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RNA measurements may yield less insight than assumed

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From Phys.org:

The majority of RNA expression differences between individuals have no connection to the abundance of a corresponding protein, report scientists from the University of Chicago and Stanford University in Science on Dec. 18. The findings point to a yet-unidentified cellular mechanism that regulates gene expression and suggest studies that rely only on RNA measurements to characterize gene function require further analysis.

“The chief assumption for studies of RNA differences is that they ultimately reflect differences in an end product, which is protein,” said senior study author Yoav Gilad, PhD, professor of human genetics at the University of Chicago. “But it turns out in most cases this may not be true.”

Interesting, when we consider the high hopes placed in RNA world.

See also: Welcome to “RNA world,” the five-star hotel of origin-of-life theories

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Comments
Secretory proteins hail a cab at the TGN doi: 10.1083/jcb.1997iti2 After moving through the secretory pathway from the ER to the Golgi apparatus, proteins are sorted at the TGN for delivery to their final destinations. How soluble proteins are selected for secretion outside of the cell is unclear,... http://jcb.rupress.org/content/199/7/1018.2.fullDionisio
December 23, 2014
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Hey Dio, at about the 1:45 mark of that new protein packing video I can't tell what those greenish things are, did you come across it by any chance?AVS
December 23, 2014
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Ok, let's not get confused so easily. Some PCB may look messy, but they handle a lot of data processing very elegantly. One of the beauties of the biological systems is that it does much more than all the most sophisticated systems humans have created, but still scientists can't figure out exactly how all that is done in details. Tremendous technological advances lately have allowed researchers to discover more details, but some old questions remain and many new ones have popped up. Much more is known today than a few years ago, but we ain't there yet. We are witnessing a system that seems designed and setup to handle even stochastic scenarios. We ain't seen nothing yet. That's why we look forward, with much anticipation, to reading the next reports coming out of research labs. This is indeed fascinating. Let's enjoy it!Dionisio
December 23, 2014
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Coordinated protein sorting, targeting and distribution in polarized cells doi:10.1038/nrm2525 http://www.nature.com/nrm/journal/v9/n11/full/nrm2525.htmlDionisio
December 23, 2014
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Wow, remember when I caught all that flak from you guys for saying the molecular environment of the cell is in reality a mess? Here's some quotes from what was said about the simulation in a post above: "Alain Viel, the director of undergraduate research at Harvard and a member of the BioVisions team, likened the inside of a cell to a rush-hour subway platform. “If there’s a big crowd in front of you, there’s a good chance you might not even see the train,” he said." "kinesin doesn’t look like a molecule out for a stroll. Its movements are barely constrained randomness." "In reality, however, the parts of our cells don’t operate with the precise movements of the springs and gears of a clock. They flail blindly in the crowd. Our cells work almost in spite of themselves." Interesting! Thanks Dio!AVS
December 23, 2014
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Hydrophobic handoff for direct delivery of peroxisome tail-anchored proteins doi:10.1038/ncomms6790 http://www.nature.com/ncomms/2014/141217/ncomms6790/full/ncomms6790.htmlDionisio
December 23, 2014
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Tracking Protein Function in Living Cells https://www.asme.org/engineering-topics/articles/bioengineering/tracking-protein-function-living-cellsDionisio
December 23, 2014
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The Inside Story of Cell Communication http://learn.genetics.utah.edu/content/cells/insidestory/Dionisio
December 23, 2014
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Directing Traffic: How Vesicles Transport Cargo http://learn.genetics.utah.edu/content/cells/vesicles/Dionisio
December 23, 2014
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The Get1/2 transmembrane complex is an endoplasmic-reticulum membrane protein insertase doi:10.1038/nature13471 http://www.nature.com/nature/journal/v512/n7515/full/nature13471.htmlDionisio
December 23, 2014
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SIMIBI twins in protein targeting and localization doi:10.1038/nsmb.2605 http://www.nature.com/nsmb/journal/v20/n7/full/nsmb.2605.htmlDionisio
December 23, 2014
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The mechanism of membrane-associated steps in tail-anchored protein insertion doi:10.1038/nature10362 Tail-anchored (TA) membrane proteins destined for the endoplasmic reticulum are chaperoned by cytosolic targeting factors that deliver them to a membrane receptor for insertion. Although a basic framework for TA protein recognition is now emerging, the decisive targeting and membrane insertion steps are not understood. http://www.nature.com/nature/journal/v477/n7362/full/nature10362.htmlDionisio
December 23, 2014
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Watch Proteins Do the Jitterbug http://www.nytimes.com/2014/04/10/science/watch-proteins-do-the-jitterbug.html?_r=0Dionisio
December 23, 2014
