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Zhu X, Yao Q, Yang P, Zhao D, Yang R, Bai H, Ning K. Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine. Front Pharmacol 2022; 13:1031051. [PMID: 36506559 PMCID: PMC9732109 DOI: 10.3389/fphar.2022.1031051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM. In this review, we concentrated on multi-omics approaches in principles and applications to gain a better understanding of TCM formulas against various diseases from several aspects. We first summarized frequently used TCM quality assessment methods, and suggested that incorporating both chemical and biological ingredients analytical methods could lead to a more comprehensive assessment of TCM. Secondly, we emphasized the significance of multi-omics approaches in deciphering the therapeutic mechanism of TCM formulas. Thirdly, we focused on TCM network analysis, which plays a vital role in TCM-diseases interaction, and serves for new drug discovery. Finally, as an essential source for storing multi-omics data, we evaluated and compared several TCM databases in terms of completeness and reliability. In summary, multi-omics approaches have infiltrated many aspects of TCM research. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired or will be gained in the future.
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Affiliation(s)
- Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Yao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ronghua Yang
- Dovetree Synbio Company Limited, Shenyang, China
| | - Hong Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Xavier JKAM, Baia TGC, Alegria OVC, Figueiredo PLB, Carneiro AR, Moreira ECDO, Maia JGS, Setzer WN, da Silva JKR. Essential Oil Chemotypes and Genetic Variability of Cinnamomum verum Leaf Samples Commercialized and Cultivated in the Amazon. Molecules 2022; 27:7337. [PMID: 36364159 PMCID: PMC9655072 DOI: 10.3390/molecules27217337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 12/01/2023] Open
Abstract
Cinnamomum verum (Lauraceae), also known as "true cinnamon" or "Ceylon cinnamon" has been widely used in traditional folk medicine and cuisine for a long time. The systematics of C. verum presents some difficulties due to genetic variation and morphological similarity between other Cinnamomum species. The present work aimed to find chemical and molecular markers of C. verum samples from the Amazon region of Brazil. The leaf EOs and the genetic material (DNA) were extracted from samples cultivated and commercial samples. The chemical composition of the essential oils from samples of C. verum cultivated (Cve1-Cve5) and commercial (Cve6-c-Cv9-c) was grouped by multivariate statistical analysis of Principal Component Analysis (PCA). The major compounds were rich in benzenoids and phenylpropanoids, such as eugenol (0.7-91.0%), benzyl benzoate (0.28-76.51%), (E)-cinnamyl acetate (0.36-32.1%), and (E)-cinnamaldehyde (1.0-19.73%). DNA barcodes were developed for phylogenetic analysis using the chloroplastic regions of the matK and rbcL genes, and psbA-trnH intergenic spacer. The psbA-trnH sequences provided greater diversity of nucleotides, and matK confirmed the identity of C. verum. The combination of DNA barcode and volatile profile was found to be an important tool for the discrimination of C. verum varieties and to examine the authenticity of industrial sources.
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Affiliation(s)
| | - Talissa Gabriele C. Baia
- Programa Institucional de Bolsas de Iniciação Científica, Universidade Federal do Pará, Belém 66075-900, Brazil
| | - Oscar Victor C. Alegria
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém 66075-900, Brazil
| | - Pablo Luis B. Figueiredo
- Departamento de Ciências Naturais, Centro de Ciências Sociais e Educação, Universidade do Estado do Pará, Belém 66050-540, Brazil
| | - Adriana R. Carneiro
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém 66075-900, Brazil
| | - Edith Cibelle de O. Moreira
- Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá 68501-970, Brazil
| | - José Guilherme S. Maia
- Programa de Pós-Graduação em Química, Universidade Federal do Pará, Belém 66075-900, Brazil
- Programa de Pós-Graduação em Química, Universidade Federal do Maranhão, São Luís 65080-805, Brazil
| | - William N. Setzer
- Aromatic Plant Research Center, 230 N 1200 E, Suite 100, Lehi, UT 84043, USA
| | - Joyce Kelly R. da Silva
- Programa de Pós-Graduação em Química, Universidade Federal do Pará, Belém 66075-900, Brazil
- Aromatic Plant Research Center, 230 N 1200 E, Suite 100, Lehi, UT 84043, USA
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Yao R, Guo R, Liu Y, Kou Z, Shi B. Identification and phylogenetic analysis of the genus Syringa based on chloroplast genomic DNA barcoding. PLoS One 2022; 17:e0271633. [PMID: 35853031 PMCID: PMC9295972 DOI: 10.1371/journal.pone.0271633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is a supplementary tool in plant systematics that is extensively used to resolve species-level controversies. This study assesses the significance of using two DNA barcoding loci (e.g., psbA-trnH and trnC-petN) in distinguishing 33 plant samples of the genus Syringa. Results showed that the average genetic distance K2P of psbA-trnH DNA marker was 0.0521, which is much higher than that of trnC-petN, which is 0.0171. A neighbor-joining phylogenetic tree based on psbA-trnH and trnC-petN indicated that the identification rate of psbA-trnH and trnC-petN alone were 75% and 62.5%, respectively. The barcode combination of psbA-trnH+trnC-petN could identify 33 samples of the genus Syringa accurately and effectively with an identification rate of 87.5%. The 33 Syringa samples were divided into four groups: Group I is series Syringa represented by Syringa oblata; Group II is series Villosae represented by Syringa villosa; Group III is series Pubescentes represented by Syringa meyeri; and Group IV is section Ligustrina represented by Syringa reticulata subsp. pekinensis. These research results provided strong evidence that the combinatorial barcode of psbA-trnH+trnC-petN had high-efficiency identification ability and application prospects in species of the genus Syringa.
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Affiliation(s)
- Ruihong Yao
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Runfang Guo
- Department of Bioengineering, Hebei Agricultural University, Baoding, P. R. China
| | - Yuguang Liu
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Ziqian Kou
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
| | - Baosheng Shi
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, P. R. China
- * E-mail:
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Liyanage NMN, Chandrasekara BCHWM, Bandaranayake PCG. A CTAB protocol for obtaining high-quality total RNA from cinnamon ( Cinnamomum zeylanicum Blume). 3 Biotech 2021; 11:201. [PMID: 33927991 DOI: 10.1007/s13205-021-02756-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022] Open
Abstract
Cinnamomum zeylanicum Blume is an endemic Sri Lankan species commonly known as Ceylon cinnamon or true cinnamon. It is considered the king of spices in addition to its medicinal benefits. Despite recent scientific evidence on its medicinal properties and the industrial demand, cinnamon breeding and crop improvement are not been improved to the expectation. It is mainly due to the limited availability of the genomic information of cinnamon, linked with technical challenges caused by abundant secondary metabolites in all plant parts. Therefore, obtaining high-quality RNA is the fundamental step of transcriptomic analysis and the gene discovery process of cinnamon. We have optimized a CTAB based protocol for high-quality RNA extraction from different cinnamon tissues at various maturity stages collected from the field. Regular pH around 8 and the presence of Polyvinylpyrrolidone (PVP) in CTAB buffer increased the viscosity of the cinnamon lysate. Adjusting the pH of the lysis buffer to 6-6.5 reduced the viscosity of lysate while chloroform precipitates protein efficiently at the adjusted pH with no phenol. Therefore, this protocol excludes PVP and phenol extraction steps. Nanodrop spectrophotometer, gel electrophoresis, and bioanalyzer readings confirmed the quality of extracted RNA. RNA-seq libraries prepared were sequenced with Illumina Sequencing by synthesis technology and obtained good quality data to be used for transcriptomic analysis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02756-1.
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