Talk:Molecular-weight size marker

Untitled

• I will add an image of one of the gels i've run at work showing the molecular weight marker. will381796 00:49, 20 August 2006 (UTC)

Wiki Project

Suggested improvements for this article:

- 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. The lone reference is from New England Biolabs. While sites for scientific companies will provide general information on the topic, one must watch out for bias as the companies are obviously trying to sell a product or products. They want to convince us as to why their product is the superior to others.

- 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. Suggested headings and subheadings include 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.

- Additional pictures would help to enhance the text. Currently, there is only one picture of two DNA ladders. At the very least, there should be a picture of DNA ladders and a picture of protein ladders.

Just some thoughts, Madscientist2007 (talk) 04:04, 22 October 2013 (UTC)

Does anyone have images of DNA/protein/RNA ladders from their own lab data that they'd like to use? Along with the different types of markers, there are some images that show the same ladder under different conditions, which effectively illustrates how ladders can be affected by buffers, charge, etc. So far though, the majority of these images seem to be provided by scientific companies trying to show the versatility (or limitations) of their particular brand.

Also, in mentioning difficulties associated with markers (to provide a broad and balanced view) perhaps we can provide images of botched gels. For example, a clumped ladder from a gel that has not been run long enough, or a ladder that has run off the gel.

It would also be interesting to see different types or brands of markers run under the same conditions for comparability. And, if possible, mention what is the most commonly used marker. I believe it could be the 1kb DNA ladder, as I've seen it most often, but we would need references to back this up. --Pozmi (talk) 01:00, 23 October 2013 (UTC)

Very good idea. I personally don't, but I can check with my coworkers on Monday.Jirwin1097 (talk) 21:44, 26 October 2013 (UTC)

Current Tasks

I think this it is a good idea to announce our current tasks, so that two of us aren't unknowingly working on the same section.

I will start to work on the types of molecular markers.Jirwin1097 (talk) 22:02, 26 October 2013 (UTC)

I am trying to put together the effects of gel conditions section. Madscientist2007 (talk) 23:40, 28 October 2013 (UTC)

I'm looking into the history/invention/development. Starting off with looking up patents. If I come across something relevant to your topics I'll post links on the group page. (Or sandbox? not sure which area we'll predominantly use to work.)--Pozmi (talk) 01:33, 29 October 2013 (UTC)

Comments from James Thissen

Hi Group 84G! I was assigned to peer review your article. I went back to the August 23rd version of the article before you made any edits and I see that your group has made many worthwhile and substantial edits. I especially appreciate the examples of markers and think that they do a good job to reflect the breadth of uses that the markers can be used for in molecular biology experiments. In addition I think the section about gel effects on the marker will be extremely useful to anyone doing experimental work looking for explanations for "weird" gel results. There are a few comments and things I would suggest to improve the article (I'm sure many of these are planned already):

1. I would suggest changing the main picture in the article...I think I already saw a note above in this talk page that you intend to. I say this because the image that is in the article now actually shows a ladder that is not very well defined and pretty crooked/smeared.
2. The Development section reads to me more of an introduction of the topic, but might need a bit of expansion to cover some of the major developments/improvements to markers. The term auto-development doesn't have much meaning to me at least...I'm not clear what this means or if there is an entry to Wikipedia that this could link to?
3. A couple of the references in the "Different Types of Molecular Markers" have the citation prior to the word, but I think the standard is to put the citation after the word. The style is mixed in the article.
4. In the "Different Types of Molecular Markers" some of the topics would seem to need a bit of expansion as I'm not sure I understand how they relate to molecular weight-size markers (especially SNP and RAPD).
5. Under the "Effects of Gel Conditions" I think the heading-subheading structure is not correct as Buffers, Charge/Voltage, and Concentration should not be at the same heading level as the DNA and Protein Electrophoresis subheadings that follow them.
6. In the "Effects of Gel Conditions" section sometimes it reads like there is a bit too much jargon or explanation of items that may not directly relate to molecular weight markers (ie some of the details of TAE vs TBE buffer and single vs gradient gels)
7. It is great that you already have so many reference (many more than my article so far), but I wonder if it would be good to include some references from peer reviewed journals. I'm sure there aren't a ton or articles just relating to molecular weight markers, but often on company websites (ie NEB, Biorad, Life, Sigma, etc) they will include links to publications that used their products...there may be some valuable references there.
8. A couple things that come to mind that you might think about adding are: RNA markers, Agilent Bioanalyzer (I use this instrument at work and it does a great job separating RNA, DNA and protein and the molecular weight marker images look great), and I also have used weight markers in an ABI 3100 Prism sequencer for very high fidelity gels, but that practice isn't done too much any more I think. Apoptosis81 (talk) 04:41, 5 November 2013 (UTC)

James, thanks for your feedback. I am the author of the "Different Types of Molecular Markers" section. I do agree that more information is needed, and that some examples may be unnecessary because they aren't very relevant. I will expand on examples that I feel are relevant, and probably do without the unrelated examples. I will also fix my references.

