Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.

BACKGROUND: Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging. MATERIALS AND METHODS: We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences. RESULTS: The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation. CONCLUSIONS: We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.

Circumscription of the East Asia clade (Apiaceae subfamily Apioideae) and the taxonomic placements of several problematic genera.

The East Asia (or Physospermopsis) clade was recognized in previous molecular phylogenetic investigations into the higher-level relationships of Apiaceae subfamily Apioideae. The composition of this clade, the phylogenetic relationships among its constituent taxa, and the placement of species previously determined to be problematic have yet to be resolved. Herein, nrDNA ITS sequences were obtained for 150 accessions of Apioideae, representing species whose distributions are in East Asia or genera having one or more species included within the East Asia clade. These data, along with published ITS sequences from other Apioideae (for 3678 accessions altogether), were subjected to maximum likelihood and Bayesian inference analyses. The results show that the East Asia clade contains representatives of 11 currently recognized genera: Hansenia, Hymenolaena, Keraymonia, Sinolimprichtia, Acronema, Hymenidium, Physospermopsis, Pimpinella, Sinocarum, Tongoloa, and Trachydium. However, the latter seven genera have members falling outside of the East Asia clade, including the generic types of all except Tongoloa. Within the clade, the species comprising these seven genera are widely intermingled, greatly increasing confusion among relationships than previously realized. The problematic species Physospermopsis cuneata is confirmed as falling within the East Asia clade, whereas P. rubrinervis allies with the generic type in tribe Pleurospermeae. Physospermopsis kingdon-wardii is confirmed as a member of the genus Physospermopsis, whereas the generic attributions of P. cuneata and Tongoloa stewardii remain unclear. Two species of Sinocarum (S. filicinum and S. wolffianum) are transferred into the genus Meeboldia. This is the most comprehensive molecular phylogenetic investigation of the East Asia clade to date, and while the results increase systematic understanding of the clade, they also highlight the need for further studies of one of the most taxonomically intractable groups in Apioideae.

Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species.

Sanghuangporus sanghuang is a medicinal macrofungus with antioxidant and antitumor activities, and it is enriched with secondary metabolites such as polysaccharides, terpenes, polyphenols, and styrylpyrone compounds. To explore the putative core genes and gene clusters involved in sanghuang biosynthesis, we sequenced and assembled a 40.5-Mb genome of S. sanghuang (SH1 strain). Using antiSMASH, local BLAST, and NCBI comparison, 12 terpene synthases (TPSs), 1 non-ribosomal peptide synthase, and five polyketide synthases (PKSs) were identified in SH1. Combining the transcriptome analysis with liquid chromatography mass spectrometry-ion trap-time of flight analysis, we determined that ShPKS1, one phenylalanine aminolyase (ShPAL), and one P450 monooxygenase (ShC4H1) were associated with hispidin biosynthesis. Structural domain comparison indicated that ShPKS2 and ShPKS3 are involved in the biosynthesis of orsellinic acid and 2-hydroxy-6-methylbenzoic acid, respectively. Furthermore, comparative genomic analysis of SH1 with 14 other fungi from the Hymenochaetaceae family showed variation in the number of TPSs among different genomes, with Coniferiporia weirii exhibiting only 9 TPSs and Inonotus obliquus having 20. The number of TPSs also differed among the genomes of three strains of S. sanghuang, namely Kangneng (16), MS2 (9), and SH1 (12). The type and number of PKSs also varied among species and even strains, ranging from two PKSs in Pyrrhoderma noxium to five PKSs in S. sanghuang SH1. Among the three strains of S. sanghuang, both the structural domains and the number of PKSs in strains MS2 and SH1 were consistent, whereas strain Kangneng exhibited only four PKSs and lacked the PKS with the structural domain KS-AT-DH-KR-ACP. Additionally, Sanghuangporus species exhibited more similar PKSs to Inonotus, with higher gene similarity around five PKSs, while showing differences from those of other fungi in the same family, including Phellinus lamaoensis. This result supports the independent taxonomic significance of the genus Sanghuangporus to some extent.

Comparative Study of the Structural Characteristics and Bioactivity of Polysaccharides Extracted from Aspidopterys obcordata Hemsl. Using Different Solvents.

