An integrated genomic and metabolomic framework for cell wall biology in rice.

BACKGROUND: Plant cell walls are complex structures that full-fill many diverse functions during plant growth and development. It is therefore not surprising that thousands of gene products are involved in cell wall synthesis and maintenance. However, functional association for the majority of these gene products remains obscure. One useful approach to infer biological associations is via transcriptional coordination, or co-expression of genes. This approach has proved useful for several biological processes. Nevertheless, combining co-expression with other large-scale measurements may improve the biological inferences. RESULTS: In this study, we used a combined approach of co-expression and cell wall metabolomics to obtain new insight into cell wall synthesis in rice. We initially created a weighted gene co-expression network from publicly available datasets, and then established a comprehensive cell wall dataset by determining cell wall compositions from 29 tissues that almost cover the whole life cycle of rice. We subsequently combined the datasets through the conversion of co-expressed gene modules into eigen-vectors, representing expression profiles for the genes in the modules, and performed comparative analyses against the cell wall contents. Here, we made three major discoveries. First, we confirmed our approach by finding primary and secondary wall cellulose biosynthesis modules, respectively. Second, we found co-expressed modules that strongly correlated with re-organization of the secondary cell walls and with modifications and degradation of hemicellulosic structures. Third, we inferred that at least one module is likely to play a regulatory role in the production of G-rich lignification. CONCLUSIONS: Here, we integrated transcriptomic associations and cell wall metabolism and found that certain co-expressed gene modules are positively correlated with distinct cell wall characteristics. We propose that combining multiple data-types, such as coordinated transcription and cell wall analyses, may be a useful approach to glean new insight into biological processes. The combination of multiple datasets, as illustrated here, can further improve the functional inferences that typically are generated via a single type of datasets. In addition, our data extend the typical co-expression approach to allow deeper insight into cell wall biology in rice.

Effect of in vitro digestion on chestnut outer-skin and inner-skin bioaccessibility: The relationship between biotransformation and antioxidant activity of polyphenols by metabolomics.

Chestnut skin is rich in polyphenols that have been linked to health for their antioxidant activity. However, chestnut outer-skin extract (COE), chestnut inner-skin extract (CIE), and their digested products have different compositions of polyphenols, and therefore their antioxidant activities might differ as well. Here, we study the effect of in vitro digestion on their total phenol content, antioxidant capacity, and individual phenolic profile to clarify the relationship between biotransformation and antioxidant activity. Compared to undigested samples, total phenol content and antioxidant activity of digested chestnut outer-skin extract (DCOE) and digested chestnut inner-skin extract (DCIE) had significantly higher values. The changes of phenolic composition and antioxidant activity after digestion were mainly due to the anthocyanin biosynthesis involving glycosylation, acylation, methoxylation and their reverse processes. All these data suggest that as chestnut processing by-products, COE and CIE are raw material sources of antioxidant-rich active substances and need more sufficient utilization.

Preparation, antioxidant activity evaluation, and identification of antioxidant peptide from black soldier fly (Hermetia illucens L.) larvae.

Black soldier fly larvae protein (BLP) was hydrolyzed using alcalase, neutrase, trypsin, and papain. The BLP hydrolysates (BLPHs) were fractionated by ultrafiltration into three peptide fractions of molecular weight (<3 kDa, 3-10 kDa and >10 kDa). Their antioxidant activities in vitro and the amino acid composition were determined. Results showed that the alcalase was more efficient in hydrolyzing the BLP into oligopeptides. BLPHs-I presented the best scavenging activity to superoxide radicals, hydroxyl radicals, DPPH, and ABTS radicals. The best scavenging activities were found in BLPHs-I containing high levels of aromatic and hydrophobic amino acids. Seventeen novel sequences with typical features of well-known antioxidant proteins were identified by LC-MS/MS. Results demonstrated that BLPHs-I possesses a great capacity as antioxidant peptides applied in functional foods. PRACTICAL APPLICATIONS: Black soldier fly larvae protein (BLP) can also be hydrolyzed to produce antioxidant peptides and their sequences were identified. It can be used in pharmaceutical products and functional foods.

Arabinose substitution degree in xylan positively affects lignocellulose enzymatic digestibility after various NaOH/H2SO4 pretreatments in Miscanthus.

Xylans are the major hemicelluloses in grasses, but their effects on biomass saccharification remain unclear. In this study, we examined the 79 representative Miscanthus accessions that displayed a diverse cell wall composition and varied biomass digestibility. Correlation analysis showed that hemicelluloses level has a strong positive effect on lignocellulose enzymatic digestion after NaOH or H(2)SO(4) pretreatment. Characterization of the monosaccharide compositions in the KOH-extractable and non-KOH-extractable hemicelluloses indicated that arabinose substitution degree of xylan is the key factor that positively affects biomass saccharification. The xylose/arabinose ratio after individual enzyme digestion revealed that the arabinose in xylan is partially associated with cellulose in the amorphous regions, which negatively affects cellulose crystallinity for high biomass digestibility. The results provide insights into the mechanism of lignocellulose enzymatic digestion upon pretreatment, and also suggest a goal for the genetic modification of hemicelluloses towards the bioenergy crop breeding of Miscanthus and grasses.