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Wikipedia:USEP/Courses/JHU MolBio Ogg SP14/Group 82H

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Article Selection Rationale for Group 82H

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We selected the article Histone Acetylation and Deacetylation due to the fact that it is an important regulatory mechanism that affects a majority of nucleosomes. The acetylation status of a nucleosome is important in many cellular processes, including transcription, DNA replication, DNA repair and heterochromatin formation[1]. Furthermore, it is a relatively new field of study with many different research projects taking place. We feel that, due to the novelty and excitement of the scienctific community for this subject, there will be plenty of information for us to take advantage of. Though a new field, already multiple evidences suggest histone acetyl-transferases (HATs) and histone deacetylases (HDACs) also play roles in different disease pathologies which attracts us to this regulatory process and its potential as a therapeutic target[2] [3] [4] . It is these aspects of acetylation and deacetylation that make it a very effective and important process not only in the knowledge base of this class, but also in the field of molecular biology as a whole. By choosing this article, we are not only taking part in an assignment where we will learn about an important subject for this class now, but it is also an investment in our knowledge for future classes, applications, and endeavors in this field[5].

References

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  1. ^ Shahbazian, MD; Grunstein, M (2007). "Functions of site-specific histone acetylation and deacetylation". Annual review of biochemistry. 76: 75–100. PMID 17362198.
  2. ^ Barnes, PJ; Adcock, IM; Ito, K (March 2005). "Histone acetylation and deacetylation: importance in inflammatory lung diseases". The European respiratory journal. 25 (3): 552–63. PMID 15738302.
  3. ^ Lazo-Gómez, R; Ramírez-Jarquín, UN; Tovar-Y-Romo, LB; Tapia, R (2013). "Histone deacetylases and their role in motor neuron degeneration". Frontiers in cellular neuroscience. 7: 243. PMID 24367290.
  4. ^ French, SW (2013). "Epigenetic events in liver cancer resulting from alcoholic liver disease". Alcohol research : current reviews. 35 (1): 57–67. PMID 24313165.
  5. ^ James D. Watson; Tania A. Baker; Alexander Gann; Michael Levine; Richard Losik (2014). Molecular biology of the gene (7th ed.). Boston: Pearson/CSH Press. ISBN 978-0-321-76243-6.

Initial article assessment from Lxu27

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Protein inhibitor of activated STAT

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The article has a very basic description of the inhibitor of STAT signaling pathway and only listed the genes that are involved. It belongs to the stub class. Further expansion on the topic should be added. Online reference to the topic includes [1] and [2]

References

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  1. ^ Shuai, K; Liu, B (August 2005). "Regulation of gene-activation pathways by PIAS proteins in the immune system". Nature Reviews. Immunology. 5 (8): 593–605. PMID 16056253.
  2. ^ Palvimo, JJ (December 2007). "PIAS proteins as regulators of small ubiquitin-related modifier (SUMO) modifications and transcription". Biochemical Society transactions. 35 (Pt 6): 1405–8. PMID 18031232.


Histone acetylation and deacetylation

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Article contains a concise description and a diagram illustration for nucleosome structure. The topic has been developed and belong to the start class. However, it does not include all the information on the topic and requires input on sources. Improvements are needed for this topic. Potential sources include [1] and [2]

References

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  1. ^ Gräff, J; Tsai, LH (February 2013). "Histone acetylation: molecular mnemonics on the chromatin". Nature Reviews. Neuroscience. 14 (2): 97–111. PMID 23324667.
  2. ^ Kurdistani, SK; Grunstein, M (April 2003). "Histone acetylation and deacetylation in yeast". Nature Reviews. Molecular Cell Biology. 4 (4): 276–84. PMID 12671650.

Initial Article Assessments from bigA726

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Acetyltransferase

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The article contains almost no meaningful content other than a definition of the article subject and some links to examples. There is one external link included which contains helpful information about specific transferases, but the article is devoid of any references. There is one picture included in the article, but is only a picture of an acetyl group. This article would greatly benefit from a schematic breakdown of a pathway or mechanism and a section detailing what happens. This article is the perfect example of a Stub. As far as the talk page is concerned, the WikiProject Molecular and Cellular Biology have posted it as a stub-class article that is of mid-importance. Other than that, nothing has been entered in the talk page of how this stub can be improved. Some references that could be used to help better this article include [1], [2], and [3].

