LEVEL 1 被report了lucene similarityy analysis，该怎么回复
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时间：2016-07-29 12:36
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真是好贴子！进来学习一下，对夏老师的热情无私感到敬佩！
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claybird 真是好贴子！进来学习一下，对夏老师的热情无私感到敬佩！对夏老师的热情无私感到敬佩！
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treesea 夏老师：你好，以下是我一篇论文的response letter，由于投稿经验不足，麻烦你帮忙看看，不甚感激~~~谢谢~~~See the attached.Good luck!
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美捷登主编 See the attached.Good luck!非常非常感谢~~~
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太精彩了，感谢夏老师！
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回复信有很多值得关注的地方，回的好改稿的次数也大大减少，努力
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回复信有很多值得关注的地方，回的好改稿的次数也大大减少，努力
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夏老师您好：非常感谢您长久以来的帮助，我最近投稿一篇meta-analysis，现在返稿意见让大修，我已修好，现将审稿人的意见及回复黏贴如下，希望夏老师给把把关，非常期盼能得到您的帮助!
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I will get back to you tomorrow.Thanks.
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快乐跑垒手 夏老师您好：非常感谢您长久以来的帮助，我最近投稿一篇meta-analysis，现在返稿意见让大修，我已修好，现将审稿人的意见及回复黏贴如下，希望夏老师给把把关，非常期盼能得到您的帮助!See attached.Good luck.
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非常感谢夏老师无私的帮助，我会认真修改，届时通报结果！
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请夏老师看看我的小修回复信，以前在夏老师的帮助下，现在感觉回答起来好多了，但还是不放心，请夏老师指教！Reviewer #1: This interesting study provides evidence for a proton-sensitive ASIC1a channel in articular chondrocytes and, as the authors point out, the study is 'a good starting point for a number of subsequent studies into the physiological and pathological roles of ASICs in non-neuronal cells'. CommentsFigure legends are missing.Answer: Thank you for pointing out the error, which has been added in the revised version.The traces shown in Figure 3D appear to be representative traces for a single experiment? It might be better to provide a graph showing mean data from several cells? Answer: It was provided a graph showing mean data from seven cells. This point has been briefly addressed in the revised version of the manuscript (page 3, line 8).In Figure 3D how can one explain the comparatively small rise in Ca2+ concentration when the cells are in Ca2+-free extracellular solution? Several possibilities: Ca2+ contamination in the extracellular fluid and entry of Ca2+ via L-type Ca2+ channels (despite blockade of these channels), leakage of Ca2+ from the SR?Answer: Thank you for sharing your experience in Ca2+ concentration experiments. We accept your comment and consider that small rise in Ca2+ concentration was entry of Ca2+ via L-type Ca2+ channelsMinor points:Reference to Figures in Results section should be checked. Page 9. No reference to Figure 1 in the Results section.Answer: Thank you for pointing out the error, which has been corrected in the revised version.Page 7. State whether confocal experiments were performed at room temperature or physiological temperature?Answer: Confocal experiments were performed at room temperature has been added in the Introduction of the revised version.Page 4, Line 16 - PBS Phosphate buffered saline. State in full first time it appears and then use abbreviation.Answer: Thank you for sharing your experience, which has been corrected in the revised version.Page 9, Line 22 - ..thapsigargin were added to the possible secondary activation…Clarification required.不知审稿人是啥意思？Page 10, Line 1. …confocal micrographs (Figure 3B)….and other references to Figures in this paragraph. Check to see that referencing to different parts of Figure 3 in text correspond to correct panels shown in Figure 3.Answer: I have re-checked the reference carefully and found that the findings of the study are accurately described.Page 12, Line 13. It has proposed…?
Page 12, Line 22. The results our study….?Answer: Thank you for carefully and patiently reviewing of our manuscript, and listing so many mistakes in the original manuscript. Specific corrections in the revised version are followings: I The results of our study.Reviewer #2: This is a straightforward study examining the role of ASIC 1a in chondrocytes.
As seen in neurons, the AS1C1a of chondrocytes transport calcium in a pH dependent manner.
This leads to injury of the chondrocytes at low pH.
The data support the proposed hypothesis.
However, the cells incubated in medium at pH 7.4 also appear to be unstable, as reflected by the increase in LDH release.
What is the source of the instability?
Does the increase in intracellular calcium concentation mediated by ASIC 1a accelerate the events responsible for the instability?Answer: We appreciate the comments, and accept your point of view.
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主编老师您好，我也才刚刚投了一篇文章，杂志是journal of neuroimmunology,内容是cepo(一种药物）对神经干细胞MHC分子表达的影响，其中一个reviewer 认为无法确定cepo在体内的作用，由于时间和资金的限制，我现在无法补充动物体内实验，但不知该如何回复来信，以使拒稿的可能性降到最低，主编老师能指导一下吗？不胜感激！下面是信的原文：Reviewer #1: The authors test the effects of carbamylated erythropoietin (CEPO) on human neural stem cells.In the introduction and discussion, the authors make the important point that a given drug can have many different effects.However, the work is done entirely in vitro.
There is no way to know if the findings have any clinical or other relevance in vivo.
Nor is this topic well-discussed.
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Please check my attached file before your post in response to your request by PM.
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美捷登主编 edited on
美捷登主编 First of all, I have to say that I am not the expert in your research area, and thus I cannot comment on how to exactly reply to the reviewer.However, I would provide some advice based on the above comments and what you described.In my opinion, the comment is critical but not so aggressive and demanding, as the reviewer did not directly request for an additional in vivo study. Thus, you have an opportunity to reply to the comment without an in vivo study.I would suggest:1. Check your Instruction and Discussion to see if you overstated the aims and the findings. Don't draw a conclusion that you cannot from your findings.2. In the Reply letter, give a praise to the reviewer for the constructive comment, and explain frankly why you cannot do the in vivo study. 3. Do some literature search to find if there are some in vivo studies supporting your in vitro findings, and then use these findings to further discuss the topic in the Discussion section.Perhaps, this may be of help.Good luck!美捷登主编三句话，一句值千金！
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夏老师好，我的回修稿件是12月2号上传cancer letters的，12月3号状态就变为under review, 怎么期间状态又从12月3号under review变为12月29号under review，这到底什么原因？不会under review是从12月29号才开始算得吧？
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163abcdc 夏老师好，我的回修稿件是12月2号上传cancer letters的，12月3号状态就变为under review, 怎么期间状态又从12月3号under review变为12月29号under review，这到底什么原因？不会under review是从12月29号才开始算得吧？You are confusing me, Dr. Jiang. What do you mean by the change from &under review& to &under review&? However, I don't think it matters. Again, you should be patient as many editors and reviewers just returned from their long holiday (I just received three papers to review over the last week). So, please give them some time to do the job. Normally, your paper should be accepted after revision by the journal.
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psyuan 请夏老师看看我的小修回复信，以前在夏老师的帮助下，现在感觉回答起来好多了，但还是不放心，请夏老师指教！Reviewer #1: This interesting study provides evidence for a proton-sensitive ASIC1a channel in articular chondrocytes and, as the authors point out, the study is 'a good starting point for a number of subsequent studies into the physiological and pathological roles of ASICs in non-neuronal cells'. CommentsFigure legends are missing.Answer: Thank you for pointing out the error, which has been added in the revised version.The traces shown in Figure 3D appear to be representative traces for a single experiment? It might be better to provide a graph showing mean data from several cells? Answer: It was provided a graph showing mean data from seven cells. This point has been briefly addressed in the revised version of the manuscript (page 3, line 8).In Figure 3D how can one explain the comparatively small rise in Ca2+ concentration when the cells are in Ca2+-free extracellular solution? Several possibilities: Ca2+ contamination in the extracellular fluid and entry of Ca2+ via L-type Ca2+ channels (despite blockade of these channels), leakage of Ca2+ from the SR?Answer: Thank you for sharing your experience in Ca2+ concentration experiments. We accept your comment and consider that small rise in Ca2+ concentration was entry of Ca2+ via L-type Ca2+ channelsMinor points:Reference to Figures in Results section should be checked. Page 9. No reference to Figure 1 in the Results section.Answer: Thank you for pointing out the error, which has been corrected in the revised version.Page 7. State whether confocal experiments were performed at room temperature or physiological temperature?Answer: Confocal experiments were performed at room temperature has been added in the Introduction of the revised version.Page 4, Line 16 - PBS Phosphate buffered saline. State in full first time it appears and then use abbreviation.Answer: Thank you for sharing your experience, which has been corrected in the revised version.Page 9, Line 22 - ..thapsigargin were added to the possible secondary activation…Clarification required.不知审稿人是啥意思？Page 10, Line 1. …confocal micrographs (Figure 3B)….and other references to Figures in this paragraph. Check to see that referencing to different parts of Figure 3 in text correspond to correct panels shown in Figure 3.Answer: I have re-checked the reference carefully and found that the findings of the study are accurately described.Page 12, Line 13. It has proposed…?
