The Osteogenic Function of Danggui Buxue Tang, a Herbal Decoction Containing Astragali Radix and Angelicae Sinensis Radix, Is Optimized by Boiling the Two Herbs Together: Signaling Analyses Revealed by Systems Biology
, Anna X. D. Yu 1,2, Tina T. X. Dong 1,2, Henry H. L. Lam 3 and Karl W. K. Tsim 1,2,*Round 1
Reviewer 1 Report
The manuscript, “The osteogenic function of Danggui Buxue Tang, a herbal decoction containing Astragali Radix and Angelicae Sinensis Radix, is optimized by boiling the two herbs together: signaling analyses revealed by systems biology” is finely designed and presented by the authors. I would recommend the publication of the manuscript with minor corrections (suggestions only).
- Abstract needs refinement with special emphasis on the outcomes of the study.
- A suitable background with relevant citations is missing in the introduction section.
- I would recommend authors to share the raw data proteomics and network analysis in the supplementary or by GitHub for the readers and reproducibility.
Author Response
1.Abstract needs refinement with special emphasis on the outcomes of the study.
Our response: We have revised the mentioned issues in the abstract.
2.A suitable background with relevant citations is missing in the introduction section.
Our response: We have included the relevant references in the introduction section.
3.I would recommend authors to share the raw data proteomics and network analysis in the supplementary or by GitHub for the readers and reproducibility.
Our response: In accordance to this comment, we have included the omics data in the supplementary files.
Reviewer 2 Report
The manuscript from Kwan et al compares a traditional Chinese medicine with a mixture of its untreated components. The manuscript focuses on the differences caused by the two treatments rather than the components of the treatments. the manuscript is well written with only minor corrections to the English required, some of which I have noted below. The science has been clearly described. However, the most interesting question to me is not addressed by this manuscript; how does boiling the components make them more active? Perhaps this is addressed elsewhere.
Many of the figure captions require more explanation of what is being displayed in the figure. Figure 6 panel A is difficult to see. perhpas making it larger or adding a grid beneath the peaks would make it easier to interpret.
Some suggested corrections are listed below.
line 86 replace "calvaries" with "calvarias"
line 92 replace "106" with "106"
line 190 replace "2" with "two"
line 206 explain "DEP" acronym when it is first used
Figure 3D The top red and blue bar has been shifted to the right slightly
line 244 explain "DEG" acronym when it is first used
Figure 5 caption needs to explain the figure better. What are the different networks? What do the colors mean? What do the differnt shapes mean? What does a dotted line vs a solid one mean? What do the circular arrows mean?
Figure 6A It is difficult to see. Can the panel be made larger?
line 271 explain acronym VIP
line 321 replace "The membrane" with "The importance of the membrane"
Figure S1 caption It is not explained what panel A is. What did the isolated fractions 1,2,3 and 4 correspond to?
Author Response
1.Many of the figure captions require more explanation of what is being displayed in the figure. Figure 6 panel A is difficult to see. perhaps making it larger or adding a grid beneath the peaks would make it easier to interpret.
Our response: We have revised all the figures for better illustration.
2.line 86 replace "calvaries" with "calvarias"
Our response: We have replaced "calvaries" with "calvarias" in line 116.
3.line 92 replace "106" with "106"
Our response: We have replaced "106" with "106" in line 124.
4.line 190 replace "2" with "two"
Our response: We have replaced "2" with "two" in line 198.
5.line 206 explain "DEP" acronym when it is first used
Our response: We have included the explanation for DEP in line 255.
6.Figure 3D The top red and blue bar has been shifted to the right slightly
Our response: We have revised the mentioned issues in Figure 3D.
7.line 244 explain "DEG" acronym when it is first used
Our response: We have included the explanation of DEG in line 299.
8.Figure 5 caption needs to explain the figure better. What are the different networks? What do the colors mean? What do the different shapes mean? What does a dotted line vs a solid one mean? What do the circular arrows mean?
Our response: We have included the mentioned captions in Figure 5.
9.Figure 6A It is difficult to see. Can the panel be made larger?
Our response: We have revised Figure 6A.
10.line 271 explain acronym VIP
Our response: We have included the explanation of VIP in line 324.
11.line 321 replace "The membrane" with "The importance of the membrane"
Our response: We have revised the wording in line 378.
12.Figure S1 caption It is not explained what panel A is. What did the isolated fractions 1,2,3 and 4 correspond to?
