Regulation of reserve carbohydrates in hull-less barley grain

(1,3;1,4)-β-Glucans, which have many health benefits, represent the major cell wall component in barley endosperm. There have been a number of studies that have altered the amount of (1,3;1,4)-β-glucan in the grain, however, the effects of modifying (1,3;1,4)-β-glucan on various carbohydrate metabolic pathways and its impact on grain development have not previously been clearly defined. Here, we used transgenic grain with increased (1,3;1,4)-β-glucan and a (1,3;1,4)-β-glucanless (bgl) mutant (OUM125) supplied by Professor K. Sato (Okayama University), to investigate the link between carbohydrate metabolism and grain development in hull-less barley. Hull-less barley was investigated as it is more suitable for food use due to absence of maternal (husk) tissues. High (1,3;1,4)-β-glucan barley grain (cv Torrens) was successfully generated by over-expressing HvCslF6, via agrobacterium-mediated transformation. Transgenic grain had up to 70% more (1,3;1,4)-β-glucan than the wild type. Examination of developing transgenic grain revealed a large fluid filled cavity in the endosperm, which resulted in shrunken grain at maturity. The endosperm transfer region of the developing grain was ruptured by 10 days after pollination (DAP), which became more pronounced through development. Quantitative real-time PCR (QPCR) analysis uncovered genes related to cell wall, starch, sucrose and fructan biosynthesis that were differentially expressed across grain development. Starch metabolic genes were downregulated in the early storage phase and the fructan biosynthetic gene, 6-SFT, was upregulated during the later storage phase. Increased amounts of sucrose and fructan were found in the cavity and endosperm tissue of the transgenic grain. The link between altered sugar homeostasis, the large endosperm cavity and the poorly formed endosperm transfer region in transgenic grain was explored by immuno-histochemical microscopy. Cell walls in the endosperm transfer region were poorly formed and variations occurred in the abundance of mannan polysaccharides. Additionally, the development of both the subaleurone and aleurone layers were altered with regards to cell number, shape and position. To further understand the relationship between cell wall, starch and fructan metabolism in barley, transcript profiles of genes related to their metabolism were examined in the (1,3;1,4)- β-glucanless OUM125 mutant. Inactive CSLF6 synthase activity in OUM125 resulted in upregulation of the CslH1 gene from 19 DAP, resulting in traces of BG1 antibody labelling in the mutant pericarp. Other cell wall-related genes including CslF3, CslF7, CslF10, CesA2, CesA3 and Gsl2 were upregulated from 15 DAP in the mutant grain. Deposition of arabinoxylan, callose and cellulose was altered in the absence of (1,3;1,4)-β-glucan in the mutant endosperm. QPCR analysis identified changes in the expression of starch and fructan biosynthetic genes during the storage phase. At grain maturity, sucrose and fructan contents had increased, while the amount of starch remained unchanged. Research findings from this project provide fundamental knowledge about carbon partitioning in grain across development and suggest that small changes in polysaccharide synthesis and deposition can have significant effects on other metabolic processes important for correct grain development. While decreasing the amount of (1,3;1,4)-β-glucan in the barley endosperm had a low impact on grain morphology and carbon partitioning, significantly increasing the (1,3;1,4)-β-glucan content had major deleterious effects on a number of key processes.Thesis (Ph.D.) (Research by Publication) -- University of Adelaide, School of Agriculture, Food and Wine, 201

Protein Palmitoylation Regulates Osteoblast Differentiation through BMP-Induced Osterix Expression

Osteoporosis is one of the most common diseases and can be treated by either anti-resorption drugs, anabolic drugs, or both. To search for anabolic drug targets for osteoporosis therapy, it is crucial to understand the biology of bone forming cells, osteoblasts, in terms of their proliferation, differentiation, and function. Here we found that protein palmitoylation participates in signaling pathways that control osterix expression and osteoblast differentiation. Mouse calvarial osteoblasts express most of the 24 palmitoyl transferases, with some being up-regulated during differentiation. Inhibition of protein palmitoylation, with a substrate-analog inhibitor, diminished osteoblast differentiation and mineralization, but not proliferation or survival. The decrease in differentiation capacity is associated with a reduction in osterix, but not Runx2 or Atf4. Inhibition of palmitoyl transferases had little effect in p53−/− osteoblasts that show accelerated differentiation due to overexpression of osterix, suggesting that osterix, at least partially, mediated the effect of inhibition of palmitoyl transferases on osteoblast differentiation. BMPs are the major driving force of osteoblast differentiation in the differentiation assays. We found that inhibition of palmitoyl transferases also compromised BMP2-induced osteoblast differentiation through down-regulating osterix induction. However, palmitoyl transferases inhibitor did not inhibit Smad1/5/8 activation. Instead, it compromised the activation of p38 MAPK, which are known positive regulators of osterix expression and differentiation. These results indicate that protein palmitoylation plays an important role in BMP-induced MAPK activation, osterix expression, and osteoblast differentiation