Page 12, Line 22. The results our study….?Answer: Thank you for carefully and patiently reviewing of our manuscript, and listing so many mistakes in the original manuscript. Specific corrections in the revised version are followings: I The results of our study.Reviewer #2: This is a straightforward study examining the role of ASIC 1a in chondrocytes.
As seen in neurons, the AS1C1a of chondrocytes transport calcium in a pH dependent manner.
This leads to injury of the chondrocytes at low pH.
The data support the proposed hypothesis.
However, the cells incubated in medium at pH 7.4 also appear to be unstable, as reflected by the increase in LDH release.
What is the source of the instability?
Does the increase in intracellular calcium concentation mediated by ASIC 1a accelerate the events responsible for the instability?Answer: We appreciate the comments, and accept your point of view.Dear Dr. Yuan,I am so sorry for missing your request post due to my heavy workload.Attached is my edited version, and I hope it is not too late to submit.Good luck.
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夏老师，谢谢！！您辛苦啦！！
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学习学习 很有收获 O(∩_∩)O谢谢
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楼主，您好！我有一篇文章，关于胃癌免疫方面的，不知投什么杂志。很着急！
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留下记号，慢慢看
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夏老师：您好， 我的回修稿件是12月2号上传投稿系统的， “Status Date”状态为12月3号， “Current Status” 状态为under review, 怎么期间“Status Date”又从12月3号变为12月29号，这到底是什么原因？到什么时间还没有结果的话，我可以写信问编辑？心里有点急.
蒋Peer Review Policy for Cancer LettersHow long does the peer review process take?
“Typically the manuscript will be reviewed within 3-8 weeks. Should the reviewers' reports contradict one another or a report is unnecessarily delayed a further expert opinion will be sought. Revised manuscripts are usually returned to the initial reviewers within 2-4 weeks. Reviewers may request more than one revision of a manuscript.”
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163abcdc edited on
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I understand your feeling. Please be patient and do give them another 2 week to make a decision on your paper.You can send a reminder to the editor by the end of the month (perhaps you have already received a positive one by the time).Good luck:)
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Dear zhanghaisen,Please download the attached file.Let me know if you need any help.
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[Hidden Post:1]
您无权限看这个帖子，您的积分需要大于 1
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zhanghaisen edited on
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Please check the attached file above your post for my revisions in your letter sent by PM.
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美捷登主编 edited on
夏老师，请帮忙指点一下。谢谢Dear Dr. XXX, & & Thank you for arranging a timely review for our manuscript. We are pleased to know that our study is of general interest for the readers of GENE. We have carefully evaluated the reviewers’ critical comments and thoughtful suggestions, responded to these suggestions point-by-point, and revised the manuscript accordingly. All changes made to the text are in red so that they may be easily identified. With regard to the reviewers’ comments and suggestions, we wish to reply as follows:& & To Reviewer #1: & Comments:& & 1. The effects observed for RAP overexpressing Arabidopsis should be compared with RAP knockdowns or knockouts in Arabidopsis.& & We thank reviewer’s suggestion, and added the data in the revised manuscript. As the supplementary figure 3 shown, RNAi-RAP transgenic plants show no significant phenotype compared with WT under normal or stress conditions.& & 2. The RAP overexpressing seedlings showed severe growth inhibition in response to glucose and to NaCl but less pronounced effects in the presence of ABA and sorbitol.Hypotheses explaining these effects should be included in the discussion.& & We believe different stress stimuli through different mechanisms. We speculated that RAP is a transcription factor, which may roles in different stress pathways. But maybe it acts different roles in different pathway. Many reports showed indicated that changes in expression level of a transcription factor may lead to varying degrees of sensitivity to different stresses, such as XERICO (Ko, et al. 2006), ABR1(Pandey,et al. 2005).& & 3. Statistical analyses of the 3 independent experiments of figure 4 should be included.& & As shown in figure 4, we have finished at least 3 independent experiments, the statistical data and significant differences are calculated.& & 4. In figure 1, wild type Arabidopsis stained with the GUS substrate should be shown as a negative control. Thus, the staining pattern in rosette leaves and in siliques should be verified as a RAP specific signal.& & In fact, when we did this control experiment, we used plants transformed with pCAMBIA1300+pBI101 as
so that we can use proper GUS staining conditions to get the RAP specific signal. Now the negative control was added in the supplemental data. & & 5 Highest tissue-specific transcript levels of RAP were observed in stems by RT-PCR but only weak signals could be detected by the GUS staining. In contrast, the GUS staining showed strong signals in roots of A. thaliana whereas the signal was weak in the RT-PCR. How might these effects be explained?& & The material used for RT-PCR analysis was 5-week old Arabidopsis, and the GUS staining plants were seedlings. The inconsistent results were because of the different stages of tissues we used in the two experiments. Also, we use quantitive RT-PCR method to further confirm the RT results.& Moreover, the GUS staining signal was affected by different factors, such as the staining time, the concentration of x-gluc, ect.Our GUS results here only showed the quantity instead of quality expression pattern.& & 6 The effect of salt-induced increase of ABA should be discussed.& & ABA plays vital role in regulating seed germination and it is considered as a plant stress hormone. When plants are subjected to abiotic stresses, the level of ABA will increase (Finkelstein, et al. 2002).Our preliminary investigation lead us suppose that the stress-induced hypersensitive phenotype may be caused by activating ABA-signaling pathway. We supposed that the enhanced activity of RAP confers the observed induction in ABA therefore, plants do not need to produce more ABA, it may reflect a balance between ABA-signaling and ABA-biosynthesis pathways. Similarly, feedback regulation in ABA levels has also been observed in the ERD15 gene study (Kariola,et al. 2006).& & 7. Transcription of RAB18 in ABA-treated plants and of COR15 in NaCl stressed wild type and transgenic Arabidopsis should be shown.& & As shown in figure 7, the results of the transcription of RAB18 in ABA-treated plants and COR15 in NaCl-treated plants are added.& & 8. The conclusion that &RAP could act as an activator of its downstream genes& is not supported by the experimental results presented in the manuscript.& & We agree with the reviewer’s this important viewpoint. Indeed, our results presented could not fully support the conclusion, and further study of downstream targets of RAP will be an important work to understand this transcription factor’s molecular function. As a response to the reviewer, and based on our results, we rephrased our conclusion as “RAP could modulate some ABA and salt-induced gene expression”.& & 9. Was the transcript level of ABI4 higher in the transgenic lines under control or under stress conditions? Experimental data of these experiments should be included.& & We added the data as the reviewer’s suggestion. Our quantitive RT-PCR result showed that ABI4 transcripts were increased under normal or stress conditions in RAP-OX transgenic plants compared with WT.& & 10. The hypothesis that the increased response to ABA might be due to increased expression of ABI4 in the RAP over expressing Arabidopsis is not supported by experimental data.& & In the present study, our results indicated the expression of ABI4, one of the important factors in ABA signaling, enhanced the abundance.& Accordingly, we have modified the sentence to address the reviewer’s point,“All these results led us to speculate that RAP may act as a positive regulator in the ABA-signaling pathway”. & & 11. Other comments:& Last paragraph of the introduction: the 3rd sentence should be rephrased.& & We have modified the sentence as suggested by the reviewer. “Here, we showed evidence for the first time that RAP is involved in Arabidopsis response to ABA and abiotic stress”.& & The selection of transgenic Arabidopsis should be described in more detail.& & We revised this section and described the point in more detail: Wild-type Arabidopsis was transformed by the floral dipping method. T2 seeds from each of the selected transgenic plants were plated on germination medium containing hygromycin as selection antibiotics, and & in total, 10 homozygous lines were selected. Homozygous T3 progeny were then examined for the expression levels of RAP by RT-PCR method, & Representative lines overexpressing RAP were used for further analysis, and results from RAP-OX1 and RAP-OX2 which have different RAP expression levels are shown in this manuscript.& & Origins of the plasmids should be included throughout the manuscript.& & We revised this point in the new manuscript& & Paragraph 2.4: The 1st sentence should be explained in more detail& & We revised the sentence as: “The encoding region without the stop codon of RAP was amplified with primers (5’-GAAGATCTGATGGTGTCTATGCTG ACTAATG-3’and 5’-GACTAGTACCAAAAGAGGAGTAATTG-3’), the fragment was fused in-frame to the 5’-terminal of YFP in the pA7-YFP vector (provided by H.