Jirwin1097 (talk) 15:20, 11 November 2013 (UTC)

Hi James,

Thank you for your thoughtful review. I greatly appreciate the fact that you took the time to go back to an earlier version of the article in order to better compare the original with our current attempt. This is especially helpful for my group as certain sections, such as the introduction, have not been tinkered with yet and remain in their original state. We do plan to tackle these particular areas as we move through the article and as we come across relevant sources in the coming weeks.

I would like to take this opportunity to address some of your specific comments:

1. I do agree that the current picture is in need of a change. This is one of several of those aforementioned areas that is in the works. Thanks to one of my partners, we already have some wonderful pictures in mind for us to use.
2. As for the heading-subheading structure in the “Effects of Gel Conditions” section, the outline at the top of the article page reflects the set up that I was trying to achieve in this section. However, I do agree that the structure in the article is misleading in terms of how it is presented. I will look into this and see if there is better way to set the headings and subheadings apart. Also, if you or Pdholak1 have any ideas or suggestions as to how to approach this, I would greatly appreciate it.
3. Again, regarding the “Effects” section. I plan to revamp this section. This part posed a little bit of a challenge as I didn’t want to miss anything that might be relevant to each subheading, but yet keep the topic focused on how these different conditions ultimately affect the markers. One of the tricky parts with researching this section was trying to sort through conditions that affect both the ladder and the sample(s) and those that are more likely to only affect the samples themselves. This was complicated by the fact the most sites presented these gel conditions in terms of how the samples are affected.
4. As for sources, I would certainly love to include more sources from peer reviewed journals or textbooks. It is, as you stated, difficult to find such articles on this topic. In the majority of cases when I do come across a peer reviewed article, I find myself mostly restricted to the information contained in the introduction. On the other hand, in doing research for Unit 10, I have taken into account your suggestion for following sources on company websites. Surprisingly though, not as many sites do this as one might think. I was excited when I originally saw this suggestion. Unfortunately, many of the sites that I have come across recently have not done this. I will keep trying though.
5. I do like the idea of including RNA markers and we do have this in our proposed outline. I am in the process of finding information on these markers. However, much of what I have come across so far is company product specific. I am trying to find something more general.

Thank you again for all of your suggestions. They will certainly be taken into account as we move forward. As I have mentioned, I have already begun to incorporate some of them as I continue my research. I very much appreciate your comments. I look forward to continuing this discussion with you and invite you to add to your initial suggestions should you or Pdholak1 think of anything else that might aid my group in improving our article. The best of luck to you and Pdholak1 with your article! Madscientist2007 (talk) 03:13, 13 November 2013 (UTC)

Hi group 84G, thank you for your detailed response to my review. I have been looking at your article again this week and see that you have made great progress! As I expected, many of the suggestions I had in my original review were already being planned to be worked on. I see that you have some great images now and have really expanded on the number of references. The article overall seems very organized and is easy to follow from section to section. My only further suggestion would be to add some additional wikilinks (especially in the Protein Markers section). I am looking forward to seeing your final edits to the article over the next couple weeks, but can really appreciate all of the content you have already added.Apoptosis81 (talk) 04:48, 21 November 2013 (UTC)

Thank you for continuing to follow our article as it evolves. It is very much appreciated. I agree that we could use more wikilinks, especially, as you mentioned, in the Protein Markers section. I will be sure to look through the article and see where we can add links in. Thanks again and keep in touch!Madscientist2007 (talk) 03:20, 23 November 2013 (UTC)

Hi Molecular Marker group, the page is looking great! I see that you added a section on RNA markers and it looks like you have also added many more Wikilinks to the article. You have really added a ton of great content. There is not much else I can think to modify...maybe as a style/design point would be to make some of your images left aligned just to change up the look of the article. Also since your Contents table is so large now it may look better to make your header image bigger, but again that is just a design suggestion. Apoptosis81 (talk) 05:43, 3 December 2013 (UTC)

Thanks James for all your suggestions! We'll also be reviewing your list for our upcoming final contribution. We're planning on adding some more images, too, so we'll keep formatting in mind to make things visually interesting.--Pozmi (talk) 01:36, 9 December 2013 (UTC)

No problem! I like the Design and Development sections under each type of molecular marker. I also like the section on the Different Uses at the end of your article and I really think this adds a lot. Your group has made tremendous project over the course of this semester and have drastically improved the quality of this article! Apoptosis81 (talk) 03:24, 12 December 2013 (UTC)

Thanks, James! I really appreciate you taking the time to keep up with our article and make additional suggestions. I especially like image formatting suggestion. I took a look at your article, and changing up the image positioning on the page certainly adds interest to the page. I know that a couple of other groups have used the strategy as well. We will certainly have to keep this in mind. The best of luck to you and Paulomi with your article! (It looks great, by the way!)Madscientist2007 (talk) 20:35, 12 December 2013 (UTC)

