Talk:Genomic library

Archived discussion of move from Gene library.

Done. Now a to-do list.

This article was moved here from Gene library, which now redirects to Library (biology). There is also a cDNA library article. All of these need some work, but this one the most, I believe. I went through and did a very quick cleanup to fix phrasing, remove redundant wikilinks, etc. All three articles could use some good references. I think they also need some rewriting, especially in the leads, so that non-specialists can get some idea of the topic before the article goes into a lot of detail. Agathman (talk) 19:32, 3 June 2009 (UTC)

Dr. kuldeep rathod —Preceding unsigned comment added by 122.168.213.175 (talk) 16:30, 1 September 2009 (UTC)

Gene library didn't redirect to Library (biology), but to this article. I have fixed that, as the term 'gene library' can mean 'genomic library', but also other things (such as a randomized mutant library, which - if it represents a gene - is usually also called a gene library).

Entelechon (talk) —Preceding undated comment added 14:08, 18 October 2011 (UTC).

Does anyone have suggestions/concerns of what additions they would like to add this page? My classmate and I have proposed a new section set up:

1. Genomic Library (Lead)

2. History

3. Construction Of A Genomic Library

a. Types of Vectors used

b. Math behind the type of vector used???

4. Applications

a. Current Use

b. Clinical Use?

5. References

This isn't set in stone, but we are retrieving peer-reviewed journals, textbook references, etc. for this page. Please also direct us to any images or PubMed articles you would like used. We will use our best judgement of what can help the flow of the page! Thank you, Jmudukes88 (talk) 02:07, 12 March 2013 (UTC)

Hi, all. I am the above mentioned classmate. We will be working on this article as part of our Molecular Biology class. I look forward to writing/editing with you all! Aluquette (talk) 14:12, 12 March 2013 (UTC)

Comments from Jessicalau90

Overall, a good start to the article. The lead section follows style guidelines by being very clear and concise. The references are also well cited and are used throughout the article-content does accurately represent the cited sources. The writing is clear and there is no use of jargon.

Some suggestions would be to include a legend for the figure that you have-a few sentences below the figure to give a quick summary. (I see that you have the steps clearly written out above it as well as in the diagram itself, but maybe just add a short sentence describing it?)

There was brief mention of restriction enzymes that can be used to digest the genomic DNA but maybe include some examples?

Also, I feel that there is a very big emphasis on the types of vectors. I like that you have included the advantages to using each vector and the capacity that each can hold but maybe include some disadvantages (if any, other than capacity constraints) as well? If there are images for some of the vectors, maybe try including those in the article too.

Perhaps in the applications section, include a specific example of how the genomic library is used. And also, in the paragraph where you mentioned that "The whole library can be plated onto filter over media. Colonies are grown and the filter (blotted) can be prepared for hybridization plus labeling by a probe. The target DNA insert of interest would be identified by detection such as autoradiography because of the hybridization", possibly include an image of that as well.

Are there any limitations overall in using the genomic library to clone a DNA fragment? I would think that a genomic library is not as suitable for organisms with complex genomes as many DNA fragments would not contain coding DNA sequences. I'm not sure if any limitations were discussed in the article. Hope these comments/suggestions help!Jessicalau90 (talk) 10:09, 11 April 2013 (UTC)

Hi Jessica! Thanks for your suggestions. When I started writing about the kinds of vectors I kept finding more of them. I didn't want to exclude any so it ended up being a large section. I think adding some disadvantages to each is a good idea. Also, genomic libraries are not generally used to look at just coding DNA sequences. I think the biggest use of them that we have found so far is for sequencing whole genomes (like the human genome). We plan to expand the applications section significantly in the next two weeks and after that I think the bigger picture of what they are for and how they are used should be more clear. Aluquette (talk) 13:36, 11 April 2013 (UTC)

Thank you, Jessica. In regards to your 2nd comment, is this due to the clarity of the text in the picture? My partner has already started to try to address this area by creating a new figure in Inkscape. If we aren’t able to figure this out, would you recommend that we supply an annotated step-by-step comment of what the figure shows?