-Q. Yang) using BglII and SpeI site, then verified by sequencing”.& & Paragraph 2.6: ss-galactosidase or ss-glucuronidase?& & As shown in the manuscript, the sentence has been modified to“ss-galactosidase”.& & Paragraph 2.8: The 1st sentence should be rephrased.& & We revised the sentence as: “Approximately 60 seeds each from the wild-type and RAP overexpression transgenic lines (RAP-OX1 and RAP-OX2) were planted in triplicate on Murashige and Skoog (MS) medium supplemented with different concentrations of ABA, NaCl, sorbitol, or glucose, and incubated at 4°C for 4 days before being placed at 22°C under long-day conditions”.& & The accession number of RAP should be included in the manuscript.& & The accession number of RAP is AY114582, and we added it in the new manuscript& & A list of the identified cis-elements and of their position should be included in the main manuscript.& & We added the table to the main manuscript.& & The analysis of transcriptional activation activity in yeast should be explained more precisely.& & We did the experiment more precisely, accordding to the reviewer ‘suggestion. We further analyzed the transcription activity of full RAP ORF, N-terminal ORF and C-terminal ORF.& & Grammar and spelling should be checked throughout the manuscript.& & Reviewer #2: & This manuscript describes characterization of the RAP gene in Arabidopsis. Overall the manuscript is of high quality and it provides novel information about RAP and provides support for a role of this gene in environmental stress response. In addition, the authors provide evidence that RAP, which is a member of the AP2/ERF family, is really a transcription factor. The protein is nuclear localized and can act as a transcriptional activator in yeast, binding to GCC and CE1 cis-elements. The authors show that expression of ABI4 is unregulated in RAP OE lines and suggest that the phenotype of these lines might be a consequence of increase ABI4 levels. & & 1. The paper would be stronger if this hypothesis was tested by introducing& abi4 mutants into the OE lines. & & We thank the reviewer to put forward this important suggestion. We now analyzed the abi4/RAP-OE line under different stress conditions.& We believe that the relationship between ABI4 and RAP is a very important topic, thus we would like to carry out a separate but more extensive experiment on this topic.& & Another area in which the paper could be strengthened is the characterization of the spatial pattern of RAP. The authors use a promoter:GUS reporter but have not shown that this promoter fragment drives proper expression of the gene. Of course, in the absence of a mutant, this is difficult to test. In situ hybridization would directly measure RAP mRNA distribution. One concern I have is that the level of RAP mRNA in leaves looks to be quite high (relative to flowers) based on the& RT-PCR results (Fig. 1. A). But is restricted to just a few cells in the GUS reporter stained leaves (Fig 1.B.v).& & We thank the reviewer’s valuable suggestion. Before the experiment, we use the software to predict the promoter (http://www.fruitfly.org/seq_tools/promoter.html), and the predicted sequence was about 1.4k. And in many studies, they use about 1-1.5kb fragment above the translation start site as the effective promoter, we also use more than 1.5kb (1639bp) sequence as the RAP promoter.& In situ hybridization is effective to determine the RAP mRNA distribution,原位杂交在研究植物发育领域应用比较广泛。我们查找了芯片结果，发现RAP的表达并不是很强，况且我们的原位杂交技术不很成熟。& In fact, the leaf used in RT-PCR was rosette leaf instead of stem leaf (we revised in the new manuscript), and we use quantitive RT-PCR method to further confirm the result. As for the GUS result, we provide the negative control data to make sure the signal was RAP specific.（我们没有条件做原位杂交，况且这个并不是很必要，我用定量pcr的方法来弥补了一下）& & However, if the reviewer feels that it is essential to add the result in this manuscript, we would be glad to carry out the additional experiments.& & Other items& & 1. page 9, line 8, should be &responds& rather than &responses&& 2. page 9, line 20 should be &Numerous& not &A numerous&& 3. page 11, line 3 should be &pHISi-GCC& instead of &pHISi-GC&& 5. page 15, line 22, should be &activating or repressing& instead of &activate or repress&& & Thank you for pointing out the error, which has been corrected in the revised version.& & 4. Is ABI4, the most closely related AP2/ERF protein to RAP?& & We did phylogenetic analyses, and find ABR1 the most closely related AP2/ERF protein to RAP (86%). ABR1 was considered as a repressor of the ABA response in Arabidopsis. And also, ABR1 may functionally interact with ABI4 in the regulation of ABA-responsive genes. However, we think the relationship between ABI4 and RAP is more crucial, first, the conserved amino acid similarity among ABI4 and RAP is nearly also very high (70%); second, ABI4 plays important role in multiple pathways including ABA signaling a third, the promoter of ABI4 have several CE1 cis-element, which RAP could bind to. Because of the reason above, we began to investigate the relationship between the two and provide our preliminarily results. We think a separate and extensive experiment is needed for settle this important issue.& & 6. Figure 3B, Are these replicate assays?& & Yes, all experiments in the manuscript are replicated. And now we provide more precise results in the revised manuscript.& & 7. Figure 4, It is hard to see much difference between WT and the OE lines for 1&mu&M ABA and 150mM NaCl& & We did statistic analysis, and our results showed that although the difference is small, but it really exists.& & 8. Figure 6 legend, line 2, should be &treatment& instead of &treated&& 9. Figure 7 legend, line 6; should be &RD22, RD29A, and COR15 gene specific primers& instead of &RAP gene specific primers&& & We thank the reviewer ’s careful review, and we revised those errors in the new manuscript.
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163abcdc 夏老师：您好， 我的回修稿件是12月2号上传投稿系统的， “Status Date”状态为12月3号， “Current Status” 状态为under review, 怎么期间“Status Date”又从12月3号变为12月29号，这到底是什么原因？到什么时间还没有结果的话，我可以写信问编辑？心里有点急.
蒋Peer Review Policy for Cancer LettersHow long does the peer review process take?
“Typically the manuscript will be reviewed within 3-8 weeks. Should the reviewers' reports contradict one another or a report is unnecessarily delayed a further expert opinion will be sought. Revised manuscripts are usually returned to the initial reviewers within 2-4 weeks. Reviewers may request more than one revision of a manuscript.”催稿信已修改。下面是我的模板。
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ygtq 夏老师，请帮忙指点一下。谢谢Dear Dr. XXX, & & Thank you for arranging a timely review for our manuscript. We are pleased to know that our study is of general interest for the readers of GENE. We have carefully evaluated the reviewers’ critical comments and thoughtful suggestions, responded to these suggestions point-by-point, and revised the manuscript accordingly. All changes made to the text are in red so that they may be easily identified. With regard to the reviewers’ comments and suggestions, we wish to reply as follows:& & To Reviewer #1: & Comments:& & 1. The effects observed for RAP overexpressing Arabidopsis should be compared with RAP knockdowns or knockouts in Arabidopsis.& & We thank reviewer’s suggestion, and added the data in the revised manuscript. As the supplementary figure 3 shown, RNAi-RAP transgenic plants show no significant phenotype compared with WT under normal or stress conditions.& & 2. The RAP overexpressing seedlings showed severe growth inhibition in response to glucose and to NaCl but less pronounced effects in the presence of ABA and sorbitol.Hypotheses explaining these effects should be included in the discussion.& & We believe different stress stimuli through different mechanisms. We speculated that RAP is a transcription factor, which may roles in different stress pathways. But maybe it acts different roles in different pathway. Many reports showed indicated that changes in expression level of a transcription factor may lead to varying degrees of sensitivity to different stresses, such as XERICO (Ko, et al. 2006), ABR1(Pandey,et al. 2005).& & 3. Statistical analyses of the 3 independent experiments of figure 4 should be included.& & As shown in figure 4, we have finished at least 3 independent experiments, the statistical data and significant differences are calculated.& & 4. In figure 1, wild type Arabidopsis stained with the GUS substrate should be shown as a negative control. Thus, the staining pattern in rosette leaves and in siliques should be verified as a RAP specific signal.& & In fact, when we did this control experiment, we used plants transformed with pCAMBIA1300+pBI101 as
