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13. Additional file 5 of Tracheostomy timing and clinical outcomes in ventilated COVID-19 patients: a systematic review and meta-analysis

Author

Ji, Yun, Fang, Yumin, Cheng, Baoli, Li, Libin, and Fang, Xiangming

Abstract

Additional file 5: Figure S1-S13. Figure S1. Time from tracheostomy to ventilator weaning in early vs late tracheostomy. Figure S2. Duration of sedation in early vs late tracheostomy. Figure S3. Sensitivity analysis of duration of IMV by excluding one study with high heterogeneity. Figure S4. Sensitivity analysis of duration of ICU stay by excluding one study with high heterogeneity. Figure S5. Sensitivity analysis of duration of IMV by restricting to studies published in peer-reviewed journals. Figure S6. Sensitivity analysis of duration of ICU stay by restricting to studies published in peer-reviewed journals. Figure S7. Sensitivity analysis of overall mortality by restricting to studies published in peer-reviewed journals. Figure S8. Subgroup analysis of duration of IMV in studies defining early tracheostomy as that done within 7 days. Figure S9. Subgroup analysis of duration of IMV in studies defining early tracheostomy as that done within 14 days. Figure S10. Subgroup analysis of duration of ICU stay in studies defining early tracheostomy as that done within 7 days. Figure S11. Subgroup analysis of duration of ICU stay in studies defining early tracheostomy as that done within 14 days. Figure S12. Subgroup analysis of overall mortality in studies defining early tracheostomy as that done within 7 days. Figure S13. Subgroup analysis of overall mortality in studies defining early tracheostomy as that done within 14 days.

Published
2022
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16. Additional file 2 of Characterization of UDP-glycosyltransferase family members reveals how major flavonoid glycoside accumulates in the roots of Scutellaria baicalensis

Author

Pei, Tianlin, Yan, Mengxiao, Li, Tian, Li, Xiaoqiang, Yin, Yijia, Cui, Mengying, Fang, Yumin, Liu, Jie, Kong, Yu, Xu, Ping, and Zhao, Qing

Abstract

Additional file 2: Figure S1. Representative 7-O flavonoid glycosides detected from roots of S. baicalensis. Red boxes indicated the different groups between sugar moieties. Figure S2. Alignment of SbUGTs and SbUGATs protein sequences. The consensus sequences were highlighted by red color. The arrows indicated the different amino acid residues between SbUGTs and SbUGATs, which were responsible for the functional divergent between these two types of glycosyltransferases. Figure S3. MS and MS2 patterns of oroxin A (A) and baicalin standard (B). Figure S4. SDS PAGE analysis of purification of SbUGT and SbUGAT proteins. A. Tracks from left to right showed protein markers (M), empty vector control (1), SbUGT1 (2), SbUGT2 (3), SbUGT3 (4), SbUGT7 (5), SbUGT8 (6) and SbUGT9 (7). B. Tracks from left to right showed protein markers (M), empty vector control (1), SbUGTA3 (2), SbUGAT4 (3), SbUGAT5 (4) and SbUGAT6 (5). Figure S5. Nonlinear regressions of the Michaelis���Menten equation for SbUGTs and SbUGATs.

Published
2022
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19. SbMYB3 transcription factor promotes root-specific flavone biosynthesis in Scutellaria baicalensis.

Author

Fang, Yumin, Liu, Jie, Zheng, Minmin, Zhu, Sanming, Pei, Tianlin, Cui, Mengying, Chang, Lijing, Xiao, Hanwen, Yang, Jun, Martin, Cathie, and Zhao, Qing

Subjects
CHINESE skullcap, BIOSYNTHESIS, TRANSCRIPTION factors, SCUTELLARIA, FLAVONES, GENETIC transcription regulation
Abstract

Scutellaria baicalensis Georgi produces abundant root-specific flavones (RSFs), which provide various benefits to human health. We have elucidated the complete biosynthetic pathways of baicalein and wogonin. However, the transcriptional regulation of flavone biosynthesis in S. baicalensis remains unclear. We show that the SbMYB3 transcription factor functions as a transcriptional activator involved in the biosynthesis of RSFs in S. baicalensis. Yeast one-hybrid and transcriptional activation assays showed that SbMYB3 binds to the promoter of flavone synthase II-2 (SbFNSII-2) and enhances its transcription. In S. baicalensis hairy roots, RNAi of SbMYB3 reduced the accumulation of baicalin and wogonoside, and SbMYB3 knockout decreased the biosynthesis of baicalein, baicalin, wogonin, and wogonoside, whereas SbMYB3 overexpression enhanced the contents of baicalein, baicalin, wogonin, and wogonoside. Transcript profiling by qRT–PCR demonstrated that SbMYB3 activates SbFNSII-2 expression directly, thus leading to more abundant accumulation of RSFs. This study provides a potential target for metabolic engineering of RSFs. [ABSTRACT FROM AUTHOR]

Published
2023
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22. Diverse specialized metabolism and their responses to lactalbumin hydrolysate in hairy root cultures of Salvia miltiorrhiza Bunge and Salvia castanea Diels f. t omentosa Stib