Comments from pdholak1

Hello Group 84G! I too am assigned to your article, and I agree that you all have made some serious progress on this article! Here are a few suggestions from my end as well:

1. Throughout the article you switch between using the words "ladder" and "markers". I feel this gets a little confusing. I would stick to using "marker" since this is the one used in the name of the article, but I like that you mention the other names for the same topic in the first line.
2. Under "Different Types of Molecular Markers", I am sure you are going to expand some, but I was wondering if it is really necessary to include so many? Maybe if a article exists about that kind of marker, a link could be used instead!
3. This is just a suggestion for formatting: You may want to consider splitting the entire article into two parts, DNA and Protein and then putting each subsection of "development", "effects of conditions" etc under each rather than doing it the other way around. Both ways work of course, but I think it may be easier for the reader to navigate the article if you split it into two sections from the get go.
4. More pictures and more peer-reviewed articles will help, but I see you already mentioned that you plan to add these!

Great job so far, I look forward to seeing the rest of your article! Pdholak1 (talk) 22:59, 5 November 2013 (UTC)

Hi Pdholak1, thank you for your suggestions. On the point of markers vs. ladders, we found the word "marker" to be a tricky term to research. Many mentions of "marker" in journal articles actually refer to genetic markers, not molecular-weight markers. Many of our references were found by searching for "ladder" instead. We certainly want to present a distinction between these types of markers so users know they've come to the right topic before they start reading it. However, as you mentioned, consistency is important too to keep the terms from being confusing. We'll keep track of this.

We'll definitely keep your DNA vs. Protein formatting idea in mind. We have an article outline, and once most of the sections are filled in we might do some rearranging for optimum navigation. I think this arrangement will also depend on how much content we have for each section -- we'd like to balance it out.

Thanks again for your comments! (Pinar) --Pozmi (talk) 21:25, 12 November 2013 (UTC)

Hi Pdholak,

Thank you for the wonderful feedback and for taking the time to read through our discussions in order to get a better idea of the entire planned layout for out article. There is a great deal that we wish to do with this article and it is still very much a work in progress. I appreciate you taking this in account when presenting your suggestions.

I would like to briefly address your suggestions on the structure of the article. I constructed the "Effects" sections. I must say that I kept changing my mind on how to best structure this section, especially since there is repetition of headings and subheadings. I know that I went back and forth at least three or four times!

I agree that splitting the entire article, and not just this section, into two main sections may be a better way to go. As my partner mentioned, we will most definitely take this into consideration, especially as our article evolves further. While we do have an outline which we are following, it will still be some time before the entire picture begins to take shape.

Our ultimate goal is to construct a well-written, well-structured article which is accessible to our audience in terms of both content and formatting. We want it to flow smoothly from section to section and certainly welcome any ideas, such as yours, that would help us to achieve this flow.

Thank you again for your suggestions. As I mentioned to James, I look forward to continuing this discussion and I welcome you both to add to your initial comments should you think of anything else. I wish the both of you the best of luck with your article! Madscientist2007 (talk) 03:34, 13 November 2013 (UTC)

Thank you MadScientist2007 and Pinar for your feedback. I'm happy I could help! Based on your feedback and your article I know its going to turn out great! I look forward to staying in touch with you! Pdholak1 (talk) 01:35, 19 November 2013 (UTC)

And help you did! Also,thanks for continuing to keep an eye on our article. It is very much appreciated. Furthermore, as I mentioned before, please feel free to make further suggestions. We are certainly open to any ideas that would help us improve our article. Madscientist2007 (talk) 03:23, 23 November 2013 (UTC)

Hello! I just wanted to say that your progress on the article is so great!! It has really come together and is very informative. Congrats! Pdholak1 (talk) 18:35, 8 December 2013 (UTC)

Thanks!!!!!!Madscientist2007 (talk) 22:32, 8 December 2013 (UTC)

Second contribution comments

So I posted my second contribution to turnitin.com and waiting to hear back. I just looked at our page and noticed there will be some overlap with the section I'm about to post. I expanded on the different types of markers. I will post my contribution as it is without making revisions, so that we as a group can do the editing. This means that there will be some redundancy on our page before we make these revisions. Jirwin1097 (talk) 01:46, 15 November 2013 (UTC)

Hi James, Given the time factor, it might be better if you went and plugged in the new information from your research. That way we can avoid redundancy and can focus on other sections or areas that need to be addressed. Just some thoughts. Madscientist2007 (talk) 02:53, 15 November 2013 (UTC)

Ok I posted and did my best to avoid redundancy. Please read my section on ladder vs. marker. If this information is correct, and im confident it is (i found multiple sources on how they differ), we have to make some changes in the lead paragraph, because it says they are the same. — Preceding unsigned comment added by Jirwin1097 (talk • contribs) 01:24, 16 November 2013 (UTC)

You raise a good point. We certainly need to make sure that we keep that distinction throughout the article, staring with the introduction. It is good that we are incorporating this distinction into the article especially as many sites use these terms interchangeably. The term "standard" or "standards" is often interchanged as well.