so that we can use proper GUS staining conditions to get the RAP specific signal. Now the negative control was added in the supplemental data. & & 5 Highest tissue-specific transcript levels of RAP were observed in stems by RT-PCR but only weak signals could be detected by the GUS staining. In contrast, the GUS staining showed strong signals in roots of A. thaliana whereas the signal was weak in the RT-PCR. How might these effects be explained?& & The material used for RT-PCR analysis was 5-week old Arabidopsis, and the GUS staining plants were seedlings. The inconsistent results were because of the different stages of tissues we used in the two experiments. Also, we use quantitive RT-PCR method to further confirm the RT results.& Moreover, the GUS staining signal was affected by different factors, such as the staining time, the concentration of x-gluc, ect.Our GUS results here only showed the quantity instead of quality expression pattern.& & 6 The effect of salt-induced increase of ABA should be discussed.& & ABA plays vital role in regulating seed germination and it is considered as a plant stress hormone. When plants are subjected to abiotic stresses, the level of ABA will increase (Finkelstein, et al. 2002).Our preliminary investigation lead us suppose that the stress-induced hypersensitive phenotype may be caused by activating ABA-signaling pathway. We supposed that the enhanced activity of RAP confers the observed induction in ABA therefore, plants do not need to produce more ABA, it may reflect a balance between ABA-signaling and ABA-biosynthesis pathways. Similarly, feedback regulation in ABA levels has also been observed in the ERD15 gene study (Kariola,et al. 2006).& & 7. Transcription of RAB18 in ABA-treated plants and of COR15 in NaCl stressed wild type and transgenic Arabidopsis should be shown.& & As shown in figure 7, the results of the transcription of RAB18 in ABA-treated plants and COR15 in NaCl-treated plants are added.& & 8. The conclusion that &RAP could act as an activator of its downstream genes& is not supported by the experimental results presented in the manuscript.& & We agree with the reviewer’s this important viewpoint. Indeed, our results presented could not fully support the conclusion, and further study of downstream targets of RAP will be an important work to understand this transcription factor’s molecular function. As a response to the reviewer, and based on our results, we rephrased our conclusion as “RAP could modulate some ABA and salt-induced gene expression”.& & 9. Was the transcript level of ABI4 higher in the transgenic lines under control or under stress conditions? Experimental data of these experiments should be included.& & We added the data as the reviewer’s suggestion. Our quantitive RT-PCR result showed that ABI4 transcripts were increased under normal or stress conditions in RAP-OX transgenic plants compared with WT.& & 10. The hypothesis that the increased response to ABA might be due to increased expression of ABI4 in the RAP over expressing Arabidopsis is not supported by experimental data.& & In the present study, our results indicated the expression of ABI4, one of the important factors in ABA signaling, enhanced the abundance.& Accordingly, we have modified the sentence to address the reviewer’s point,“All these results led us to speculate that RAP may act as a positive regulator in the ABA-signaling pathway”. & & 11. Other comments:& Last paragraph of the introduction: the 3rd sentence should be rephrased.& & We have modified the sentence as suggested by the reviewer. “Here, we showed evidence for the first time that RAP is involved in Arabidopsis response to ABA and abiotic stress”.& & The selection of transgenic Arabidopsis should be described in more detail.& & We revised this section and described the point in more detail: Wild-type Arabidopsis was transformed by the floral dipping method. T2 seeds from each of the selected transgenic plants were plated on germination medium containing hygromycin as selection antibiotics, and & in total, 10 homozygous lines were selected. Homozygous T3 progeny were then examined for the expression levels of RAP by RT-PCR method, & Representative lines overexpressing RAP were used for further analysis, and results from RAP-OX1 and RAP-OX2 which have different RAP expression levels are shown in this manuscript.& & Origins of the plasmids should be included throughout the manuscript.& & We revised this point in the new manuscript& & Paragraph 2.4: The 1st sentence should be explained in more detail& & We revised the sentence as: “The encoding region without the stop codon of RAP was amplified with primers (5’-GAAGATCTGATGGTGTCTATGCTG ACTAATG-3’and 5’-GACTAGTACCAAAAGAGGAGTAATTG-3’), the fragment was fused in-frame to the 5’-terminal of YFP in the pA7-YFP vector (provided by H.-Q. Yang) using BglII and SpeI site, then verified by sequencing”.& & Paragraph 2.6: ss-galactosidase or ss-glucuronidase?& & As shown in the manuscript, the sentence has been modified to“ss-galactosidase”.& & Paragraph 2.8: The 1st sentence should be rephrased.& & We revised the sentence as: “Approximately 60 seeds each from the wild-type and RAP overexpression transgenic lines (RAP-OX1 and RAP-OX2) were planted in triplicate on Murashige and Skoog (MS) medium supplemented with different concentrations of ABA, NaCl, sorbitol, or glucose, and incubated at 4°C for 4 days before being placed at 22°C under long-day conditions”.& & The accession number of RAP should be included in the manuscript.& & The accession number of RAP is AY114582, and we added it in the new manuscript& & A list of the identified cis-elements and of their position should be included in the main manuscript.& & We added the table to the main manuscript.& & The analysis of transcriptional activation activity in yeast should be explained more precisely.& & We did the experiment more precisely, accordding to the reviewer ‘suggestion. We further analyzed the transcription activity of full RAP ORF, N-terminal ORF and C-terminal ORF.& & Grammar and spelling should be checked throughout the manuscript.& & Reviewer #2: & This manuscript describes characterization of the RAP gene in Arabidopsis. Overall the manuscript is of high quality and it provides novel information about RAP and provides support for a role of this gene in environmental stress response. In addition, the authors provide evidence that RAP, which is a member of the AP2/ERF family, is really a transcription factor. The protein is nuclear localized and can act as a transcriptional activator in yeast, binding to GCC and CE1 cis-elements. The authors show that expression of ABI4 is unregulated in RAP OE lines and suggest that the phenotype of these lines might be a consequence of increase ABI4 levels. & & 1. The paper would be stronger if this hypothesis was tested by introducing& abi4 mutants into the OE lines. & & We thank the reviewer to put forward this important suggestion. We now analyzed the abi4/RAP-OE line under different stress conditions.& We believe that the relationship between ABI4 and RAP is a very important topic, thus we would like to carry out a separate but more extensive experiment on this topic.& & Another area in which the paper could be strengthened is the characterization of the spatial pattern of RAP. The authors use a promoter:GUS reporter but have not shown that this promoter fragment drives proper expression of the gene. Of course, in the absence of a mutant, this is difficult to test. In situ hybridization would directly measure RAP mRNA distribution. One concern I have is that the level of RAP mRNA in leaves looks to be quite high (relative to flowers) based on the& RT-PCR results (Fig. 1. A). But is restricted to just a few cells in the GUS reporter stained leaves (Fig 1.B.v).& & We thank the reviewer’s valuable suggestion. Before the experiment, we use the software to predict the promoter (http://www.fruitfly.org/seq_tools/promoter.html), and the predicted sequence was about 1.4k. And in many studies, they use about 1-1.5kb fragment above the translation start site as the effective promoter, we also use more than 1.5kb (1639bp) sequence as the RAP promoter.& In situ hybridization is effective to determine the RAP mRNA distribution,原位杂交在研究植物发育领域应用比较广泛。我们查找了芯片结果，发现RAP的表达并不是很强，况且我们的原位杂交技术不很成熟。& In fact, the leaf used in RT-PCR was rosette leaf instead of stem leaf (we revised in the new manuscript), and we use quantitive RT-PCR method to further confirm the result. As for the GUS result, we provide the negative control data to make sure the signal was RAP specific.（我们没有条件做原位杂交，况且这个并不是很必要，我用定量pcr的方法来弥补了一下）& & However, if the reviewer feels that it is essential to add the result in this manuscript, we would be glad to carry out the additional experiments.& & Other items& & 1. page 9, line 8, should be &responds& rather than &responses&& 2. page 9, line 20 should be &Numerous& not &A numerous&& 3. page 11, line 3 should be &pHISi-GCC& instead of &pHISi-GC&& 5. page 15, line 22, should be &activating or repressing& instead of &activate or repress&& & Thank you for pointing out the error, which has been corrected in the revised version.& & 4. Is ABI4, the most closely related AP2/ERF protein to RAP?& & We did phylogenetic analyses, and find ABR1 the most closely related AP2/ERF protein to RAP (86%). ABR1 was considered as a repressor of the ABA response in Arabidopsis. And also, ABR1 may functionally interact with ABI4 in the regulation of ABA-responsive genes. However, we think the relationship between ABI4 and RAP is more crucial, first, the conserved amino acid similarity among ABI4 and RAP is nearly also very high (70%); second, ABI4 plays important role in multiple pathways including ABA signaling a third, the promoter of ABI4 have several CE1 cis-element, which RAP could bind to. Because of the reason above, we began to investigate the relationship between the two and provide our preliminarily results. We think a separate and extensive experiment is needed for settle this important issue.& & 6. Figure 3B, Are these replicate assays?& & Yes, all experiments in the manuscript are replicated. And now we provide more precise results in the revised manuscript.& & 7. Figure 4, It is hard to see much difference between WT and the OE lines for 1&mu&M ABA and 150mM NaCl& & We did statistic analysis, and our results showed that although the difference is small, but it really exists.& & 8. Figure 6 legend, line 2, should be &treatment& instead of &treated&& 9. Figure 7 legend, line 6; should be &RD22, RD29A, and COR15 gene specific primers& instead of &RAP gene specific primers&& & We thank the reviewer ’s careful review, and we revised those errors in the new manuscript.ygtq,Please check the attached file.Good luck!
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非常感谢老师耐心回复！
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土蚂蚁,Please check the attached file.Good luck.
