OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology

Effects of Storage and Roasting Condition on the Antioxidant Activity of Soybeans with Different Colors of Seed Coat

The DPPH radical scavenging activity and ORAC value of soybeans (yellow soybean, blue soybean, and black soybean) were increased by roasting at above 190 °C. Concerning raw beans, black soybeans with the darkest seed coat color had the strongest antioxidant activity, indicating the effect of the coat pigment. However, the degree of increased antioxidant activity by roasting was almost similar regardless of seed coat color, suggesting that coat color is independent of the increased antioxidant activity. Concerning aged beans stored at 37 °C/75% RH for 60 days, the antioxidant activity increased in yellow soybean and decreased in blue and black soybean compared to before storage. Conversely, when roasted at 190 °C for 20 min, the DPPH values of all the aged beans were significantly increased. Other analyses of roasted beans with and without seed coat showed that changes in the components of cotyledons during storage may have contributed to the increased antioxidant activity of aged beans, regardless of seed coat color. These results revealed that roasting effectively improves the antioxidant activity of aged soybeans, regardless of seed coat color. We concluded that roasting is recommended for antioxidant properties, particularly regarding the effective use of aged beans

A STUDY OF SERUM ACID SPHINGOMYELINASE ACTIVITY AND CLINICAL SEVERITY IN INFANTS WITH RESPIRATORY SYNCYTIAL VIRUS BRONCHIOLITIS

Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of hospitalization in infants without any effective treatment strategies. Identification of biomarkers associated with disease severity may be significant in improving management. However, several studies have failed to identify specific biomarkers for bronchiolitis. Serum secretory acid sphingomyelinase (S-ASM) activity has been considered a biomarker of cytokine release, inflammation, and oxidative stress in various diseases. This study aimed to evaluate whether serum S-ASM activity increases and correlates with disease severity in infants with RSV bronchiolitis. Serum S-ASM activity was measured in 31 infants with RSV bronchiolitis, 9 infants with RSV-negative febrile infection, and 8 healthy infants. Laboratory data and clinical observational findings were analyzed for correlation with serum S-ASM activity. Serum S-ASM activity was significantly higher in the 31 infants with RSV bronchiolitis (9.5±5.4 nmol/mL/h) than individuals in the control groups (RSV-negative febrile infection patients : 4.3±1.9 mol/mL/h, p<0.005 ; healthy infants : 4.0±1.4 nmol/mL/h, p<0.005). Serum S-ASM activity was negatively correlated with interferon-γ levels (rho=−0.448, p=0.012) but not with any other outcomes. Serum S-ASM activity was significantly higher in infants with RSV bronchiolitis than in individuals in the control groups ; however, its clinical significance requires further investigation