Wikipedia talk:USEP/Courses/JHU MolBio Ogg FA13/Group 84G

Selecting an Article

Hi James and Pinar,

It is hard to believe that it is time to pick our article. After analyzing our initial articles, do either of you have any preferences? My initial assessments were on the Capping Enzyme article and the Isomerase article. They both have their pros and cons. However, the biggest things that I would like to point out with these articles are as follows:

1) I found it easier to find references, especially review-type references, for the Capping Enzyme article than the article on Isomerase.

2) The manner in which the Isomerase article is currently structured lends itself well to subheadings and subsections, especially in terms of the classifications of isomerases.

3) The capping enzyme is a more focused topic.

4) For the Isomerase article, it will take some time just to sort through and sort out the information on the different classes.

5) Both need inline citations.

6) Both need pictures, diagrams, and/or charts.

7) Both are linked to multiple pages.

Both articles obviously need a great deal of work. I am certainly open to any thoughts on these two articles, or any of the articles that you analyzed or are interested in. Let me know what you guys think. We should decided on article soon as it is first come, first serve. Also, the sooner we choose an article, the sooner we can start planning a strategy for how to best tackle this assignment.

Thanks, Madscientist2007 (talk) 03:04, 11 October 2013 (UTC)

Thanks for starting off the discussion, Erin!

The capping enzyme article is nearly empty but does have a lot of links to other topics. I've never studied it before, but this suggests to me that it's a complex and specialized topic.

Regarding isomerase, it seems to be an umbrella term for a type of enzyme. As a wiki user, I would want a detailed explanation of the topic, along with comprehensive list of examples (not every single isomerase, but all classifications, and examples within each once plus links to their pages, providing they exist.). Although both are new topics for me, as a personal preference I would rather research isomerases.

From the articles that I reviewed, I thought exogenous DNA touched on a lot of topics that can be expanded on. I was even a bit surprised it's still a stub since it's a broad and somewhat common topic.

As for the inverted repeats article, I can see us being able to improve it a lot visuallly. I think the concept of inverted repeats really needs some visual aid and examples to be explained properly. And although the main focus should remain inverted repeats, there is a lot to discuss in mentioning other DNA motifs and their significance.

From the rest of the stub list, I would pick molecular-weight size markers. I've used DNA ladders myself and so have many others so it would be quite useful to have a good article written on the topic (pun not intended, really!). Perhaps areas to add can include its history, invention, development, how it works, what it's used for, what it's composed of, types/variations on the market, improvements, problems, and alternatives.

When tackling a big project I like to section it off into parts. I suppose that's why the articles that interest me are the ones that lend themselves to more structure and have lists and categories. Of course, this then requires some very specific research so the article can be more complete (and also areas that may need to be updated with time).

So, let's play article Survivor! Here's my rankings of article preference (from most preferred to least):

1. Inverted Repeats or Molecular-weight size marker (tied for first)

3. Isomerase

4. Exogenous DNA

5. Capping enzyme

Also, at the time of posting, from what I've peeked at from the other groups' talk pages, none of the above topics are currently under discussion so I don't think there would be a conflict in claiming one. Still, better to decide sooner than later! That said, feel free to add other articles to your ranking if you like.

--Pozmi (talk) 08:11, 13 October 2013 (UTC)

Hi, Pinar!

I, too, like to break a large project into smaller sections both in terms of how to handle such an undertaking, and in terms of final presentation. When it comes to writing, I have often been taught/told to approach a paper as if you are telling a story. As such, you want the information to be presented in a manner than makes sense and has a smooth flow to it. In a sense, our Wiki page should be no different. We can achieve this by splitting our topic into logical sections with appropriate headings.

Not to be too cliché, but it is true that a picture is worth a thousand words. Regardless of our chosen topic, pictures are certainly a great way to enhance an article, and to provide a visual accompaniment to the explanation in the text. I, personally, find diagrams, pictures, charts, table, etc. particularly helpful and informative as I am a very visual learner. I noticed that a few of the possible topics already have at least one picture, such as the Molecular-weight size marker that you suggested. The pages for leucine zipper and for DNA adduct do as well just to name two others.

I have read over both your initial assessments and the assessments that you wrote on this page. You did a wonderful job on both in terms of analyzing the pages as they are and as they could be. I agree with what you had to say about each of the articles.

