User talk:Houq/sandbox

This topic is very underexplored on Wikipedia. It lists more than 50 references on the page but cites only three, going into only minimal detail. Its sister binding domains (which contain the coiled coil leucine-zipper motif) are explored in articles spanning numerous sections and topics and yet this stub spans only a single paragraph. Its structure and function are well defined and there is a wealth of available information on the topic. It has well-known and characterized example proteins, including the c-Fos and c-Jun proteins, which are involved in cellular proliferation and apoptosis. We are looking forward to discussing the mechanisms by which it operates, its biological and cellular significance, and its clinical relevance. We could also explore the structure, binding mechanism, and specificity of this binding domain.

Houq (talk) 16:52, 15 October 2015 (UTC)

AP-1 Peer Review 1
The Wikipedia page covered all important concepts of AP-1 and was significantly more detailed than the original. The topic choice for each section was very appropriate as they all played a role in the development of AP-1 concepts. I liked the bolded parts under the Function section, Cell Growth, Proliferation, Cellular Differentiation and Apoptosis, because first, it helped with the overall organization of the Wikipedia page and second, they linked back to ideas that were previously talked about in the general summary. The "Physiological Relevance" section was also a good addition as it demonstrated the importance of studying AP-1. However, the Structure and History sections proved to be slightly confusing and difficult to read, so perhaps simplification of words and concepts as well as addition of extra pictures would be helpful. The rest were clear and easy to understand and the length of each section was suitable for the topic, not too brief or excessively detailed. The group did an excellent job linking important concepts to respective Wikipedia pages and highlighting key words in each section. Furthermore, the materials added were new and differed from the original Wikipedia contents.

The figure added was helpful in terms of clarifying the ideas under the Structure section, especially the description underneath the picture. However, the Structure section was the most confusing, so addition of extra pictures would make this section more comprehensible.

The group did an excellent job with references, about 18 in total. Also, most of the sources came from journal articles, which is reassuring as it demonstrates accuracy of the contents written.

Overall, the page is well organized and the role and importance of AP-1 is clearly explained. Important concepts were linked to other Wikipedia pages and the amount of references exceeded the expectation. However, some of the language used is difficult to comprehend for non-experts, so simplification of words and along with addition of extra pictures would help with clarification.

Chemistrychemistry (talk) 16:57, 21 October 2015 (UTC)Chemistrychemistry

AP-1 Peer Review 2
The original Wikipedia page goes into very minimal detail about the AP-1 transcription factor. Additionally, the original page was not very accessible for non-experts to be able to comprehend what the AP-1 TF is really all about. The introduction section and basic history/structure sections do a good job of introducing the topic of AP-1 and is accessible for non-experts, but likely will require the reader to have some basic biology background to fully understand the significance. The contents in each section do a great job of providing the respective information. I was particularly impressed with the function section and how it provided specific examples. There is only one figure on the new Wikipedia page but I think that is plenty for this topic. The figure is the crystal structure of the transcription factor and shows how it interacts with DNA and provides the reader with a visual representation of what they are reading about, as well as showing what structural motifs are present and how they might play a role in the activity. Are there any other crystal structures for other subunits of the transcription factor that might be beneficial to add? The reference list on the new article looks good with a total of 18 references, indicating thorough research in preparation for this project. It appears that all of the references come from journals, which gives me confidence in the information given in the article. Perhaps your group could find additional information on the topic that comes from a non-journal source to be more inclusive of readers that may not have access to the journals already referenced. Overall, the presentation and formatting of the new page is really good. It is extremely well organized and maintains good flow throughout the page.

Scott5485 (talk) 15:41, 22 October 2015 (UTC)

AP-1 Peer Review 3
In the original Wikipedia page about the AP-1 transcription factor, there is only 2 very short paragraphs and an image explaining what it is, what it does, and how it works. In addition, there is an image on the right hand side. To someone who doesn't know anything about biochemistry and the mechanics of how DNA replication works, this page is difficult to comprehend because it just lists all the facts about the AP-1 Transcription factor without explaining anything. This is ineffective and I thought you guys did a good job in expanding on the existing post. In response to the edits you made to the Wikipedia page, you really went into a lot more detail than what was provided previously. In addition to adding more information, you added a more detailed image and explained your image clearly as well. Although I think that the addition of information is great, one with little knowledge in biochemistry would not be able to make sense of your page. This Wikipedia page is supposed to be aimed toward an audience of non-experts, however, what you wrote was definitely for someone with a lot of background in chemistry and biochemistry. Although I realize that it may be difficult to write about this subject in a simpler way, this can somewhat be made up for by giving more examples and applications. One aspect that I thought you did well was the explanations of cell growth and proliferation, cellular differentiation, and apoptosis (the 3 subjects that were briefly mentioned in the original page). I think that being able to explain to the reader what these three topics are helps increase reader comprehension, and does indeed help a less knowledgeable reader. Another aspect of your page that I really liked was the physiological relevance. I think that after explaining what this complicated transcription factor does, it's nice to see its physiological application as well. Therefore, I think that expanding this applications section would be beneficial to your page, perhaps through adding more examples. In conclusion, I think you guys did a great job but tone down the vocabulary for the average reader.

