1.Universality Assessment of matK Primer Pairs in Seed Plants
Linchun SHI ; Jinxin LIU ; Hui YAO ; Xiaolan XU ; Tianyi XIN ; Caixiang XIE ; Jingyuan SONG
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):381-386
matK is one of the core DNA barcode markers for plant DNA barcode identification and its universality using single makers has been in controversy. However, the universalities of different matK primer pairs in same seed plant group (order) and same matK primer pairs in different seed plant groups (order) are lack of systematic research. In this study, we collected 14563 full-length matK sequences of 11429 species of 3292 genera in 239 families belonging to 36 orders in seed plants. The universalities of 13 matK primer pairs and its 78 primer com-binations have been assessed using bioinformatics methods. The results indicated that xf/5r, 1F/8R, 390F/1326R and 3F_KIM/1R_KIM were the four most universality primer pairs. The four markers' universalities were 91.18%, 84.65%, 79.81% and 80.94% respectively in all 11429 seed plants. The most universality primer pairs in different orders were different. For each order, the primer pair with maximum universality was different. the xf/5r was the basal primer pair for primer combination and 1F/8R, 1F/1R, M3/M4 and 3F_KIM/1R_KIM could be the complementary primer pairs. This study could be a valuable resource for the primer selection of the research DNA barcoding identification in seed plants.
2.Relationship between DNA Barcoding and Chemical Classification of Salvia Medicinal Herbs
Jianping HAN ; Chang LIU ; Minhui LI ; Linchun SHI ; Jingyuan SONG ; Hui YAO ; Xiaohui PANG ; Shilin CHEN
Chinese Herbal Medicines 2010;2(1):16-29,封3
Objective To make the identification of medicinal herbs in Salvia L. quickly and accurately. Methods In this work,DNA barcoding and chemical fingerprint were compared for the identification of herbs in Salvia L. First, the nucleotide sequences of the internal transcribed spacer region two amplified from 48 medicinal plants in Salvia L., and three other groups of medicinal plants in Lamiaceae were sequenced. A molecular phylogeny was constructed using the minimum evolution and maximum parsimony methods according to their sequence diversity. Second, the water-solution bioactive components and lipid soluble components were tested by HPLC. Then a chemical phylogeny was built using HPLC fingerprint data. Comparing the molecular and chemical phylogenetic trees revealed many similarities. Results DNA barcoding was sequencing based and could therefore provide more accurate results within a shorter time especially in large-scale studies. Conclusion The results show that ITS2 region is a novel DNA barcode for the authentication of the species in Salvia L. This is the first work to show the relationship between DNA barcoding and chemical components.
3.Identification of Cistanche species (Orobanchaceae) based on sequences of the plastid psbA-trnH intergenic region.
Jianping HAN ; Jingyuan SONG ; Chang LIU ; Jun CHEN ; Jun QIAN ; Yingjie ZHU ; Linchun SHI ; Hui YAO ; Shilin CHEN
Acta Pharmaceutica Sinica 2010;45(1):126-30
The dried succulent stems of Cistanche (Cistanche deserticola Y. C. Ma and Cistanche tubulosa Wight.) are one of the most widely used components of traditional Chinese medicines. However, it is often confused and substituted with the roots of Orobanche pycnostachya, Boschniakia rossica (Cham. & Schltdl.) Standl., Cistanche sinensis Beck, and Cistanche salsa (C. A. Mey.) Beck. In this study, we identified psbA-trnH regions from species and tested their suitable for the identification of the above mentioned taxa. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Cistanche species. Additionally, the average genetic distance of psbA-trnH ranging from 0.077% to 0.743%. In contrast, the intra-specific variation among Cistanche species was found to be significantly different from those of other species, with percentages of variation studied ranged from 0% to 0.007%. The sequence difference between the psbA-trnH sequences of Cistanche species and Orobanche pycnostachya ranged from 0.979% to 1.149%. The distance between the Cistanche species and Boschniakia rossica ranged from 1.066% to 1.224%. Our results suggest that the psbA-trnH intergenic spacer region represent a barcode that can be used to identify Cistanche species and other morphologically undistinguishable species.