Our response: We have revised the captions in Figure S1.
Reviewer 3 Report
In this work, the authors optimized the process for boiling the two herbs together called Danggui Buxue Tang (DBT: a herbal decoction containing Astragali Radix and Angelicae Sinensis Radix) and studies its osteogenic function. The decoction was tested by various cell culture techniques, shotgun proteomics, protein identification, and lipid analysis by lipidomics. Overall the manuscript is well written and is recommended given the fact that the author addresses the following comments.
The authors have shown a stack HPLC chromatogram for DBT, AR, ASR in the suppl. Figure 1. They also showed a known marker chemical. I would suggest showing a comparative HPLC chromatogram with the standard marker chemical.
Figure S1, A/B the arrow markings are offset that needs to be fixed. S1C: the unit ‘ng’ for the column ‘samples’ should be mentioned.
Fig 2: please show the µm bar inside the box from the software.
Please write briefly about the use of Dex.+Vit C control? Why it was selected as a positive control?
Fig 3B: Those dotted line boxes are suppressing the main data points, please change.
How did the author perform analysis of signaling induced by DBT and AR+ASR? I would suggest giving details about the analysis and experiments. What are KEGG, Reactome, BioCye, PANTHER, and GO?
Fig 5: Lines are bold, and fonts are not clearly visible. Improvement is needed.
Line 254; what is the cent wave method? Reference and a piece of brief information are needed.
Where is the data for control lipid analysis? Total how many control lipids were analyzed and did the author optimized the method for control lipids or samples?
Did the authors notice any changes in the nitric oxidase protein expression or nitric acid product changes through other downstream pathways? See reference Planta Med 2016; 82(05): 418-423 (DOI: 10.1055/s-0035-1558332) OR changes in mitochondrial energetics? (see https://doi.org/10.3389/fphar.2019.00614)
Author Response
1.The authors have shown a stack HPLC chromatogram for DBT, AR, ASR in the suppl. Figure 1. They also showed a known marker chemical. I would suggest showing a comparative HPLC chromatogram with the standard marker chemical.
Our response: Thank you for your suggestion. In accordance to your comment, we have revised Supplementary figure 1, and the profiles of markers have been included.
2.Figure S1, A/B the arrow markings are offset that needs to be fixed. S1C: the unit ‘ng’ for the column ‘samples’ should be mentioned.
Our response: We have revised the Figure S1, and “ng” has been included in S1C.
3.Fig 2: please show the µm bar inside the box from the software.
Our response: We have revised the bar location in Figure 2.
4.Please write briefly about the use of Dex.+Vit C control? Why it was selected as a positive control?
Our response: Dex.+Vit C is well-defined positive control for bone differentiation in culture. In addition, this positive control has been used in our previous studies on DBT. The corresponding reference has been added on line 134, Page 5.
5.Fig 3B: Those dotted line boxes are suppressing the main data points, please change.
Our response: We have revised Fig 3B.
6.How did the author perform analysis of signaling induced by DBT and AR+ASR? I would suggest giving details about the analysis and experiments. What are KEGG, Reactome, BioCye, PANTHER, and GO?
Our response: We have provided detailed description re those analyses in the text, line 214, Page 7.
7.Fig 5: Lines are bold, and fonts are not clearly visible. Improvement is needed.
Our response: We have revised the mentioned issues in Figure 5.
8.Line 254; what is the cent wave method? Reference and a piece of brief information are needed.
Our response: We have included the reference and information in the section of method, line 300, page 9.
9.Where is the data for control lipid analysis? Total how many control lipids were analyzed and did the author optimized the method for control lipids or samples?
Our response: The data is the fold change in comparing to DBT or AR+ASR with control. Total 28 lipid classes were analyzed. The method for control lipids or sample was optimized. After feature alignment, the total number of 5,611 and 6,690 grouped features were obtained from +ve and -ve ionization profiles, respectively (Figure 6A). The untargeted lipdomics analysis is sufficient to identify the changes.
10.Did the authors notice any changes in the nitric oxidase protein expression or nitric acid product changes through other downstream pathways? See reference Planta Med 2016; 82(05): 418-423 (DOI: 10.1055/s-0035-1558332) OR changes in mitochondrial energetics? (see https://doi.org/10.3389/fphar.2019.00614)
Our response: Thank you for your suggestion. We have revealed the changed in mitochondrial energetics, as shown in Figure 4E