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夏老师您好：第一次投sci，现在返稿意见让小修（不过我感觉是大修，因为好多问题），我已修好，现将回复信以文件形式附上，请夏老师帮忙修改，非常感谢。
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主编您好，我投的期刊返稿让补实验，我已经补上了，不知道需不需要将所补内容全部贴上，只是标明位置可不可以。现将回复信附上，请帮忙修改，感激不尽！
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真是好贴子！进来学习一下，对夏老师的热情无私感到敬佩！
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claybird 真是好贴子！进来学习一下，对夏老师的热情无私感到敬佩！对夏老师的热情无私感到敬佩！
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treesea 夏老师：你好，以下是我一篇论文的response letter，由于投稿经验不足，麻烦你帮忙看看，不甚感激~~~谢谢~~~See the attached.Good luck!
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美捷登主编 See the attached.Good luck!非常非常感谢~~~
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太精彩了，感谢夏老师！
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回复信有很多值得关注的地方，回的好改稿的次数也大大减少，努力
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回复信有很多值得关注的地方，回的好改稿的次数也大大减少，努力
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夏老师您好：非常感谢您长久以来的帮助，我最近投稿一篇meta-analysis，现在返稿意见让大修，我已修好，现将审稿人的意见及回复黏贴如下，希望夏老师给把把关，非常期盼能得到您的帮助!
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I will get back to you tomorrow.Thanks.
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快乐跑垒手 夏老师您好：非常感谢您长久以来的帮助，我最近投稿一篇meta-analysis，现在返稿意见让大修，我已修好，现将审稿人的意见及回复黏贴如下，希望夏老师给把把关，非常期盼能得到您的帮助!See attached.Good luck.
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非常感谢夏老师无私的帮助，我会认真修改，届时通报结果！
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请夏老师看看我的小修回复信，以前在夏老师的帮助下，现在感觉回答起来好多了，但还是不放心，请夏老师指教！Reviewer #1: This interesting study provides evidence for a proton-sensitive ASIC1a channel in articular chondrocytes and, as the authors point out, the study is 'a good starting point for a number of subsequent studies into the physiological and pathological roles of ASICs in non-neuronal cells'. CommentsFigure legends are missing.Answer: Thank you for pointing out the error, which has been added in the revised version.The traces shown in Figure 3D appear to be representative traces for a single experiment? It might be better to provide a graph showing mean data from several cells? Answer: It was provided a graph showing mean data from seven cells. This point has been briefly addressed in the revised version of the manuscript (page 3, line 8).In Figure 3D how can one explain the comparatively small rise in Ca2+ concentration when the cells are in Ca2+-free extracellular solution? Several possibilities: Ca2+ contamination in the extracellular fluid and entry of Ca2+ via L-type Ca2+ channels (despite blockade of these channels), leakage of Ca2+ from the SR?Answer: Thank you for sharing your experience in Ca2+ concentration experiments. We accept your comment and consider that small rise in Ca2+ concentration was entry of Ca2+ via L-type Ca2+ channelsMinor points:Reference to Figures in Results section should be checked. Page 9. No reference to Figure 1 in the Results section.Answer: Thank you for pointing out the error, which has been corrected in the revised version.Page 7. State whether confocal experiments were performed at room temperature or physiological temperature?Answer: Confocal experiments were performed at room temperature has been added in the Introduction of the revised version.Page 4, Line 16 - PBS Phosphate buffered saline. State in full first time it appears and then use abbreviation.Answer: Thank you for sharing your experience, which has been corrected in the revised version.Page 9, Line 22 - ..thapsigargin were added to the possible secondary activation…Clarification required.不知审稿人是啥意思？Page 10, Line 1. …confocal micrographs (Figure 3B)….and other references to Figures in this paragraph. Check to see that referencing to different parts of Figure 3 in text correspond to correct panels shown in Figure 3.Answer: I have re-checked the reference carefully and found that the findings of the study are accurately described.Page 12, Line 13. It has proposed…?
Page 12, Line 22. The results our study….?Answer: Thank you for carefully and patiently reviewing of our manuscript, and listing so many mistakes in the original manuscript. Specific corrections in the revised version are followings: I The results of our study.Reviewer #2: This is a straightforward study examining the role of ASIC 1a in chondrocytes.
As seen in neurons, the AS1C1a of chondrocytes transport calcium in a pH dependent manner.
This leads to injury of the chondrocytes at low pH.
The data support the proposed hypothesis.
However, the cells incubated in medium at pH 7.4 also appear to be unstable, as reflected by the increase in LDH release.
What is the source of the instability?
Does the increase in intracellular calcium concentation mediated by ASIC 1a accelerate the events responsible for the instability?Answer: We appreciate the comments, and accept your point of view.
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主编老师您好，我也才刚刚投了一篇文章，杂志是journal of neuroimmunology,内容是cepo(一种药物）对神经干细胞MHC分子表达的影响，其中一个reviewer 认为无法确定cepo在体内的作用，由于时间和资金的限制，我现在无法补充动物体内实验，但不知该如何回复来信，以使拒稿的可能性降到最低，主编老师能指导一下吗？不胜感激！下面是信的原文：Reviewer #1: The authors test the effects of carbamylated erythropoietin (CEPO) on human neural stem cells.In the introduction and discussion, the authors make the important point that a given drug can have many different effects.However, the work is done entirely in vitro.
There is no way to know if the findings have any clinical or other relevance in vivo.
Nor is this topic well-discussed.
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Please check my attached file before your post in response to your request by PM.
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美捷登主编 edited on
美捷登主编 First of all, I have to say that I am not the expert in your research area, and thus I cannot comment on how to exactly reply to the reviewer.However, I would provide some advice based on the above comments and what you described.In my opinion, the comment is critical but not so aggressive and demanding, as the reviewer did not directly request for an additional in vivo study. Thus, you have an opportunity to reply to the comment without an in vivo study.I would suggest:1. Check your Instruction and Discussion to see if you overstated the aims and the findings. Don't draw a conclusion that you cannot from your findings.2. In the Reply letter, give a praise to the reviewer for the constructive comment, and explain frankly why you cannot do the in vivo study. 3. Do some literature search to find if there are some in vivo studies supporting your in vitro findings, and then use these findings to further discuss the topic in the Discussion section.Perhaps, this may be of help.Good luck!美捷登主编三句话，一句值千金！
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夏老师好，我的回修稿件是12月2号上传cancer letters的，12月3号状态就变为under review, 怎么期间状态又从12月3号under review变为12月29号under review，这到底什么原因？不会under review是从12月29号才开始算得吧？
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163abcdc 夏老师好，我的回修稿件是12月2号上传cancer letters的，12月3号状态就变为under review, 怎么期间状态又从12月3号under review变为12月29号under review，这到底什么原因？不会under review是从12月29号才开始算得吧？You are confusing me, Dr. Jiang. What do you mean by the change from &under review& to &under review&? However, I don't think it matters. Again, you should be patient as many editors and reviewers just returned from their long holiday (I just received three papers to review over the last week). So, please give them some time to do the job. Normally, your paper should be accepted after revision by the journal.
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psyuan 请夏老师看看我的小修回复信，以前在夏老师的帮助下，现在感觉回答起来好多了，但还是不放心，请夏老师指教！Reviewer #1: This interesting study provides evidence for a proton-sensitive ASIC1a channel in articular chondrocytes and, as the authors point out, the study is 'a good starting point for a number of subsequent studies into the physiological and pathological roles of ASICs in non-neuronal cells'. CommentsFigure legends are missing.Answer: Thank you for pointing out the error, which has been added in the revised version.The traces shown in Figure 3D appear to be representative traces for a single experiment? It might be better to provide a graph showing mean data from several cells? Answer: It was provided a graph showing mean data from seven cells. This point has been briefly addressed in the revised version of the manuscript (page 3, line 8).In Figure 3D how can one explain the comparatively small rise in Ca2+ concentration when the cells are in Ca2+-free extracellular solution? Several possibilities: Ca2+ contamination in the extracellular fluid and entry of Ca2+ via L-type Ca2+ channels (despite blockade of these channels), leakage of Ca2+ from the SR?Answer: Thank you for sharing your experience in Ca2+ concentration experiments. We accept your comment and consider that small rise in Ca2+ concentration was entry of Ca2+ via L-type Ca2+ channelsMinor points:Reference to Figures in Results section should be checked. Page 9. No reference to Figure 1 in the Results section.Answer: Thank you for pointing out the error, which has been corrected in the revised version.Page 7. State whether confocal experiments were performed at room temperature or physiological temperature?Answer: Confocal experiments were performed at room temperature has been added in the Introduction of the revised version.Page 4, Line 16 - PBS Phosphate buffered saline. State in full first time it appears and then use abbreviation.Answer: Thank you for sharing your experience, which has been corrected in the revised version.Page 9, Line 22 - ..thapsigargin were added to the possible secondary activation…Clarification required.不知审稿人是啥意思？Page 10, Line 1. …confocal micrographs (Figure 3B)….and other references to Figures in this paragraph. Check to see that referencing to different parts of Figure 3 in text correspond to correct panels shown in Figure 3.Answer: I have re-checked the reference carefully and found that the findings of the study are accurately described.Page 12, Line 13. It has proposed…?
