Wake up, make breakfast. Espresso, two slices of bread from a French batard from Clear Flour Bread with some mouhamara spread from Arax. In the newspaper I read about the primaries, the financial crisis and nothing too important. I waste an hour with email, signing up to some HHMI online system, reading teh intertubes and blogging. Time to work on the grant. I read the background and significance section ... did I compose that crap? After rewriting a bit I move down to preliminary data. Not so bad. I add some clarifications here and there ... man I have to finish the methods section and it's already noon! Eat a quick lunch - I finish the batard with some mortadella, some crotonese cheese and a tomato. Back to writing. No no all this is wrong. Damn. Write write write. What the hell am I proposing? Call up baymate. "How did you do that?" "I got the prep from her, check the paper" I look at the pdf. "were prepared as previously described by Walter et al. 83" Do I have that? No. And the reference is some methods paper not available online. Damn. Look at Dirk's paper. Ah yes, exactly. Write write write. Oh yeah mention p180. Go onto pubmed. Hmm no one's done that? strange. Read some obscure manuscript (well ok it wasn't so obscure - JCB '02) Wow! This could actually be it! Email baymate. Go back look up p180's sequence. Hunh? p180 and only 980 amino acids? That's too small. And where are all the famous repeats? Click, click, click. I don't get it?
Reread pubmed page.
Analysis of cDNA clones indicates that ribosome binding protein 1 may exist in different forms due to removal of tandem repeats, or partial intraexonic splicing of RRBP1. The form presented here is lacking the canine p180 ribosome-binding domain, NQGKKAEGAQ, which is tandemly repeated close to the N-terminus in other forms that haven't been fully characterized. RRBP1 has been excluded as a candidate gene in the cause of Alagille syndrome. Alternate splicing results in multiple transcript
What so they omitted the repeats in pubmed?? Click on the dog version of the gene. Ha! 1530 amino acids ... and the repeats? Oh my.
>gi|50978924|ref|NP_001003179.1| ribosome binding protein 1 [Canis lupus familiaris]
MDIYDTQTLGVMVFGGFMVVSAIGIFLVSTFSMKETSYEEALAN
QRKEMAKTHHQKVEKKKKEKTVEKKGKTKKKEEKPNGKIPDH
EPAPNVTILLKDPVRAPAVPVAPTPVQPPVVIAPVATVPAMPQ
EKLAPSPKDKKKKEKKVAKVEPAVSSVVNSVQVLASKAAILE
TAPKEVPMVVVPPVGAKAGTPATSTAQGKKAEGAQNQSR
KAEGAPNQGKKAEGALNQGKKAEGAQNQGKKVEVAPNQGK
KAEGGQNQGKKVEGAQNQGKKAEGTPNQGKKAEGAPNQGK
KTDGAPNQGKKSEGAPNQGKKAEGAQNQGKKVEVAPNQGK
KAEGGQNQGKKVEGAQNQGKKAEGTPNQGKKAEGAPNQGK
KTDGAPNQGKKSEGAPNQGKKVEGAQNQGKKVEGVQNQGK
KAEGAQNQGKKAEGTSSQGRKEEGTPNLGKKAEGSPNQGK
KVEVVQNQSKKVEGAPNQGKKAEGSQNQGKKTEGASNQGK
KVDGAQNQGKKAEGAPNQGKKVEGAQNQGKKAEGTPNQGK
KAEGAQNQGKKAEGAPNQGKKAEGAPNQGKKAEGAPNQGK
KAEGAPNQGKKAEAAPNQGKKAEGAPNQGKKAEGAPNQGK
KAEAAPNQGKKAEGAPNQGKKAEGAPNQGKKAEGAPNQGK
KAEGAQNQGKKAEGAPNQGKKADLVANQGTKAEGVAGQGK
KAEGAPNQGKKGEGTPNQGKKSEGSPNQGKKVDASANQSK
RAESAPIQGKNADMVQSQEAPKQEAPAKKKSGSKKKG
EPGPPDSDSPLYLPYKTLVSTVGSMVFNEGEAQRLIEILSEKA
GVIQDTWHKATQKGDPVAILKRQLEEKEKLLATEQEDAAVAKS
KLREVNKELAAEKAKAAAGEAKVKKQLVAREQEITAVQARIEA
SYREHVKEVQQLQGKIRTLQEQLENGPNTQLARLQQENSILRDA
LNQATSQVESKQNTELAKLRQELSKVSKELVEKSEAARQEEQQ
