DISCUSSION of Rosetta@home Journal (3)

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Keith Akins

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Message 40463 - Posted: 7 May 2007, 3:53:48 UTC

That's Ok.

I guess that the main point I was making, where DNA is concerned, a number of mechanisms keep the DNA in a relatively high energy state. When a DNA containing organism dies, the DNA begins to uncoil and rapidly looses energy. It's almost like these mechanisms keep the cellular batteries charged and charged batteries contain energy. That's probably the energy of life.

That was my concern with RNA. Is RNA considered a "living" part of the cell? If so, then I don't think that the energy question can be answered by lowest energy.

Anyway I appreciate your response.
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Lee Carre

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Message 40464 - Posted: 7 May 2007, 4:11:09 UTC

I'm starting to see some new work units using a "(beta) strand pairing" search method.
Could someone knowledgeable on the subject of "(beta) strand pairing" elaborate, in layman's terms, what the term means and how it affects the way the search is performed?
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David Baker
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Message 40465 - Posted: 7 May 2007, 4:31:54 UTC - in response to Message 40464.  

I'm starting to see some new work units using a "(beta) strand pairing" search method.
Could someone knowledgeable on the subject of "(beta) strand pairing" elaborate, in layman's terms, what the term means and how it affects the way the search is performed?


Yes--these are my work units which are testing a new idea we have had. I'll give an explanation in my journal tonight or tomorrow.
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Lee Carre

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Message 40467 - Posted: 7 May 2007, 5:43:46 UTC - in response to Message 40465.  
Last modified: 7 May 2007, 5:45:39 UTC

I'm starting to see some new work units using a "(beta) strand pairing" search method.
Could someone knowledgeable on the subject of "(beta) strand pairing" elaborate, in layman's terms, what the term means and how it affects the way the search is performed?


Yes--these are my work units which are testing a new idea we have had. I'll give an explanation in my journal tonight or tomorrow.

thanks very much, I look forward to reading it
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svincent

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Message 40490 - Posted: 7 May 2007, 18:19:16 UTC

There's been no news for a couple of months on the approaches to carbon dioxide fixation that were discussed here; such as an improved Rubisco and a new reaction cycle that would convert carbon dioxide to simple sugars. Are these projects still going to happen?
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Tom Philippart
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Message 40493 - Posted: 7 May 2007, 19:32:17 UTC - in response to Message 40490.  

There's been no news for a couple of months on the approaches to carbon dioxide fixation that were discussed here; such as an improved Rubisco and a new reaction cycle that would convert carbon dioxide to simple sugars. Are these projects still going to happen?

any news on the HIV vaccine candidates?
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Profile dcdc

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Message 40605 - Posted: 9 May 2007, 21:15:11 UTC - in response to Message 40490.  

There's been no news for a couple of months on the approaches to carbon dioxide fixation that were discussed here; such as an improved Rubisco and a new reaction cycle that would convert carbon dioxide to simple sugars. Are these projects still going to happen?

My guess would be that the Bakerlab is too busy for this ATM, but such a project would be perfect for a dissertation/thesis subject for students...
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David Baker
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Message 40626 - Posted: 10 May 2007, 3:49:43 UTC - in response to Message 40490.  

There's been no news for a couple of months on the approaches to carbon dioxide fixation that were discussed here; such as an improved Rubisco and a new reaction cycle that would convert carbon dioxide to simple sugars. Are these projects still going to happen?


Yes! Graduate student Justin and postdoc Yasuo are just testing their first designs in this area, and have been brainstorming with me about possibilities since my last post--there are lots of things to explore!
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Profile rochester new york
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Message 40990 - Posted: 15 May 2007, 1:21:51 UTC

cancer research................http://news.yahoo.com/s/ap/20070514/ap_on_he_me/cancer_discovery;_ylt=Aip5FPvPmCuDD7miHy549cjMWM0F
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Message 41120 - Posted: 18 May 2007, 12:59:56 UTC

Nice stats
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Profile dcdc

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Message 43152 - Posted: 4 Jul 2007, 11:10:25 UTC

can someone explain where the electrons could come from for the proposed carbon capture reaction? Could you just put an annode/cathode into the mix with a generator and have the electrons free like that or would it need to be in the form of ATP or something similar?
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Message 43249 - Posted: 5 Jul 2007, 15:40:13 UTC

Which work units were working on the enzymes mentioned in Dr. Baker's last post? Were these work units designing the enzyme? Or testing how it will dock?
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David Baker
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Message 43295 - Posted: 6 Jul 2007, 6:10:03 UTC - in response to Message 43152.  

can someone explain where the electrons could come from for the proposed carbon capture reaction? Could you just put an annode/cathode into the mix with a generator and have the electrons free like that or would it need to be in the form of ATP or something similar?


excellent question. you could just put in an annode/cathode, but this still begs the question of where the current comes from. one possibility is nuclear power plants at night when demand for electricity is way down. the problem of course is that reducing C02 requires energy input; the options are sunlight (put the engineered enzymes into photosynthesizing organisms) and not too many other possibilities.