Page 12, Line 22. The results our study….?Answer: Thank you for carefully and patiently reviewing of our manuscript, and listing so many mistakes in the original manuscript. Specific corrections in the revised version are followings: I The results of our study.Reviewer #2: This is a straightforward study examining the role of ASIC 1a in chondrocytes.
As seen in neurons, the AS1C1a of chondrocytes transport calcium in a pH dependent manner.
This leads to injury of the chondrocytes at low pH.
The data support the proposed hypothesis.
However, the cells incubated in medium at pH 7.4 also appear to be unstable, as reflected by the increase in LDH release.
What is the source of the instability?
Does the increase in intracellular calcium concentation mediated by ASIC 1a accelerate the events responsible for the instability?Answer: We appreciate the comments, and accept your point of view.Dear Dr. Yuan,I am so sorry for missing your request post due to my heavy workload.Attached is my edited version, and I hope it is not too late to submit.Good luck.
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夏老师，谢谢！！您辛苦啦！！
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学习学习 很有收获 O(∩_∩)O谢谢
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楼主，您好！我有一篇文章，关于胃癌免疫方面的，不知投什么杂志。很着急！
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留下记号，慢慢看
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夏老师：您好， 我的回修稿件是12月2号上传投稿系统的， “Status Date”状态为12月3号， “Current Status” 状态为under review, 怎么期间“Status Date”又从12月3号变为12月29号，这到底是什么原因？到什么时间还没有结果的话，我可以写信问编辑？心里有点急.
蒋Peer Review Policy for Cancer LettersHow long does the peer review process take?
“Typically the manuscript will be reviewed within 3-8 weeks. Should the reviewers' reports contradict one another or a report is unnecessarily delayed a further expert opinion will be sought. Revised manuscripts are usually returned to the initial reviewers within 2-4 weeks. Reviewers may request more than one revision of a manuscript.”
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163abcdc edited on
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I understand your feeling. Please be patient and do give them another 2 week to make a decision on your paper.You can send a reminder to the editor by the end of the month (perhaps you have already received a positive one by the time).Good luck:)
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Dear zhanghaisen,Please download the attached file.Let me know if you need any help.
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[Hidden Post:1]
您无权限看这个帖子，您的积分需要大于 1
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Please check the attached file above your post for my revisions in your letter sent by PM.
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美捷登主编 edited on
夏老师，请帮忙指点一下。谢谢Dear Dr. XXX, & & Thank you for arranging a timely review for our manuscript. We are pleased to know that our study is of general interest for the readers of GENE. We have carefully evaluated the reviewers’ critical comments and thoughtful suggestions, responded to these suggestions point-by-point, and revised the manuscript accordingly. All changes made to the text are in red so that they may be easily identified. With regard to the reviewers’ comments and suggestions, we wish to reply as follows:& & To Reviewer #1: & Comments:& & 1. The effects observed for RAP overexpressing Arabidopsis should be compared with RAP knockdowns or knockouts in Arabidopsis.& & We thank reviewer’s suggestion, and added the data in the revised manuscript. As the supplementary figure 3 shown, RNAi-RAP transgenic plants show no significant phenotype compared with WT under normal or stress conditions.& & 2. The RAP overexpressing seedlings showed severe growth inhibition in response to glucose and to NaCl but less pronounced effects in the presence of ABA and sorbitol.Hypotheses explaining these effects should be included in the discussion.& & We believe different stress stimuli through different mechanisms. We speculated that RAP is a transcription factor, which may roles in different stress pathways. But maybe it acts different roles in different pathway. Many reports showed indicated that changes in expression level of a transcription factor may lead to varying degrees of sensitivity to different stresses, such as XERICO (Ko, et al. 2006), ABR1(Pandey,et al. 2005).& & 3. Statistical analyses of the 3 independent experiments of figure 4 should be included.& & As shown in figure 4, we have finished at least 3 independent experiments, the statistical data and significant differences are calculated.& & 4. In figure 1, wild type Arabidopsis stained with the GUS substrate should be shown as a negative control. Thus, the staining pattern in rosette leaves and in siliques should be verified as a RAP specific signal.& & In fact, when we did this control experiment, we used plants transformed with pCAMBIA1300+pBI101 as
so that we can use proper GUS staining conditions to get the RAP specific signal. Now the negative control was added in the supplemental data. & & 5 Highest tissue-specific transcript levels of RAP were observed in stems by RT-PCR but only weak signals could be detected by the GUS staining. In contrast, the GUS staining showed strong signals in roots of A. thaliana whereas the signal was weak in the RT-PCR. How might these effects be explained?& & The material used for RT-PCR analysis was 5-week old Arabidopsis, and the GUS staining plants were seedlings. The inconsistent results were because of the different stages of tissues we used in the two experiments. Also, we use quantitive RT-PCR method to further confirm the RT results.& Moreover, the GUS staining signal was affected by different factors, such as the staining time, the concentration of x-gluc, ect.Our GUS results here only showed the quantity instead of quality expression pattern.& & 6 The effect of salt-induced increase of ABA should be discussed.& & ABA plays vital role in regulating seed germination and it is considered as a plant stress hormone. When plants are subjected to abiotic stresses, the level of ABA will increase (Finkelstein, et al. 2002).Our preliminary investigation lead us suppose that the stress-induced hypersensitive phenotype may be caused by activating ABA-signaling pathway. We supposed that the enhanced activity of RAP confers the observed induction in ABA therefore, plants do not need to produce more ABA, it may reflect a balance between ABA-signaling and ABA-biosynthesis pathways. Similarly, feedback regulation in ABA levels has also been observed in the ERD15 gene study (Kariola,et al. 2006).& & 7. Transcription of RAB18 in ABA-treated plants and of COR15 in NaCl stressed wild type and transgenic Arabidopsis should be shown.& & As shown in figure 7, the results of the transcription of RAB18 in ABA-treated plants and COR15 in NaCl-treated plants are added.& & 8. The conclusion that &RAP could act as an activator of its downstream genes& is not supported by the experimental results presented in the manuscript.& & We agree with the reviewer’s this important viewpoint. Indeed, our results presented could not fully support the conclusion, and further study of downstream targets of RAP will be an important work to understand this transcription factor’s molecular function. As a response to the reviewer, and based on our results, we rephrased our conclusion as “RAP could modulate some ABA and salt-induced gene expression”.& & 9. Was the transcript level of ABI4 higher in the transgenic lines under control or under stress conditions? Experimental data of these experiments should be included.& & We added the data as the reviewer’s suggestion. Our quantitive RT-PCR result showed that ABI4 transcripts were increased under normal or stress conditions in RAP-OX transgenic plants compared with WT.& & 10. The hypothesis that the increased response to ABA might be due to increased expression of ABI4 in the RAP over expressing Arabidopsis is not supported by experimental data.& & In the present study, our results indicated the expression of ABI4, one of the important factors in ABA signaling, enhanced the abundance.& Accordingly, we have modified the sentence to address the reviewer’s point,“All these results led us to speculate that RAP may act as a positive regulator in the ABA-signaling pathway”. & & 11. Other comments:& Last paragraph of the introduction: the 3rd sentence should be rephrased.& & We have modified the sentence as suggested by the reviewer. “Here, we showed evidence for the first time that RAP is involved in Arabidopsis response to ABA and abiotic stress”.& & The selection of transgenic Arabidopsis should be described in more detail.& & We revised this section and described the point in more detail: Wild-type Arabidopsis was transformed by the floral dipping method. T2 seeds from each of the selected transgenic plants were plated on germination medium containing hygromycin as selection antibiotics, and & in total, 10 homozygous lines were selected. Homozygous T3 progeny were then examined for the expression levels of RAP by RT-PCR method, & Representative lines overexpressing RAP were used for further analysis, and results from RAP-OX1 and RAP-OX2 which have different RAP expression levels are shown in this manuscript.& & Origins of the plasmids should be included throughout the manuscript.& & We revised this point in the new manuscript& & Paragraph 2.4: The 1st sentence should be explained in more detail& & We revised the sentence as: “The encoding region without the stop codon of RAP was amplified with primers (5’-GAAGATCTGATGGTGTCTATGCTG ACTAATG-3’and 5’-GACTAGTACCAAAAGAGGAGTAATTG-3’), the fragment was fused in-frame to the 5’-terminal of YFP in the pA7-YFP vector (provided by H.-Q. Yang) using BglII and SpeI site, then verified by sequencing”.& & Paragraph 2.6: ss-galactosidase or ss-glucuronidase?& & As shown in the manuscript, the sentence has been modified to“ss-galactosidase”.