Interpreting Patterns of Gene Expression: Signatures of Coregulation, the Data Processing Inequality, and Triplet Motifs

Various methods of reconstructing transcriptional regulatory networks infer transcriptional regulatory interactions (TRIs) between strongly coexpressed gene pairs (as determined from microarray experiments measuring mRNA levels). Alternatively, however, the coexpression of two genes might imply that they are coregulated by one or more transcription factors (TFs), and do not necessarily share a direct regulatory interaction. We explore whether and under what circumstances gene pairs with a high degree of coexpression are more likely to indicate TRIs, coregulation or both. Here we use established TRIs in combination with microarray expression data from both Escherichia coli (a prokaryote) and Saccharomyces cerevisiae (a eukaryote) to assess the accuracy of predictions of coregulated gene pairs and TRIs from coexpressed gene pairs. We find that coexpressed gene pairs are more likely to indicate coregulation than TRIs for Saccharomyces cerevisiae, but the incidence of TRIs in highly coexpressed gene pairs is higher for Escherichia coli. The data processing inequality (DPI) has previously been applied for the inference of TRIs. We consider the case where a transcription factor gene is known to regulate two genes (one of which is a transcription factor gene) that are known not to regulate one another. According to the DPI, the non-interacting gene pairs should have the smallest mutual information among all pairs in the triplets. While this is sometimes the case for Escherichia coli, we find that it is almost always not the case for Saccharomyces cerevisiae. This brings into question the usefulness of the DPI sometimes employed to infer TRIs from expression data. Finally, we observe that when a TF gene is known to regulate two other genes, it is rarely the case that one regulatory interaction is positively correlated and the other interaction is negatively correlated. Typically both are either positively or negatively correlated

Magnetic field generation in finite beam plasma system

For finite systems boundaries can introduce remarkable novel features. A well known example is the Casimir effect [1, 2] that is observed in quantum electrodynamic systems. In classical systems too novel effects associated with finite boundaries have been observed, for example the surface plasmon mode [3] that appears when the plasma has a finite extension. In this work a novel instability associated with the finite transverse size of a beam owing through a plasma system has been shown to exist. This instability leads to distinct characteristic features of the associated magnetic field that gets generated. For example, in contrast to the well known unstable Weibel mode of a beam plasma system which generates magnetic field at the skin depth scale, this instability generates magnetic field at the scales length of the transverse beam dimension [4]. The existence of this new instability is demonstrated by analytical arguments and by simulations conducted with the help of a variety of Particle - In - Cell (PIC) codes (e.g. OSIRIS, EPOCH, PICPSI). Two fluid simulations have also been conducted which confirm the observations. Furthermore, laboratory experiments on laser plasma system also provides evidence of such an instability mechanism at work

Performance Limits of Stochastic Sub-Gradient Learning, Part II: Multi-Agent Case

The analysis in Part I revealed interesting properties for subgradient learning algorithms in the context of stochastic optimization when gradient noise is present. These algorithms are used when the risk functions are non-smooth and involve non-differentiable components. They have been long recognized as being slow converging methods. However, it was revealed in Part I that the rate of convergence becomes linear for stochastic optimization problems, with the error iterate converging at an exponential rate $\alpha^i$ to within an $O(\mu)-$neighborhood of the optimizer, for some $\alpha \in (0,1)$ and small step-size $\mu$. The conclusion was established under weaker assumptions than the prior literature and, moreover, several important problems (such as LASSO, SVM, and Total Variation) were shown to satisfy these weaker assumptions automatically (but not the previously used conditions from the literature). These results revealed that sub-gradient learning methods have more favorable behavior than originally thought when used to enable continuous adaptation and learning. The results of Part I were exclusive to single-agent adaptation. The purpose of the current Part II is to examine the implications of these discoveries when a collection of networked agents employs subgradient learning as their cooperative mechanism. The analysis will show that, despite the coupled dynamics that arises in a networked scenario, the agents are still able to attain linear convergence in the stochastic case; they are also able to reach agreement within $O(\mu)$ of the optimizer