The introduction section in general needs some work as it is, especially in terms of tying references to what is written there. Unfortunately, this will take some time as the introduction was already written when we took on the article.

Madscientist2007 (talk) 02:59, 21 November 2013 (UTC)

Comments from Agulati4

This is a stark improvement over the previous article on molecular-weight size marker. The article is very well developed and the sections add greatly to the understanding of a molecular-weight size marker. Since DNA markers and protein markers are used twice as section headers, I would consider changing one of them. The headings may be a bit misleading as one might click on the DNA marker section under Development and expect to find all information on DNA markers. Under the Development section, I would change “DNA markers” to “Discovery of DNA Markers” and “Protein markers” to “Discovery of Protein Markers” so that people do not confuse the headings with those of the following section. Another option is using a timeline format. Also, under the DNA markers section in Development, the “in” is missing from the sentence: a kit for Southern Blot analysis was developed 1990. The introduction needs to be referenced as well, but I see that you are already discussing that above!

For the DNA Markers section, I would consider writing about the methods used to construct DNA markers before listing the examples of DNA markers. Under Choosing the Correct Protein Standard, you have listed two types of molecular-weight size markers: molecular weight markers and molecular ladder markers. Are molecular ladders the same as the protein ladders discussed below? If it is, I would change the name of one of them to keep it consistent and to limit any confusion. Also, for the “Effects of Gel Conditions” section, make sure to relate each condition back to the molecular-weight size marker and describe specifically how each condition impacts the marker. You could even discuss how these conditions affect which type of marker should be used. Also make sure to appropriately wikilink any scientific terms! I hope these suggestions help. The article is coming along very well and I’m very excited to see it how it turns out! Please let me know if you have any questions regarding the suggestions I have made. Thanks! - Agulati4 (talk) 04:18, 21 November 2013 (UTC)

Hi Agulati, Thank you for the wonderful feedback. It is very much appreciated! I would like to take this opportunity to address some of your suggestions:

• You raise a good point about the headings and alternative ones that you suggest would certainly make things less confusing. I would like to mention that we are considering splitting the article into two sections , one for proteins and one for DNA, in order to have our article flow more smoothly (We may also add a third for RNA). We have already done this with the “Effects” section and are looking into extending this division to the entire article. Should that be the case, sections such as “Discovery” would be moved and both the protein and DNA portions of the article would have their own “Discovery” section.
• As you noted, we are working on the introduction. This section is a bit touchy as it was already written (and not referenced) when we took on the article. We are in the process of attaching references to the information listed.
• I like your suggestion of switching the order on the DNA markers section. This switch would put it more in line with the Protein markers section and would help the flow of the article.
• You raise another good point about the nomenclature. It is my understanding that molecular ladder markers and protein ladders are the same. Jirwin1097, please feel to correct me if I am mistaken in my thinking. The name game, in general, has been a little bit of a thorn in our side as different sites handle the terms differently, with many using the terms markers, ladders, and standards interchangeably. It recently came to our attention that molecular weight markers and molecular ladder markers are indeed somewhat different. This has further complicated an already tricky situation. Especially since we were already in the process of making sure that the same term was used throughout the article. With that being said, we will work on eliminating any confusion in this regard.
• As for your comments on the “Effects” section, this part has been a work in progress. In terms of addressing your concerns here, I offer the following. I plan to revamp this section. This part posed a little bit of a challenge as I didn’t want to miss anything that might be relevant to each subheading, but yet keep the topic focused on how these different conditions ultimately affect the markers. One of the tricky parts with researching this section was trying to sort through conditions that affect both the ladder and the sample(s) and those that are more likely to only affect the samples themselves. This was complicated by the fact the most sites presented these gel conditions in terms of how the samples are affected. As we have been trying to fill in empty portions of our outline, I have not had a chance to address this as of yet.
• As for wikilinks, I plan to go back through the article and examine where we can add more.

We are always looking for ways to improve our article. As such, we are certainly open to new ideas. It is always helpful to have others take a look at projects like this and get their perspective on it. Chances are good that the reviewers will pick up something that the authors missed (e.g. the missing “in” that you caught) or come up with a suggestion that the authors did not think of. This is what makes reviews such as yours so valuable. Again, my thanks for your feedback. Please keep in touch, and certainly feel free to add suggestions should you think of anything else. The best of luck to you and your partner on your article! Madscientist2007 (talk) 04:23, 23 November 2013 (UTC)

Hi Madscientist, Thank you for your response! I am very happy to see that my suggestions were useful. I really like how you, Jirwin, and Pozmi have reorganized the article. It looks great and flows very well. As for the nomenclature issue, I have a suggestion. Since molecular ladder markers and protein markers are the same, you could mention this at the beginning of the protein ladder section and then continue to use them interchangeably throughout the section. For instance, under the "Development" section in the "Protein Ladder" category, you could edit the first sentence to "Previously, protein markers or molecular ladder markers...". I hope that's helpful! - Agulati4 (talk) 19:03, 5 December 2013 (UTC)

