Multiple model species selection for transcriptomics analysis of non-model organisms.

BACKGROUND: Transcriptomic sequencing (RNA-seq) related applications allow for rapid explorations due to their high-throughput and relatively fast experimental capabilities, providing unprecedented progress in gene functional annotation, gene regulation analysis, and environmental factor verification. However, with increasing amounts of sequenced reads and reference model species, the selection of appropriate reference species for gene annotation has become a new challenge. METHODS: We proposed a novel approach for finding the most effective reference model species through taxonomic associations and ultra-conserved orthologous (UCO) gene comparisons among species. An online system for multiple species selection (MSS) for RNA-seq differential expression analysis was developed, and comprehensive genomic annotations from 291 reference model eukaryotic species were retrieved from the RefSeq, KEGG, and UniProt databases. RESULTS: Using the proposed MSS pipeline, gene ontology and biological pathway enrichment analysis can be efficiently achieved, especially in the case of transcriptomic analysis of non-model organisms. The results showed that the proposed method solved problems related to limitations in annotation information and provided a roughly twenty-fold reduction in computational time, resulting in more accurate results than those of traditional approaches of using a single model reference species or the large non-redundant reference database. CONCLUSIONS: Selection of appropriate reference model species helps to reduce missing annotation information, allowing for more comprehensive results than those obtained with a single model reference species. In addition, adequate model species selection reduces the computational time significantly while retaining the same order of accuracy. The proposed system indeed provides superior performance by selecting appropriate multiple species for transcriptomic analysis compared to traditional approaches.

Effects of Substituting Polyisoprenyl Carbanions for Ethoxyl Groups of Bis-[3-(triethoxysilyl)propyl] Tetrasulfide on the Properties of Carbon Black and Silica-Reinforced NR/SSBR.

The coupling agent TESPT (bis-[3-(triethoxysilyl)propyl] tetrasulfide) was modified by substituting polyisoprenyl (PI) carbanions for the ethoxyl groups on silicon for increasing the interaction of rubber with its fillers. The modification was carried out by the reaction of TESPT with polyisoprenyllithium, which had been previously prepared by anionic polymerization of isoprene using butyllithium. The success of the substitution was confirmed by Fourier-transform infrared spectroscopy, and the molecular weight of the modified TESPT (PI-TESPT) was determined from gel permeation chromatography measurements. The effects of tethered PI, as well as of its chain length, on the mechanical and dynamic properties of rubber compounds were examined using a universal testing machine and dynamic mechanical analysis (DMA). In rubber sample preparation, the amount of PI3-TESPT (PI of 2900 g/mol) used in rubber compounding is equal to that of the reference sample with TESPT (S TESPT). For S PI-TESPT samples, the amounts of PI6-TESPT (PI of 5500 g/mol) and PI14-TESPT (PI of 13,700 g/mol) used were calculated as molar ethoxyl groups which are nearly equivalent to those of PI3-TESPT. At the same wt % (parts per hundred, phr) of elemental sulfur in rubber compounds, despite the order of cross-linking density being S TESPT (sample prepared with TESPT) > S PI3-TESPT > S PI6-TESPT > S PI14-TESPT, the exhibited tensile strength is of the order of S PI3-TESPT > S PI6-TESPT > S TESPT ≈ S PI14-TESPT. The better mechanical properties of S PI3-TESPT, as opposed to those of S TESPT, could be attributed to the extra reinforcement from the PI-rubber chain linkage and better silica dispersion, as suggested by the mixing torque and Payne effect (ΔG') measurements. While the dynamic properties of S PI3-TESPT are inferior to those of S TESPT, these properties can be improved by adding more elemental sulfur to increase the cross-linking density.