{"id":1362,"date":"2011-10-17T20:58:38","date_gmt":"2011-10-17T20:58:38","guid":{"rendered":"http:\/\/occamstypewriter.org\/mindthegap\/?p=1362"},"modified":"2011-10-19T07:24:37","modified_gmt":"2011-10-19T07:24:37","slug":"in-which-i-embark-on-one-last-hurrah","status":"publish","type":"post","link":"https:\/\/occamstypewriter.org\/mindthegap\/2011\/10\/17\/in-which-i-embark-on-one-last-hurrah\/","title":{"rendered":"In which I embark on one last hurrah"},"content":{"rendered":"

So, there is<\/em> life after a high-throughput screen after all.<\/p>\n

As the dust settles after publication of my big screen in the Journal of Cell Biology<\/a>, I\u2019ve been thinking back on the last four years of my lab life and wondering where it all went. I knew when we embarked on the project \u2013 a visual survey of cell shape phenotypes across the entire fly genome, and in a targeted subset of 500+ human genes \u2013 that it was ambitious. But I\u2019d had a real mental block about envisioning its aftermath. <\/p>\n

I remember having particular difficulty in my Wellcome Trust fellowship application, in the section where I had to describe long-term aims and milestones for when the screen was \u201cfinished\u201d. It\u2019s really hard to plan experiments when you don\u2019t know what sort of genes will shake out of the tree: you are reduced to banal generalities in the subjunctive mood \u2013 if I were to get X as a hit, I\u2019d do Y to follow it up<\/em>. Fortunately the Wellcome panel of experts were sufficiently convinced that the screen would yield good fruit, no matter how hypothetically, and by and large I am happy with the outcome as well.<\/p>\n

But there is a strange feeling when you come to the end of such a long project. The momentum that carried you up to that point suddenly dissipates \u2013 you are both lighter, but also newly unstructured. In my case, the sense of being cut loose is exacerbated by the imminent end of my contract at the close of January. I think I have found the means to stay in research afterwards, though until the funding comes through and the contract is signed, I don\u2019t want to go public about it. I\u2019m very optimistic about the appointment, but by its nature, I will probably be leaving behind the work I am doing now.<\/p>\n

So what do you do with a few months? What can<\/em> you do? I\u2019ve turned to a second screen \u2013 the product of an EMBO short-term fellowship sabbatical<\/a> I carried out<\/a> for a few months<\/a> at the EMBL a few years back. The dataset comprises two terabytes of timelapse video footage of each and every one of those 500+ human genes manifesting their actin phenotypes in real time. After having failed to find any collaborators who had the time and money to help me analyze this massive dataset computationally, and knowing that I couldn\u2019t physically watch all the movies myself, I came up with a cunning plan: to use my fixed J Cell Biol<\/em> screen to identify one phenotypic cluster of interest and then visually inspect the movies for all the genes in that set to see if anything looked intriguing.<\/p>\n

Dear reader, it worked a treat. I have found one gene that gives an amazing and unique phenotype in dynamic timelapse that wasn\u2019t evident from the fixed screen. Like the best hits, there is a little known about it, but not very much. I\u2019ve also got in touch with the researcher who\u2019s published the sole paper on this gene, and we\u2019ve embarked on a really friendly and stimulating overseas collaboration \u2013 I don\u2019t want to reveal any details just yet, but we have high hopes of getting a paper together. It\u2019s been so long since I\u2019ve worked on just one gene that I\u2019d forgotten how good it feels to abandon the general for the highly specific. When you work on one gene, instead of hundreds, you can make and test mutants \u2013 you can lavish care and attention onto your approach; you can read the literature in detail and allow yourself the indulgence of entertaining a few crazy ideas.<\/p>\n

Will I ever do a screen again? Quite probably. But for now, I\u2019m basking in the glow of reverting to my previous one-gene-sort-of-girl phenotype at long last.<\/p>\n","protected":false},"excerpt":{"rendered":"

So, there is life after a high-throughput screen after all. As the dust settles after publication of my big screen in the Journal of Cell Biology, I\u2019ve been thinking back on the last four years of my lab life and … Continue reading →<\/span><\/a><\/p>\n","protected":false},"author":6,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8,34],"tags":[],"class_list":["post-1362","post","type-post","status-publish","format-standard","hentry","category-careers-2","category-scientific-thinking"],"_links":{"self":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/1362","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/comments?post=1362"}],"version-history":[{"count":0,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/posts\/1362\/revisions"}],"wp:attachment":[{"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/media?parent=1362"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/categories?post=1362"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/occamstypewriter.org\/mindthegap\/wp-json\/wp\/v2\/tags?post=1362"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}