Solar wind collisional heating

To properly describe heating in weakly collisional turbulent plasmas such as the solar wind, inter-particle collisions should be taken into account. Collisions can convert ordered energy into heat by means of irreversible relaxation towards the thermal equilibrium. Recently, Pezzi et al. (Phys. Rev. Lett., vol. 116, 2016, p. 145001) showed that the plasma collisionality is enhanced by the presence of fine structures in velocity space. Here, the analysis is extended by directly comparing the effects of the fully nonlinear Landau operator and a linearized Landau operator. By focusing on the relaxation towards the equilibrium of an out of equilibrium distribution function in a homogeneous force-free plasma, here it is pointed out that it is significant to retain nonlinearities in the collisional operator to quantify the importance of collisional effects. Although the presence of several characteristic times associated with the dissipation of different phase space structures is recovered in both the cases of the nonlinear and the linearized operators, the influence of these times is different in the two cases. In the linearized operator case, the recovered characteristic times are systematically larger than in the fully nonlinear operator case, this suggesting that fine velocity structures are dissipated slower if nonlinearities are neglected in the collisional operator

Locus model for space-time fabric and quantum indeterminacies

A simple locus model for the space-time fabric is presented and is compared with quantum foam and random walk models. The induced indeterminacies in momentum are calculated and it is shown that these space-time fabric indeterminacies are, in most cases, negligible compared with the quantum mechanical indeterminacies. This result restricts the possibilities of an experimental observation of the space-time fabric

Some Remarks about the Complexity of Epidemics Management

Recent outbreaks of Ebola, H1N1 and other infectious diseases have shown that the assumptions underlying the established theory of epidemics management are too idealistic. For an improvement of procedures and organizations involved in fighting epidemics, extended models of epidemics management are required. The necessary extensions consist in a representation of the management loop and the potential frictions influencing the loop. The effects of the non-deterministic frictions can be taken into account by including the measures of robustness and risk in the assessment of management options. Thus, besides of the increased structural complexity resulting from the model extensions, the computational complexity of the task of epidemics management - interpreted as an optimization problem - is increased as well. This is a serious obstacle for analyzing the model and may require an additional pre-processing enabling a simplification of the analysis process. The paper closes with an outlook discussing some forthcoming problems

Ferromagnetic and insulating behavior of LaCoO3 films grown on a (001) SrTiO3 substrate. A simple ionic picture explained ab initio

This paper shows that the oxygen vacancies observed experimentally in thin films of LaCoO3 subject to tensile strain are thermodynamically stable according to ab initio calculations. By using DFT calculations, we show that oxygen vacancies on the order of 6 % forming chains perpendicular to the (001) direction are more stable than the stoichiometric solution. These lead to magnetic Co2+ ions surrounding the vacancies that couple ferromagnetically. The remaining Co3+ cations in an octahedral environment are non magnetic. The gap leading to a ferromagnetic insulating phase occurs naturally and we provide a simple ionic picture to explain the resulting electronic structure.Comment: 7 pages, 7 figure

Wave-like Decoding of Tail-biting Spatially Coupled LDPC Codes Through Iterative Demapping

For finite coupling lengths, terminated spatially coupled low-density parity-check (SC-LDPC) codes show a non-negligible rate-loss. In this paper, we investigate if this rate loss can be mitigated by tail-biting SC-LDPC codes in conjunction with iterative demapping of higher order modulation formats. Therefore, we examine the BP threshold of different coupled and uncoupled ensembles. A comparison between the decoding thresholds approximated by EXIT charts and the density evolution results of the coupled and uncoupled ensemble is given. We investigate the effect and potential of different labelings for such a set-up using per-bit EXIT curves, and exemplify the method for a 16-QAM system, e.g., using set partitioning labelings. A hybrid mapping is proposed, where different sub-blocks use different labelings in order to further optimize the decoding thresholds of tail-biting codes, while the computational complexity overhead through iterative demapping remains small.Comment: presentat at the International Symposium on Turbo Codes & Iterative Information Processing (ISTC), Brest, Sept. 201