Also, great comment on the “Applications” section. I will look into specific examples to throw in. If not, maybe including a real-world example in the mathematics on vector selection that has already been included. In terms of adding another image/figure to the article, I believe adding one to the vectors area, or to the applications area, would be the best fit. In regards to the last comment, I don’t think we explicitly state limitations of using a gene library to clone a specific DNA fragment in complex genomes, so this is definitely something to consider as well. Thanks again! Jmudukes88 (talk) 23:36, 16 April 2013 (UTC)

Again, thank you for the comments, Jessica. We added a brief summary of the tabled figure as you suggested. We didn't add any mention of restriction enzymes. While this is obviously important, the restriction enzyme Wiki page may suffice. If we had more time, however, this would be a great add. We are about to add a few disadvantages to the vector section too. We took your suggestion about adding some images to the vector section and actually added two more to the applications section, plus modified our original image in how to create a library.

We extended the applications section with more content, giving brief examples of how it could be used. You will see an image there as you had also suggested. We haven't explicitly made a section or subsection on limitations; however, we have briefly hinted or mentioned them through how to select vectors. The numerous vectors and the numerous aspects to consider entails just how much work needs to be done when creating a library. Also, it entails just how much more can be added to this Wiki page! Jmudukes88 (talk) 03:03, 26 April 2013 (UTC)

Hi Aluquette and Jmudukes88, great to see that my suggestions were helpful. I took a brief look again at your article and you guys have done an awesome job at improving the article! Jessicalau90 (talk) 08:14, 10 May 2013 (UTC)

comments from Jengel11

First off, good work! The article looks great and really flows well. I like the addition of the various vector applications; there’s some good information there. On my initial read through I added some internal wiki links to some of the sections. I may have missed a few though. And I’m curious if they should be added to every single usage of the term or if just the first time they are used? I’m going to look into what the norm is.

• “The lead should be able to stand alone as a concise overview”

The article opens with a good description of the topic and summarizes the most important points before diving into the body of the article.

• Does the content accurately represent the cited sources?

All internal wiki links are functional and direct the reader to the proper wiki page. Cited sources are accurate and represent a good basis to establish the topic. Maybe add a few more wiki links where needed.

• Is the writing clear, comprehensible, and doesn't use too much jargon?

The writing is clear and comprehensible, but the opening paragraph may have some grammatical error?

• Do the contents of each section belong in that section? Is each section coherent, and in concord with the section heading?

Sections are coherent and lead with a heading. Each sections flows well and the article gives more in depth knowledge as it progresses.

• Are there gaps in the content? (What is missing?)

A section on genetic engineering might really compliment the material in the article. Or an internal link to the wiki page added to the opening section would probably suffice.

• Are there places where there is ambiguity or inaccuracy over which sources are supporting what content?

No ambiguity or inaccuracy over sourcing content was observed.

• Could the content be structured differently?

Organization of the opening paragraph is good but sentence structure may need to be altered. Maybe Include some additional basic knowledge in the opening paragraph. Some suggestions: What is a genome? How long are they? Maybe compare different species to the length of their genome. In the history section you could add some information on next generation sequencing and how entire genomes are relatively easy to produce and cost continues to decrease.

• Is the content within Wikipedia's guidelines (such as neutral point of view) and does it avoid plagiarism or too-close paraphrasing?

The article has no obvious signs of plagiarism and is written from a neutral point of view. Jengel11 (talk) 02:42, 12 April 2013 (UTC)

Thank you for the positive compliment, and for adding internal wiki links to some areas. We were going to look through these a bit more. I believe we are to just link the first time the term is used, by the way (in case this helps your proj.). My question is regarding the lead section- you mentioned it may have some grammatical errors. Do you mind pointing us to what particular area or sentence you felt had errors?... Genetic engineering may be a great sub-section we can use under “Applications” since I feel this area can be utilized a bit more. Thanks for suggesting that. As for the second to last comment, those are perfect questions to be answered in the lead. We were looking into strengthening that first section to really include the overall scope of the article. Great comments. Jmudukes88 (talk) 23:26, 16 April 2013 (UTC)

Thank you once again for the accolades. We have added a few more wiki links and will continue to add more as suggested by our moderator by the completion of this project. We haven't added a section specifically for genetic engineering, but I will integrate it w/ a link shortly! I like your suggestions for the lead section, but some aspects may be too specific to add such as: comparing lengths different species genomes or that in general. Your comment for adding to the history section was great. Hopefully, we get a chance to add this for the final paper. We used most of our time adding content to the applications section, finding images (plus modifying them), and even creating one based off an older image. The math section was quite laborious as well. Jmudukes88 (talk) 03:11, 26 April 2013 (UTC)

