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

Energy Efficient Ant Colony Algorithms for Data Aggregation in Wireless Sensor Networks

In this paper, a family of ant colony algorithms called DAACA for data aggregation has been presented which contains three phases: the initialization, packet transmission and operations on pheromones. After initialization, each node estimates the remaining energy and the amount of pheromones to compute the probabilities used for dynamically selecting the next hop. After certain rounds of transmissions, the pheromones adjustment is performed periodically, which combines the advantages of both global and local pheromones adjustment for evaporating or depositing pheromones. Four different pheromones adjustment strategies are designed to achieve the global optimal network lifetime, namely Basic-DAACA, ES-DAACA, MM-DAACA and ACS-DAACA. Compared with some other data aggregation algorithms, DAACA shows higher superiority on average degree of nodes, energy efficiency, prolonging the network lifetime, computation complexity and success ratio of one hop transmission. At last we analyze the characteristic of DAACA in the aspects of robustness, fault tolerance and scalability.Comment: To appear in Journal of Computer and System Science

Approximation and Generalization of DeepONets for Learning Operators Arising from a Class of Singularly Perturbed Problems

Singularly perturbed problems present inherent difficulty due to the presence of a thin boundary layer in its solution. To overcome this difficulty, we propose using deep operator networks (DeepONets), a method previously shown to be effective in approximating nonlinear operators between infinite-dimensional Banach spaces. In this paper, we demonstrate for the first time the application of DeepONets to one-dimensional singularly perturbed problems, achieving promising results that suggest their potential as a robust tool for solving this class of problems. We consider the convergence rate of the approximation error incurred by the operator networks in approximating the solution operator, and examine the generalization gap and empirical risk, all of which are shown to converge uniformly with respect to the perturbation parameter. By utilizing Shishkin mesh points as locations of the loss function, we conduct several numerical experiments that provide further support for the effectiveness of operator networks in capturing the singular boundary layer behavior

Mechanisms of leucyl-tRNA synthetase dependent group I intron splicing

Leucyl-tRNA synthetase (LeuRS) plays dual roles within the yeast mitochondria. In addition to protein synthesis, it is also essential to RNA splicing of critical respiratory genes. The LeuRS collaborates with a maturase to excise the bI4 and aI4α introns from the cob and cox1α genes respectively. The LeuRS-based suppressor mutations have been isolated within the amino acid editing CP1 domain and restore native RNA splicing activity in the presence of an inactive maturase. Mutational analysis of these sites and the regions that surround them demonstrated that certain substitutions can also inactivate LeuRS-dependent splicing activity under in vivo and in vitro conditions. Binding measurements suggest that these suppressor sites are important in maintaining interaction between LeuRS and the group I intron RNA. Thus, CP1 domain binds specifically to the bI4 and aI4α intron to promote RNA splicing. In addition to LeuRS from yeast mitochondria (ymLeuRS), diverse LeuRSs from varied origins such as M. tuberculosis and human mitochondria complement the ymLeuRS activities. Similarly, wild-type E. coli LeuRS (EcLeuRS) complemented a ymLeuRS null strain. Interestingly, at reduced levels of EcLeuRS expression in yeast mitochondria, the heterologous synthetase supported protein synthesis, but not intron splicing. Thus, it is a weak splicing suppressor. Surprisingly, a gain of splicing activity was exhibited by positive charge substitutions at the Ala293 position, suggesting that this Ala293 can be adapted for alternative activities. Preliminary footprinting data suggest that LeuRS binds to the P4-P6 core region of the bI4 intron that is cognate to LeuRS. The RNA duplex mimics of the P6 helix were designed and it was shown that LeuRS promotes their annealing in an ATP-independent manner. Domain analysis of LeuRS shows that the C-terminal domain is critical to the RNA annealing activity. Yeast mitochondrial tRNALeu (ymtRNALeu) competitively inhibit annealing. Also, an ymtRNALeu variable-stem-like region was identified on the P6 stem that is important for LeuRS-dependent annealing. These data support that the annealing and tRNA variable arm binding sites overlap on the C-terminal domain of LeuRS. It was shown that the overhang location and length of the duplexes are important features that LeuRS recognizes. It was hypothesized that LeuRS plays a key role in remodeling specific group I intron ribozymes so that they can productively self-splice