Author

Zongsuo Liang, Fang Yumin, Dongfeng Yang, Xiaodan Zhang, and Zhuoni Hou

Subjects
0106 biological sciences, 0301 basic medicine, Environmental Engineering, biology, Traditional medicine, Rosmarinic acid, Biomedical Engineering, Bioengineering, Metabolism, Phenolic acid, biology.organism_classification, 01 natural sciences, Salvia miltiorrhiza, 03 medical and health sciences, chemistry.chemical_compound, 030104 developmental biology, chemistry, Biosynthesis, Caffeic acid, Medicinal plants, 010606 plant biology & botany, Biotechnology, Salvia castanea
Abstract

Salvia miltiorrhiza Bunge (S. miltiorrhiza) and Salvia castanea Diels f. tomentosa Stib (S. castanea) are both important medicinal plants which have been widely used to treat cardiovascular diseases. Tanshinone and phenolic acid are active and specialized metabolites in the two species. However, the divergent mechanism of specialized metabolism in the two species is yet unknown. We found that S. castanea produced higher levels of cryptotanshinone, tanshinone IIA, caffeic acid, and rosmarinic acid, but lower levels of dihydrotanshinone I and salvianolic acid B than S. miltiorrhiza. Some key genes involved in specialized metabolism were potentially associated with the diverse metabolism between the two species. LH with 1 g l−1 contributed more to tanshinone accumulation in S. castanea than that in S. miltiorrhiza. Genes involved in tanshinone biosynthesis in S. castanea were also more sensitive to LH than those in S. miltiorrhiza. Knowledge about diverse specialized metabolism in the two species will help us understand mechanism of tanshinone and phenolic acid biosynthesis.

Published
2018

28. The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis

Author

Zhao, Qing, primary, Yang, Jun, additional, Cui, Meng-Ying, additional, Liu, Jie, additional, Fang, Yumin, additional, Yan, Mengxiao, additional, Qiu, Wenqing, additional, Shang, Huiwen, additional, Xu, Zhicheng, additional, Yidiresi, Reheman, additional, Weng, Jing-Ke, additional, Pluskal, Tomáš, additional, Vigouroux, Marielle, additional, Steuernagel, Burkhard, additional, Wei, Yukun, additional, Yang, Lei, additional, Hu, Yonghong, additional, Chen, Xiao-Ya, additional, and Martin, Cathie, additional

Published
2019
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29. Oxalate promoted iron dissolution of hematite viaproton coupled electron transferElectronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d1en01190a

Author

Zhan, Guangming, Fang, Yumin, Zhang, Meng, Cao, Shiyu, Xu, Tianyuan, Ling, Cancan, Gu, Huayu, Liu, Xiao, and Zhang, Lizhi

Abstract

Oxalate, a typical natural ligand, plays a significant role in promoting iron dissolution from iron (oxyhydr)oxide minerals to improve iron bioavailability in nature. However, the mechanism of oxalate promoted iron dissolution remains obscure due to the complicated interactions between oxalate and iron (oxyhydr)oxide minerals. Herein, oxalate promoted iron dissolution of hematite {001} nanoplates was examined at a molecular level with in situattenuated total reflectance-Fourier transform infrared reflection (ATR-FTIR) spectroscopy, open circuit potential, H/D exchange experiments, and density functional theory (DFT) simulations. The results revealed that oxalate (C2O42−) would be gradually protonated with decreasing pH from 6.0 to 2.0, and then its protonated form (HC2O4−) was adsorbed on hematite in a deprotonated bidentate mononuclear configuration, accompanied with the proton transfer from HC2O4−to the surface hydroxyl groups of hematite viaa proton coupled electron transfer (PCET) mechanism during the adsorption to increase the acidity of the hematite surface, along with the injection of 0.65 electrons from the adsorbed C2O42−into the bonded iron atom. Subsequently, the strength of Fe–O bonds on the hematite surface decreased to the same level as that of Fe(iii)·H2O cluster formed between homogeneous Fe(iii) and H2O, as followed with the breakage of these weakened Fe–O bonds on the hematite surface, resulting in the final iron dissolution as Fe(C2O4)(H2O) clusters from the hematite surface into solution. This study clarifies the intrinsic mechanism of oxalate promoted iron dissolution of hematite, and also sheds light on the iron dissolution of iron (oxyhydr)oxide minerals promoted by natural ligands.

