Wikipedia talk:USEP/Courses/JHU MolBio Ogg SP14/Group 81F

Hi, Mitch!

I hope you are doing well. It looks like this week we need to pick an article. Article choice is first come first serve basis, so we should probably decide which topic we would like rather soon. The articles that I summarized for last week's assignment have been taken; however, yours have not. Between the two that were summarized, I feel that gene cluster would be a better option. As you stated, differentiation-inducing factor is ongoing, so there may not be sufficient research for us to use. Gene cluster is also a rather broad subject. Do we want to do something more specific?

I also looked at some other articles in the table as not to limit ourselves to just the four we used. Considering our backgrounds, I think we would do exceptionally well with the following articles: Bacteriolysis, Viral Transformation, T7 RNA polymerase, CAG promoter, and AP-1 Binding Site. Autosome and Non-Disjunction are also other articles which would also suit us well. We could also readily find a vast amount of information regarding either topic.

Let me know what you think and/or if you have other article suggestions! :) Kneal0627 (talk) 20:06, 28 February 2014 (UTC)

Hi Katelyn! I looked through your suggestions and the ones that I find most interesting are gene clusters, non-disjunction, and the CAG promoter. Viral transformation also looks very interesting, and I think we could find quite a bit of relevant research on it. The CAG promoter will probably be the most specific topic. Let me know what you think out of these options and we can narrow it down. I guess if I had to narrow it down to 3 it would be Viral transformation, the CAG promoter, and gene clusters, but I'm open to exploring any of the topics. Talk to you again soon (I'll check this page often). Mnemcek (talk) 20:29, 1 March 2014 (UTC)

It looks like viral transformation has already been taken; however, the remaining ones mentioned are still available. I'm fine with any of the three, but I think I'm leaning more toward gene clusters or non-disjunction. There seems to be a lot of information that could potentially be useful on our project.Kneal0627 (talk) 00:29, 2 March 2014 (UTC)

Ok, let's do gene clusters then. I went ahead and claimed it for us. For the summary, do we do 2 separate 200-300 word summaries or just one? 2600:1010:B02E:FD08:2454:5329:139A:9579 (talk) 16:14, 2 March 2014 (UTC)

Ok, sounds great! Thank you for claiming it for us! I believe we only do one summary. It says in the grading rubric that we have an individual grade for participation on the talk page and then a group grade for the summary. Perhaps we should email her to double check? Kneal0627 (talk) 17:57, 2 March 2014 (UTC)

Hi, Mitch! I went ahead and started working on the article summary. I also emailed our professor to clarify that only one summary should be written per group. I cc'd you the email. The working summary that I've typed up is only 94 words. The required length is roughly 200-300 words. Please add/edit the summary within the next day as I will do the same. Kneal0627 (talk) 17:34, 3 March 2014 (UTC)

Sounds good, I'll add to it tonight (3/3) and you can check it over and make any final edits. I'll check it again tomorrow before the deadline. Thanks!Mnemcek (talk) 03:21, 4 March 2014 (UTC)

I made one final edit. Feel free to review and change as you see fit though. Other than that, I thought the summary sounded great. Kneal0627 (talk) 15:04, 4 March 2014 (UTC)

Preliminary Outline

This is the preliminary outline and references (with notes) I have right now. Please let me know what you think.