The polysaccharides extracted from Aspidopterys obcordata are thought to have anti-urolithiasis activity in Drosophila kidney stones. This study aimed to assess the effects of different extraction solvents on the yield, chemical composition, and bioactivity of polysaccharides from A. obcordata. A. obcordata polysaccharides were extracted by using four solutions: hot water, HCl solution, NaOH solution, and 0.1 M NaCl. The results revealed that the extraction solvents significantly influenced the extraction yields, molecular weight distribution, monosaccharide compositions, preliminary structural characteristics, and microstructures of polysaccharides. The NaOH solution's extraction yield was significantly higher than the other extraction methods. Vitro antioxidant activity assays revealed that the NaOH solution extracted exhibited superior scavenging abilities towards DPPH and ABTS radicals and higher FRAP values than other polysaccharides. The vitro assays conducted for calcium oxalate crystallization demonstrated that four polysaccharides exhibited inhibitory effects on the nucleation and aggregation of calcium oxalate crystals, impeded calcium oxalate monohydrate growth, and induced calcium oxalate dihydrate formation. The NaOH solution extracted exhibited the most pronounced inhibition of calcium oxalate crystal nucleation, while the hot water extracted demonstrated the most significant suppression of calcium oxalate crystal aggregation. Therefore, it can be inferred that polysaccharides extracted with NaOH solution exhibited significant potential as a viable approach for extracting polysaccharides from stems due to their superior yield and the remarkable bioactivity of the resulting products.

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses.

BACKGROUND: Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. RESULTS: The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029-155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61-67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. CONCLUSIONS: The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

The complete chloroplast genome of Ligusticopsis acaulis (Shan et Sheh) Pimenov (Apiaceae), an endemic species from China.

Ligusticopsis acaulis, belonging to the family Apiaceae (Umbelliferae), is endemic to China. The complete chloroplast genome sequence of L. acaulis was assembled and annotated for the first time in this study. The results showed that the plastome was 148,509 bp in length and consisted of a pair of inverted repeat regions (IRs: 19,468 bp), a large single-copy region (LSC: 91,902 bp), and a small single-copy region (SSC: 17,671 bp). A total of 114 unique genes were annotated, including 80 protein-coding, 30 tRNA, and four rRNA genes. According to the phylogenetic analysis, L. acaulis belongs to the tribe Selineae, with a close relationship to Ligusticum hispidum (Franch.) Wolff.

Resurrection of Pleurospermumlecomteanum H.Wolff (Apiaceae) based on molecular and morphological evidence.

The taxonomic placement of Pleurospermumlecomteanum, previously synonymized with Pleurospermumwilsonii, was carefully examined using herbarium specimens and molecular evidence. The results showed that Pleurospermumlecomteanum is distinguished from P.wilsonii by several morphological characters. Its phylogenetic position is separate from P.wilsonii in the ML tree. Therefore, Pleurospermumlecomteanum should be restored as a distinct species.

Cyclorhizapuana (Apiaceae), a new species from Sichuan, China.

A new species, Cyclorhizapuana J. Zhou & Z.W. Liu (Apiaceae) from Sichuan Province of China, is described and illustrated here. Morphological comparisons with congeneric species revealed that it is distinguished by its slender habit, sparse annular scars, 4-pinnatisect leaf blade with ultimate segments linear (2-4×0.5-1 mm), subequal rays, oblong fruits with slightly thickened ribs, obconic stylopodium and slightly concave seed face. A molecular analysis based on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences indicated that C.puana is genetically distinct from the other two species of the genus. A distribution map, as well as an updated key, are provided for the species of Cyclorhiza.

MicroRNA-20a-3p regulates the host immune response to facilitate the mycobacterium tuberculosis infection by targeting IKKß/NF-κB pathway.

BACKGROUND: Mycobacterium tuberculosis (M.tb) has evolved to utilize different mechanisms to evade the host immune response. Several microRNAs (miRNAs) have been found to regulate innate immune response in M.tb replication and infection, but the roles and detailed molecular mechanisms of miRNAs in M.tb infection remain to be clarified. METHODS: Previously published dataset GSE94007 from GEO database was used for screening differential-expressed miRNAs, and a significant up-regulated miR-20a-3p was chosen for further investigation. Cells were transfected with miR-20a-3p mimics, inhibitors, IKKß siRNA, or their controls to verify the role of miR-20a-3p and IKKß in M.tb infection and host immune response. IL-ß, IL-6 and TNF-α contents in supernatant were measured by ELISA kits. The expression level of IKKß/NF-κB pathway were also detected by western blot. RESULTS: We found that miR-20a-3p was dose-and time-dependently increased during M.tb infection. Subsequently, our results demonstrated that upregulation of miR-20a-3p promoted intracellular growth of bacterial, and suppressed the release of proinflammatory cytokines in both M.tb-infected RAW264.7 and BMDM cells, while downregulation of miR-20a-3p had an opposite effect. Moreover, miR-20a-3p suppressed the activity of NF-κB pathway by directly targeting IKKß, resulting in the suppression of pro-inflammatory cytokines, attenuation of immune response and promotion of M.tb survival. CONCLUSION: Our findings uncover a role of miR-20a-3p and its target IKKß in regulating M.tb induced immune responses and provide a better understanding of pathogenesis of M.tb infection.