4.Application of COI-based DNA Barcoding for Identifying Animal Medical Materials in the Chinese Pharmacopoeia
Hui ZHANG ; Hui YAO ; Lina CUI ; He DU ; Zhe LIN ; Xiaochen GAO ; Xue LANG ; Jingyuan SONG ; Kun LUO ; Linchun SHI ; Shilin CHEN
World Science and Technology-Modernization of Traditional Chinese Medicine 2013;(3):371-380
Medicinal animals are important part of Traditional Chinese medicine resources in China. Cytochrome c oxidase subunit I (COI) was selected as the standard DNA barcoding sequence for animal medical materials. In this study, the 51 animal species from 45 animal medical materials in the Chinese Pharmacopoeia were selected and the intra-specific variation and the inter-specific divergence, the barcoding gap, the identification efficiency of their COI sequences were analyzed. The results showed that the inter-specific divergence is higher than intra-specific distance. The barcoding gap existed between inter-specific sequence divergence and intra-specific dis-tance. The identification efficiencies were 100% both at the genus and species level except the Arthropoda. The cluster dendrogram exhibited that different species distinguished from others. Therefore, COI sequence as a bar-code is suitable to identify the species of animal medical materials in Chinese Pharmacopoeia.
5.DNA Extraction Method Optimization for Animal Medicines and Identification of Commercial Animal Medicines Using DNA Barcoding
Xuzhao LIU ; Jinxin LIU ; Wei SUN ; Jingyuan SONG ; Linchun SHI ; Zhiying SUN
World Science and Technology-Modernization of Traditional Chinese Medicine 2017;19(4):602-609
The DNA extraction method of animal medicine material is difficult and un-unified,which limits the application of molecular identification to identify animal medicines.In this study,based on the DNA extraction theory of SDS,we assessed the effects of three elements including different EDTA concentrations (0.025 mol·L-1,0.25 mol· L-1,and 0.5 mol· L-1) and whether containing NaCl and Triton X-100 in the lysis buffer on the quality of DNA extracted from different kinds of animal medicine.The optimized lysis buffer was used to extract DNA from 121 commercial animal medicines for original and species identification.The results showed that the lysis buffer of 1% SDS,0.03 mol· L-1 Tris-HCl,0.25 mol· L-1 EDTA and 0.2 mol· L-1 NaCl had the optimum effect on DNA extraction.This lysis buffer can obtain DNA from animal medicine which is difficult to extract,such as Cicadae periostracum.The DNA extractions of 121 commercial animal medicines by optimized lysis buffer can satisfy the experimental requirements for molecular identification.All samples of commercial animal medicines can be accurately identified to the level of species.It was concluded that optimized lysis buffer can be used in the DNA extraction of different kinds of animal medicines except shells,secretions and processed products.This method provides technique support for the molecular identification of animal medicines.
6.Effect of Buyang Huanwutang in Treating Diabetic Peripheral Neuropathy by Inhibiting Pyroptosis Through AMPK/ULK1 Mitophagy Pathway
Jingwen AN ; Linchun SONG ; Die CHEN ; Wang ZHANG ; Jiaxin TIAN ; Tianya ZHANG ; Ying BEN
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(15):1-10
ObjectiveTo observe the effect of Buyang Huanwutang in treating diabetic peripheral neuropathy (DPN) by inhibiting pyroptosis through AMP-activated protein kinase (AMPK)/UNC-51-like kinase 1 (ULK1) mitophagy pathway. MethodSixty male SPF SD rats (6-7 weeks old) were used in animal experiments and numbered according to their body mass. They were then randomly divided into four groups by computer: normal group, model group, α-lipoic acid group(60 mg·kg-1), and Buyang Huanwutang group(15 g·kg-1), with 15 rats in each group. The diabetic model was established by injection of streptozocin (STZ). After successful modeling, the α-lipoic acid group and the Buyang Huanwutang group were given corresponding drugs, and the normal group and the model group were given normal saline. Sensory nerve conduction velocity (SNCV) and paw withdrawal threshold (PWT) were measured at the end of administration for 12 weeks. Immunohistochemistry and Western blot were used to detect the expression of phosphorylated AMP activated protein kinase (p-AMPK), phosphorylated UNC-51-like kinase 1 (p-ULK1), protein involved in microtubule-associated protein 1 light chain 3 (LC3), selective autophagy receptors (p62/SQSTM1), Beclin1, NOD receptor protein structure domain-related proteins 3 (NLRP3), Caspase-1 (Caspase-1), and interleukin-1 beta (IL-1β) in dorsal root ganglia (DRG). Immunofluorescence was used to detect the expression of the N-terminal gasdermin D (N-GSDMD). ResultCompared with those in the normal group, rats in the model group had increased fasting blood glucose (P<0.01) and significantly reduced SNCV, PWT (P<0.01), LC3Ⅱ/LC3Ⅰ, Beclin1, p-AMPK/AMPK, and p-ULK1/ULK1 (P<0.01). In addition, p62, NLRP3, N-GSDMD/GSDMD, IL-1β, and cleaved Caspase-1/Caspase-1 were significantly increased (P<0.01). Compared with those in the model group, SNCV and PWT were increased (P<0.01) in each administration group, and LC3Ⅱ/LC3Ⅰ, Beclin1, p-AMPK/AMPK, and p-ULK1/ULK1 were significantly increased (P<0.05, P<0.01). p62, N-GSDMD/GSDMD, cleaved Caspase-1/Caspase-1, NLRP3, and IL-1β decreased (P<0.05, P<0.01). Compared with the α-lipoic acid group, the Buyang Huanwutang group had significantly increased SNCV, PWT (P<0.05), LC3Ⅱ/LC3Ⅰ, and p-ULK1/ULK1 (P<0.05) and significantly decreased NLRP3 and N-GSDMD/GSDMD (P<0.05). ConclusionBuyang Huanwutang regulates mitophagy and inhibits pyroptosis through the AMPK/ULK1 pathway to prevent and treat DPN, and its therapeutic effect may be better than α-lipoic acid.