Hi everyone! The article is looking great! My only suggestion is to make sure that the statements are properly cited. For instance, there are some statements under the Design section of DNA markers and the Concentration section of Protein markers that should be referenced. Overall, great work! I am very excited to see the final version! - Agulati4 (talk) 00:43, 13 December 2013 (UTC)

Thanks for letting us know. We will take a look. Thanks, again! Madscientist2007 (talk) 02:13, 13 December 2013 (UTC)

Hi Pinar and James, Agulati brings up a good point (see above). I fixed the citations in the Concentration section of Protein markers that should be referenced. However, we need to take a look at last two paragraphs of the Design section of DNA markers. We inherited those two paragraphs, along with the lone reference, from the previous author(s). Any thoughts about how we should handle this? Obviously, the easiest thing to do is to cut these paragraphs out completely. However, at least some of the material probably should stay. Anything that we leave in of course has to be cited. Madscientist2007 (talk) 02:38, 13 December 2013 (UTC)

Comments from Adimart1

Hi! I can tell you have done a lot of work on this article and have been thoughtfully condsidering the suggestions made by your reviewers. As such, I am not going to go through making the same comments I have seen the others makes. I think your writing is very good, over all, and you are clearly paying attention to the rules of grammar. I wanted to comment on the DNA Markers section. I was wondering if it would be possible/advisable to consider adding in some diagrams, pictures, and commentary on some of the equipment you would use to perform these assays? I realize that you may have left this out on purpose as you do link to the southern blot page, and I haven't looked at that page. Also, I was thinking it might be good to talk about some of the other assays (beisides southern blot)that use this technology like ELISAs, COMET, etc. It might help you with adding some more "scholarly" references which people have been asking for and it would give you a chance at some really good images. Just my thought. It might make things clearer about how the markers are used and would help people who are completely unfamiliar with the process visualize what is happening.

I hope this is helpful. Keep up the good work!Adimart1 (talk) 02:51, 4 December 2013 (UTC)

Hi Adimart1, Thank you for the great feedback. You certainly provided us with some food for thought, especially in terms of other techniques and technologies for us to look at and potentially incorporate. Also, it would definitely be nice to be able to add some "scholarly" references to our bibliography, especially as they have been hard to come by (hence the lack of them in our bib). Furthermore, as I mentioned to Jim892, I love pictures, diagrams, etc. and what they can bring to an article such as this. Thanks again for the wonderful suggestions. Please feel free to contact us if you think of anything else. The best of luck to you and WillPugart with your article! Madscientist2007 (talk) 21:01, 7 December 2013 (UTC)

Comments from Jim892

Hello Jirwin1097, Madscientist2007 and Pozmi!   I will be posting my comments in multiple sub-sections under this heading and will be working on it a piece at a time over then next several days. I thought that breaking the comments into smaller sections might make it easier for us to dialog on the separate topics. --Jim Perry (Jim892) (talk) 22:35, 4 December 2013 (UTC)

First Impression

This is now a great article! You have added a lot of good content and the whole thing is just really impressive. I do have a suggestion in the "layout" category. This is a "soft suggestion" meaning it is one of those for you to "think about and reflect and consider" and then feel free to reject the idea - I won't mind at all.

Here is the idea: When the article opens up, most of what I see is a super long "contents box" that kind of overwhelms me. And, as I scroll through the article, I hit the major sections, sub-sections, and sub-sub-sections and I can't really tell what is a "sub-section" and what is a "sub-sub-section". (If I look real close, I can see that the font size is very slightly smaller, but it is hard to tell.) So, one idea is the make the sub-sub-sections just "indented bullets". This will help to visually separate sub-sections from sub-sub-sections and also will take the sub-sub-sections out of the contents box (making it much shorter). To illustrate this, I did a copy/paste of part of your article into my "sandbox3". Click this link to get to it: Jim892/sandbox3   Good luck thinking through this. Note that I replaced the sub-sub-sections (that have 4 equal signs on each side) with a "*" at the beginning of the line and then bolded the sub-sub-section text. Then, I added two ":" at the beginning of each block of text below the sub-sub-section. The editing required to do the indenting is a little tedious, but might be worth it for the visual effect.

--Jim Perry (Jim892) (talk) 22:40, 4 December 2013 (UTC)

Hi Jim,

Thank you for your "first impression" comments. They are very much appreciated. In looking back over my article, you are right in saying that the content box has become overwhelming. I took a look at the example that you set up in your sandbox. I like the way that you have it formatted. Even in the small portion that you have there, this type of formatting is certainly easier on the eyes. It also makes it easier to delineated between sections, sub-sections, and sub-sub-sections. We will definitely have to keep this in mind, especially as we approach the end of the semester (it is hard to believe that it is here already!) Thanks again. I look forward to any additional comments, ideas, or suggestions that you may have. We certainly appreciate any and all feedback! Madscientist2007 (talk) 02:12, 6 December 2013 (UTC)

Limiting content box and first image

Some more "food for thought"... I found an idea for limiting the content box without a lot of work. Try putting this at the end of the introduction.