RKALETKTAALEKQVLQLQASHKESEEALQKRLDEVSRELCRS
QTSHASLRADAEKAQEQQQQMAELHSKLQSSEAEVKSKSEE
LSGLHGQLKEARAENSQLMERIRSIEALLEAGQARDTQDAQASR
AEHQARLKELESQVWCLEKEATELKEAVEQQKVKNNDLREKN
WKAMEALASAERACEEKLRSLTQAKEESEKQLSLTEAQTKEA
LLALLPALSSSAPQSYTEWLQELREKGPELLKQRPADTDPSSD
LASKLREAEETQNNLQAECDQYRTILAETEGMLKDLQKSVEEE
EQVWKAKVSATEEELQKSRVTVKHLEDIVEKLKGELESSEQV
REHTSHLEAELEKHMAAASAECQSYAKEVAGLRQLLLESQSQ
LDAAKSEAQKQSNELALVRQQLSEMKSHVEDGDVAGSPAAPP
AEQDPVELKAQLERTEATLEDEQALRRKLTAEFQEAQSSACRL
QAELEKLRSTGPLESSAAEEATQLKERLEKEKKLTSDLGHAATK
LQELLKTTQEQLAKERDTVKKLQEQLDKTDDSSSKEGTSV//
Write write write. Baymate emails me back. "Duh. Didn't I tell you about this paper?" Write write write. Damn it's 6PM and I need to work on that talk. Wife calls. "I've been cooped up in this apartment for 3 days. Lets go out for, dinner." Write write write. Almost there. Wife comes home. "You didn't shower?" Jump in the shower, jump out. Head to Casa Romero's ... wow its so busy. No tables??? Head to Kashmir. "The place has changed quite a bit." Eat, talk about ribosomes. My wife rightfully thinks I'm deranged (just kidding). "Did you hear about the artificial chromosome - they were talking about it on NPR?" "No, I've been too busy writing" Head home. Sit down write write write. Time for bed. Read Barzun. So the Puritans were kind of pro-freedom, and tolerant but they were ... zealots. Read about Cromwell. Wow great quote:
we are very apt, all of us, to call faith which perhaps may be but carnal imagination and carnal reasoning
- Oliver Cromwell
Good night.
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For some reasons I find this a very interesting day. Science student talking here.
I've been looking for a recipe for mouhamara since I had it at least every week in an Armenian restaurant in Ft Lauderdale that closed 12 years ago. Thank you.
I don't know if the sole focus of this post on the research project section of your K99 app reflects the proportion of your effort you are putting in to that part in comparison to others, in particular, the mentored career development plan.
You should make absolutely sure that you clearly, explicitly, and comprehensively describe what training you already have received, what additional training and mentoring you have planned, and how that additional training and mentoring will substantially increase the likelihood of a successful independent career relative to the training and mentoring you have already received. It is also absolutely essential that the letter from the mentor describing her participation in the mentored career development plan be equally comprehensive and consistent with yours in every detail.
I am sure Harvard (that's where you're at, right?) has K99 recipients. If you can look at a successful application *and* the summary statement, that will be hugely helpful.
Finally, if you want a fresh set of eyes on it, I'm happy to look at it and provide you with comments. You know how to find me.
Much more detail on this topic posted at DrugMonkey just now:
http://scienceblogs.com/drugmonkey/2008/01/fellowship_mentored_career_d…
Thanks a lot! I may take you up on that offer. I haven't yet touched on the mentored career development plan, but I'm 75% done with the research plan.