I. Gene Cluster defined

a. Creation of gene clusters

i. Gene Duplication

ii. Tandem arrays vs. Gene Clusters

b. Examples

II. Bioinformatics

a. Cluster trees

b. Maps

III. Research

References

1. Sherwood EJ, Hesketh AR, Bibb MJ. Cloning and analysis of the planosporicin lantibiotic biosynthetic gene cluster of Planomonospora alba. J Bacteriol. 2013;195(10):2309-21. http://www.ncbi.nlm.nih.gov/pubmed/23475977
2. Higgs DR, Vickers MA, Wilkie AO, Pretorius IM, Jarman AP, Weatherall DJ. A review of the molecular genetics of the human alpha-globin gene cluster. Blood. 1989;73(5):1081-104. http://www.ncbi.nlm.nih.gov/pubmed/2649166
3. Hardison R, Miller W. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol Biol Evol. 1993;10(1):73-102. http://www.ncbi.nlm.nih.gov/pubmed/8383794
4. Graham, G. (1995). Tandem genes and clustered genes. Journal of Theoretical Biology, 175(1), 71-87. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/7564393 (This is a great article about the difference between tandem arrays and gene clusters and how they can turn into each.)
5. Caron, H. et al. (2001). The human transcriptome: clustering of highly expressed genes in chromosomal domains. Science, 291, Retrieved from http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.169.4274&rep=rep1&type=pdf (This article contains great figures and elaborates on human gene clusters.)
6. I’m not sure we can actually use this as a reference since it is technically a lecture; however, it does present some great figures and information. Perhaps we can look for something similar. http://www.discoveryandinnovation.com/BIOL202/notes/lecture26.html
7. Garcia-Fernàndez, J. (2005). Genesis and evolution of homeobox gene clusters. Nature Reviews Genetics, 6, 881-892. doi: 10.1038/nrg1723. http://www.nature.com/nrg/journal/v6/n12/box/nrg1723_BX2.html (Excellent specific example)
8. Haselkorn, R. (1998). The use of gene clusters to infer functional coupling. Proceedings of the National Academy of Sciences, 96(6), 2896-2901. doi: 10.1073/pnas.96.6.2896 http://www.pnas.org/content/96/6/2896.short (Research)
9. Blanco, E., Pignatelli, M., Beltran, S., Punset, A., Pérez-Lluch, S., Serras, F., Guigó, R., & Corominas, M. (2008). Conserved chromosomal clustering of genes governed by chromatin regulators in drosophila. Genome Biology, 9(R134), doi: 10.1186/gb-2008-9-9-r134 http://genomebiology.com/2008/9/9/R134 (Research)
10. http://david.abcc.ncifcrf.gov/gene2gene.jsp (Bioinformatics)
11. http://segmine.ijs.si/use_cases/ (Bioinformatics)

Forgot to sign my post Kneal0627 (talk) 18:58, 10 March 2014 (UTC) — Preceding unsigned comment added by Mnemcek (talk • contribs)

I like the outline you have so far. I think it will be able to give a good overview of the work going on with gene clusters, without getting to detailed. I have also found that when you search gene clusters, some bioinformatics articles and approaches come up, so I like your idea to include this in the outline.

Now that we've started to discuss this here, we actually need to migrate this again (oops!) to one of our sandboxes. Do you want to copy/paste your outline and references to your sandbox so we can work on it there?

In the meantime, I will try to find some figures/images to add, and maybe some more references. I will also post to the "talk" page of the Gene Cluster page, to start a discussion on what we might want to add. Talk to you soon!

Mnemcek (talk) 22:17, 10 March 2014 (UTC)

Hi, Mitch! Thanks for moving this to the correct talk page. I apologize for the mix up! I'll copy and past it to my sandbox. I'll look at the discussion as well. Kneal0627 (talk) 23:37, 10 March 2014 (UTC)

Progress Report

Hi, Mitch! I went ahead and did our progress report for this unit. Since we didn't really add figures/images, I simply stated that all of our contributions were prose as instructed in the assignment guidelines for this unit. If you wind up adding a figure for this unit, please update the progress report. Thanks! Kneal0627 (talk) 22:59, 25 March 2014 (UTC)

Second Contribution to Article

Hi, Mitch! Hope you are doing well. I just wanted to touch base with you on our article. So this week, it looks like we are making our second contribution to our article. I've already been working on it throughout the week. In particular, I have been focusing on section "Creation of Gene Clusters." Per one of the suggestions made by another user during our week of peer review, I consolidated some of the sections under this section as well as expanded upon material and added some figures. I'm hoping to add one more figure; however, I'm awaiting to hear back from the author for approval. Take a look and let me know what you think. Also, this week it states that we should have at least 50% of the article put down. Please elaborate on the section you've been working on. I know you mentioned adding an image as well. I was doing some reading on tandem repeats and gene clusters, and it looks like they can turn in to each. Perhaps that's something we should incorporate into the article? I think we should also create and add something substantive to the Bioinformatics and Research sections. Kneal0627 (talk) 05:49, 4 April 2014 (UTC)

I'm going to add a Bioinformatics section and Research section this week, and I may make some additions to our other sections (including an image as mentioned). I had one thought about the title of "Types of Gene Clusters". Are we planning on adding to this section? It only mentions operons right now, which I think is something we definitely need to include but maybe in its own section titled something like "Operon-like gene clusters". What are your thoughts here? Mnemcek (talk) 22:39, 6 April 2014 (UTC)

That sounds great! I look forward to reading it. Yes, I plan on adding to this section. I will be working on it tomorrow. I was going to include prokaryotic gene clusters vs. eukaryotic gene clusters as suggested by another user. Kneal0627 (talk) 01:59, 8 April 2014 (UTC)

Hi Katelyn, I'm having a hard time figuring out what to discuss in the "Research" section. Do you have any suggestions? When I look at PubMed, there is such a variety that I don't know what to really focus on, or how to structure this section. Mnemcek (talk) 02:48, 8 April 2014 (UTC)