{{TOC limit}}

This will limit the Table-Of-Contents to just 2 levels and keep it much shorter. Also, the TOC will display where you place the {{TOC limit}}, so you want to be sure to put it at the end of the intro text and not at the beginning.

Additionally, try moving your first image to the end of the last sentence of the introduction and then follow that with {{TOC limit}}. This will put the TOC box and the image in line with each other.

You might also want to consider moving the image into the section on DNA markers. The image is about DNA ladders so I thinnk that would work ok. The DNA section would then wrap around the image nicely. --Jim Perry (Jim892) (talk) 16:44, 6 December 2013 (UTC)

Thank you for providing us with another option for handling our overwhelming contents box! However, am I correct in thinking that this option would only deal with the contents box and not the section/sub-section/sub-sub-section heading issue discussed above? If that is this case, I think your first suggestion might be a better way to go, as it will neaten up the heading format in the article as well. Then again, would it be possible to fuse the two suggestion, i.e. add the {{TOC limit}} at the end of the intro plus use indenting and bullets to fix up the article formatting? Or, do you think that this might cause more problems then it will solve? Thanks, Madscientist2007 (talk) 17:07, 6 December 2013 (UTC)

You are correct. The "TOC limit" just changes what displays in the Contents Box. You can do the "TOC limit" and the indenting/bulleting together or do just one and not the other. They won't interfere with each other. Now, one concern I have about my own suggestion on the indenting and bulleting... You might want to check with an Online Volunteer concerning my approach to be sure it doesn't violate Wikipedia's style guidelines or something. I got a comment on my own article about "bolding" items in a list, so I'd hate for you to do all that work and then find out it isn't "legal" to do it that way. --Jim Perry (Jim892) (talk) 17:21, 6 December 2013 (UTC)

Thanks for getting back to me and thanks for the heads up about the formatting. I will check with one of the OAs before tackling this change. Madscientist2007 (talk) 17:40, 6 December 2013 (UTC)

I wrote to both Klortho and Neelix about this issue. Neelix wrote back with the following advice:

"I'm glad that you are experimenting with formatting on Wikipedia. I would recommend against bolding and bulleting sub-subsection headings, both because words should not be bolded for this reason and also because it requires all of the text in each sub-subsection to be indented in a way that is contrary to established practice. Nonetheless, I understand your desire to distinguish between the subsections and the sub-subsections. Having taken a look at the Molecular-weight size marker article, I have two recommendations. One option is to simply remove the sub-subection headings. The sub-subsections are so short that they probably don't need to be sectioned off; most sections on well-developed articles consist of several paragraphs. If you really want to retain the headings, a second option is to create a table with one column being the sub-subsection headings and the second column being the paragraphical text currently in those sub-subsections. What do you think?"

Thanks again for contacting me about this concern.Madscientist2007 (talk) 04:04, 7 December 2013 (UTC)

Hi, I have mixed feelings about Jim's suggestions. On the one hand, I can see his concern about the structure of the article being difficult to discern when you are reading through it. On the other, I'm not crazy about his proposed solution, and also, I think that you are using the heading levels in the way that they were intended.

I also agree with Neelix, for the most part. But in my opinion, some of the subsections should stay as they are, and for others, I agree that you could just remove the subsection headings. I don't like his idea about making them into a table -- I don't think a table is appropriate. So, specifically:

• I think you could do away with the subsection headings under the Effects of gel conditions sections (both of them).
• On the other hand, under Choosing the correct protein marker, I think the subsection headings are good and helpful, albeit I agree that the difference in the style isn't very good -- but that's Wikipedia's fault.
• Under Protein markers, it might be marginally helpful if you were to put Choosing the correct protein marker after Effects of Gel Conditions.
• For the level-3 subsections underneath 4.2, 4.3, and 4.4, you might consider using description lists. These are similar to Jim's suggestions, but I think more "standard", and more appropriate in this case. For the wiki-syntax, see here. Klortho (talk) 04:48, 8 December 2013 (UTC)

Thank you for the suggestions, Klortho! The description list seems to be a good fit, as it puts clear distinctions between the paragraphs without elongating the table of contents. I've updated the article with your suggestions in my sandbox1 so my group members can see the formatting before we post it. Also, Erin, James, and others -- thoughts on using the description list in the "Effects of gel conditions" and/or "Choosing the correct protein marker" sections? (Pinar) --Pozmi (talk) 02:26, 9 December 2013 (UTC)

Hi Pinar,

• I agree that the description list appears to be a good fit. I took a look at the "updated" article, and this new formatting certainly makes things a little easier on the eyes. Thank you for taking the time to put that sample together by the way!