In terms of capping enzymes, it does seem to be a very specific and focused topic. In terms of general references, we might only be able to get so far before having to delve into the nitty-gritty of the topic. The existing Wikipedia page mentions that " it is specific to RNAs synthesized by this polymerase (RNA polymerase II) rather than those synthesized by RNA polymerase I or RNA polymerase III." We would have to get into the type or types of RNA synthesized by RNA polymerase II. We could also compare those types of RNA to RNAs synthesized by RNA polymerase I or III and then explain why the enzyme can only deal with RNA polymerase II.

In terms of isomerases, I agree that this a broader topic. In regards to providing examples, we should/could also insert pictures with in-text explanation of those examples. This would be especially helpful if we cannot link the example to another page.

Between the capping enzyme page and the isomerase page, I, too, would lean towards isomerases. However, as I mentioned in my initial post on this page, I found it difficult to find information from general review-type sources online for this topic. Most of the pages that I came across were for primary research articles. We may have our work cut out for us in that respect. On the other hand, we could look at the reference lists of some of those primary articles and see if we can find more generalized sources by backtracking from there.

In terms of Inverted repeats, there seems to be a good deal of things that we could do with it, both visually (as you mentioned) and in terms of how these repeats are tied into different biology techniques. A quick search online brought up topics such as inverted repeats in PCR, gene silencing using inverted repeats, and inverted repeats and RNA interference. This is just for starters. It also led to topics such as mirror repeats and direct repeats, both of which could be compared to inverted repeats. Furthermore, we could add a picture to show the difference between the three. However, as you noted, the main topic should be on inverted repeats; while it seems that there is a fair amount of information available, we do not want to stray too far off course.

In terms of Exogenous DNA, you are right in saying that there is a lot that we can do with it. While the article certainly needs work, even as it currently stands, there are obvious places where the topic could be split into sections and sub-sections. For instance, there is what is exogenous DNA, examples, transmission, transfection, uses in research, uses industry, medical implications, and transgenesis. In terms of transmission, we can even break things down further in sub-sections dealing with transfection in bacteria, in plant cells, and in animal cells. In doing a quick search online, I found NIH guidelines for the use of recombinant DNA in animals, especially in rodents as they are so commonly used in research. Among some of these guidelines, were specific mentions of exogenous DNA. I am not sure if we would find enough on this last subject to warrant a whole section or even sub-section, but it is something that could be mentioned in a section on research uses.

In terms of Molecular-weight size markers, I like the idea of throwing this this topic into the mix. It certainly has a wider appeal in terms of the audience we would be writing for than some of the other topics. Like you, I have used these type of markers numerous times when running agarose gels. I have also used markers for Western blots. As the page stands, there is definitely more information on DNA markers than protein markers. When it comes to this topic, I think that you have a wonderful outline going in terms of how to break this topic down into sections. One caveat that I would like to make is that we would need to watch out for manufacturer bias. I did a quick search online and many of the websites that I found are from scientific companies trying to sell their product(s). While I am sure that these site also contain general info on DNA and or protein markers, their ultimate concern is to convince us as to why their product is the best. This is just something we should keep in mind should we decide to go this route.

I took a look at the other possible articles on this list. There was one other topic that I would possibly put up for consideration: DNA adduct. As is, this article lends itself pretty well to section headings. Some examples for sections are what is a DNA adduct, types, how are they formed, consequences of DNA adducts, how are they repaired, and possible uses in research. The article already has two pictures, but I think for this topic pathway diagrams/pictures might be a good way to explain details such as how they are formed and how they are repaired.

Now for article Survivor! For starters, I would like to vote Capping enzyme off the island. I feel that this topic is so specific that we are only going to be able to take it so far without going crazy with all the technical details that we might end up running into. I think that we are better off with a topic that allows for flexibility, as well as a level of creativity.

With that said, I would like to provide my rankings of article preference (from most preferred to least):

1) Exogenous DNA or Molecular-weight size markers (tie for first)

2) DNA adduct

3) Inverted repeat

4) Isomerases

As such, it looks as if we both have Molecular-weight size markers as one of our two first place choices. I agree with you that we should choose soon, especially since it first come, first serve. Once chosen, we also need to put together a brief essay on why we chose our article. Both are due Tuesday.

I don't know if James has any thoughts on the matter, but if we don't hear from him soon, we may have to go ahead and pick something. I would hate for us to lose our top pick because we waited too long.

Let me know what you think! Thanks, Madscientist2007 (talk) 19:16, 13 October 2013 (UTC)

Pinar and Erin,

I like your rationale behind topic possibilities. All the topics mention need a great deal of work, and I think some are much better than others. Here is my opinion.