The article looks to be improving nicely, good work. I can appreciate the time and effort it takes to get images altered and in the right location but what a difference it makes! As for the grammatical errors you mentioned, I would check on the use of commas in the lead section. There might be a way to more easily convey your thoughts without using so many of them. And one last comment would be to maybe add a little more information to the lead section. Jengel11 (talk) 12:17, 29 April 2013 (UTC)

Hi Jengel11! Thanks for the clarification on the grammatical errors in the lead section. I think that has been one of the toughest sections to write just because it's hard to summarize the topic so that it's understandable to non-science readers. We plan to continue working on it during the final edit. I'd also like to add a little bit about applications for genomic libraries in the lead section before talking about how to make one. Aluquette (talk) 01:06, 30 April 2013 (UTC)

Article Writing Project

Hi Jmudukes88! I guess we should decide who will be working on what... I found a really good book (Molecular Cloning) that gives thorough descriptions of the different kinds of vectors used for genomic libraries. So if it's ok with you I would like to start writing sections about each one. I have a few other books too (already listed in our outline on your sandbox) that discuss vectors. Would you want to work on the history section and how to choose a vector since you had good references for those? And then we can always add to or change each others sections if needed. What do you think? Aluquette (talk) 21:06, 30 March 2013 (UTC)

That sounds great! We can certainly add more as we go. I'm going to try and get as much in tonight and tomorrow as I can. I'll follow up with you once complete for any revisions or edits you think are necessary. Enjoy the Holiday and March Madness! Jmudukes88 (talk) 21:51, 31 March 2013 (UTC)

I just added descriptions for each kind of vector. I am planning to update the chart soon to include some that were not already in it. I will also add links to other pages and hopefully find some more references too. Do you think the history section might go better under applications? Like "early appications" or something like that. It seems a little out of place to read about the history before you know about how to make a library... what do you think? Aluquette (talk) 02:45, 2 April 2013 (UTC)

Ahhh! Sorry I forgot to respond to your question. I'm fine with making that move from History to Applications if it will make the flow a bit better. I only put the History first as a way to show this had happened at this time; then we show this is how you would do something like that in the following section. This may be a rough read! Let me know if you want me to attempt to explain it better. Jmudukes88 (talk) 02:09, 12 April 2013 (UTC)

My turn to forget to respond! What you said makes sense... like it's in chronological order. I just think if someone who doesn't know anything about the topic reads it, it might be more helpful to read about what they are before all the history/uses. Maybe once we start filling in the applications we can see where the history part fits best. Aluquette (talk) 00:13, 17 April 2013 (UTC)

Hey Jmudukes88! I got the new figure up for construction of a genomic library. Let me know what you think. It seems kinda big... I'm not sure if there's a way to resize it aside from shrinking it myself and resubmitting it. I also added a section on hierarchical sequencing to applications and I'm going through everything tonight and trying to fix things that were mentioned in the reviews. Good finds on the other figures you added! Aluquette (talk) 00:41, 26 April 2013 (UTC)

Never mind, I figured out how to resize the figure. :) I think I covered most things from Klortho's review. I moved your sentence about the human genome project from the history section to the hierarchical sequencing section. We still need to add some more links but we can do that later. Aluquette (talk) 01:46, 26 April 2013 (UTC)

Review from Klortho

• In the opening sentence, links should not appear in the boldface reiteration of the title (so, unlink "library")
• Link the first occurrance of "DNA"
• "DNA is extracted" from what?
• Maybe, "ligated" is a bit jargony for the lead -- could you use a different verb? Same for "transformed".
• After reading the lead, I have some questions: if the description is of how to make a library, and a library is stored as a population of vectors, then why do I care that the vector can be transformed into a host organism? (I'm not suggesting this is wrong, just that it needs to be clarified.)
• More stuff should be linked. For example bacteriophage, sequencing, gene therapy, polymorphisms, all those diseases, etc. This should be done throughout the article.
• The last sentence of "History", "The human genome sequencing ...", seems out-of-place. Either tie it in with the earlier material, or drop it, I'd think.
• For section headings, only capitalize the first word (this is just weird Wikipedia house style, different from academic writing).
• "Steps for large genomes:" this should be a complete sentence
• The first sentence of bullet #3 is confusing (what does "by mixing with ligase" refer to?)
• The figure is very good and appropriate!
• I think the table should get an introduction, like "The following table lists ..."
• "small amount of clones" → "small number of clones"
• If you have time, try to do the math in LaTeX. It is easier than you think. I did the first equation for you at User:Klortho/sandbox

Klortho (talk) 03:40, 20 April 2013 (UTC)

