Group talk:The Spiral
A place to discuss the group's goals and purpose, or simple mindless chat :)
== TRS LAB ==
5-9-2013 hey, it's wilf. Been reading some stuff on theophylline riboswitches, and reviewing the designs from past labs. In a link Nando posted on the other Spiral page there is this detail: "CONSENSUS SEQUENCE OF THE THEOPHYLLINE BINDING RNA APTAMER FLANKED BY A FOUR BASE-PAIR STEM, A THREE BASE-PAIR STEM, AND CAPPED BY A GAAA TETRALOOP" this is in papers 1O15 and 1EHT. The part I was curious about was specifically the 4 base-pair / 3 base-pair part. In randl/AndrewM2A's 51 scored lab the 1NT bulge created @ leaves a 4 pair stack before the binding site Nando was talking about , followed by a 3 pair stack. In the other labs I looked at that closely matched this native state none had this bulge at 62. Am I taking the quote from the paper too literally , or over-simplifying, if I ask if this 1 NT/ 4 pair stack/ binding site/ 3 pair stack set-up was what made randl/Andrew's lab a winner?
Also, I was reading this : http://europepmc.org/articles/PMC390306/reload=0;jsessionid=kY0rWVNZZ983fzJNxYzo.6
thought it was interesting. A little more than I can quite get my head around just yet, but still interseting :)
Have a good night all.
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Hey wilf :)
It's interesting that you should bring this up now. Not many players may know this, but we EteRNA players, are going to have to face another TRS challenge very soon, but this time with freedom of choice as to the length of the "communication module". So instead of having a TRS 5-0, with exactly 5 "manipulable" bases on the 5' side and exactly 0 on the 3' side, we will have a TRS X-Y, with X and Y being user-selectable (within certain limits).
This said, without visual help, I'm having a hard time following your idea, wilf... I think I can say this though : none of the papers I've read about Theophylline conformational switches consider the context of a Hammerhead ribozyme. I believe that this factor is important in the evaluation/design/success of a sequence for a TRS-type lab. I presented my thoughts about the TRS 5-0 challenge in this forum post and this follow-up, and I will probably make a wiki-copy of them very soon.
Other than that, really cool paper. Just for information, this is the link to the NCBI version of it : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC390306/
-- ElNando888 (talk) 07:06, 10 May 2013 (UTC)
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Hi Nando :) I fail at explaining myself, and I am not suprised. More generically, I was wondering about how the immediate structure surrounding the '13-mer RNA' (ACGGUUCC and pairing CCA) affected the success of theophylline binding. And if it does, is that structure something specific only to that lab (or 'test subject'), or could it carry over to others? Also was recently reading about codons and wondered if coding for certain amino acids made a difference in this instance. Anyways, I'll look at the old labs again and keep pondering :) I read the forums posts and what you're describing with the energy makes very good sense. Also it is interesting to see the differences between the eterna model vs current vienna models vs RNA Composer image. I knew eterna's model doesn't account for everything and kindof wondered how much of a hindrance that becomes in a lab like TRS.
I did know about the "freestyle" TRS... I lurk on chat all the time, not really social myself, but I have seen some of you discussing this new TRS as upcoming. It will be interesting to see what is designed.
Think that's all I had to add tonight. Back to my reading, just getting through 'Molecular and Cell Biology for Dummies'. Laugh if you want, but I had to start somewhere :D
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Hey wilf :) you're not failing at explaining, more likely it is me failing at understanding. Although now that you've rephrased, I see better where you're going.
In short, I don't have a clue :) It could be. That molecule is very small, but some 3D features of the immediate environment could possibly disturb, impair or simply reduce the likelihood of the "docking". Hard to tell...
As for the codons, in theory, we don't really have to worry about them for the moment. It will be time to, the day we start in vivo experiments, which I don't foresee happening this year (but I'd love to be proven wrong of course)
And no, not gonna laugh, I would have read that too if I had known it existed !
-- ElNando888 (talk) 21:23, 10 May 2013 (UTC)
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== General ==
eternacac here: system says I'm not logged in, where would I do that? And I edit to post a comment?
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Hi eternacac, yes, currently, this server is not directly linked with EteRNA, so you have to create account here too. Well, actually, you don't absolutely have to, since you can interact as an anonymous user, but it would probably be more comforable for you and for us too.
And yes, everything in wikis is just that, edits, edits and more edits. Nothing to worry about, all changes are reversible. At the moment, it would seem like I'm the only guy in charge here, so if any of you guys think you messed something, drop by my talk page and leave a message there, I'll fix it :)
-- ElNando888 (talk) 22:37, 22 April 2013 (UTC)
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== JASP 6 ==
ElNando888: You guys having any luck ? :P
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yeah, got that awhile ago :P So if I want to reply to something, I just use this edit feature?
Sorry for the dumb question, never used wiki before -wilf
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Basically yes, that's it, just edit. Welcome to the wiki world wilf
-- ElNando888 (talk) 13:45, 22 April 2013 (UTC)
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== Chimera in Ubuntu ==
I installed Chimera on Ubuntu 12.10 Just in case someone else uses Linux and isn't exactly fluent in termial-speak, like me....
after downloading chimera for linux, and after you've run the chmod +x filename.bin command, the install instructions say "Then run the chimera-installer.bin in a terminal window to install Chimera." OK, I didn't know the command to run a .bin file, and to do that you'll need- ./
so
./chimera-alpha-linux.bin is what will run the program.
-wilf