& & Paragraph 2.8: The 1st sentence should be rephrased.& & We revised the sentence as: “Approximately 60 seeds each from the wild-type and RAP overexpression transgenic lines (RAP-OX1 and RAP-OX2) were planted in triplicate on Murashige and Skoog (MS) medium supplemented with different concentrations of ABA, NaCl, sorbitol, or glucose, and incubated at 4°C for 4 days before being placed at 22°C under long-day conditions”.& & The accession number of RAP should be included in the manuscript.& & The accession number of RAP is AY114582, and we added it in the new manuscript& & A list of the identified cis-elements and of their position should be included in the main manuscript.& & We added the table to the main manuscript.& & The analysis of transcriptional activation activity in yeast should be explained more precisely.& & We did the experiment more precisely, accordding to the reviewer ‘suggestion. We further analyzed the transcription activity of full RAP ORF, N-terminal ORF and C-terminal ORF.& & Grammar and spelling should be checked throughout the manuscript.& & Reviewer #2: & This manuscript describes characterization of the RAP gene in Arabidopsis. Overall the manuscript is of high quality and it provides novel information about RAP and provides support for a role of this gene in environmental stress response. In addition, the authors provide evidence that RAP, which is a member of the AP2/ERF family, is really a transcription factor. The protein is nuclear localized and can act as a transcriptional activator in yeast, binding to GCC and CE1 cis-elements. The authors show that expression of ABI4 is unregulated in RAP OE lines and suggest that the phenotype of these lines might be a consequence of increase ABI4 levels. & & 1. The paper would be stronger if this hypothesis was tested by introducing& abi4 mutants into the OE lines. & & We thank the reviewer to put forward this important suggestion. We now analyzed the abi4/RAP-OE line under different stress conditions.& We believe that the relationship between ABI4 and RAP is a very important topic, thus we would like to carry out a separate but more extensive experiment on this topic.& & Another area in which the paper could be strengthened is the characterization of the spatial pattern of RAP. The authors use a promoter:GUS reporter but have not shown that this promoter fragment drives proper expression of the gene. Of course, in the absence of a mutant, this is difficult to test. In situ hybridization would directly measure RAP mRNA distribution. One concern I have is that the level of RAP mRNA in leaves looks to be quite high (relative to flowers) based on the& RT-PCR results (Fig. 1. A). But is restricted to just a few cells in the GUS reporter stained leaves (Fig 1.B.v).& & We thank the reviewer’s valuable suggestion. Before the experiment, we use the software to predict the promoter (http://www.fruitfly.org/seq_tools/promoter.html), and the predicted sequence was about 1.4k. And in many studies, they use about 1-1.5kb fragment above the translation start site as the effective promoter, we also use more than 1.5kb (1639bp) sequence as the RAP promoter.& In situ hybridization is effective to determine the RAP mRNA distribution,原位杂交在研究植物发育领域应用比较广泛。我们查找了芯片结果，发现RAP的表达并不是很强，况且我们的原位杂交技术不很成熟。& In fact, the leaf used in RT-PCR was rosette leaf instead of stem leaf (we revised in the new manuscript), and we use quantitive RT-PCR method to further confirm the result. As for the GUS result, we provide the negative control data to make sure the signal was RAP specific.（我们没有条件做原位杂交，况且这个并不是很必要，我用定量pcr的方法来弥补了一下）& & However, if the reviewer feels that it is essential to add the result in this manuscript, we would be glad to carry out the additional experiments.& & Other items& & 1. page 9, line 8, should be &responds& rather than &responses&& 2. page 9, line 20 should be &Numerous& not &A numerous&& 3. page 11, line 3 should be &pHISi-GCC& instead of &pHISi-GC&& 5. page 15, line 22, should be &activating or repressing& instead of &activate or repress&& & Thank you for pointing out the error, which has been corrected in the revised version.& & 4. Is ABI4, the most closely related AP2/ERF protein to RAP?& & We did phylogenetic analyses, and find ABR1 the most closely related AP2/ERF protein to RAP (86%). ABR1 was considered as a repressor of the ABA response in Arabidopsis. And also, ABR1 may functionally interact with ABI4 in the regulation of ABA-responsive genes. However, we think the relationship between ABI4 and RAP is more crucial, first, the conserved amino acid similarity among ABI4 and RAP is nearly also very high (70%); second, ABI4 plays important role in multiple pathways including ABA signaling a third, the promoter of ABI4 have several CE1 cis-element, which RAP could bind to. Because of the reason above, we began to investigate the relationship between the two and provide our preliminarily results. We think a separate and extensive experiment is needed for settle this important issue.& & 6. Figure 3B, Are these replicate assays?& & Yes, all experiments in the manuscript are replicated. And now we provide more precise results in the revised manuscript.& & 7. Figure 4, It is hard to see much difference between WT and the OE lines for 1&mu&M ABA and 150mM NaCl& & We did statistic analysis, and our results showed that although the difference is small, but it really exists.& & 8. Figure 6 legend, line 2, should be &treatment& instead of &treated&& 9. Figure 7 legend, line 6; should be &RD22, RD29A, and COR15 gene specific primers& instead of &RAP gene specific primers&& & We thank the reviewer ’s careful review, and we revised those errors in the new manuscript.
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163abcdc 夏老师：您好， 我的回修稿件是12月2号上传投稿系统的， “Status Date”状态为12月3号， “Current Status” 状态为under review, 怎么期间“Status Date”又从12月3号变为12月29号，这到底是什么原因？到什么时间还没有结果的话，我可以写信问编辑？心里有点急.
蒋Peer Review Policy for Cancer LettersHow long does the peer review process take?
“Typically the manuscript will be reviewed within 3-8 weeks. Should the reviewers' reports contradict one another or a report is unnecessarily delayed a further expert opinion will be sought. Revised manuscripts are usually returned to the initial reviewers within 2-4 weeks. Reviewers may request more than one revision of a manuscript.”催稿信已修改。下面是我的模板。
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谢谢夏老师
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ygtq 夏老师，请帮忙指点一下。谢谢Dear Dr. XXX, & & Thank you for arranging a timely review for our manuscript. We are pleased to know that our study is of general interest for the readers of GENE. We have carefully evaluated the reviewers’ critical comments and thoughtful suggestions, responded to these suggestions point-by-point, and revised the manuscript accordingly. All changes made to the text are in red so that they may be easily identified. With regard to the reviewers’ comments and suggestions, we wish to reply as follows:& & To Reviewer #1: & Comments:& & 1. The effects observed for RAP overexpressing Arabidopsis should be compared with RAP knockdowns or knockouts in Arabidopsis.& & We thank reviewer’s suggestion, and added the data in the revised manuscript. As the supplementary figure 3 shown, RNAi-RAP transgenic plants show no significant phenotype compared with WT under normal or stress conditions.& & 2. The RAP overexpressing seedlings showed severe growth inhibition in response to glucose and to NaCl but less pronounced effects in the presence of ABA and sorbitol.Hypotheses explaining these effects should be included in the discussion.& & We believe different stress stimuli through different mechanisms. We speculated that RAP is a transcription factor, which may roles in different stress pathways. But maybe it acts different roles in different pathway. Many reports showed indicated that changes in expression level of a transcription factor may lead to varying degrees of sensitivity to different stresses, such as XERICO (Ko, et al. 2006), ABR1(Pandey,et al. 2005).& & 3. Statistical analyses of the 3 independent experiments of figure 4 should be included.& & As shown in figure 4, we have finished at least 3 independent experiments, the statistical data and significant differences are calculated.& & 4. In figure 1, wild type Arabidopsis stained with the GUS substrate should be shown as a negative control. Thus, the staining pattern in rosette leaves and in siliques should be verified as a RAP specific signal.& & In fact, when we did this control experiment, we used plants transformed with pCAMBIA1300+pBI101 as