Thanks for your suggestions, Klortho! We will work on fixing the things you mentioned as we make our second contribution to the article. I do have a question for you... you mentioned adding more links. What is the general rule for how often to add links for certain words? Should we link a word only the first time it's used, or the first time in each section, or more often? Thanks! Aluquette (talk) 21:39, 21 April 2013 (UTC)

See Wikipedia:Linking#Overlinking_and_underlinking. The quote specific to your question is, "A term should be linked, generally, at most once in an article's lead, perhaps once again in the main article body, and perhaps once at first occurrence in each infobox, table, caption, and footnote." Klortho (talk) 16:47, 22 April 2013 (UTC)

Ok, thanks! That sounds like a good rule of thumb. Aluquette (talk) 00:35, 26 April 2013 (UTC)

Thank you for the comments as well as guiding us toward LaTeX. We actually were able to tackle this and it was a bit easier as you had said! It was still very time-consuming, though, because there is a ton of trial and error... Speaking of an error, I have had no luck in creating the correct language to close-out my bracketed material with this, "]". This error occurs in the actual mathematical example that we created (after the basepairs). Would you be able to help us out? I gave it quite a bit of time yesterday and today, but had no luck. We made changes based off all of the suggestions, so thank you for them. We should be able to add more links within the next week or so in the newer sections. Jmudukes88 (talk) 03:45, 26 April 2013 (UTC)

Suggestions

One of our prime suggestions is to add some material on titering libraries. Does anyone have good, reputable sources on how this is completed? Me and my partner wanted to sort through what is out there on this procedures. Feel free to add any other comments of what you would like us to edit, add, delete, etc. Thank you, Jmudukes88 (talk) 04:00, 26 April 2013 (UTC)

I just added a subsection on titering a genomic library to the applications section. Let me know what you think and feel free to edit it further! I'm planning to do a bit of polishing the article in the next few days before the deadline. Aluquette (talk) 13:32, 7 May 2013 (UTC)

Comments from Mhk5600, Second peer review

Greetings! I was assigned to do the second peer review of genomic library. I quickly read both article and talk page moments ago. That is very well done in the first impression. I can read a very active talk page from the first peer-reviewers. I’d like to follow a guideline that listed in the class wiki page for Unit 13. For the next few days, I will read over a few times with focus on immediate problem rather than major structural issues. /Mhk5600 (talk) 07:07, 28 April 2013 (UTC)

Thanks! We look forward to reading your review! Aluquette (talk) 01:08, 30 April 2013 (UTC)

Hi, I did not intend to look for sections that need major structural changes, a flow of contents, accuracy of references. I read along with sections. As authors and the first peer-reviewers looked through, article is in a great shape.

• Lead section

In a lead section, can you consider the following sentence into two? It is such a long one. “In order to construct a genomic library, …. and the fragments are inserted into the vector using the enzyme DNA ligase.”

• Table

In 3. types of vectors, I can see a column for Capacity in a table. Plasmids, Capacity for Phage Lambda and Cosmids are not a fixed size. As description said, listed numbers are the maximum length of insertion. I think either a column title is needed to be changed or use “up to” words before each of those numbers.

• Figures

I don’t see any caption in each of those figures. Is that intended or forgotten? I wish a resolution of three figures better. Nevertheless, thanks you for your time and effort to create Genomic Library Construction.png. Although I have not read all of other team’s articles from Molecular Biology’s Wiki project, I think it is the only one that was created from this Wiki class.

• References

I can see one warning message in reference 12, “Wikilink embedded in URL title (help)” A book, “Molecular cloning: a laboratory manual.”, has been cited 6 times. Is that a primary sources or just book you are using? If a primary source is available, a primary source needs to be cited rather than a whole book itself.

After all, I learned what genomic library is and how it could be used in a real world application. Thanks for a good article. /Mhk5600 (talk) 13:33, 2 May 2013 (UTC)

Hi, thank you for the comments. These are the exact type of comments I think our Professor was looking for (and us), plus they are issues we can resolve immediately. I assure you, we didn't mean to have that warning message pop up, so we'll have to look into this over the weekend. The others may be quick fixes as well. In regards to the "Capacity" comment, wouldn't the capacity denote up to that specific basepair limit as you had suggested? Jmudukes88 (talk) 00:41, 3 May 2013 (UTC)

Thanks for your suggestions, Mhk5600! Regarding the table, I might change the column title to say "insert size" instead of "capacity" so that I can list the range commonly used for each vector and not just the upper limit. That way it will be consistent and also more informative. Thanks for catching that! Aluquette (talk) 20:14, 4 May 2013 (UTC)

We switched the “,” with a “:” to breakup that sentence in the lead section a bit better. It will read “In order to construct a genomic library: …”

In terms of the first figure in “Genomic library construction”, we didn’t include any information explaining it afterwards due to the fact the preceding information does sufficiently. All of the following figures now contain a reference to the figure in the content section or can be inferred by the placement of the information and the image, so thank you for pointing that out!

