The complete chloroplast genome of Tripterygium wilfordii Hook. f. (Celastraceae).

Tripterygium wilfordii is a perennial vine plant with medicinal value and belongs to the family of Celastraceae. In this study, we sequenced and analyzed the complete chloroplast genome of T. wilfordii. The chloroplast genome was 156,700 bp in length with a GC content of 37.47%. It contained two inverted repeat (IR) regions of 26,461 bp; each region was separated by large single-copy and small single-copy regions of 85,409 bp and 18,369 bp, respectively. In total, we annotated 134 unique genes, consisting of 89 protein-encoding genes, 8 rRNAs and 37 tRNAs. Phylogenetic analysis revealed that T. wilfordii was sister to T. regelii in a clade of Tripterygiumii species that was sister to a clade of Euonymus species.

Selection and validation of reference genes for quantitative real-time PCR normalization in Psoralea corylifolia (Babchi) under various abiotic stress.

Psoralea corylifolia L. is a popular herb and has long been used in traditional Ayurvedic and Chinese medicine owing to its extensive pharmacological activities, especially in the treatment of various shin diseases. To date, the systematic evaluation and selection of the optimum reference genes for gene expression analysis of P. corylifolia were not reported. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a method for gene expression quantification. Selecting appropriate reference genes is the prerequisite for accurate normalization of RT-qPCR results. This study assessed the expression stability of 10 candidate reference genes under different abiotic stresses. First, amplification primers for RT-qPCR were designed and received testing and optimization. Then, expression data from each candidate gene were evaluated based on three statistical algorithms, and their results were further integrated into a comprehensive ranking based on the geometric mean. Additionally, one target gene, i.e., 1-aminocyclopropane-1-carboxylate oxidase (ACO), was used to validate the effectiveness of the selected reference. Our analysis suggested that thioredoxin-like protein YLS8 (YLS8), TIP41-like family protein (TIP41), and cyclophilin 2 (CYP2) genes provided superior expression normalization under different abiotic stresses. Overall, this work constitutes the first effort to select optimal endogenous controls for RT-qPCR studies of gene expression in P. corylifolia. It also provides a reasonable normalization standard and basis for further analysis of the gene expression of bioactive components in P. corylifolia.

Evaluation of Angelica decursiva reference genes under various stimuli for RT-qPCR data normalization.

Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the RT-qPCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This RT-qPCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the RT-qPCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of RT-qPCR for an accurate and far-reaching gene expression analysis in this medicinal plant.

Selection of Suitable Reference Genes for qPCR Gene Expression Analysis of HepG2 and L02 in Four Different Liver Cell Injured Models.

Quantitative real-time PCR (qPCR) has become a widely used approach to analyze the expression level of selected genes. However, owing to variations in cell types and drug treatments, a suitable reference gene should be selected according to special experimental design. In this study, we investigated the expression level of ten candidate reference genes in hepatoma carcinoma cell (HepG2) and human hepatocyte cell line (L02) treated with ethanol (EtOH), hydrogen peroxide (H2O2), acetaminophen (APAP), and carbon tetrachloride (CCl4), respectively. To analyze raw cycle threshold values (Cp values) from qPCR run, three reference gene validation programs, including Bestkeeper, geNorm, and NormFinder, were used to evaluate the stability of ten candidate reference genes. The results showed that TATA-box binding protein (TBP) and tubulin beta 2a (TUBB2a) presented the highest stability for normalization under different treatments and were regarded as the most suitable reference genes of HepG2 and L02. In addition, this study not only identified the most stable reference genes of each treatment, but also suggested that ß-actin (ACTB), glyceraldehade-3-phosphate dehydrogenase (GAPDH), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ), and beta-2 microglobulin (B2M) were the least stable reference genes in HepG2 and L02. This work was the first report to systematically explore the stability of reference genes in injured models of HepG2 and L02.

Identification and Selection of Reference Genes for Quantitative Transcript Analysis in Corydalis yanhusuo.

Key word: qPCR; Corydalisyanhusuo; reference genes; geNorm; NormFinder; BestKeeper.

Validation of Reference Genes for Gene Expression Normalization in RAW264.7 Cells under Different Conditions.

RAW264.7 is a macrophage strain derived from mice tumour and shows a significant ability in antigen uptake. Real-time quantitative PCR (RT-qPCR) is one of the most commonly used methods in gene studies and requires suitable reference genes to normalize and quantitate the expression of gene of interest with sensitivity and specificity. However, suitable reference genes in RAW264.7 cells have not yet been identified for accurate gene expression quantification. In the current study, we evaluated expression levels of ten candidate reference genes in RAW264.7 cells under different conditions. RT-qPCR results indicated significant differences in the expression levels among the ten reference genes. Statistical analyses were carried out using geNorm, NormFinder, and BestKeeper software to further investigate the stability of the reference genes. Integrating the results from the three analytical methods, cytochrome c-1 and hydroxymethylbilane synthase were found to be the most stable and therefore more suitable reference genes, while ribosomal protein L4 and cyclophilin A were the least stable. This study emphasises the importance of identifying and selecting the most stable reference genes for normalization and provides a basis for future gene expression studies using RAW264.7 cells.

The complete chloroplast genome of Changium smyrnioides Wolff.

Changium smyrnioides Wolff, which could only be found in Eastern China, is a monotypic species of the genus Changium Wolff. In this study, the complete chloroplast genome sequence of C. smyrnioides was assembled and characterized by the 42.33 M high-throughput sequencing data. The chloroplast genome was 155,221 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 84,793 bp and 17,828 bp, respectively, which were separated by a pair of 26,300 bp inverted repeat (IR) regions. The genome is predicted to contain 131 genes, including 8 rRNA genes, 37 tRNA genes, and 86 protein-coding genes. The overall GC content of the genome is 37.7%. A phylogenetic tree reconstructed by 37 chloroplast genomes reveals that Chuanminshen violaceum is mostly related species to C. smyrnioides. The work reported here is the first complete chloroplast genome of C. smyrnioides which may provide useful information to the evolution of Changium genus.

The complete chloroplast genome of Saposhnikovia divaricata.

Saposhnikovia divaricata (Trucz.) Schischk. is a traditional Chinese herbal medicine widely distributed in Eastern Siberia and Northern Asia. In this research, we assembled and characterized the complete chloroplast genome sequence of S. divaricata from high-throughput sequencing data. The chloroplast genome was 147,834 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 93,202 bp and 17,324 bp, respectively, which were separated by a pair of 18,654 bp inverted repeat (IR) regions. The genome is expected to contain 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The total GC content of the genome is 37.5%. A phylogenetic tree reconstructed by 40 chloroplast genomes reveals that S. divaricata is mostly related to Ledebouriella seseloides.

Two hybrid transition metal triphosphonates decorated with a tripodal imidazole ligand: synthesis, structures and properties.

Two isostructural transition-metal (TM) triphosphonates decorated with neutral rigid N-containing ligands 1,3,5-tris(1-imidazolyl)benzene (tib), [Zn3(L1)(tib)]·8H2O (1) and [Co3(L1)(tib)]·9H2O (2) (H6L1 = N(CH2PO3H2)3), nitrilotris(methylenephosphonic acid), have been solvothermally prepared and structurally characterized by infrared spectroscopy, elemental analysis, thermogravimetric analysis and single-crystal/powder X-ray diffraction. The title compounds exhibit a pillar-layer structure with the TM-triphosphonates as layers and the rigid tib ligand as a pillar. The luminescence and magnetic properties have been investigated. Compound 1 exhibits intense blue luminescence, while compound 2 shows weak ferromagnetic behaviour.