16 research outputs found
Metabolic pathways expressed in different libraries.
<p>The classification of the contigs according to the NCBI NR and KEGG databases <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone.0088689-Kanehisa2" target="_blank">[46]</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone.0088689-Kanehisa1" target="_blank">[28]</a> indicates which metabolic pathway is active under a specific culture condition.</p
Molecular functions, biological process distribution and cellular localization of the transcriptome assembly.
<p>Contigs were assigned putative classifications based on homology and evaluated for their predicted involvement in molecular functions (A), biological processes (B) and cellular localization (C).</p
K-means clustering of differentially expressed genes identified as CAZymes (summarized in Table 3).
<p>K-means clustering of differentially expressed genes identified as CAZymes (summarized in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088689#pone-0088689-t003" target="_blank">Table 3</a>).</p
Expression profiles of selected glycosyl hydrolase genes determined by RT-qPCR.
<p>The squalene-epoxidase gene was used as endogenous control. The differences between groups were considered significant at P<0.05 (Student's t test) and are indicated by *.</p
Encoded genes related to cellulose and hemicellulose depolymerization.
<p>Genes classified in the transcriptome analysis of <i>T. harzianum</i> fermentation on sugarcane bagasse.</p
Contig sequences classified according to their putative hydrolytic activity.
<p>Contig sequences classified according to their putative hydrolytic activity.</p
Identified sequences that catalyze reactions that are potentially involved in biomass degradation.
<p>The results of identification based on homology using the NCBI NR database indicate the presence of genes that are related to the depolymerization of biomass in the transcriptome.</p
Filter paper activity enzymatic profiles (FPU mL<sup>−1</sup> h<sup>−1</sup>).
<p><i>T. harzianum</i> fermentation on a complex substrate (DSB) from extracts grown on preculture media using DSB (â–µ), cellulose (â—Š) or lactose (â–¡) as the carbon source. The differences were considered significant at P<0.05 (Student's t-test) and are indicated by (a) for cellulose, (b) for DSB and (c) for lactose samples.</p
The identified genes (summarized in Table 3) were resolved into three clusters.
<p>The identified genes were further classified into one of three response profiles based on where they were most highly expressed: (A) in the DSB library, (B) in the CEL library or (C) in the LAC library.</p
Results of next-generation sequencing, trimming analysis, <i>de novo</i> assembly and mapping.
<p>The raw reads were <i>de novo</i> assembled to generate contigs for further analysis and annotation.</p