AP-1 Peer Review 4
Content The introduction section is accessible to the layperson, as it is simple and provides external links for reference when more complex terms are mentioned. However, I found the introduction section to be a bit vague, as I did not really further my understanding on the function of AP-1 from reading that it regulates gene expression and controls various cellular processes. This is a very common feature of many transcription factors and does not give me information on what exactly makes AP-1 unique in its function. I realize that this information is expanded upon later in the article, but I think a sentence or even a short phrase further explaining cellular function would help a reader get a quicker grasp on the topic. The history section is bit too focused on the structural discoveries that have been made in relation to AP-1. Upon reading articles related to the topic, I have found additional information that might be helpful to include here, such as discoveries related to regulation including effects by hypoxia, retinoic acid, and thyroid hormone receptor, to name a few (Bandyopadhyay, et. al., 1995 & Desbois, et. al., 1991). It might also be interesting to include recent research findings that correlate AP-1 with various physiological processes or diseases (though this information may be more appropriate to the physiological relevance section). Upon further research, I found that AP-1 has implications in breast cancer, influenza virus infections, cervical cancer, and human papilloma virus (HPV) (Ludwig, et. al., 2002; Shen, et. al., 2007; Prusty & Das, 2005). The “Structure” section is very comprehensive, and I commend the additions here, but I think the section could be a bit more visually friendly. In other words, the one large paragraph could easily be broken up into smaller sections, and that might make the text seem a bit less intimidating to the layperson reader. The “Function” and “Regulation of AP-1” sections are presented well, but the “Physiological relevance” is once again a bit vague. I would have appreciated a bit more information regarding how exactly AP-1 is believed to be involved in tissue regeneration, unless that is still unknown. If that is the case, the authors may want to add that its specific role is currently unknown. Overall, most of the terms that should be linked to external Wikipedia pages are linked, but I noticed a few that could be added to the page for additional reference. Those are listed below:

History “TPA-inducible transcription factor” “p39 protein”

Structure “residues”

Function “basal levels” “DNA synthesis” “palindromic DNA motif”

Physiological relevance “skin metabolism” “undifferentiated” [cells]

Finally, while I think this group did a phenomenal job expanding upon the already-existing Wikipedia page on the topic, I was disappointed to find that the editors eliminated the section from the original page titled “Regulome.” This section included information on what hormones, transcription factors, and overall signaling pathways AP-1 activates and inhibits, as well as what agents activate and inhibit the activator protein. I think this information could have been presented in a more visually comprehensive way, such as including a diagram with arrows to represent activation and inhibition. It also would have helped to group these factors by pathway or anatomical system (i.e. digestive, immune, etc.). The original authors of the page used an unnecessarily large number of sources to cite each hormone and did not really convey the complexity of AP-1’s activity, but I do think the information was key to providing an understanding of how AP-1 acts within the body.

Figures

The one figure incorporated into the Wikipedia draft page was pulled from the original Wikipedia site, but I wonder if the authors of the revised draft looked into whether the figure had violated any copyright infringements. If the picture is cited appropriately and intended for public use, I think it adds a lot to the page because it shows a component of AP-1’s basic structure.

References

Regarding references (and I could be wrong here), I believe the source numbers at the end of each sentence should be outside of the period instead of inside. Also, there are no non-journal references cited on the page.

Overview

Overall, I commend Group 7 on their efforts in producing this initial draft. It is structured well, inclusive of many different sources, and serves as a significant improvement to the already-existing AP-1 page on Wikipedia. If I were to make a single suggestion in editing, I would recommend that they make the “Introduction” and “Physiological relevance” sections a bit less vague. Moving onto more detailed critiques, the “Structure” section could be broken up into separate paragraphs, the number citations should be placed outside of periods, a few additional external Wikipedia page links could be added, and the “Regulome” section from the original article should be considered to keep in the page. Otherwise, it is a very well written and extensively researched page!

Peer Review References

Bandyopadhyay, Ram; Phelan, Michael; Faller, Douglas. (1995). Hypoxia induces AP-1-regulated genes and AP-1 transcription factor binding in human endothelial and other cell types. Biochimica et Biophysica Acta (BBA) - Gene Stucture and Expression, 1264(1), pp. 72-78. doi:10.1016/0167-4781(95)00116-X

Desbois, Christelle; Aubert, Denise; Legrand, Claude; Pain, Bertrand; Samarut, Jacques. (1991). A novel mechanism of action for v-ErbA: Abrogation of the inactivation of transcription factor AP-1 by retinoic acid and thyroid hormone receptors. Cell, 67(4), pp. 731-740. doi:10.1016/0092-8674(91)90068-A

Ludwig, Stephan; Wang, Xiuyan; Ehrhardt, Christina; Zheng, Hongyong; Donelan, Nicola; Planz, Oliver; Pleschka, Stephan; Garcia-Sastre, Adolfo; Heins, Gudrun; Wolff, Thorsten. (2002). The Influenza A Virus NS1 Protein Inhibits Activation of Jun N-Terminal Kinase and AP-1 Transcription Factors. J. Virol., 76(21), pp. 11166-11171. doi: 10.1128/JVI.76.21.11166-11171.2002

Prusty, Bhupesh K.; Das, Bhudev. (2005). Constitutive activation of transcription factor AP‐1 in cervical cancer and suppression of human papillomavirus (HPV) transcription and AP‐1 activity in HeLa cells by curcumin. International Journal of Cancer, 113(6), pp. 951-960.

