Project description:The total RNA were extracted from pooled tissues of leaves and flowers from several plants of sacred lotus using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Then small RNAs ranging in 18–30 nucleotides were size fractionated electrophoretically, isolated from the gel, ligated with the 5′ and 3′ RNA adapters. The ligated product was reverse transcribed and subsequently amplified using 10–12 PCR cycles. The purified PCR product was sequenced using Illumina Genome Analyzer II. The qualified reads were used to predict phased small interfering RNAs from Chinese sacred lotus (Nelumbo nucifera Gaertn.).
Project description:Very little is known about the mechanism controlling petiole rigidity in sacred lotus (Nelumbo nucifera Gaertn.). To investigate the mechanism controlling the lotus petiole rigidity, morphological and proteomic analyses were performed. Anatomically, there is a great variation between the petioles of floating and vertical leaves. The number of vascular bundles, ligneous cells and thickness of cell wall were higher in the initial vertical leaf petiole (IVP) compared to the initial floating leaf petiole (IFP). A total of 4855 proteins were quantified through comparative proteomic analysis, among which 421 proteins expressed 1.5 folds higher in IFP and 483 proteins expressed 1.5 folds higher in IVP. Protein function categories indicated hundreds of proteins involved in cell wall organization and biosynthesis, and cell wall assembly. Functional enrichment analysis for the differentially abundant proteins indicated the enrichment of 105 proteins in 6 different pathways, while 43 out the total proteins were enriched in lignin biosynthesis pathway. In consistent with genes and proteins expressions in lignin biosynthesis, the contents of lignin monomers precursors were significantly different in IFP and IVP. These findings support the involvement of lignin in lotus petioles rigidity.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