Capping enzyme: Article is very bare; needs a ton of work, however (as Pinar mentioned) due to had specifics of the enzyme it would require us to be real technical. I agree that we should pass up on this :::one.

Isomerase: Article also needs a lot of work; as it only contains a vague definition and classifications of isomerases. As Erin pointed out, the fact that it is semi-organized will make our jobs easier. I :::think that this is definitely a viable topic.

Exogenous DNA: This topic needs a lot of help as well. Article talks about the process of transformation and transfection; we could break this information into subsections I feel there needs more of an :::explanation of exogenous DNA. I feel that this is also a very doable article.

Molecular-weight size markers: Article presents very basic information. We can definitely expand on the sections already created and add a few more. I also like this article as a possibility.

DNA adduct: Article only really gives a vague definition, provides examples, and mentions consequences. There is no mention of why it occurs or mechanism of action. I think this could also be a great :::article.

Here is my Ranking

1) DNA adduct

2) Molecular-weight size markers

3) Isomerase

4) Exogenous DNA

5) Capping enzyme

I think the winner is molecular size markers

Jirwin1097 (talk) 21:45, 14 October 2013 (UTC)

Hi James and Pinar!

As you put it, James, the winner seems to be Molecular-weight size markers. Is that our final answer? If so, we should go ahead and claim it before another group does. Also, we need to put together an explanation (about 200-300 words) for why we chose this article.

Please let me know if you agree with this choice within the next hour or so. If I don't hear from you by then, I am going to assume that this article is our final choice and I will go ahead and claim it for the group.

Thanks, Madscientist2007 (talk) 00:12, 15 October 2013 (UTC)

Hi again!

I just wanted to let you both know that I claimed the Molecular-weight size marker article for our group.

Thanks, Madscientist2007 (talk) 01:46, 15 October 2013 (UTC)

Hi James and Pinar!

I am writing to you to let you know that I have posted an explanation for our article choice on our project page. In writing this part, I tried to pull from each of our contributions to the selection process. Please feel free to make changes and/or additions. I am certainly open to suggestions. (Please note that Dr. Safford wants our explanation to be around 200-300 words. We are currently just shy of 300 words.)

Thanks, Madscientist2007 (talk) 03:36, 15 October 2013 (UTC)

Hi Erin, thanks for claiming the article and writing the rationale. I made a few grammar revisions and added a piece about references and the caveat you mentioned above. I'm not sure how strict the word limit is, but this has taken us to 318. I tried shaving off a few words where I could, but I left the last paragraph untouched since I found it very well-put and inspirational! But, if we definitely want to be under 300 words then perhaps we could tighten the first or last paragraph, or remove the sentence "Additional pictures can be used to illustrate the history and evolution of these markers, the different types in terms of composition, uses, etc., and potential problems and alternatives." since most of the points are mentioned in the paragraph above. --Pozmi (talk) 04:25, 15 October 2013 (UTC)

Hi Pinar,

No problem. If anything, I hope that I am not being to pushy. (I am a worrier!) I really like the changes you made and your choice of wording. Your revisions certainly give a more sophisticated and polished sound to our explanation. I hope you don't mind but I made a few minor punctuation changes. Also, I had a question regarding one of your sentences: " From here, there is great potential to expand sections include sub-sections using ideas we have already discussed." I think a word is missing. I wasn't sure if you wanted to use "to" or "and" where it says "expand sections include sub-sections." Either word works there. I put in "and," but please feel free to change it this to "to," especially if that is what you intended on in the first place.

In terms of the number of words, I don't think that the word limit will be that strict. I think the range is more of a ballpark figure. I think Dr. Safford is looking to see that we took the time and effort to really sit back and analyze the reasons behind our choice. This is especially important since we will be spending a lot of time with this topic over the next few weeks. With that said, I think that we should be fine with what we have, i.e. 318 words. Madscientist2007 (talk) 05:14, 15 October 2013 (UTC)

Ok cool, DNA molecular markers is a great topic to expand on. I agree that neutrality is going to be very important. Some companies may make false claims about their product, so we must make sure we get our information from reputable sources. Also (as you guys mentioned) we must put our work/school experience aside. I think is will be a great topic!Jirwin1097 (talk) 22:42, 15 October 2013 (UTC)

Ok so let’s start delegating some tasks. Here is a list:

Simple tasks

-Choose sandbox

-Move references to sandbox

Other tasks

-Find high quality references (and explanation)

