Transfer RNAs (tRNAs) are the most heavily modified RNA species in life entities. Post-transcriptional modifications severely impact the structure and function of tRNAs. To date, hundreds of modifications have been identified in tRNAs, mainly from microorganisms and animals. However, tRNAs in plant roots or tubers that have been widely used for food and medical purpose for centuries are rarely studied because isolation of RNA from plants still remains a challenge. In this paper, a polysaccharase-aided RNA isolation (PARI) method for extraction of high-quality RNA from plants containing large quantities of polysaccharides is developed. This method presents a new strategy of "digesting" polysaccharides that is completely different from the conventional method of "dissolving" the contaminants. By using this method, RNA of high integrity and purity were successfully extracted from ginseng roots because polysaccharide contaminations were removed efficiently with α-amylase digestion. Ginseng tRNAs were first sequenced by NGS and a total of 41 iso acceptors were identified. ChloroplastictRNAGly(GCC) in ginseng root was purified and four modified nucleosides, including m7G, D, T, and Ψ, were identified by LC-MS/MS. The results also revealed that the m7G occurs at a novel position 18, which may be related to the deformation of D-loop. PARI is the first enzyme-assisted technique for RNA isolation from plants, which could fundamentally solve the problem of polysaccharide contaminations. By using the PARI method, more individual tRNAs could be isolated easily from polysaccharide-rich plant tissues, which would have a positive impact on the feasibility of research on structure and function of tRNA in plants.

LC-MS/MS Profiling of Post-Transcriptional Modifications in Ginseng tRNA Purified by a Polysaccharase-Aided Extraction Method

Reactivities of human urinary prokallikrein and kallikrein toward rabbit antibodies with special reference to enzyme immunoassay

This study was attempted to focus on the pattern of codon usage bias (CUB) of chloroplast genes in two species of Pisum viz. P. fulvum and P. sativum and to identify the factors which influence CUB...

Mutation pressure and natural selection on codon usage in chloroplast genes of two species in Pisum L. (Fabaceae: Faboideae).

Panax ginseng is usually used as a famous plant medicine in many countries. In order to study the codon usage in whole chloroplast genome in Panax ginseng, whole chloroplast genome sequence is analyzed via codonW software and some results such as relationships between the codon adaptation index, frequency of optimal codons, codon bias index, effective number of codons, especially the relative synonymous codon usage are all discussed. Furthermore, PR2-bias plot, histogram GC content, Codon Bias Index are also analyzed for exploring the sequence characteristics of chloroplast genome in Panax ginseng. These results showed that codon usage bias in the chloroplast genome from Panax ginseng is weak, and the relative results could lay a foundation for other further study on the medicinal plant Panax ginseng.

/pdf/codon-usage-study-on-chloroplast-genome-in-medicinal-plant-49trabw3ka.pdf

Codon Usage Study on Chloroplast Genome in Medicinal Plant Panax Ginseng

ARC Journal of Urology Page |9 Abstract: Urinary prokallikrein in human participates in the regulation of water and electrolyte balance. In this paper, several characteristics of urinary prokallikrein are studied via some bioinformatics tools. First, the chemical and physical properties such as the molecular weight, the isoelectric point and the hydrophobicity, etc, of urinary prokallikrein are predicted via ProtParam tool. The results show that the molecular formula is C1168H1764N310O363S14, the instability index is 37.98, the theoretical pI is 4.57, et al. the secondary structure of urinary prokallikrein is predicted via the SOPMA tool, the result shows that there are 57(23.95%) Alpha helix, 60(25.21%) Beta sheet, 31(13.03%) Turn and 90(37.82%) Coil. Finally, phosphorylation sites and the protein-protein interaction of urinary prokallikrein are respectively studied by the netphos tool and the STRING system.

/pdf/bioinformatics-tools-stuty-on-the-sequence-and-structure-3ztxfo3dxf.pdf

Bioinformatics Tools Stuty on the Sequence and Structure Characteristics of Urinary Prokallikrein

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Codon Usage Study on Chloroplast Genome in Medicinal Plant Panax Ginseng

Bioinformatics Tools Stuty on the Sequence and Structure Characteristics of Urinary Prokallikrein