Published
2022
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30. Diverse responses of tanshinone biosynthesis to biotic and abiotic elicitors in hairy root cultures of Salvia miltiorrhiza and Salvia castanea Diels f. tomentosa

Author

Fang Yumin, Xiaodan Zhang, Zongsuo Liang, Dongfeng Yang, and Pengguo Xia

Subjects
0106 biological sciences, 0301 basic medicine, Silver, Salvia miltiorrhiza, Salvia, 01 natural sciences, Plant Roots, Copalyl diphosphate synthase, 03 medical and health sciences, chemistry.chemical_compound, Biosynthesis, Cytochrome P-450 Enzyme System, Gene Expression Regulation, Plant, Transferases, Botany, Genetics, Farnesyltranstransferase, Medicine, Chinese Traditional, Salvia castanea, Plant Proteins, Alkyl and Aryl Transferases, ATP synthase, biology, General Medicine, Metabolism, biology.organism_classification, Bioactive compound, 030104 developmental biology, chemistry, Abietanes, biology.protein, 010606 plant biology & botany
Abstract

Salvia miltiorrhiza (S. miltiorrhiza) and Salvia castanea Diels f. tomentosa (S. castanea) are both used for treatment of cardiovascular diseases. They have the same bioactive compound tanshinones, but whose contents are hugely different. This study illustrated diverse responses of tanshinone biosynthesis to yeast extract (YE) and Ag+ in hairy roots of the two species. YE enhanced both the growth and tanshinone biosynthesis of two hairy roots, and contributed more to tanshinone accumulation in S. castanea than that in S. miltiorrhiza. Genes encoding 1-deoxy-d-xylulose 5-phosphate synthase (DXS2), geranylgeranyl diphosphatesynthase (GGPPS1), copalyl diphosphate synthase (CPS1), and two cytochromes P450 (CYP76AH1 and CYP76AH3) were also more responsive to YE in S. castanea than those in S. miltiorrhiza. Accumulations of dihydrotanshinone I and tanshinone I, and most biosynthetic genes in S. miltiorrhiza were more responsive to Ag+ than those in S. castanea. Accumulations of dihydrotanshinone I and cryptotanshinone were more responsive to YE, while tanshinone IIA accumulation was more responsive to Ag+ in S. miltiorrhiza. However, accumulations of other four tanshinones and related genes in S. castanea were more responsive to YE than Ag+. This study provides foundations for studying diverse specialized metabolism between the related species.

Published
2017

33. Gap-free genome assembly and CYP450gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis

Author

Pei, Tianlin, Zhu, Sanming, Liao, Weizhi, Fang, Yumin, Liu, Jie, Kong, Yu, Yan, Mengxiao, Cui, Mengying, and Zhao, Qing

Abstract

Scutellaria baicalensisGeorgi, a member of the Lamiaceae family, is a widely utilized medicinal plant. The flavones extracted from S. baicalensiscontribute to numerous health benefits, including anti-inflammatory, antiviral, and anti-tumor activities. However, the incomplete genome assembly hinders biological studies on S. baicalensis. This study presents the first telomere-to-telomere (T2T) gap-free genome assembly of S. baicalensisthrough the integration of Pacbio HiFi, Nanopore ultra-long and Hi-C technologies. A total of 384.59 Mb of genome size with a contig N50 of 42.44 Mb was obtained, and all sequences were anchored into nine pseudochromosomes without any gap or mismatch. In addition, we analysed the major cyanidin- and delphinidin-based anthocyanins involved in the determination of blue-purple flower using a widely-targeted metabolome approach. Based on the genome-wide identification of Cytochrome P450 (CYP450)gene family, three genes (SbFBH1, 2, and 5) encoding flavonoid 3′-hydroxylases (F3′Hs) and one gene (SbFBH7) encoding flavonoid 3′5′-hydroxylase (F3′5′H) were found to hydroxylate the B-ring of flavonoids. Our studies enrich the genomic information available for the Lamiaceae family and provide a toolkit for discovering CYP450genes involved in the flavonoid decoration.

Published
2023
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34. Diverse specialized metabolism and their responses to lactalbumin hydrolysate in hairy root cultures of Salvia miltiorrhiza Bunge and Salvia castanea Diels f. tomentosa Stib.

Author

Fang, Yumin, Hou, Zhuoni, Zhang, Xiaodan, Yang, Dongfeng, and Liang, Zongsuo

Subjects
*LACTALBUMIN, *SALVIA miltiorrhiza, *PLANT roots, *MEDICINAL plants, *PLANT metabolism, *CARDIOVASCULAR disease treatment
Abstract

Salvia miltiorrhiza Bunge ( S. miltiorrhiza ) and Salvia castanea Diels f. t omentosa Stib ( S. castanea ) are both important medicinal plants which have been widely used to treat cardiovascular diseases. Tanshinone and phenolic acid are active and specialized metabolites in the two species. However, the divergent mechanism of specialized metabolism in the two species is yet unknown. We found that S. castanea produced higher levels of cryptotanshinone, tanshinone IIA, caffeic acid, and rosmarinic acid, but lower levels of dihydrotanshinone I and salvianolic acid B than S. miltiorrhiza . Some key genes involved in specialized metabolism were potentially associated with the diverse metabolism between the two species. LH with 1 g l −1 contributed more to tanshinone accumulation in S. castanea than that in S. miltiorrhiza . Genes involved in tanshinone biosynthesis in S. castanea were also more sensitive to LH than those in S. miltiorrhiza . Knowledge about diverse specialized metabolism in the two species will help us understand mechanism of tanshinone and phenolic acid biosynthesis. [ABSTRACT FROM AUTHOR]

Published
2018
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