Shen, Q.; Uray, I.P.; Li, Y.; Krisko, T.I.; Strecker, T.E.; Kim, H.-T.; Brown, P.H. (2007). The AP-1 transcription factor regulates breast cancer cell growth via cyclins and E2F factors. Oncogene, 27, pp. 366-377. doi:10.1038/sj.onc.1210643

Chem4551221 (talk) 18:23, 22 October 2015 (UTC)Chem4551221

Suggestions from ChemLibrarian
Excellent job with expanding the article! Here are my suggestions.


 * 1) There is one section called Regulome in the original article AP-1 transcription factor. Please make sure you keep it there when you move your article to the formal space.
 * 2) You may want to consider use a Protein Info Box to make your article more standardized. See Template:Infobox protein for more information.
 * 3) I see that you have not added any images to the article yet. Please check out slide 21 and 37 of the Slides for Wikipedia Editing Basics I posted on the CTools site for link to video tutorials and notices about copyright issues.
 * 4) Great additions of images. Change the size and location of the images using the syntax examples on Picture tutorial

ChemLibrarian (talk) 17:41, 23 October 2015 (UTC)

Review from GSI
This is a well organized, nicely written compact article. A few little changes can make it better.

1. In the introduction part, it would be better if the technical terms, like c-Fos, c-Jun, can be explained in a general way. My suggestion would be to re-write the first sentence as "In the field of molecular biology, the activator protein 1 (AP-1) is a transcription factor that is a heterodimer composed of different proto-oncogene associated and transcription factors activating proteins ( belonging to c-Fos, c-Jun, ATF, JDP protein family)."

2. Under the heading Regulation of AP-1, link couple of terms to the associated existing wikipedia pages (e.g. transcriptional, post-translational).

Soumigchem (talk) 03:01, 24 October 2015 (UTC)

A Brief Note on the Included Image (from the Authors)
We would like to point out that the image that we have included in this sandbox is, in fact, an original image, even though it has the same subject as that on the original wiki. We have specifically highlighted hydrophobic residues in the coiled coil dimerization domain of the AP-1 binding complex, since we discuss these in detail, and felt it relevent to point them out on the structure. We also highlighted the basic residues involved in DNA binding. Since the image shown is entirely of our own creation (we would be happy to provide both the source pymol and gimp files for your verification), we feel it is a little inaccurate to say that we did not follow the guidelines on image inclusion in the article. Even though our image is on the same subject mater as the original, it is definitely not the same image, and copyright should not be an issue.

D.A.H-M (talk) 03:34, 24 October 2015 (UTC)

Changelog 11/3/15
Below is a list of updates to the page in response to the preceding comments:

Introduction It was suggested that we rewrite the first sentence, be less vague, be more specific on AP-1 function, and include information on cellular function. On review, we believe that our original wording, with some minor cosmetic edits, is sufficiently specific given what we cover in following sections. We mention cellular function as “[controlling] a number of cellular processes including differentiation, proliferation, and apoptosis,” and we believe that this section should inherently be fairly broad as an introduction.

History It was suggested that this section was too focused on the structural discoveries, and that additional info could be added on specific regulatory and physiological processes. We felt that our section effectively addressed the context of the discovery of the AP-1 system without being too structurally focused, and felt that the history section was not the right place to discuss specific regulatory or physiological relationships. However, we did add a brief note that since the discovery, AP-1 has been associated with numerous regulatory and physiological processes. We also attempted to simplify and clarify some of the language.

Images It was suggested that our images were too similar to the original to be distinguishable, so we altered our color scheme further from the original and added two additional images to clarify our focus.

Structure It was suggested that we break this up into smaller paragraphs, which we did. We also ran a few cosmetic edits on citation style and punctuation.

Regulation It was suggested that we re-add the “Regulome” section from the original page and a few visual aids to show regulatory pathways. We did the first, but decided that the second would be immensely difficult to do well, given the complexity of the AP-1 system, and felt that any diagram would likely have serious insufficiencies and perhaps cause more issues than it would solve. We additionally linked a few new terms in this section.

Physiological relevance It was recommended that we provide more examples here. We have since added material.

Formatting / minor points Several additional sources have been cited that are not journals Multiple new terms have been linked to other wiki pages Periods have been moved to precede citation number — Preceding unsigned comment added by D.A.H-M (talk • contribs) 11:04, 3 November 2015 (UTC)