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

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Mishasubz's and Crandel5425's Group page.Crandel5425 (talk) 02:44, 26 February 2014 (UTC)[reply]

Unit 7

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In this unit, you will get started working on your article, in a user sandbox page. Crystal Clear action apply Graded milestone at the end of this unit: 10 points. We should be able to find your initial work on your article in one of the team members' sandbox pages. This should include your preliminary outline located in one team members sandbox, your list of references, and your suggested improvements added to the 'talk page of the article'. Details In order to prepare for the next unit, read or skim the following, for more information about style and structure of Wikipedia articles Manual of Style - Lead section Do some initial work on your article: Pick one of your team members' sandboxes in which to work ... it does not matter which. As a team, begin to research the topic of the article, identify key points that should be in the Wikipedia article for this topic. Discuss this on your group talk page. Move the list of references found in Unit 5 from your group page to the working sandbox page. Find more high-quality references, and add them to a list. As you add them, it would probably be a good idea to skim them over and, for your teammate's benefit, add a few bullet points explaining what useful material the reference contains. Search for any suitably-licensed images that you can add. If you find some, create a list for these on the working sandbox page, and add them to it. As a team, prepare a preliminary outline for the article, and write that in a new section of the working sandbox page. Add your ideas for how you would like to improve the article to the talk page of the article. This will open communication between your group and other wiki editors who are interested in improving the article.

Initial article assessments from Crandel5425

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Aminoallyl Nucleotide

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Need more information on each nucleotide, maybe include images of each modified nucleotide. Current work with these modified nucleotides. Crandel5425 (talk) 04:06, 26 February 2014 (UTC) [1] [2] [3][4] [5] [6][reply]

Based on our email/phone conversation we have decided to go with Aminoallyl nucleotidesCrandel5425 (talk) 19:35, 1 March 2014 (UTC)[reply]
I would like to add some more information which might be useful.[7]

Article selection rationale

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We decided on aminoallyl nucleotides due to their application in molecular biology labs where radioactive labeling is not allowed or is banned. This type of labeling is available for use in producing cDNA, PCR nick-translation, random-primed labeling, or primer extension. We wanted to learn more about how its florescence works with the addition of biotin or hapten. What are the benefits and disadvantages of using post-synthesis labeling over pre-synthesis labeling like cyanine (cy) labeling. Is this labeling available on all types of nucleotides? What research used this type of labeling and what did they get out of the data? What are its effects on DNA structure, stability, and function for transcription or translation in the lab? Can these nucleotides be coupled with other molecular biological techniques? We are interested in learning more about these nucleotide modifications and how they play an important role in assay development. They are of critical use in DNA microarray which measures the level of gene expression. We would like to know more information on the cost of aminoallyl nucleotides vs other labeling techniques and when to use aminoallyl nucleotides. Learning more about the uses of the different aminoallyl nucletiodes will be a helpful contribution to Wikipedia for students and scientists looking for not only basic information but also ways to advance their research.

Unit 8 Progress Report

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Write a very brief progress report on your group page, in a new section titled "Unit 8 progress report". As a guideline, this should be a bulleted list of up to five items, with one or two lines per item, highlighting specific contributions that we otherwise might miss. For example, don't include "Wrote the introduction section", because that kind of contribution will be obvious. Do include things like "Used Inkscape to make the figure 'small nucleic acid lipid particle', and uploaded it to Wikimedia Commons", or "Updated the infobox-disease with several external links." If all of your contributions were prose, then your progress report might consist of only one line, "All of our contributions were prose."

  • Added citation
  • Added new headings
  • Added figure (new figure to reflect topic)- uploaded to wikimedia commons
  • Added list of types of AA-nucleotides
  • Added external links and internal links
  • prose

Unit-10 Progress Report

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Misha's contributions:

  • I was able to address some of the concerns laid out by the peer reviews
  • I made an attempt to give a description in the beginning of what aa-ntp's are..work in progress
  • added a history section...but work in progress

Mishasubz (talk) 10:26, 9 April 2014 (UTC)[reply]

Unit-12 Progress Report

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  • Edit lead to make it more clear and concise along with more wiki linking
  • create and add image that labels the carbon rings for clarification per request
  • expanded on history - still unable to find the initial date of aminoallyl nucleotide use
  • expand on synthesis and explain the image per request
  • more wiki links
  • move list to the last portion of the article instead of the middle.
  • Prose

Crandel5425 (talk) 03:10, 22 April 2014 (UTC)[reply]

  • worked on citation corrections
  • grammar corrections
  • added a paragraph in the post-synthesis section
  • added a few wiki links
  • added vendor information
  • prose

Mishasubz (talk) 09:31, 22 April 2014 (UTC)[reply]

Final progress report

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Progress Report Overall:

  • Added 5 images (4 were self created) and one was cited in PLOS1
  • Removed incorrect material
  • Added multiple subheadings
  • added formation of aa-UTP
  • added how its added to DNA/RNA
  • added uses
  • lots of grammar modification
  • lots of wiki linking and citing sources
  • Followed reviews by our peers and admins (and outside sources for images)

More recently within the last unit:

Crandel5425 (talk) 21:36, 1 May 2014 (UTC)[reply]

So I have fixed up the 'use' section as per Martins review. I am not sure what we are doing about the citations from 6-11, do you know what needs to be fixed? thanksMishasubz (talk) 05:54, 1 May 2014 (UTC)[reply]

I think you fixed them as they don't show red anymore. Crandel5425 (talk) 18:41, 1 May 2014 (UTC)[reply]

References

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  1. ^ Berti, L; Medintz, IL; Alessandrini, A; Facci, P (10 June 2009). "A one-pot functionalization strategy for immobilizing proteins onto linear dsDNA scaffolds". Nanotechnology. 20 (23): 235101. PMID 19448298.
  2. ^ Schoetzau, T; Langner, J; Moyroud, E; Roehl, I; Vonhoff, S; Klussmann, S (September–October 2003). "Aminomodified nucleobases: functionalized nucleoside triphosphates applicable for SELEX". Bioconjugate chemistry. 14 (5): 919–26. PMID 13129394.
  3. ^ Xiang, CC; Kozhich, OA; Chen, M; Inman, JM; Phan, QN; Chen, Y; Brownstein, MJ (July 2002). "Amine-modified random primers to label probes for DNA microarrays". Nature Biotechnology. 20 (7): 738–42. PMID 12089562.
  4. ^ Thermo. "Aminoallyl-dUTP". Retrieved 26 February 2014.
  5. ^ Life Technologies. "Amino Allyl Labeling for Array Analysis". Retrieved 26 February 2014.
  6. ^ Jena Bioscience. "Dye-labeled Uridine Nucleotides - Aminoallyl-dUTP". Retrieved 26 February 2014.
  7. ^ Scheler, Ott; Barry Glynn; Sven Parkel; Priit Palta; Kadri Toome; Lauris Kaplinski; Maido Remm; Majella Maher; Ants Kurg (15 May 2009). "Fluorescent labeling of NASBA amplified tmRNA molecules for microarray applications". {{cite journal}}: Cite journal requires |journal= (help)
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