As far as reference 12, there was an issue with an attempt to embed a URL for the work “genomic library”. Haha I may have messed that up previously. It’s been fixed. Thanks again! Jmudukes88 (talk) 23:03, 4 May 2013 (UTC)

I actually just changed the lead quite a bit so that sentence is now two sentences. Sorry, Jmudukes88, I changed it right after you made your change. Thanks for checking the rest! Aluquette (talk) 23:13, 4 May 2013 (UTC)

Thanks for taking my suggestions in a constructive manner. I read the lead section with those 2 extra paragraphs that recently added. I have somewhat different feeling. Let me step back and read it again at the beginning of week. We know that the lead section is the most important part of article to give our audience the first impression and scope. Let me write a small note how well I accept it later. Thanks. /Mhk5600 (talk) 22:15, 5 May 2013 (UTC)

I can guess why the lead section is changed. You tried to give a reader a general overview how it could be used, before you describe type and application of genomic library. BTW, I think this line does not need to be there, "The capacity represents the size an insert of DNA may approach." in Type of vectors section. Now, I don't have any further comment on your article. Thanks. /Mhk5600 (talk) 18:15, 7 May 2013 (UTC)

Thanks, Mhk5600! I forgot to take that sentence out when I changed the column title in the table. I fixed it. Aluquette (talk) 19:29, 7 May 2013 (UTC)

Comments from Sharkeyr

I was assigned to do the second peer review of this article. Overall the article was well written and easy to get the information you might need, be it a general overview or the more detailed information. I particularly liked the example of vector selection, it made the concept of the math easier to visualize and understand. I know since it is late in the game there isn't much time to add much more detail, but if you were looking to add more applications, just from personal experience in clinical labs, plasmids can also be used for controls in studies, having a positive and a negative plasmid for a particular gene/marker you are looking for. Everything is cited very well throughout, and there appropriate linking to other articles without repeating or being overwhelming. I read through the other reviews you've had and it looks like the comments mentioned earlier have all been addressed. The article is in great shape. Sharkeyr (talk) 21:36, 30 April 2013 (UTC)

Thanks, Sharkeyr! I'm glad you think the article is in good shape. Question about your idea for applications... is that just with plasmids in general or for genomic libraries? I guess I don't see the connection but maybe I'm missing something. Anyway, thanks again for your comments! Aluquette (talk) 12:08, 1 May 2013 (UTC)

I guess I was just thinking that based off of the data contained in the genomic library, the plasmid (vector) can be purchased to use as a point of reference for screening type assays.Sharkeyr (talk) 16:27, 2 May 2013 (UTC)

We appreciate your suggestion! Would you be able to point us to the direction of maybe a study or study lesson (.edu website) where that was used so maybe we can incorporate a bit of that into the application section? Thanks, Jmudukes88 (talk) 00:35, 3 May 2013 (UTC)

http://www.sciencedirect.com/science/article/pii/S0006291X03024537 is just one example I found on a quick google scholar search that shows a plasmid being used as a control. Sharkeyr (talk) 16:04, 4 May 2013 (UTC)

Oh, ok. I think I see what you mean now. We'll look into this and see if we can incorporate it into the applications. Thanks for the idea! Aluquette (talk) 20:01, 4 May 2013 (UTC)

Hi Sharkeyr, we looked into your applications idea but since we don't have much time left in class we weren't able to really compile a good summary of the concept. We did add a section on how to titer a library and also made the part about screening libraries its own section so now there is a little more in the applications section. We appreciate your idea, though! Good luck in the rest of class! or what's left of it :) Aluquette (talk) 23:53, 9 May 2013 (UTC)

Yes, we hope that future contributors may add the concepts from your example. We moved the screening and titering subsections to the more aptly suited "Genomic library construction" section. Jmudukes88 (talk) 04:01, 10 May 2013 (UTC)

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Construction of genomic Library - human antibody gene library

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