Acetyltransferase References

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  1. ^ Fan, HK; Yang, C; Zhang, YY; Le, XP; Zheng, CG; Shi, L; Zhang, Q (July 2013). "[Expression of choline acetyltransferase in the rat barrel cortex by electrical stimulation]". Zhongguo ying yong sheng li xue za zhi = Zhongguo yingyong shenglixue zazhi = Chinese journal of applied physiology. 29 (4): 312–6. PMID 24175550.
  2. ^ Zhang, X; Ouyang, S; Kong, X; Liang, Z; Lu, J; Zhu, K; Zhao, D; Zheng, M; Jiang, H; Liu, X; Marmorstein, R; Luo, C (19 February 2014). "Catalytic Mechanism of Histone Acetyltransferase p300: From the Proton Transfer to Acetylation Reaction". The Journal of Physical Chemistry B. PMID 24521098.
  3. ^ Cox, David L. Nelson, Michael M. (2013). Lehninger principles of biochemistry (6th ed.). New York: W.H. Freeman. ISBN 978-1-42923414-6.{{cite book}}: CS1 maint: multiple names: authors list (link)


Ubiquitin-Conjugating Enzyme

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The article contains a very small but concise introduction to the topic. Aside from the initial introduction, there is a small section that contains bits of information on a pathway (slightly more in depth than the introduction). The following section is for identifying genes that contain genetic codes for ubiquitin-conjugating enzymes and after that is a section that refers the reader to other articles that are related. There is a small reference section with two references to PubMed articles and a section of external links to an additional Wiki source and a link for the US National Library of Medicine. There are no entries in the talk page that discuss how to further improve the article, but the topic is in the scope of the WikiProject Molecular and Cellular Biology group which has classified this article as a stub-class at mid-importance. I’m not sure how to grade in the middle of two grade criteria, but I would slightly disagree on the classification as a stub. Although not containing a lot of information, this article presents more information than would a stub based on the criteria listed from Wikipedia. The information included is sufficient to someone wanting to gain a general working knowledge on the subject of the article. The article also contains a helpful picture on the pathway it beings to describe. Much more information is needed, as well as many more sources and section, but I feel that this article comes close to being a very basic “Start,” or at least in the middle of a start and a stub. Some resources that could be used to help make this article better include [1], [2], and [3]

Ubiquitin-Conjugating Enzyme References

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  1. ^ Xie, C; Powell, C; Yao, M; Wu, J; Dong, Q (February 2014). "Ubiquitin-conjugating enzyme E2C: A potential cancer biomarker". The international journal of biochemistry & cell biology. 47: 113–7. PMID 24361302.
  2. ^ Dong, M; Pang, X; Xu, Y; Wen, F; Zhang, Y (24 May 2013). "Ubiquitin-conjugating enzyme 9 promotes epithelial ovarian cancer cell proliferation in vitro". International Journal of Molecular Sciences. 14 (6): 11061–71. PMID 23708104.
  3. ^ Cipressa, F; Cenci, G (2 October 2013). "Effete, an E2 ubiquitin-conjugating enzyme with multiple roles in Drosophila development and chromatin organization". Fly. 7 (4). PMID 24088712.

BigA726 (talk) 22:26, 25 February 2014 (UTC)[reply]

Unit 8 Progress Report

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1) I started the Pathway section in the official article. I think there is some good beginning information included, but i'm having trouble locating a detailed mechanism for the actual acetylation/deacetylation process. Hopefully i can find that soon. I also included some preliminary information as to what nucleosomes and histones were. I wasn't sure if i was including too much extraneous information, but i figured a small intro to the subject at hand was slightly necessary.

2) I started a HAT/HDAC section for the official article. In this section so far, i've outlined which HATs and HDACs we find commonly in humans. I have a source that outlines nice information and i'm in the process of getting it together (it should be up in the next day or so). I was struggling as to whether or not to include this section since there are pages dedicated solely to HATs and HDACs that include a lot of the information. I figured i'd outline some general functions and a few other details about each.

