This paper presents a weighted support vector machine (WSVM) to improve the outlier sensitivity problem of standard support vector machine (SVM) for two-class data classification. The basic idea is to assign different weights to different data points such that the WSVM training algorithm learns the decision surface according to the relative importance of data points in the training data set. The weights used in WSVM are generated by a robust fuzzy clustering algorithm, kernel-based possibilistic c-means (KPCM) algorithm, whose partition generates relative high values for important data points but low values for outliers. Experimental results indicate that the proposed method reduces the effect of outliers and yields higher classification rate than standard SVM does when outliers exist in the training data set.
BackgroundTrametes trogii is a member of the white-rot fungi family, which has a unique ability to break down recalcitrant lignin polymers to CO2 and water, and they have enormous potential to biodegrade a wide range of toxic environmental pollutants. Because of its industrial potential, the identification of lignin-degrading enzyme systems in Trametes is an important area of research. Development and utilization of industrial value genes are suffering due to deficiency knowledge of genome available for their manipulation.ResultsIn the present study, Homokaryotic strains of T. trogii S0301 were screened and sequencing by PacBio Sequel II platform. The final draft genome is ~ 39.88 Mb, with a contig N50 size of 2.4 Mb, this was the first genome sequencing and assembly of T. trogii species. Further analyses predicted 14,508 protein-coding genes. Results showed that T. trogii S0301 contains 602 genes encoding CAZymes, include 211 glycoside hydrolase and 117 lignin-degrading family genes, nine laccases related genes. Small subunit ribosomal RNA gene (18S rRNA) sequencing confirms its phylogenetic position. Moreover, T. trogii S0301 has the largest number of cytochromes P450 (CYPs) superfamily genes compare to other fungi. All these results are consistent with enzymatic assays and transcriptome analysis results. We also analyzed other genome characteristics in the T. trogii S0301genome.ConclusionHere, we present a nearly complete genome for T. trogii S0301, which will help elucidate the biosynthetic pathways of the lignin-degrading enzyme, advancing the discovery, characterization, and modification of novel enzymes from this genus. This genome sequence will provide a valuable reference for the investigation of lignin degradation in the Trametes genus.
A thermo-activation and thermostable laccase isoenzyme (Lac 37 II) produced by Trametes trogii S0301 at 37 • C was purified to apparent homogeneity by anionic exchange chromatography and sephadex G-75 chromatography, with 12.3% of yeiled and a specific activity of 343.1 U mg −1 . The molecular weight of the purified Lac 37 II was estimated to be approximately 56 kDa in 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The optimal pH and temperature for the protein was 2.7 and 60 • C, respectively. The purified Lac 37 II showed higher resistance to all tested metal ions and organic solvents except for Fe 2+ and Cd 2+ at 37 • C and the activity of the purified Lac 37 was significantly enhanced by Cu 2+ at 50 mM. The K cat , K m , and K cat /K m of Lac 37 II were 2.977 s −1 , 16.1 µM, and 184.9 s −1 µM −1 , respecively, in the condition of pH 2.7 and 60 • C using ABTS as a substrate. Peptide-mass fingerprinting analysis showed that the Lac 37 II matched to the gene-deduced sequences of lcc3 in T. trogii BAFC 463, other than Lcc1, Lcc 2, and Lcc 4. Compared with laccase prepared at 28 • C, the onset of thermo-activation of Lac 37 II activity occurred at 30 • C with an increase of 10%, and reached its maximum at the temperatures range of 40-60 • C with an increase of about 40% of their original activity. Furthermore, Lac 37 II showed the efficient decolorization ability toward triphenylmethane dyes at 60 • C, with decolorization rates of 100 and 99.1% for 25 mg L −1 malachite and crystal violet in 5 h, respectively, when hydroxybenzotriazole (HBT) was used as a mediator. In conclusion, it is the first time to report a thermoactivation laccase from a thermophilic T. trogii strain, which has a better enzyme property and higher decolorization ability among fungal laccases, and it also has a further application prospective in the field of biotechnology.
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