Talk:CH391L/S14/CRISPR

Here is something you e-mailed me: "The CRISPR/Cas system is an RNA-guided endonuclease system found naturally in many prokaryotes. CRISPR stands for Clustered Regularly Inter-Spaced Palindromic Repeats. This small genomic region (less than 1kb) is a critical part of the bacterial defense system against foreign DNA, mainly because it is known to retain genetic information about previous encounters with phage or plasmid DNA. Cas genes, are CRISPR associated genes that encode for several proteins with roles in the formation of the RNA-guided endonuclease complex."
 * --Dennis Mishler (talk) 08:38, 1 April 2014 (CDT) Gabo, you have a ton of information, which is great.  My concern though is in the ordering of that information...

Maybe you needed to change this paragraph a bit, but this was a very good introduction/starting description. I would add a paragraph like this before you go into the background/details. Originally, my one big request from this starting paragraph was to add a one-sentence simple explanation of what CRISPR does... (relating to bacterial defenses). When introducing material, you should start with the bigger/general picture, and then focus on the details.


 * --Dennis Mishler (talk) 08:38, 1 April 2014 (CDT) Assuming you add an introduction, I would change the current "background" section to something indicating a comparison of different nuclease-mediated genome editing. This could (perhaps) be the second or third section, after the introduction.


 * --Dennis Mishler (talk) 08:38, 1 April 2014 (CDT) I might move the "How the CRISPR/Cas system works" section to part of the introduction. Perhaps this would follow a first paragraph, which ends with hints of using CRISPR/Cas for genome engineering... and then describe the natural-occurring system and its elements... This is one idea, not sure if it is the best idea.

Thank you Dennis! Check out intro modifications, mostly as you suggested.
 * --Dennis Mishler (talk) 08:38, 1 April 2014 (CDT)Applications of CRISPR/Cas should be more fleshed out. A single sentence describing some applications is okay, but we should also have more information regarding one or two experiments... and what about in mammalian cells?  Or Embryos?  Could you take 20 fertilized eggs, perform CRISPR/Cas engineering and get a designer baby?  This last question is more speculative, but if you can easily re-engineer mammalian cells...
 * --Gabriel Suarez (talk) 21:35, 1 April 2014 (CDT)

--Chen-Hsun Tsai (talk) 02:14, 4 April 2014 (CDT) The structure of this wiki is well organized and make the story easy to understand. I like you have the advantage and disadvantage compared, and the figures also help readers to understand the complicate mechanisms. I only have few minor things; for example, I think some statements need a reference, such as "Advantage: Works on all cell types", or some of them could be more specific, such as "Disadvantage: Efficiency: it can be improved". Another thing is you said CRISPR could still have many non-specific editing, so are there any interesting studies focusing on solving this? Thanks Chen! I added the requested references and wrote it a bit more specific. Regarding improving specificity, I found a paper (Fu et al., 2014) that demonstrates that shortening the guide RNA increases specificity. I included it in the report.
 * --Gabriel Suarez (talk) 10:50, 7 April 2014 (CDT)

--Liz (talk) 07:26, 4 April 2014 (CDT)Well done. I think the intro and description of how the system works in nature are both very clear. For the CRISPR/Cas gene editing I feel that you start speeding up in a way (if possible in an article?) and maybe skipping over some things that - if defined/explained/rearranged could make this section much more understandable. Ie invert the Type II best sequence: Because all that is needed in Type II is .... it is the best. What is Cas9 compared to other Cas? Anything special there? The three steps at the end seem like the interesting/ meaty part but it also read kinda crammed on the end. Also I really like the figure under Applications. A short description of what we are looking at - even just what the parts we are looking at (ie what is recognition sequence, what is nuclease etc ...) for clarity, and maybe elaboration on how some of the more complex editing takes place- will be nice and helpful. Overall good job!
 * --Gabriel Suarez (talk) 11:15, 7 April 2014 (CDT) Thank you Liz! Type II is just better in terms of simplicity, as expressed in this report you only need Cas9, whereas in the other CRISPR types you'd need to incorporate various other Cas genes for it to work. I'm fleshing out the editing section with more juicy stuff.