-Find images and add to sandbox

-Outline to article

- Individual Research (key points)

My thoughts of approaching this is to first take a look at our outline we made for the last unit: basic information on DNA and protein markers, history, invention, development, how they work, what they are used for, what they are composed of, types/variants on the market, improvements, problems, and alternatives. Let’s first make sure that enough information exists to allow for viable sections. This is just my opinion; I’m open to other ideas. Also, whose sandbox should we use? I really don’t have a preference.Jirwin1097 (talk) 23:27, 17 October 2013 (UTC)

Starting Our Article

Hi James and Pinar,

In reviewing the work due for tomorrow night, we really need to have all of our postings up by 6:00. I am going to start posting information for our article in my sandbox. Please check there and comments as appropriate.

Thanks,Madscientist2007 (talk) 03:48, 22 October 2013 (UTC)

Hi again,

Pinar, you came up with a great list of topics that could be added to our article: history, invention, development, how it works, what it's used for, what it's composed of, types/variations on the market, improvements, problems, and alternatives. I took this list and put together a general, preliminary outline in my sandbox. Feel free to make changes.

During the last unit, we also talked about adding additional pictures as a great way to complement the text.

We also discussed watching out for information bias, especially on company websites. However, we may need to rely on company websites to a point as they constitute a large number of search hits for this topic. Primary research articles are another big source that comes up in search. I don't know about you, but I am finding it difficult to locate review articles on this topic.

Also, in searching online, we needed to be careful in our search terminology. Terms such as protein markers, and especially DNA markers, turn up hits that deal with topics such as microsatellites. Using the term "ladder" or "standards" might be more profitable.

Just some thoughts. Madscientist2007 (talk) 05:10, 22 October 2013 (UTC)

Unit 7 Summary for Molecular-weight size marker article

There is a lot going on in this unit. We have information and ideas posted in several different spots on Wikipedia. With that said, I thought that it might be a good idea to put together a summary section here.

Information to Add

- Add additional references and inline citations. Currently there is only one reference for this article and there is no inline citation for it.

- Add information from a variety of sources, i.e. textbooks and review articles.

- Bolster the existing sections with additional information. It may also be possible to break these sections down even further. Add additional sections and subsections to the article. (Refer to outline below)

- Additional pictures would help to enhance the text. (Refer to image section below)

Outline (This is posted on my sandbox page (Madscientist2007/sandbox). Please make any changes in my sandbox and not on our group page.)

I. Introduction Section

II. History

A. Invention

B. Development

III. Classifications

A. DNA markers

B. RNA markers

C. Protein markers

IV. General principle

A. Effect of gel conditions

i. Buffer

ii. Charge

iii. Concentration

iv. Type

V. Applications

A. Gel electrophoresis

B. Western blot

C. Southern blot

D. Northern blot

E. PCR

VI. Problems

VII. Improvements

VIII. Alternatives

IX. Markers currently on the market

Images

- Pinar, you posted some great images on my sandbox page(Madscientist2007/sandbox).

- You also posted some great ideas for additional pictures (talk page for Molecular-weight size marker ):

- Does anyone have images of DNA/protein/RNA ladders from their own lab data that they'd like to use?

- Some images that show the same ladder under different conditions, which effectively illustrates how ladders can be affected by buffers, charge, etc. (However, most seem to be provided by scientific companies.) trying to show the versatility (or limitations) of their particular brand)

- Provide images of botched gels (i.e. a clumped ladder from a gel that has not been run long enough, or a ladder that has run off the gel.)

- Images showing different types or brands of markers run under the same conditions for comparability.

- Mention and/or show the most commonly used marker.

Issues to Keep Under Consideration

- Watch out for bias, especially when it comes to websites for scientific companies.

- Wikipedia is not a place for primary research. Sources should be more along the lines of review papers and not primary research articles. However, we can probably take a look at the introductory sections of primary papers. They are usually summaries of existing information that is pertinent to the main topic of the paper.

- Be careful when using search terms for our topic. Molecular-weight size markers and Molecular markers are not the same thing. Instead of "markers," search terms such as "ladders" and "standards" can be used.

Current Areas of Difficulty

- Finding information for the alternatives and improvements sections

As mentioned above, I put this section together in order for us to see our Unit 7 information in one place. In flipping back and forth between pages, chances are good that I missed something. Please feel free to add to or change anything in this summary. Let me know what you think. Thanks,Madscientist2007 (talk) 02:48, 23 October 2013 (UTC)