7.Buyang Huanwutang Treats Diabetic Peripheral Neuropathy via Mitochondrial Transport in Rats
Jiaxin TIAN ; Jingwen AN ; Tianya ZHANG ; Zhihong ZHANG ; Wang ZHANG ; Linchun SONG ; Tianmeng DUAN ; Ying BEN
Chinese Journal of Experimental Traditional Medical Formulae 2023;29(13):27-36
ObjectiveTo investigate the mechanism of Buyang Huanwutang in treating diabetic peripheral neuropathy (DPN) via mitochondrial transport. MethodDiabetes in SD rats was induced by a high-carbohydrate/high-fat diet and intraperitoneal injection of streptozotocin (STZ). The 45 diabetic rats were randomly assigned into a DPN group, an alpha-lipoic acid (60 mg·kg-1·d-1) group, and a Buyang Huanwutang (15 g·kg-1·d-1) group, with 15 rats in each group. Fifteen normal SD rats were fed with the standard diet and set as the control group. The rats were administrated with corresponding drugs by gavage for 12 weeks. The paw withdraw threshold (PWT) and motor nerve conduction velocity (MNCV) were measured at the end of medication, and the sciatic nerve and the bilateral dorsal root ganglia of L4-5 were collected. The injury model of NSC34 cells was established by treating with 50 mmol·L-1 glucose and 250 μmol·L-1 sodium palmitate. The NSC34 cells were then randomly assigned into a blank (10% blank serum) group, a DPN (10% blank serum) group, an apha-lipoic acid (10% apha-lipoic acid-containing serum) group, a Buyang Huanwutang (10% Buyang Huanwutang-containing serum) group, and a Buyang Huanwutang + Compound C (CC) (10% Buyang Huanwutang-containing serum + 10 μmol·L-1 CC) group. The cell intervention lasted for 24 h. The immunofluorescence method, immunohistochemistry, and Western blot were employed to determine the expression levels of phosphorylated adenosine monophosphate-activated protein kinase (p-AMPK), phosphorylated cAMP-response element binding protein (p-CREB), kinesin family member 5A (KIF5A), and dynein cytoplasmic 1 intermediate chain 2 (DYNC1I2). ResultCompared with the control group, the DPN group of rats showed increased fasting blood glucose (P<0.01), decreased MNCV and PWT (P<0.01), down-regulated expression of KIF5A, p-AMPK/AMPK, and p-CREB/CREB (P<0.01), and up-regulated expression of DYNC1I2 (P<0.01). Compared with the DPN group, drug intervention groups showed increased MNCV and PWT (P<0.01), up-regulated expression of KIF5A, p-AMPK/AMPK, and p-CREB/CREB (P<0.05, P<0.01), and down-regulated expression of DYNC1I2 (P<0.05, P<0.01). The Buyang Huanwutang group had higher levels of MNCV and KIF5A (P<0.05) and lower level of DYNC1I2 (P<0.01) than the apha-lipoic acid group. Compared with the blank group, the DPN group of NSC34 cells showed decreased levels of KIF5A, p-AMPK/AMPK, and p-CREB/CREB (P<0.01) and increased level of DYNC1I2 (P<0.01). The apha-lipoic acid group and Buyang Huanwutang group had higher levels of KIF5A, p-AMPK/AMPK, and p-CREB/CREB (P<0.05, P<0.01) and lower level of DYNC1I2 (P<0.01) in NSC34 cells than the DPN group. Buyang Huanwutang group had higher KIF5A level (P<0.05) in NSC34 cells than the apha-lipoic acid group. Moreover, the Buyang Huanwutang + CC group had lower levels of KIF5A, DYNC1I2, p-AMPK/AMPK, and p-CREB/CREB (P<0.01) in NSC34 cells than the Buyang Huanwutang group. ConclusionBuyang Huanwutang may regulate mitochondrial anterograde transport via the AMPK/CREB pathway to prevent and treat DPN.