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The authors have responded in detail to the comments from the reviewers and have addressed them in a satisfactory manner, as noted by the reviewers in their response to this version. The manuscript is much improved.
The only remaining issue is the presence of some English language or formatting errors. The following are a few examples:
Line 25: "the testis produces sperm and secrete androgens," should be: "the testis produces sperm and secretes androgens,"
Line 30: "The testis of three giant pandas..." would be better phrased: "Samples from the testes of three giant pandas..."
Line 82: "Maria Paz et al. (2006)" - the font is a different size.
Line 134: "...Sichuan Province, PRC. which derived.." This should be rewritten, for example: "...Sichuan Province, PRC. The samples were derived from..."
Throughout the manuscript, there should be a space before and after any citations, but this is not always the case. For example, Line 59 "130 grams(Cao et al. 2020)"; Line 65: "(Lu et al. 2018).Proteomics"; Line 70 "pathways(Rozanova et al. 2021;" The authors should check and correct as required.
These are all minor issues and if the authors can do one final careful check of the manuscript to correct these errors, I believe it will be acceptable for publication.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
The authors have revised the manuscript based on the previous comments. Now it looks great, and is ready to go forward. I have no comments now.
It's OK.
The conclusion is reasonable.
The authors have addressed all of my issues. I suggest to aceept the manuscript to publish in PeerJ.
The authors have addressed all of my issues. I suggest to aceept the manuscript to publish in PeerJ.
The authors have addressed all of my issues. I suggest to aceept the manuscript to publish in PeerJ.
As has been noted by the reviewers, because giant pandas are an endangered species and have low reproductive capacity this study presents important information. However, two of the three reviewers have suggested that major revisions are required, and all their comments need to be addressed.
In particular, the authors should clarify the health status of the animals from which the tissue samples were derived, and ensure appropriate information is provided regarding access to the raw data.
The authors should also clearly state any limitations of their study. The main one is the very small sample size (n=3). While this is, of course, justified given the difficulty in obtaining samples from pandas, it still limits the validity of any conclusions. The authors should note this.
Giant pandas have low fertility, not only females, but also males with low sperm production, but related studies are lacking. This study can provide valuable data for further study of giant panda reproduction, so it has certain publication value.
The experimental method is correct and the design is reasonable.
The results of this study are basically credible and provide meaningful basic data for the further study of giant panda reproduction. However, I would like the author to provide the health status of the sample.
1. The number of samples is only 3,which may have some influence on the conclusion of the article. But I also know it is difficult to obtain these samples of giant pandas as endangered animals. However, the authors need to explain the source of the giant panda testicles in Materials, such as whether they come from healthy or diseased tissues, which has a great impact on the validity of the research results.
2. Group T don’t have a frame and the spacing between font and image is too small in Figure 3C. 60.41% of proteins not annotated in COG does not mean that the function of these proteins is unknown in line 251-254.
3. The head label is wrong in Figure 3D, which should be KEGG. It is recommended to align the font to the right, which will make the picture more beautiful and easier to read.
4. Digital fonts should not be compressed and items should be ordered by the number of proteins in Figure 3D and E.
5. The domain should be proven by other studies for its connection to function, not just “believe” in line 276.
6 The value is wrong in figure of Coexpressed top-ten proteins of three pandas in Table S2.
7. “in-depth” maybe not suitable in line 369, because only annotation and quantification were implied in this study. The results of the annotation analysis are too general and specific proteins need further characterization, for example, proteins involved in spermatogenesis in signal transduction. Additional analysis about the age-related difference and functional enrichment are recommend proceeding.
no comment
no comment
This is an interesting study. Here are some minor comments:
(1) Please compare the composition among three individuals (different ages).
(2) The discussion is descriptive.
In this manuscript Peng et al proteomic analysis of testicular tissue from three giant pandas of different ages (22 years, 18 years, 8 days). This work is the first proteomic study of testicular tissue in giant pandas, which provides an important dataset, and the results reveal the important role of testicular tissue proteins in spermatogenesis, testosterone production, and testicular microenvironment. Overall, the results of the study provide clues for further research on male giant panda reproduction. It is commendable that the methodology adopted in this paper is largely reasonable, which guarantees the reliability of the results, but the author's partial description of the results is not very clear, which is easy to confuse the reader, and there are some problems that need to be solved in order to be suitable for publication.
Major issues:
1) Data availability and reproducibility of analyses: I didn't find any description of the raw data in the manuscript. In order to facilitate access to the raw data by readers, and to maximize the impact of this work in the community, authors need to publish the raw data to a public database (e.g., PRIDE Archive, etc.). This is essential to replicate this study.
2) Introduction: In lines 46-48: Captive giant pandas have a low reproductive capacity, both male and female pandas have reproductive problems, such as low sperm count in males and uterine issues in females. Several studies have explored the genetic mechanisms of low fertility in giant pandas, these studies should be listed here.
3) Introduction: The third paragraph of the introduction lists a number of proteomic studies of testicular tissue from other mammals, but none of them describe the specific conclusions drawn from these studies, and the results of these studies and their significance for the study of the giant panda testis should be more detail here.
4) Introduction: The last paragraph of the introduction should briefly describe the main study and results of this study.
5) Proteomic profiling of testis of three pandas: In lines 185-186, The authors mentioned that: the total protein numbers of the three giant panda testicular tissue samples were 10,090, 10,178, and 10,176, respectively. Although the total number of proteins is certainly an important parameter, I think the juxtaposition or crossover of these three datasets should be further characterized by focusing on proteins specifically expressed in testicular tissue at different ages. The function of these age-specific expressed proteins can be analyzed by functional enrichment, which will help us understand the temporal patterns of the reproductive system of male giant pandas.
6) Functional analysis of identified testis proteins: In lines 234-235, The authors mentioned that: GO analysis was performed on the proteins identified from the testicular tissues of giant pandas to extract functional information about the proteins. The proteins used here for GO analysis are all the proteins identified from testicular tissue from three different ages? If so, why not use functional enrichment of testicular proteins based on different ages separately? I have the same confusion about KEGG and COG mentioned below.
7) Protein quantification and differential analysis: In lines 299-302, The authors mentioned that: Ultimately, nine unique proteins were highly abundant in the three pandas, and we analyzed their abundance patterns from young to old times and found that these proteins were more abundant in the young and old periods, except for G1LEJ5, which had the opposite characteristics (Table S2). I think it is necessary to briefly describe the relevant functions of these proteins in the discussion section.
8) Figure-2: The figures are too cramped. Make the individual ones larger, some are hard to read.
no comment
no comment
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