Talk:Reviews:Directed evolution/Library construction

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General Comments

This is adapated more or less directly from the original text. The major modification is that Figure 2 has been removed as this was adapated from a paper in Nature Biotech. I could check up on the copyright issues but as this is a part of the review that needs modifications anyway I probably won't bother.

Todo List

Good place to list the things that need to be done on this review.

General presentation and logistics

References have been converted to biblio format. There is also now an Endnote style for generating a properly formatted text and reference list for biblio. The bibliography for the review has been placed on a separate page as I think this is probably the best way to do it as it will ultimately allow for linked bibliographies for a set of reviews in the area of directed evolution. The catch is that I've given them references that are just numbers (which correspond to record numbers in an Endnote file I have) so maintaining multiple bibliographies that are all cross compatible could get challenging.

Email appropriate editor at NAR to enquire about writing a short paper to get a primary citation for the WikiReview.

• Cameron Neylon 26 April 2007: Will wait on this until the review is more up to date before doing this.

Contact some directed evolution people to help out with curation.

• Cameron Neylon 26 April 2007: Done. Sent this email to people who cited the original review in papers describing new and improved methods for library construction.

It occurs to me it would be good to link the review to consensus protocols on OWW. Need to think about how to get a relatively large number of such protocols up on the system. If enough of the relevant people sign up as curators for the review then hopefully they can be persuaded to put up the relevant protocols as well.

Other issues?

Science and updating

Several areas need work to bring this up to date. If anyone has some particular references that they feel should be included it would be helpful to categorise them below. General criteria is that they need to give a good description of the methodology and any practical issues as well as apply it to a real experiment.

In vivo error prone methods

http://aem.asm.org/cgi/content/full/67/8/3645?view=long&pmid=11472942

Error-prone PCR methods

DOne some work here but needs cleaning up. Need to make some decisisons about what (not) to include

http://dx.doi.org/10.1016/j.ab.2004.11.032

pmid=15585138 - this link seems to be broken, currently checking

http://journals.humanapress.com/index.php?option=com_opbookdetails&task=articledetails&category=humanajournals&article_code=ABAB:117:2:115

http://nar.oxfordjournals.org/cgi/content/full/32/22/e176 - see nbt paper below

http://www.biomedcentral.com/1472-6750/7/18 - in

http://dx.doi.org/10.1016/j.jbiotec.2004.10.016 - this may belong in RID methods below

http://www.nature.com/nbt/journal/v22/n6/abs/nbt974.html - need discussion of various polymerases (?)

http://nar.oxfordjournals.org/cgi/content/full/32/19/e145 - in

http://dx.doi.org/10.1016/j.bioeng.2004.10.004 - in

http://pubs.acs.org/cgi-bin/article.cgi/bipret/2004/20/i06/html/bp049925z.html - generation of random sequences

http://www.nature.com/nprot/journal/v1/n5/abs/nprot.2006.403.html - protocol for whole plasmid error prone RCA - in

Random insertion/deletion methods

The importance of insertions and deletions to protein engineering is highlighted in this review http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-45765WK-37&_user=129520&_coverDate=12%2F31%2F1995&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010758&_version=1&_urlVersion=0&_userid=129520&md5=e6e7b40edbf64c5d407e1e64b84982ef

http://nar.oxfordjournals.org/cgi/content/full/33/9/e80 And the benefit of these mutations are highlighted here http://linkinghub.elsevier.com/retrieve/pii/S0014-5793(07)00775-2

The original article concerning the commercially available transposon-based pentapeptide scanning mutagenesis method. http://nar.oxfordjournals.org/cgi/content/full/25/9/1866 Which is also reviewed here http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-41V88G6-N&_user=129520&_coverDate=12%2F01%2F2000&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010758&_version=1&_urlVersion=0&_userid=129520&md5=3e698ade6a1f2403fe95bea372f7df98

