Endosperm enrichment and physicochemical properties of superior and inferior grain starch in super hybrid rice

• A significant asynchronous phenomenon exists in super hybrid rice because of the differences in spike and spikelet positions, which affect the accumulation and properties of starch. However, little is known about the endosperm enrichment and physicochemical properties of starch in superior and inferior grains in super hybrid rice.
• Rice YY2640 was selected as study material to investigate the enrichment and physicochemical properties of starch in superior and inferior grains in super rice using semi‐thin sections, X‐ray diffraction and related technologies.
• Superior grain filling was a continuous process, whereas inferior grain only started 8–10 days after anthesis. The order of starch accumulation starts in the central endosperm, then in the endosperm of the proximal vascular bundle and finally in the aleurone layer. Compared with the inferior grains, the superior grains have a higher 1000‐grain weight, apparent amylose content, total starch content, average starch granule size, relative crystallinity, solubility and a resonance peak ratio at 1022/995 cm^?1, whereas the swelling power and ratio of the resonance peak at 1045/1022 cm^?1 were lower. The final degree of hydrolysis of HCl, AAG and PPA of the superior grains were significantly lower than those of the inferior grains.
• The findings indicate that the different physicochemical properties of starch were mainly related to the development order of superior and inferior grains and the spatial enrichment of starch.

     

Optimizing comparative genomic hybridization probes for genotyping and SNP detection in Plasmodium falciparum

Microarray-based comparative genomic hybridizations (CGH) interrogate genomic DNA to identify structural differences such as amplifications and deletions that are easily detected as large signal aberrations. Subtle signal deviations caused by single nucleotide polymorphisms (SNPs) can also be detected but is challenged by a high AT content (81%) in P. falciparum. We compared genome-wide CGH signal to sequence polymorphisms between parasite strains 3D7, HB3, and Dd2 using NimbleGen microarrays. From 23,191 SNPs (excluding var/rif/stevor genes), our CGH probe set detected SNPs with > 99.9% specificity but low (< 10%) sensitivity. Probe length, melting temperature, GC content, SNP location in the probe, mutation type, and hairpin structures affected SNP sensitivity. Previously unrecognized variable number tandem repeats (VNTRs) also were detected by this method. These findings will guide the redesign of a probe set to optimize an openly available CGH microarray platform for high-resolution genotyping suitable for population genomics studies.     

Bayesian covariance selection in generalized linear mixed models

The generalized linear mixed model (GLMM), which extends the generalized linear model (GLM) to incorporate random effects characterizing heterogeneity among subjects, is widely used in analyzing correlated and longitudinal data. Although there is often interest in identifying the subset of predictors that have random effects, random effects selection can be challenging, particularly when outcome distributions are nonnormal. This article proposes a fully Bayesian approach to the problem of simultaneous selection of fixed and random effects in GLMMs. Integrating out the random effects induces a covariance structure on the multivariate outcome data, and an important problem that we also consider is that of covariance selection. Our approach relies on variable selection-type mixture priors for the components in a special Cholesky decomposition of the random effects covariance. A stochastic search MCMC algorithm is developed, which relies on Gibbs sampling, with Taylor series expansions used to approximate intractable integrals. Simulated data examples are presented for different exponential family distributions, and the approach is applied to discrete survival data from a time-to-pregnancy study.     

Maximally selected chi-square statistics for ordinal variables

The association between a binary variable Y and a variable X having an at least ordinal measurement scale might be examined by selecting a cutpoint in the range of X and then performing an association test for the obtained 2 x 2 contingency table using the chi-square statistic. The distribution of the maximally selected chi-square statistic (i.e. the maximal chi-square statistic over all possible cutpoints) under the null-hypothesis of no association between X and Y is different from the known chi-square distribution. In the last decades, this topic has been extensively studied for continuous X variables, but not for non-continuous variables of at least ordinal measurement scale (which include e.g. classical ordinal or discretized continuous variables). In this paper, we suggest an exact method to determine the finite-sample distribution of maximally selected chi-square statistics in this context. This novel approach can be seen as a method to measure the association between a binary variable and variables having an at least ordinal scale of different types (ordinal, discretized continuous, etc). As an illustration, this method is applied to a new data set describing pregnancy and birth for 811 babies.     

Impact of variable domain glycosylation on antibody clearance: an LC/MS characterization

Variable (Fv) domain N-glycosylation sites are found in approximately 20% of human immunoglobulin Gs (IgGs) in addition to the conserved N-glycosylation sites in the C(H)2 domains. The carbohydrate structures of the Fv glycans and their impact on in vivo half-life are not well characterized. Oligosaccharide structures in a humanized anti-Abeta IgG1 monoclonal antibody (Mab) with an N-glycosylation site in the complementary determining region (CDR2) of the heavy chain variable region were elucidated by LC/MS analysis following sequential exoglycosidase treatments of the endoproteinase Lys-C digest. Results showed that the major N-linked oligosaccharide structures in the Fv region have three characteristics (core-fucosylated biantennary oligosaccharides with one or two N-glycolylneuraminic acid [NeuGc] residues, zero or one alpha-linked Gal residue, and zero or one beta-linked GalNAc residue), whereas N-linked oligosaccharides in the Fc region contained typical Fc glycans (core-fucosylated, biantennary oligosaccharides with zero to two Gal residues). To elucidate the contribution of Fv glycans to the half-life of the antibody, a method that allows capture of the Mab and determination of its glycan structures at various time points after administration to mice was developed. Anti-Abeta antibody in mouse serum was immunocaptured by immobilized goat anti-human immunoglobulin Fc(gamma) antibody resin, and the captured material was treated with papain to generate Fab and Fc for LC/MS analysis. Different glycans in the Fc region showed the same clearance rate as demonstrated previously. In contrast to many other non-antibody glycosylated therapeutics, there is no strong correlation between oligosaccharide structures in the Fv region and their clearance rates in vivo. Our data indicated that biantennary oligosaccharides lacking galactosylation had slightly faster clearance rates than other structures in the Fv domain.     

A structural study of the synergic envelopment of acetonitrile by a Cd(II) activated molecular receptor formed from cyclen with appended 2-hydroxy-3-phenylpropyl moieties

The newly synthesised metal ion activated molecular receptor [Cd{1,4,7,10-tetrakis((R)-(−)-2-hydroxy-3-phenylpropyl)-1,4,7,10-tetraazacyclododecane}](ClO₄)₂ (hereafter [CdL](ClO₄)₂) acts as a molecular receptor for acetonitrile. The receptor was characterised by X-ray crystallography in its metal free form, as its Cd(II) complex with no included molecule, as its Cd(II) complex with an included acetonitrile molecule and, for comparative purposes, as its Zn(II) complex with a partially included acetonitrile molecule. These structural studies demonstrated that the Cd(II) complex is eight-coordinate, with the potential to form a well defined hydrophobic cavity that can contain one acetonitrile molecule through four hydrogen-bonds, whereas the Zn(II) complex is six-coordinate, with a less rigidly constituted binding cavity, such that when solvated by acetonitrile the solvating molecule is retained by only a single hydrogen-bond.