• In looking back over the Gel Effects sections, I think that Klortho might be right with his suggestion about eliminating the subheadings in these sections. My only suggestion, should we decide to go that route, is that for the protein version of this section, we should have a sentence or two as an intro instead of just launching into buffers. It can be something simple like "As with DNA markers....." or "As with DNA electrophoresis....". Then we could just reformat the first sentence of the buffer paragraph, as it starts in a similar fashion.

• Should we decide to keep the subheadings in the Gel Effects sections, I think that we should consider employing the description lists. However, if we use it here, we should also consider using it in the "Choosing the correct protein marker" section, as it will help the article look more uniform.

• I agree with Klortho that we should move the "Choosing the correct protein marker" section. While it is only a minor change in the grand scope of things, it does seem to help the flow of the paper.

Just some thoughts.Madscientist2007 (talk) 03:11, 9 December 2013 (UTC)

Images

You have a bunch of DNA ladder images on User:Madscientist2007/sandbox and I think they would look GREAT in the DNA section. That section has lots of prose and it could use 1 or 2 or even 3 pictures. I especially like the colorful image that "glows". Keep in mind that you can limit the display size of the image with "|300px|" or whatever size (large or small) seems right. You could really dress that section up with multiple images and it would also improve the "first impression". --Jim Perry (Jim892) (talk) 16:59, 6 December 2013 (UTC)

One of my partners found the wonderful images that are in my sandbox. I agree that pictures would dress up the DNA section, and the article in general. While our topic is not nearly as mechanistic in scope as other ones, pictures, etc. certainly help to elaborate on the text regardless. They also add to the accessibility of an article, especially one of a technical nature. I am a very visual learner, and as such, I love pictures, diagrams, illustrations, tables, graphs, charts, etc. alongside textual information. My group will certainly have to keep this suggestion in mind. Thanks,Madscientist2007 (talk) 17:19, 6 December 2013 (UTC)

Content, wikilinks, references

No special suggestions here. Just praise... Content is super! You have done a great job with this article. Wikilinks also look to be in great shape. Everytime I thought I and found one that was needed I discovered it had already been wikilinked earlier in the article. Great work! References also look good and I really like the references in two columns. It looks really professional. One very minor comment on layout. In the very last section (DNA Sequence Polymorphism) you have a single sub-sub-section on "SNPs". Both sections are reasonably short, so unless you have plans to add another sub-sub-section, I would just make that a separate paragraph under "DNA Sequence Polymorphism" and remove the "SNPs" sub-sub-section.

That's it for my review. You have done really nice work here! Best of luck with the final weeks of this semester!

--Jim Perry (Jim892) (talk) 17:11, 6 December 2013 (UTC)

I agree with your suggestion about that last section of the article. I will be sure to discuss this with the group. At this point in time, I do not know if the group member who constructed this section has any plans to further elaborate on what is written there. Thanks, Madscientist2007 (talk) 17:28, 6 December 2013 (UTC)

Hi Jim,

Thank you very much for all of your wonderful suggestions and feedback. I really appreciate you taking the time to put together such a thorough and well-thought out review. Please feel free to make additional recommendations should you think of anything. The best of luck to you as well. I still can't believe that we are coming upon the last week of the semester!

Also, the best of luck to you and Godwin with your article! I took a gander at it the other day and it looks awesome. You have both done an amazing job with it. I can't wait to read it when it is all finished! Keep up the good work!

Madscientist2007 (talk) 17:37, 6 December 2013 (UTC)

Hi Jim, thanks so much for taking the time to give us both your "first impression" and a further review. This helps us see the article from the POV of both users who are skimming it, perhaps to carry on to another topic, and users who are reading through it all. We want the information to be accessible to both types of users.

I really appreciate you putting your formatting suggestion in your sandbox! In recent weeks, we reformatted the article by molecular marker type, and although it cut down on the number of major sections, we accumulated many (sub)subsections. With most of our prose contributions in place, we'll spend the final week reformatting, adding images, and clarify/expanding on certain points -- and using these reviews as a checklist! --Pozmi (talk) 01:53, 9 December 2013 (UTC)

Brief suggestion

Impressive expansion of such a stub. An extra example for you to consider:

• gel electrophoresis of stained carbohydrates (e.g. Kosik O, Bromley JR, Busse-Wicher M, Zhang Z, Dupree P. (2012) Studies of enzymatic cleavage of cellulose using polysaccharide analysis by carbohydrate gel electrophoresis (PACE). Methods Enzymol.510:51-67)

Keep up the good work, T. Shafee (Evo&Evo) (talk) 13:42, 7 December 2013 (UTC)

Thank you for the suggestion!Madscientist2007 (talk) 17:19, 7 December 2013 (UTC)

Notes for Our Final Contribution

I put this section together as a place to keep running tab on what we still need to address over this last week. Feel free to jot things down as you see fit. Thanks,Madscientist2007 (talk) 03:18, 9 December 2013 (UTC)