Suppression of miR-147b contributed to H37Rv-infected macrophage viability and migration in tuberculosis in vitro.

BACKGROUND: Tuberculosis (TB) is a severe infectious disease. It was reported that microRNAs played important roles in tuberculosis. However, the role of miR-147b in the disease remained unveiling. METHODS: Tuberculosis cell model was established using macrophage THP-1 cells infected with H37Rv strain. RT-qPCR was first for examination of miR-147b relative expression. Cell viabilities were then measured with MTT. Cell transfection was to interfere the relative expression of miR-147b or C11orf87 in infected cells. RT-qPCR was adopted to confirm the transfection efficiency. Luciferase assay verified the binding sites between miR-147b and C11orf87. Migration was examined by scratch and relative protein expression of EMT biomarkers and phosphorylation of Pi3K and AKT were assessed via Western blot. RESULT: MiR-147b expression was higher and cell viability decreased in H32Rv-THP-1 cells. Cell viability was shown higher after miR-147b downregulation. Luciferase assay confirmed the binding. RT-qPCR found C11orf87 expression was lower in the H32Rv-THP-1 cells. MTT suggested that cell viability fell with the decrease of C11orf87 in infectious cells. Moreover, when H32Rv-THP-1 cells were co-transfected with miR-147b inhibitor and si-C11orf87, cell viability, migration and EMT and activation of Pi3K/AKT pathway was partially reversed compared with mere downregulation of miR-147b. CONCLUSION: miR-147b might regulate macrophage proliferation and migration through targeting C11orf87 via Pi3K/AKT pathway in Tuberculosis in vitro, which calls for in-depth inter-cellular researches and animal researches to further support that miR-147b/C11orf87 axis might be a potential therapeutic target for the molecular treatment of Tuberculosis in the future.

Prognostic value of serum macrophage migration inhibitory factor levels in pulmonary tuberculosis.

BACKGROUND: Macrophage migration inhibitory factor (MIF) makes chemokine-like functions and plays critical roles in various inflammatory diseases. This study was designed to explore the significance of MIF serum levels in predicting the prognosis of pulmonary tuberculosis (PTB) following anti-TB treatment. METHODS: Patients diagnosed with culture-confirmed PTB without treatment were included and the serum was collected. Levels of MIF in serum were quantified with immunoassay, and the levels of established biomarkers were also determined, including C-reactive protein (CRP) and Interleukin 6 (IL-6). The outcome was estimated with all-cause mortality, with the mortality in 12 months as the primary outcome and the mortality in 3, 6, 9 months as other outcomes. The prognostic value of MIF and other factors in PTB were tested. RESULTS: Two hundred eighty-seven PTB patients were included. The median MIF levels in patients with advanced disease, disseminated and drug-resistant TB were significantly higher than that observed in mild -to- moderate disease, non-disseminated and drug-sensitive TB. MIF levels in patients with the outcome of death were higher than those survived [28.0 ng/ml (Inter-quartile range [IQR]: 24.2-33.1) vs. 22.3 ng/ml (IQR: 18.7-26.5); P < 0.001]. Multivariate model analysis was performed for comparing the highest quartiles to the lowest quartile of MIF levels. MIF levels were related to the mortality, with an elevated mortality risk of 236% [Odds ratio (OR) = 3.36; 95% Confidence interval (CI): 1.21-15.14; P = 0.012]. The model was re-analysis after combing MIF with currently established risk indicators. The obtained Area Under the Receiver Operating Characteristic Curve (±standard error) was elevated from 0.81 (±0.035) to 0.84 (±0.031), with a significant difference before and after adding the MIF (difference, 0.03[0.004]; P = 0.03). CONCLUSION: Serum level of MIF was a better biomarker than CRP or IL-6 for predicting death in HIV-negative PTB patients, and increased MIF serum levels were related to higher mortality.

Invasion inhibition by a MEK inhibitor correlates with the actin-based cytoskeleton in lung cancer A549 cells.

Metastasis remains the primary cause of lung cancer. The molecules involved in metastasis may be candidates for new targets in the therapy of lung cancer. The MEK/ERK signaling pathway has been highlighted in a number of studies on invasiveness and metastasis. In this paper, we show that the MEK inhibitor U0126 induces flattened morphology, remodels the actin-based cytoskeleton, and potently inhibits chemotaxis and Matrigel invasion in the human lung cancer A549 cell line. Furthermore, downregulation of ERK by small interfering RNA significantly inhibits the invasion of A549 cells and induces stress fiber formation. Taken together, our findings provide the first evidence that the inhibition of invasion of lung cancer A549 cells by inhibiting MEK/ERK signaling activity is associated with remodeling of the actin cytoskeleton, suggesting a novel link between MEK/ERK signaling-mediated cell invasion and the actin-based cytoskeleton.