative effects on the contents of dietary fibre components in durum wheat. However, comparison of material grown over two years indicated that the content and composition of arabinoxylan and β-glucan were more stable in the older than in the modern genotypes. The identification of modern cultivars with high viscosity associated with a high content of β-glucan suggests that they are good sources of fibre for human health

Improving Rice Dietary Fibre Content and Consumption for Human Health

Soft textured rice is the major source of calories in the diet of most South East (SE) Asian countries. However, it is most often consumed after polishing which removes the bran and embryo and hence most of the vitamins, minerals and dietary fibre (DF) are lost. Consequently, white rice comprises over 90% starch with only trace amounts of DF and is rapidly digested in the human gastrointestinal tract, resulting in a high glycaemic index (GI). The excessive consumption of high GI foods is associated with increased risks of a range of chronic diseases including type-2 diabetes, cardiovascular disease (CVD) and some types of cancer. Furthermore, the incidence of these conditions is dramatically increasing in areas where white rice is the staple food, notably Asia, with the prevalence of diabetes in SE Asia alone predicted to reach 120 million by 2030. It is therefore necessary to develop rice lines in which high energy content is combined with low GI. This may be achieved by combining acceptable levels of resistant starch (RS) with an increased content of the cell wall derived-dietary fibre components

Balancing the double‐edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms

Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome‐wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low‐to‐intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non‐starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water‐insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia

Wheat with greatly reduced accumulation of free asparagine in the grain, produced by CRISPR/Cas9 editing of asparagine synthetase gene TaASN2

Free asparagine is the precursor for acrylamide, which forms during the baking, toasting and high-temperature processing of foods made from wheat. In this study, CRISPR/Cas9 was used to knock out the asparagine synthetase gene, TaASN2, of wheat (Triticum aestivum) cv. Cadenza. A 4-gRNA polycistronic gene was introduced into wheat embryos by particle bombardment and plants were regenerated. T1 plants derived from 11 of 14 T0 plants were shown to carry edits. Most edits were deletions (up to 173 base pairs), but there were also some single base pair insertions and substitutions. Editing continued beyond the T1 generation. Free asparagine concentrations in the grain of plants carrying edits in all six TaASN2 alleles (both alleles in each genome) were substantially reduced compared with wildtype, with one plant showing a more than 90 % reduction in the T2 seeds. A plant containing edits only in the A genome alleles showed a smaller reduction in free asparagine concentration in the grain, but the concentration was still lower than in wildtype. Free asparagine concentration in the edited plants was also reduced as a proportion of the free amino acid pool. Free asparagine concentration in the T3 seeds remained substantially lower in the edited lines than wildtype, although it was higher than in the T2 seeds, possibly due to stress. In contrast, the concentrations of free glutamine, glutamate and aspartate were all higher in the edited lines than wildtype. Low asparagine seeds showed poor germination but this could be overcome by exogenous application of asparagine

A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activation of defence responses in Arabidopsis

Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. However, despite their prominence, their biological roles have remained largely elusive so far. In this study we report the characterization of an Arabidopsis mutant named crk10-A397T in which alanine 397 has been replaced by a threonine in the αC helix of the kinase domain of CRK10, known to be a crucial regulatory module in mammalian kinases. The crk10-A397T mutant is a dwarf that displays collapsed xylem vessels in the root and hypocotyl, whereas the vasculature of the inflorescence develops normally. In situ phosphorylation assays with His-tagged wild type and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of autophosphorylation, with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Transcriptomic analysis of wild type and crk10-A397T mutant hypocotyls revealed that biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant, and a root-infection assay with the vascular pathogen Fusarium oxysporum demonstrated that the mutant has enhanced resistance to this pathogen compared with wild type plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10, the first such mutant to have been identified for a CRK in Arabidopsis