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BackgroundResearchers interested in analysing the expression patterns of functionally related genes usually hope to improve the accuracy of their results beyond the boundaries of currently available experimental data. Gene ontology (GO) data provides a novel way to measure the functional relationship between gene products. Many approaches have been reported for calculating the similarities between two GO terms, known as semantic similarities. However, biologists are more interested in the relationship between gene products than in the scores linking the GO terms. To highlight the relationships among genes, recent studies have focused on functional similarities.ResultsIn this study, we evaluated five functional similarity methods using both protein-protein interaction (PPI) and expression data of S. cerevisiae. The receiver operating characteristics (ROC) and correlation coefficient analysis of these methods showed that the maximum method outperformed the other methods. Statistical comparison of multiple- and single-term annotated proteins in biological process ontology indicated that genes with multiple GO terms may be more reliable for separating true positives from noise.ConclusionThis study demonstrated the reliability of current approaches that elevate the similarity of GO terms to the similarity of proteins. Suggestions for further improvements in functional similarity analysis are also provided.

A mutant chlorophyll‐reduced (Cr) seedling with yellow‐green cotyledons and leaves was obtained from the Brassica napus inbred line 3529 induced by fast neutron and diethyl sulphate (DES). Genetic analysis revealed that the Cr seedling marker trait was controlled by a pair of recessive genes. A randomized complete block design was used to evaluate its agronomic performance. Results from 2 years of tests indicated that the seed yield of Cr lines was significantly lower than that of normal green plants; however, when the Cr gene was in the heterozygous condition, no deleterious effects on yield characteristics and disease resistance were observed. The Cr seedling marker trait was introduced into male‐sterile lines, and Cr male‐sterile lines revealed the same superior combining ability as normal chlorophyll (Nc) lines. The Cr trait can therefore be used as a marker to produce hybrid seed.

Carbon dioxide (CO 2 ) injection into shale enables enhanced gas recovery (EGR) associated with geological CO 2 sequestration. Although primary research has been conducted on the CO 2 -based EGR technique in shale, the factors that influence the EGR efficiency remain unclear and need to be examined. This study presents a novel nuclear magnetic resonance (NMR)-based methodology to measure the EGR efficiency caused by CO 2 injection into shale samples with various properties. Accordingly, the effects of shale properties on the CO 2 -based EGR efficiency were revealed, and a calculation model for estimating the EGR efficiency was established. The results indicated that CO 2 injection enables significant production enhancement of shale gas, with the EGR efficiency averaging 23.54% and ranging from 16.22 to 34.34%, thus indicating that the EGR efficiency varies with the shale properties. The results also indicated that a higher CO 2 -based EGR efficiency, while adhering to a higher CO 2 -sequestration capacity, usually occurs in shales with a higher content of total organic carbon, higher methane-adsorption capacity, lower permeability, and lower clay mineral content. Moreover, an estimation model is developed to forecast the CO 2 -based EGR efficiency according to the shale properties. In general, these far-reaching results are of significance for predicting the benefit of CO 2 utilization in different shale reservoirs.

A trypsin inhibitor was isolated from Cassia obtusifolia by ammonium sulfate precipitation, Sepharose 4B-trypsin affinity and Sephadex G-75 chromatography. The inhibitor consisted of a single polypeptide chain with a molecular mass of 19, 812.55 Da. It was stable from pH 2 to 12 for 24 h, whereas it was unstable either above 70 degrees C for 10 min or under reduced conditions. The inhibitor, which inhibited trypsin activity with an apparent Ki of 0.3 microM, had one reactive site involving a lysine residue. The native inhibitor was resistant to pepsin digestion, whereas the heated inhibitor produced 40% degree of susceptibility. The disulfide linkage and lysine residue were important in maintaining its conformation. Partial amino acid sequence of the purified protein showed a high degree of homology with various members of the Kunitz inhibitor family. Moreover, the inhibitor showed significant inhibitory activity against trypsin-like proteases present in the larval midgut on Pieris rapae and could suppress the growth of larvae.

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Lung cancer is the main health threat in the world. Recently, oleuropein has been reported to have potent antioxidant and anticancer activities. However, the antitumor effects of oleuropein on H1299 cells are not well understood. Therefore, the purpose of this paper is tantamount to explore the effects of oleuropein on H1299 cells and its underlying mechanism that may be involved. Oleuropein treatment in H1299 cells resulted in cell cycle distribution at G2/M arrest and apoptosis in a dose‐dependent manner. Mitochondria‐mediated apoptosis was verified by the increase in Bax/Bcl‐2 ratio, release of cytochrome c, and activation of caspase‐3 on oleuropein‐induced H1299 cells. In addition, our data also demonstrated that the p38 mitogen‐activated protein kinase (MAPK) signaling pathway has a critical role in oleuropein‐induced apoptosis. Moreover, we used transcriptome analysis to identify differentially expressed genes (DEGs) in H1299 cells by oleuropein and SB203580 treatment. Many DEGs were annotated to metabolic pathways, cell cycle, pathways in cancer, MAPK signaling pathway by Kyoto Encyclopedia of Genes and Genomes and Gene ontology enrichment methods. Network and expression analysis found that DEGs, including RPS6A5, GADD45A, and MKP, play a key role in the p38 MAPK signaling pathway. In H1299 cells, oleuropein resulted in the expression of numerous genes related to cell signaling, metabolism pathway and directly associated with apoptosis. These results illustrated that oleuropein‐induced apoptosis via mitochondrial apoptotic cascade was activated by the p38 MAPK signaling pathway in H1299 cells. Thus, oleuropein as a natural compound and therapeutic drug has potential application value in the treatment of lung cancer.

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