Recognizing Proteins with Binding Function in Elymus nutans Based on Machine Learning Methods.

BACKGROUND: We research the binding function proteins in Elymus nutans. Recognition for proteins is essential for study of biology. Machine learning methods have been widely used for the prediction of proteins. METHODS: We used BLAST software for the function annotations of Elymus nutans. Besides, we used machine learning methods to recognize proteins which are not annotated by the software. In the process, we focused on identifying the proteins with binding functions. In our research, features are extracted by four algorithms, and then selected by mutual information estimator. Here three classifiers are constructed based on K-nearest neighbour algorithm and gradient boosting algorithm. RESULTS AND CONCLUSION: Experimental results show that there are 848 proteins with ATP binding function, 113 proteins with heme binding function, 315 proteins with zinc-ion binding function, 135 proteins with GTP binding function and 21 proteins with ADP binding function. Furthermore, we have successfully predicted the functions of 10 special protein sequences whose function annotations cannot be obtained by making sequence alignment with seven famous protein databases. Among them, seven sequences have ATP binding functions, one sequence has heme binding function, one sequence has zinc-ion binding function and the other one has GTP binding function.

Flavonolignans from Elymus natans L. and Phytotoxic Activities.

Elymus natans, a perennial gramineous grass, plays an important role in animal husbandry and environmental sustenance in the Qinghai-Tibet plateau as a result of its high forage quality and good adaptability to the local environment. A bioassay showed that the extracts of green grasses of E. natans (GG) exhibited stronger phytotoxic activities than withered grasses (WG) against crops and grasses. In view of the secondary metabolites, which may be responsible for the resistance of the plant, the chemical components of GG were investigated. The flavone tricin, E1, and 10 flavonolignans, E2-E11, including three new flavonolignans, E2, E10, and E11, were isolated and identified. As far as we know, this is the first report on the chemical constitutions of the plant until now. The contents of compounds E1 and E4-E7 in GG were significantly higher than those in WG in high-performance liquid chromatography analysis, and they also showed observably phytotoxic activities against lettuce and Festuca arundinacea.

Dahurelmusin A, a Hybrid Peptide-Polyketide from Elymus dahuricus Infected by the Epichloë bromicola Endophyte.

One novel hybrid peptide-polyketide, dahurelmusin A (1), was isolated from Elymus dahuricus infected by the Epichloë bromicola endophyte. Comprehensive spectroscopic analysis revealed that 1 is the first example of hybrid peptide-polyketide possessing an unprecedented 5-hydroxy-2,2,4,6-tetramethyl-3-oxooctanoic acid moiety. The single-crystal X-ray diffraction analyses allowed the absolute configuration assignment of this compound. Compound 1 also exhibited significant insecticidal activities against Rhopalosiphum padi and Brevicoryne brassicae with LC50 values of 0.092 and 0.251 mM, respectively.

Isolation and analysis of vitamin B12 from plant samples.

Based on increased demands of strict vegetarians, an investigation of vitamin B12 content in plant sources, was carried out. The vitamin B12 concentration was determined by RP-HPLC with UV detection, after prior matrix isolation by immunoaffinity chromatography (IAC). Vitamin B12 was extracted in the presence of sodium cyanide, to transform all forms of cobalamin into cyanocobalamin. Diode array detector was used to monitor vitamin B12, after its chromatographic separation under gradient elution with a mobile phase consisting of acetonitrile and trifluoroacetic acid 0.025% (w/v). The method demonstrated excellent linearity with a limit of detection 0.004µg/ml. The method precision was evaluated for plant samples and it was below 0.7% (n=6). Significant amounts of vitamin B12 in plants were detected in Hippophae rhamnoides (37µg/100g dry weight), in Elymus (26µg/100g dry weight) and in Inula helenium (11µg/100g dry weight).

Nitric Oxide Mediates 5-Aminolevulinic Acid-Induced Antioxidant Defense in Leaves of Elymus nutans Griseb. Exposed to Chilling Stress.

Nitric oxide (NO) and 5-aminolevulinic acid (ALA) are both extremely important signalling molecules employed by plants to control many aspects of physiology. In the present study, the role of NO in ALA-induced antioxidant defense in leaves of two sources of Elymus nutans Griseb. (Damxung, DX and Zhengdao, ZD) was investigated. Chilling stress enhanced electrolyte leakage, accumulation of malondialdehyde (MDA), hydrogen peroxide (H2O2) and superoxide radical in two E. nutans, which were substantially alleviated by exogenous ALA and NO application. Pretreatment with NO scavenger PTIO or NOS inhibitor L-NNA alone and in combination with ALA induced enhancements in electrolyte leakage and the accumulation of MDA, H2O2 and superoxide radical in leaves of DX and ZD exposed to chilling stress, indicating that the inhibition of NO biosynthesis reduced the chilling resistance of E. nutans and the ALA-enhanced chilling resistance. Further analyses showed that ALA and NO enhanced antioxidant defense and activated plasma membrane (PM) H+-ATPase and decreased the accumulation of ROS induced by chilling stress. A pronounced increase in nitric oxide synthase (NOS) activity and NO release by exogenous ALA treatment was found in chilling-resistant DX plants exposed to chilling stress, while only a little increase was observed in chilling-sensitive ZD. Furthermore, inhibition of NO accumulation by PTIO or L-NNA blocked the protective effect of exogenous ALA, while both exogenous NO treatment and inhibition of endogenous NO accumulation did not induce ALA production. These results suggested that NO might be a downstream signal mediating ALA-induced chilling resistance in E. nutans.

[Effect of lactic acid bacteria isolated from Tibetan Plateau on silage fermentation quality of Elms nutans].

OBJECTIVE: In order to detect the effect of lactic acid bacteria isolated from Tibetan Plateau on silage fermentation quality of Elms nutans. METHODS: We used 3 isolated lactic acid bacteria with better growth at low temperatures of 10 and 15 degrees C at ensiling of Elymus nutans. Subsequently, effects of the selected lactic acid bacteria on fermentation profiles of Elymus nutans silages stored at 15 and 25 degrees C were evaluated by using the same species of commercial inoculants as the control. RESULTS: PP-6 isolated from Tibetan Plateau could ferment raffinose, lactose, sorbitol, melibiose and sucrose, and LS-5 could ferment cottonseed sugar, laetrile, rhamnose, lactose, sorbitol, xylose, arabinose, melibiose and sucrose, but the same species of commercial strains could not use these sugars. Inoculation of these three strains into Elymus nutans at 15 and 25 degrees C ensiled for 50 d, we found that LS-5 significantly reduced silage pH, propionic acid concentration and ratio of ammonia nitrogen/total nitrogen at 15 degrees C (P < 0.05), salvaged more water-soluble carbohydrate and crude protein; Application of LP-2 and PP-6 as a combined inoculant to Elymus nutans significantly improved lactic acid concentration (P < 0.05), resulting in a lower ratio of ammonia nitrogen/total nitrogen, saved more crude protein and significantly reduced neutral detergent fiber content (P < 0.05) as compared with the commercial strains. CONCLUSION: The three isolated strains can improve silage quality of Elymus nutans growing on the Qinghai-Tibetan Plateau at low temperature, but these strains have no obvious advantages at 25 degrees C in comparison with the commercial inoculants.