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Message 43414 - Posted: 9 Jul 2007, 9:26:41 UTC - in response to Message 43295.  
Last modified: 9 Jul 2007, 9:49:04 UTC

can someone explain where the electrons could come from for the proposed carbon capture reaction? Could you just put an annode/cathode into the mix with a generator and have the electrons free like that or would it need to be in the form of ATP or something similar?


excellent question. you could just put in an annode/cathode, but this still begs the question of where the current comes from. one possibility is nuclear power plants at night when demand for electricity is way down. the problem of course is that reducing C02 requires energy input; the options are sunlight (put the engineered enzymes into photosynthesizing organisms) and not too many other possibilities.

thanks David. In that case (if a simple anode/cathode could be used) this would be perfect. If it could produce ethanol or something similar then that would be fantastic, although i guess you can always produce ethanol from sugars using traditional methods anyway :)

(Enviromission video is here: http://www.enviromission.com.au/project/video/video.htm)
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Message 43447 - Posted: 9 Jul 2007, 19:59:44 UTC - in response to Message 43414.  

hyh
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Budak

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Message 43501 - Posted: 11 Jul 2007, 1:57:28 UTC - in response to Message 43447.  

hyh



i still agree ^^
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hugothehermit

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Message 43553 - Posted: 12 Jul 2007, 10:27:26 UTC
Last modified: 12 Jul 2007, 10:31:56 UTC

I must admit that I am very interested in the severe combined immunodeficiency disorder target, I'm not a scientist but the first thing I would do (and I'm assuming that a lab would do) is find the lethal dose in mice, has this happened yet? What is it? More than they can ingest?

Is it docking with anything other than the specified target that you know about?

Am I asking too quickly, of course I am :) I'm just curious as to what's happening

Keep up the good work R@H
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Picard2UK
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Message 44369 - Posted: 26 Jul 2007, 22:29:48 UTC - in response to Message 43414.  

can someone explain where the electrons could come from for the proposed carbon capture reaction? Could you just put an annode/cathode into the mix with a generator and have the electrons free like that or would it need to be in the form of ATP or something similar?


excellent question. you could just put in an annode/cathode, but this still begs the question of where the current comes from. one possibility is nuclear power plants at night when demand for electricity is way down. the problem of course is that reducing C02 requires energy input; the options are sunlight (put the engineered enzymes into photosynthesizing organisms) and not too many other possibilities.

thanks David. In that case (if a simple anode/cathode could be used) this would be perfect. If it could produce ethanol or something similar then that would be fantastic, although i guess you can always produce ethanol from sugars using traditional methods anyway :)

(Enviromission video is here: http://www.enviromission.com.au/project/video/video.htm)


Watched the video and an awe inspiring concept for the future generations to marvel at

(Climbs on soap box)

Only one drawback to this is the constant problems of people not wanting something "Blotting There Landscape"

In the UK putting up wind farms are a constant battle from local inhabitants not wanting something so hideous in there "Back Yard", but also being contradictory in the fact they want to,or, want someone else to something to help the environment as the carbon footprint is getting larger.

Governmental papers that have been posted are now looking to place wind farms off shore, but are also having opposition because of environmental issues being raised,
sea life degradation due to installation of said wind farms
impact of tourism on towns/villages of proposed sites

As we have seen Y2K come and go we are still in a mind set opinion "its not going to happen in my life time",that we fail to see what impact it is going to have on future generations.
In short we need to wake the world up to what is actually happening and also what is going to happen if we don't act now in years to come.

(climbs off soap box)
thanks for reading
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Message 44640 - Posted: 3 Aug 2007, 3:51:17 UTC

Could you tell us more about the members of the Rosetta developers conference? From what I've heard and gathered, these are other scientists that are using/enhancing and colaborating on the Rosetta algorythm... but that is all in addition to the folks in BakerLab in Seattle?

Are these other scientific teams developing any of the techniques being used on the @home project?

Is the conference more based around the techie computer stuff? Or the bio-techie protein stuff?

How is Ian doing with the task of explaining it all? Is there a Rosetta@home home game?
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Christian L.

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Message 44915 - Posted: 12 Aug 2007, 21:03:18 UTC
Last modified: 12 Aug 2007, 21:04:59 UTC

Hello, Dr. Baker!

I am new to Rosetta and would like to ask a question concerning DNA- cutting enzymes (endonuclease ?) that you mentioned in the journal. How do you get the enzymes into the cell nucleus? From my understanding this is the actual place where these enzymes work.
Thanks in advance,

Chris L.
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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3)



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