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16493137 - I guess this belongs here

http://nar.oxfordjournals.org/cgi/content/full/32/3/e26

http://www.nature.com/nbt/journal/v20/n1/abs/nbt0102-76.html

http://nar.oxfordjournals.org/cgi/content/full/32/17/e136

http://www.pnas.org/cgi/reprint/89/8/3581

http://nar.oxfordjournals.org/cgi/content/full/26/8/1927

http://nar.oxfordjournals.org/cgi/content/full/30/8/e35

The construction of artificial molecular switches by domain insertion using non-homologous recombination

Nicely reviewed here http://peds.oxfordjournals.org/cgi/content/full/18/8/359 and here http://www.microbialcellfactories.com/content/5/1/15

http://www.pnas.org/cgi/content/full/102/32/11224

http://linkinghub.elsevier.com/retrieve/pii/S1074552104002765

http://nar.oxfordjournals.org/cgi/content/full/26/21/4946

Directed methods

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17446890&query_hl=4&itool=pubmed_docsum

http://www.biomedcentral.com/1472-6750/4/2 - added

http://nar.oxfordjournals.org/cgi/content/full/32/14/e115 - added

http://jbt.abrf.org/cgi/content/full/18/3/147 - left out

http://dx.doi.org/10.1016/j.ab.2003.10.012 - added

http://ajpcell.physiology.org/cgi/content/full/288/6/C1273 - added

http://nar.oxfordjournals.org/cgi/content/full/30/16/e84 - added

Recombination methods

http://nar.oxfordjournals.org/cgi/content/full/33/13/e117

http://www.nature.com/nbt/journal/v20/n10/abs/nbt736.html

http://nar.oxfordjournals.org/cgi/content/full/29/20/e97

http://www3.interscience.wiley.com/cgi-bin/abstract/110489948/ABSTRACT

http://aem.asm.org/cgi/content/full/68/12/6146?view=long&pmid=12450839

http://nar.oxfordjournals.org/cgi/content/full/33/9/e82

http://www.nature.com/nprot/journal/v1/n4/abs/nprot.2006.309.html - protocol on Nature Protocols

• Cameron Neylon 17 July 2007: I've added a bunch of things here as I came across them while looking for ep-PCR related papers.

Other tools

http://bioinformatics.oxfordjournals.org/cgi/content/full/21/15/3314

http://dx.doi.org/10.1006/jtbi.2000.2082

Analysis of mutation methods

There is now a significant amount of work on analysis, both functional and theoretical of mutations methods and how this relates to results of the DE experiment. Perhaps a new section is required to cover this?

http://www.blackwell-synergy.com/doi/abs/10.1046/j.1462-2920.2002.00326.x

http://dx.doi.org/10.1016/j.jmb.2005.05.023

http://nar.oxfordjournals.org/cgi/content/full/33/11/3667

http://www.liebertonline.com/doi/abs/10.1089%2F10665270050081423

http://peds.oxfordjournals.org/cgi/content/full/16/6/451

http://peds.oxfordjournals.org/cgi/content/full/19/6/245 (?)

http://www.pnas.org/cgi/content/full/101/25/9205

http://dx.doi.org/10.1016/j.bioeng.2005.06.001

http://dx.doi.org/10.1016/j.jmb.2005.10.082

License

Hi there, this is a good article, but I'm puzzled about how this can be licensed under the "Creative Commons Attribution-ShareAlike 3.0 Unported" license since the Nucleic acids research license contains conditions and restrictions on commercial use. Surely these two licenses are incompatible? Tim Vickers 12:46, 23 October 2007 (CDT)

Cameron Neylon 14:59, 23 October 2007 (CDT) Yes I need to check back on this with OUP. When I first set it up the NAR license seemed to be different than it is now and I thought it was a CC license (if you look at the history you can see I changed the reference a month or so back when I realised it wasn't). There is this potential issue with commercial re-use of this. Although there is a grey area in as much as the article is now significantly changed as well (which is allowed under the NAR license). But there is a more general issue because as NAR retain copyright of the original article they can arbitrarily change any license as well.

Yes, it would be a pity if this didn't work out. This kind of thing is why Wikipedia is so strict about all content being freely-available, since although all-free content is harder to set up it is much easier to administer. Tim Vickers 16:30, 23 October 2007 (CDT)