Talk:CH391L/S14/Directed protein evolution

--drewtack (talk) 20:18, 16 February 2014 (CST)I know you haven't given your presentation yet, but, looking through this I'm surprised you didn't mention Frances Arnold at all. There is a citation at the end from her group, but I can't actually find where it is cited in the wiki. You might consider some mention of her lab in the wiki, and you might want to look into source #9.

--Ella Watkins (talk) 20:56, 27 February 2014 (CST)I noticed that there was no detail about the amplification step, was that left blank on purpose? And, after the genes have been selected/screened and amplified, what do they do with them? Are they inserted into plasmids etc...?

Ajv684 (talk) 08:15, 28 February 2014 (CST) In general is a very good wiki article. I liked the way it was structured and it is very comprehensive for the most part. I liked how it started giving a general outline of what Directed Protein Evolution is. Very small comments: In the first paragraph, when mentioning "strong selective force" I would probably add e.g. examples. Also, I would recommend not to use contractions like "don't" (1st paragraph of Library construction section) and instead spell it out. In the Error-Prone PCR paragraph, in the 4th sentence "The following..." I guess you wanted to refer to method previously explained not the following. In addition, I would have liked to see more about DNA shuffling and a little explanation as to what is the difference between screening and selection (but I understand that the latter is not really your job, I suggest it just as a way to better introduce your reader). Lastly, there is a subheading "Amplification" that seems to be void. Other than this, I think you did a very good job.

--Dennis Mishler (talk) 09:54, 28 February 2014 (CST) Good job, Nathan. Given the importance of DNA shuffling, I think it would be nice to explain a little bit of the "how/why". Not necessarily the "how do you make the new molecules", but more of the "how does it work so well" and "why is it a beneficial technique".

--Liz (talk) 10:04, 28 February 2014 (CST) Nice layout and good explanation of technique. You do touch on the applications, but what is the scale of change we are seeing? Maybe in the applications section say what improvements those references were able to make. Similarly, how much faster does PACE turn out to be vs traditional methods?

--Dennis Mishler (talk) 08:24, 11 February 2014 (CST) Gabo's Critique

Overall Format and structure: Nice layout, practical and overall easy to follow. Just a mini-detail: take off the ‘s’ from “This methods” in third sentence. Also, the PACE method kind of interrupts the flow of the report. Maybe it should have another title like “Novel methods for directed evolution” and would then go on to describe this method.

Introduction and background material:

Although short, I found introduction and background to be good and precise enough.

Methods and main body/concepts:

The description of error-prone PCR is quite good, but should also mention the need to avoid using polymerases with proofreading capabilities. The section on “Screening and selection” is a bit confusing and kind of jumps steps giving an incomplete view. Why would DNA be easier to isolate (I know it’s kind of obvious but should say “compared to proteins”) and why is it an ideal tag for proteins? (I guess it just needs rephrasing) Why the need for high-throughput?

Consider what the Lim 2002 paper said: “High-throughput assays are essential for determining the activity of the large % of all proteins whose functions are not known.” or specify that what has really been difficult is the development of high-throughput assays to test millions of proteins at once.

Relation to iGEM and future directions:

None found? I didn’t check around much but I guess this one is somehow related: http://sb6.biobricks.org/poster/engineering-transcription-with-a-novel-platform-for-directed-evolution/

Figures, Figure legends, and citations:

There are very good images around for Screening and selection methods. It would be nice to include one of these showing the basic methods such as physical linkage, phage display, ribosome display and such.