hypervalent_iodine Posted July 25, 2014 Posted July 25, 2014 I have a somewhat rookie request. Recently I was offered a 2 year research position in a lab funded by the Gates foundation. My work will primarily be with a certain species of algae and working on ways to optimise output of various commercially valuable fatty acids, though there will also be some organic chem work in there somewhere for the pharmaceutical branch of the institute. Most people who have been here long enough will know that my background is in organic chemistry. I have a decent enough understanding of the broader concepts of molecular biology and have some practical experience in genetics labs, though it was limited to RNA extraction, library preps for NGS platforms and cleaning up and running samples for Sanger sequencing. I don't really want to go into this new position unprepared or unable to contribute to my own work intellectually (though I'm sure I will pick it up as I go) and so I was hoping someone would have a good recommendation for a practical molecular biology text. I'm looking for something similar to what the Vogel text is for chemistry or like another text I've read, From Genes to Genomes, which I found invaluable for troubleshooting and modifying my experiments while doing undergraduate research.
CharonY Posted July 25, 2014 Posted July 25, 2014 A standard book is Molecular cloning (Sambrook, Maniatis). It offers thorough descriptions of protocols and, more importantly, the reasoning behind those. I read it cover to cover as an undergrad and highly recommend it (I am not sure what they added in the new editions, but it seems to be updated fairly often). It has to be said that protocols for NGS have become so ridiculously easy and streamlined that I fear that those are dumbing down my students... 1
chadn737 Posted July 25, 2014 Posted July 25, 2014 Molecular Cloning is fully online now as part of CSHL protocols I believe. Not sure if they are releasing print editions anymore, but the print editions were great at explaining basic concepts. Still expensive for all three, but you can usually find second hand copies. 1
hypervalent_iodine Posted July 25, 2014 Author Posted July 25, 2014 Thank you for the suggestion! I'll check if the library has them. It has to be said that protocols for NGS have become so ridiculously easy and streamlined that I fear that those are dumbing down my students... I was working with RNA transcript libraries from various non-model species for sequencing on the IonTorrent platforms. Maybe not as difficult as the older emulsion PCR technologies, but boy did they not want to play ball 99% of the time. I think the lab has a Nextseq now, which does seem trivially easy in comparison.
CharonY Posted July 26, 2014 Posted July 26, 2014 IonTorrent has some snags, but to be fair, I was still comparing it to Sanger setups starting with BAC libraries....
chadn737 Posted July 27, 2014 Posted July 27, 2014 No paper anymore? I am sad now. Actually it looks like they just came out with a fourth edition in paper. For a while there it looked like they were moving everything online, but I haven't looked for copies since probably ~2011 and this came out in 2012. Thank you for the suggestion! I'll check if the library has them. I was working with RNA transcript libraries from various non-model species for sequencing on the IonTorrent platforms. Maybe not as difficult as the older emulsion PCR technologies, but boy did they not want to play ball 99% of the time. I think the lab has a Nextseq now, which does seem trivially easy in comparison. Illumina has so dominated the sequencing market the last 3-4 years that nearly all real advancements in library prep have been made for Illumina. There was a ton of excitement about Ion Torrent challenging Illumina, but they overplayed the output and quality. Meanwhile Illumina has been holding back updates and releasing them as new competitors arise to completely swamp them out. It really is amazing the pace of development when I started with next-gen back in 2008 and 454 and Solid was still competitive. With a chemistry background, I think you will find much of the benchwork behind molecular biology to be relatively easy. If you've worked with RNA, then you've already worked with the most sensitive of the three (DNA, Protein, RNA)....although certain proteins can be a huge pain in the ass. By the way, it looks like for a limited time they have knocked 30% off of the 3 volume set of the new Molecular Cloning....still expensive as hell, but much better at $255 than $365
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