--Ella Watkins (talk) 08:17, 4 April 2014 (CDT) While your section describing How crispr works in nature is very well written, I would have only understood it if I had already seen that video on it. Maybe consider including a link to the video for the more visual of learners! Maybe also include the fact that each spacer represents a different virus' DNA that is now being held as memory in the cell. Actually, I am a little confused, so are all of the spacers made, and then just the one that is needed is used? That is what it looks like in the figure, but I am not able to tell from the text, maybe consider a little tweaking of your wording of those paragraphs. Ok, added video link. I see what you mean, yes, all the spacers are made, that is, they all get incorporated into independent CRISPR/Cas complexes that basically float around the cell looking for target DNA, just like our immune system works with antibodies ready for target antigens! I'll work on the phrasing a bit to clear this out. Thanks!
 * --Gabriel Suarez (talk) 11:20, 7 April 2014 (CDT)

Got it!
 * Jorge Vazquez (talk) 09:01, 4 April 2014 (CDT) I really have very little to critique here. I think you did an awesome jobs in general. I personally would've preferred less background and more on current synbio uses of CISPR system. However I see the need of having a detailed background for people who are not familiar with the topic. I agree with Dennis in that you have a very comprehensive wiki but organization might be something that you might want to focus on.
 * --Gabriel Suarez (talk) 11:20, 7 April 2014 (CDT)

--Ashley Kessel (talk) 12:00, 4 April 2014 (CDT) Like Dennis said, would recommend expanding the "Applications of CRISPR/Cas systems" section. I like the image in the section and I would recommend providing more of a description of the different roles the system plays in each function. In general, this article is very well written, and there is not much else I have to critique about it. Cool Ashley! I've added more details to the applications section.
 * --Gabriel Suarez (talk) 11:20, 7 April 2014 (CDT)

--Dennis Mishler (talk) 15:24, 4 April 2014 (CDT) Drew's Critique

Nuts and bolts: This is a pretty good article overall. The wiki page is has a nice layout, you do a reasonable job explaining everything. There are times where something seems out of place, but this is mostly ordering of sentences and paragraphs, and doesn’t not significantly disrupt the conveyance of information.

Bigger picture: Again, this is pretty good in overall information content. I’m just a little concerned at the ordering of information. I feel like a stronger foundation would really be beneficial for the entirety of the document. I’m aware this can be difficult. But after your intro, you move on to adaptation. You should try to say this in a simple way somewhere before you go into this section, something simple like “bacteria keep small sequences of DNA from invading species or virus to use as a “memory” for future encounters. Also, it seems like you might want to compare it to the human immune system somewhere, since people might be more familiar with this (they would be familiar with the idea, not necessarily the mechanisms humans use).

Overall Format and structure: Looks pretty good up until the application of crisper/cas systems section, where all of a sudden there is a lot of white space. I would put that image somewhere, and maybe include a little more actual writing in this section. Introduction and background material: I think I have covered this in the nuts and bolts and bigger picture section. Look to those for guidance. A final thing, your image really encompasses what I think is missing in this section. If you could somehow say what the image is showing, it would greatly enhance your introduction.

Methods and main body/concepts: I feel like this section is a little off. It needs to start from some framework and move up. What is the IDT reference doing here, if you’re going to go to that point you should probably then mention the cloning requirements for CRISPR/Cas guide RNA. How do you go from a primer to a guide RNA, actually that’s a good questions, I have no idea, and I don’t think that the article has really explained it. Also, you simply mention “it can be improved” in the disadvantages, what can be improved? I guess the efficiency, but does that mean it’s really slow? Or that it is very inaccurate, or that it doesn’t fold properly when expressed in any organism besides the bacteria it came from. I don’t know what you mean here.

Relation to iGEM and future directions: Very good section on iGEM. Future directions? Maybe everything.

Figures, Figure legends, and citations: Images and citations are good. Your images could use some captions though.

Excellent Drew! I really appreciate this. You are right, the order of the concepts could be improved and I changed a lot in the intro and all throughout the article. Hopefully it's clearer now. I also moved the IDT reference to the end of the editing section, and included an ADDGENE reference cause I feel these are valuable tools in the design of CRISPR/Cas systems. The ADDGENE reference gives all the details and protocols on designing RNA-guide sequences and I believe is the best resource out there.
 * --Gabriel Suarez (talk) 21:35, 1 April 2014 (CDT)