Much of my contributions were prose, but i felt a small explanation was necessary.BigA726 (talk) 01:32, 19 March 2014 (UTC)[reply]
Update on progress - I completed the sections (so far) for the pathway of histone acetylation and deacetylation, but still trying to find a more in depth mechanism. The HAT and HDAC sections are also completed (so far). I think the next best step is some feedback to make sure that the information is easily understood and in correct order. Again, much of the contributions were prose. BigA726 (talk) 11:17, 25 March 2014 (UTC)[reply]

3) I started looking into the effects of histone acetylation and deacetylation. I do think this should be a big part of our topic. I roughfully divided diseases into three sections, inflammatory diseases, cancer, neuological diseases. I feel the sections may have been too wide and may need to focus more finely on the process of acetylation/deacetylation.

4)I looked at the introduction section, and feel like we should talk about three main points in mechanism. First, briefly introduce the histone physical structure in the beginning. Then move on the talk about histone modification and acetylation/deacetylation processes. This then can lead to three different key points, including histone acetylation in newly formed chromatin, compaction regulation of acetylation/deacetylation, and lastly transcriptional regulation.Luyao Kevin Xu (talk) 00:05, 25 March 2014 (UTC)[reply]

5)I also changed the figure that illustrated the overall structure of nucleosome. I feel it is a better representation of the structure than the original one.Luyao Kevin Xu (talk) 00:51, 25 March 2014 (UTC)[reply]


This is the official group page for bigA726 and Lxu27! BigA726 (talk) 14:13, 24 February 2014 (UTC)Luyao Kevin Xu (talk) 00:05, 25 March 2014 (UTC)[reply]

Unit 12 Progress Report

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Overall, I am satisfy with the structure and information included in our article. We maintained neutral view and have included multiple sources to support out article. We will continue to improve the quality of our article and make changes.

  1. I have added additional information under human diseases section. Majority of the materials are added under each topic. I have cited primary research journals and included wikilinks in the section.
  2. Both group members have discussed the order of images and we have decided to change the order of images to fit our general structure.
  3. I have taken into consideration of our review's comments and reworded sentences accordingly.Revised several paragraphs under the biological function section as well as the human diseases section.
  4. Minor editing was done through out the unit and I will continue to read through the article and make small changes in the following week.
  5. We have added more wikilinks and references in response to reviewer's comments.Luyao Kevin Xu (talk) 22:59, 22 April 2014 (UTC)[reply]


I think our article is coming along incredibly well. We've added a substantial amount of information to the article and many details, such as sources and wikilinks, are coming along well. In terms of the past few weeks:
  1. I went ahead and proofread the article, checking for grammatical and spelling mistakes. I also fixed up any structural problems in a couple of sections where messages didn't seem very clear. I'll make sure to do a couple more checks to make sure that sources are correctly shown and that no errors are made in the writing.
  2. I contacted the OA about additional fixes for the article and got some very positive feedback. I fixed a few details in the article that were suggested which definitely made an improvement for the article. I also inquired about the current grade status for our article and was pleasantly surprised to see that we had achieved a B rating!
  3. While reading through the article, I added a large amount of wikilinks to suggested and nonsuggested subjects in the article. I figured some terms for us may not be completely well known to others and tried to make the article as easily accessible and understandable as possible. I feel a few more wikilinks are needed for some of the esoteric terms that are in the article and will be added shortly.
  4. I made sure to read each of the reviewers comments and to fix as much as possible. Many of them made similar comments about organization. In the past few weeks, I did a lot of reading a put together a new HAT section that i think will be easier to read through and find information. Like the HDAC section, i wanted to create a structure that could be identified easily and, if need be, sorted through easily to find the subject needed. So i divided up the HAT section by family in a similar way i divided the HDAC section. I'll be making a few more small improvements throughout the next few weeks (especially after the coming reviews) to make sure the sections are as good as possible. I'll also be making a few more contributions to the pathway section. Kevin has also done an excellent job in adding a lot of great information and sources to the article!
Overall, i think the article is coming along great and we are definitely on track to having a great article by the end of the class. We've stuck to the guidelines of Wikipedia well and i look forward to finishing the semester strong. BigA726 (talk) 01:08, 23 April 2014 (UTC)[reply]
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