so that we can use proper GUS staining conditions to get the RAP specific signal. Now the negative control was added in the supplemental data. & & 5 Highest tissue-specific transcript levels of RAP were observed in stems by RT-PCR but only weak signals could be detected by the GUS staining. In contrast, the GUS staining showed strong signals in roots of A. thaliana whereas the signal was weak in the RT-PCR. How might these effects be explained?& & The material used for RT-PCR analysis was 5-week old Arabidopsis, and the GUS staining plants were seedlings. The inconsistent results were because of the different stages of tissues we used in the two experiments. Also, we use quantitive RT-PCR method to further confirm the RT results.& Moreover, the GUS staining signal was affected by different factors, such as the staining time, the concentration of x-gluc, ect.Our GUS results here only showed the quantity instead of quality expression pattern.& & 6 The effect of salt-induced increase of ABA should be discussed.& & ABA plays vital role in regulating seed germination and it is considered as a plant stress hormone. When plants are subjected to abiotic stresses, the level of ABA will increase (Finkelstein, et al. 2002).Our preliminary investigation lead us suppose that the stress-induced hypersensitive phenotype may be caused by activating ABA-signaling pathway. We supposed that the enhanced activity of RAP confers the observed induction in ABA therefore, plants do not need to produce more ABA, it may reflect a balance between ABA-signaling and ABA-biosynthesis pathways. Similarly, feedback regulation in ABA levels has also been observed in the ERD15 gene study (Kariola,et al. 2006).& & 7. Transcription of RAB18 in ABA-treated plants and of COR15 in NaCl stressed wild type and transgenic Arabidopsis should be shown.& & As shown in figure 7, the results of the transcription of RAB18 in ABA-treated plants and COR15 in NaCl-treated plants are added.& & 8. The conclusion that &RAP could act as an activator of its downstream genes& is not supported by the experimental results presented in the manuscript.& & We agree with the reviewer’s this important viewpoint. Indeed, our results presented could not fully support the conclusion, and further study of downstream targets of RAP will be an important work to understand this transcription factor’s molecular function. As a response to the reviewer, and based on our results, we rephrased our conclusion as “RAP could modulate some ABA and salt-induced gene expression”.& & 9. Was the transcript level of ABI4 higher in the transgenic lines under control or under stress conditions? Experimental data of these experiments should be included.& & We added the data as the reviewer’s suggestion. Our quantitive RT-PCR result showed that ABI4 transcripts were increased under normal or stress conditions in RAP-OX transgenic plants compared with WT.& & 10. The hypothesis that the increased response to ABA might be due to increased expression of ABI4 in the RAP over expressing Arabidopsis is not supported by experimental data.& & In the present study, our results indicated the expression of ABI4, one of the important factors in ABA signaling, enhanced the abundance.& Accordingly, we have modified the sentence to address the reviewer’s point,“All these results led us to speculate that RAP may act as a positive regulator in the ABA-signaling pathway”. & & 11. Other comments:& Last paragraph of the introduction: the 3rd sentence should be rephrased.& & We have modified the sentence as suggested by the reviewer. “Here, we showed evidence for the first time that RAP is involved in Arabidopsis response to ABA and abiotic stress”.& & The selection of transgenic Arabidopsis should be described in more detail.& & We revised this section and described the point in more detail: Wild-type Arabidopsis was transformed by the floral dipping method. T2 seeds from each of the selected transgenic plants were plated on germination medium containing hygromycin as selection antibiotics, and & in total, 10 homozygous lines were selected. Homozygous T3 progeny were then examined for the expression levels of RAP by RT-PCR method, & Representative lines overexpressing RAP were used for further analysis, and results from RAP-OX1 and RAP-OX2 which have different RAP expression levels are shown in this manuscript.& & Origins of the plasmids should be included throughout the manuscript.& & We revised this point in the new manuscript& & Paragraph 2.4: The 1st sentence should be explained in more detail& & We revised the sentence as: “The encoding region without the stop codon of RAP was amplified with primers (5’-GAAGATCTGATGGTGTCTATGCTG ACTAATG-3’and 5’-GACTAGTACCAAAAGAGGAGTAATTG-3’), the fragment was fused in-frame to the 5’-terminal of YFP in the pA7-YFP vector (provided by H.-Q. Yang) using BglII and SpeI site, then verified by sequencing”.& & Paragraph 2.6: ss-galactosidase or ss-glucuronidase?& & As shown in the manuscript, the sentence has been modified to“ss-galactosidase”.& & Paragraph 2.8: The 1st sentence should be rephrased.& & We revised the sentence as: “Approximately 60 seeds each from the wild-type and RAP overexpression transgenic lines (RAP-OX1 and RAP-OX2) were planted in triplicate on Murashige and Skoog (MS) medium supplemented with different concentrations of ABA, NaCl, sorbitol, or glucose, and incubated at 4°C for 4 days before being placed at 22°C under long-day conditions”.& & The accession number of RAP should be included in the manuscript.& & The accession number of RAP is AY114582, and we added it in the new manuscript& & A list of the identified cis-elements and of their position should be included in the main manuscript.& & We added the table to the main manuscript.& & The analysis of transcriptional activation activity in yeast should be explained more precisely.& & We did the experiment more precisely, accordding to the reviewer ‘suggestion. We further analyzed the transcription activity of full RAP ORF, N-terminal ORF and C-terminal ORF.& & Grammar and spelling should be checked throughout the manuscript.& & Reviewer #2: & This manuscript describes characterization of the RAP gene in Arabidopsis. Overall the manuscript is of high quality and it provides novel information about RAP and provides support for a role of this gene in environmental stress response. In addition, the authors provide evidence that RAP, which is a member of the AP2/ERF family, is really a transcription factor. The protein is nuclear localized and can act as a transcriptional activator in yeast, binding to GCC and CE1 cis-elements. The authors show that expression of ABI4 is unregulated in RAP OE lines and suggest that the phenotype of these lines might be a consequence of increase ABI4 levels. & & 1. The paper would be stronger if this hypothesis was tested by introducing& abi4 mutants into the OE lines. & & We thank the reviewer to put forward this important suggestion. We now analyzed the abi4/RAP-OE line under different stress conditions.& We believe that the relationship between ABI4 and RAP is a very important topic, thus we would like to carry out a separate but more extensive experiment on this topic.& & Another area in which the paper could be strengthened is the characterization of the spatial pattern of RAP. The authors use a promoter:GUS reporter but have not shown that this promoter fragment drives proper expression of the gene. Of course, in the absence of a mutant, this is difficult to test. In situ hybridization would directly measure RAP mRNA distribution. One concern I have is that the level of RAP mRNA in leaves looks to be quite high (relative to flowers) based on the& RT-PCR results (Fig. 1. A). But is restricted to just a few cells in the GUS reporter stained leaves (Fig 1.B.v).& & We thank the reviewer’s valuable suggestion. Before the experiment, we use the software to predict the promoter (http://www.fruitfly.org/seq_tools/promoter.html), and the predicted sequence was about 1.4k. And in many studies, they use about 1-1.5kb fragment above the translation start site as the effective promoter, we also use more than 1.5kb (1639bp) sequence as the RAP promoter.& In situ hybridization is effective to determine the RAP mRNA distribution,原位杂交在研究植物发育领域应用比较广泛。我们查找了芯片结果，发现RAP的表达并不是很强，况且我们的原位杂交技术不很成熟。& In fact, the leaf used in RT-PCR was rosette leaf instead of stem leaf (we revised in the new manuscript), and we use quantitive RT-PCR method to further confirm the result. As for the GUS result, we provide the negative control data to make sure the signal was RAP specific.（我们没有条件做原位杂交，况且这个并不是很必要，我用定量pcr的方法来弥补了一下）& & However, if the reviewer feels that it is essential to add the result in this manuscript, we would be glad to carry out the additional experiments.& & Other items& & 1. page 9, line 8, should be &responds& rather than &responses&& 2. page 9, line 20 should be &Numerous& not &A numerous&& 3. page 11, line 3 should be &pHISi-GCC& instead of &pHISi-GC&& 5. page 15, line 22, should be &activating or repressing& instead of &activate or repress&& & Thank you for pointing out the error, which has been corrected in the revised version.& & 4. Is ABI4, the most closely related AP2/ERF protein to RAP?& & We did phylogenetic analyses, and find ABR1 the most closely related AP2/ERF protein to RAP (86%). ABR1 was considered as a repressor of the ABA response in Arabidopsis. And also, ABR1 may functionally interact with ABI4 in the regulation of ABA-responsive genes. However, we think the relationship between ABI4 and RAP is more crucial, first, the conserved amino acid similarity among ABI4 and RAP is nearly also very high (70%); second, ABI4 plays important role in multiple pathways including ABA signaling a third, the promoter of ABI4 have several CE1 cis-element, which RAP could bind to. Because of the reason above, we began to investigate the relationship between the two and provide our preliminarily results. We think a separate and extensive experiment is needed for settle this important issue.& & 6. Figure 3B, Are these replicate assays?& & Yes, all experiments in the manuscript are replicated. And now we provide more precise results in the revised manuscript.& & 7. Figure 4, It is hard to see much difference between WT and the OE lines for 1&mu&M ABA and 150mM NaCl& & We did statistic analysis, and our results showed that although the difference is small, but it really exists.& & 8. Figure 6 legend, line 2, should be &treatment& instead of &treated&& 9. Figure 7 legend, line 6; should be &RD22, RD29A, and COR15 gene specific primers& instead of &RAP gene specific primers&& & We thank the reviewer ’s careful review, and we revised those errors in the new manuscript.ygtq,Please check the attached file.Good luck!
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非常感谢老师耐心回复！
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土蚂蚁,Please check the attached file.Good luck.
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夏老师您好：第一次投sci，现在返稿意见让小修（不过我感觉是大修，因为好多问题），我已修好，现将回复信以文件形式附上，请夏老师帮忙修改，非常感谢。
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主编您好，我投的期刊返稿让补实验，我已经补上了，不知道需不需要将所补内容全部贴上，只是标明位置可不可以。现将回复信附上，请帮忙修改，感激不尽！
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