• Formatting issues

• Use of description lists
• Wrapping text around pictures? (see Jim892's suggestion above; also take a look at his article Inverted repeats for examples) Madscientist2007 (talk) 03:18, 9 December 2013 (UTC)

• I am working on write up for polysaccharide analysis by carbohydrate gel electrophoresis (PACE) (Please refer to the "Brief Suggestion" section on this page.) Madscientist2007 (talk) 05:21, 13 December 2013 (UTC)

• In this case, the marker is made up of oligosaccharides. The paper T. Shafee recommended focuses on PACE, and only very briefly mentions markers. As such, would we be better putting it under the Different Uses section, instead of creating a whole carbohydrate markers section? Let me know what you think. Thanks, Madscientist2007 (talk) 05:42, 13 December 2013 (UTC)

• To help with the decision, I am including a rough draft of what I have:

Carbohydrate markers are employed in a technique known as polysaccharide analysis by carbohydrate gel electrophoresis (PACE), which is a quantitative separation technique. It allows for the analysis of enzyme hydrolysis products. (Kosik, et al., 2012) It has been used in applications such as characterizing enzymes involved in hemicellulose degradation, determining the structure of hemicellulose polysaccharides, and analysis of enzymatic cleavage of cellulose products. (Kosik, et al., 2012)

PACE depends on derivitization, which is the conversion of a chemical compound into a derivative. (Kosik, et al., 2012; Cammack, et al., 2006) Here mono-, oligo-, and polysaccharides are the compounds of interest. They are labeled at their reducing ends with a fluorescent label (i.e. a fluorophore). (Kosik, et al., 2012) This derivitization with a fluorophore permits both separation on a gel under the desired circumstances and fluorescence imaging of the gel. In this case, a polyacrylamide gel is used. (Kosik, et al., 2012)

As with DNA, RNA, and protein electrophoresis, markers are run alongside the samples of interest in carbohydrate gel electrophoresis. (Kosik, et al., 2012) The markers consist of oligosaccharides of known molecular weight. Like the samples of interest, the marker is also derivitized with a fluorophore (usually with 8-aminonapthalene-1,3,6-trisulfonic acid (ANTS) or 2-aminoacridone). (Kosik, et al., 2012)

Feel free to make changes and/or suggestions. This section will also allow us to add additional wikilinks.Thanks,Madscientist2007 (talk) 05:56, 13 December 2013 (UTC)

Comments from Opalite3579

Great work on this article! I compared the article at the beginning of the assignment to the one that is currently up, and there has been an impressive amount of work. I like the organization of the article and the illustrations you have chosen to incorporate. The writing is clear and has a flow to it, which results in easy reading and easy comprehension. I think you have done a wonderful job explaining a complex subject clearly and without any bias one way or another. A couple of suggestions are:

• You use the letters MW. Although I know it stands for molecular weight, I think it would be useful to define this somehow, such as molecular "weight (MW)" so that the reader is aware that that is what you mean.
• If I wasn't familiar first hand with how molecular weight size markers and gel conditions are related, I would be a little lost reading these sections. A good idea would be to make it clear to the reader how these two topics relate. Right now what is making the link in my head is first-hand experience, but for those who don't have this, it might be a little difficult to bridge the gap with the information as it is.
• Do we have a reference for the shelf life of RNA markers?

This is a work in progress, and so I am excited to see how it will turn out. Keep it up! Opalite3579 (talk) 06:59, 9 December 2013 (UTC)

Thank you for your helpful feedback. I agree that "MW" should be defined in the beginning of the article to avoid confusion. Also, addressing your second point, we should work on making this section more reader friendly for those not familiar with this topic.Jirwin1097 (talk) 02:15, 10 December 2013 (UTC)

Hi Opalite3579, Thank you for the feedback. I agree with both points. Concerning the second point, given our exposure to the topic, especially over the last few most months, it is all too easy for us to take for granted the familiarity, or there lack of, of our audience with this subject.Madscientist2007 (talk) 23:24, 10 December 2013 (UTC)

Hi James and Pinar, As we work to add the final touches to this article, we should try to take a step back and take a last look at this article from the perspective of someone who knows little, or even nothing, of our topic, in an effort to make this article as user friendly as possible.Madscientist2007 (talk) 23:24, 10 December 2013 (UTC)

Hi James, Thank you for getting the final progress report started! Madscientist2007 (talk) 23:27, 10 December 2013 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:Molecular-weight size marker/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

I do not think this article should be merged with "molecular markers" because these objects indicate the presence of something. A molecular weight marker is used as a comparative measure of how large a polynucleotide or protein is. In my opinion, merging these articles would be a large mistake. Also, an example of a molecular weight marker is already found in a picture attached to the Gel Electrophoresis article. Gerbilfluff (talk) 06:16, 13 September 2009 (UTC)gerbilfuff

Substituted at 21:52, 26 June 2016 (UTC)