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Three-part handoff delivers proteins to membrane surface http://www.uchospitals.edu/news/2011/20110824-proteins.htmlDionisio
December 23, 2014
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Golgin proteins specify destination of vesicle traffic http://www2.mrc-lmb.cam.ac.uk/golgin-proteins-specify-destination-vesicle-traffic/Dionisio
December 23, 2014
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There is no "proper destination" in the cell. Just random bumping of molecules into other molecules. Stuff happens.Mung
December 23, 2014
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It's ok, biology isn't for everyone. UD is a perfect example of that.AVS
December 23, 2014
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That must be it AVS. :)Box
December 23, 2014
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That would be because you haven't taken a basic biology course boxy.AVS
December 23, 2014
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'How do molecules in the cell find their proper destinations', is a profound question in my book.Box
December 23, 2014
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That still seems like asking how to PCR primers find their targets to me.wd400
December 23, 2014
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WD400 #128, Even if you are correct, the question remains how thousands of DNA fragments are selected on suitability and aligned in the correct sequence.Box
December 23, 2014
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The wrong bits can just as easily been put together. No. The "stitching" process requires homologous sequences which can bind to each other. If the sequences aren't homolgous they oant be put together (absent the chance similarity I discussed above)wd400
December 23, 2014
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I still don’t understand what was wrong about that text you were pointing to
I don't think it's hard to understand. 1) "News" said these results where interesting with regards the "RNA world". In fact, they have nothing to do with any RNA world hypothesis. Indeed it's bizarre someone could think these data could having any bearing on that topic 2) The press release refers to some 'unknown' process regulating the rate at which proteins are produced from mRNA. In fact, many means of regulating that process are known, there doesn't seem to be any reason to invent another unknown one to explain these results (interesting as they may be). I don't think a clearer explanation is possible.wd400
December 23, 2014
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Wd400: The “wrong” bits can’t be put together, unless they happened to share identical streches by chance.
The wrong bits can just as easily been put together. That is the whole point. Drad reconstructs its genome from the fragments of the genome and the fragments of the copies of the genome. From these thousands of fragments it 'chooses' suitable (overlapping) fragments and aligns them in the correct sequence. Any sequence is equally possible but the correct sequence is 'chosen'. Which raises the question: 'How?'Box
December 23, 2014
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You can of course leave it whereever you want, but I'll reiterate my point about PCR. When a molecular biologists sets up a PCR (s)he basically puts some genomic DNA fragments n a tube, adds small DNA molecules homlogous to some part of larger fragments and an enzyme, puts the tube in a heating-machine then walks away. The PCR reaction can only work if those small fragments anneal to the corresponding sections of the target DNA. Nothing in the PCR reaction mediates that binding (apart from the buffers etc that chemically help this process), it's just chemistry. THe process in D. rad. is a good deal more involved that PCR, and there are still "mysteries", in the sense of unsolved parts of the problem. But I don't know why you think there needs to be a top-down process. Moreover, "sequence matters" of course, but it's only the correct (actually ancestral) sequence that can be put back together because the reconstruction is primed from existing sequencees. The "wrong" bits can't be put together, unless they happened to share identical streches by chance. (I don't know, but I bet D. rad. has relatively few "low complexity" regions..)wd400
December 23, 2014
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WD400 #121,
Box: the mystery is how Drad lines them up in the correct sequence
WD400: Why would it need to?
Because, after radiation, there are only isolated fragments of DNA left. And because the sequence matters? Drad restores its genome in the original sequence BTW. After it has repaired its DNA it is as if nothing has happened. Humpty Dumpty has been put back together again. You fail to see why this is mysterious. I fail to see why you don't see the mystery. Let's leave it at that.Box
December 23, 2014
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I still don’t understand what was wrong about that text you were pointing to.
You, the person who supposedly post relevant scientific papers, extracts supposedly salient bits and highlight other parts, you fail to understand what is wrong with the statements? And even after clarification you still don't understand? I would strongly suggest you stop reading papers and start investing in an extremely basic textbook. You have then no chance at all to understand the papers you have been citing.
You seem confused again. Are you referring to my comments addressed to Box? Are you sure you’re not misquoting my comments? Apparently, Box was trying to engage in a serious discussion with some folks in this blog, but things didn’t seem to go quite right, so I expressed my opinion about discussion requirements. I don’t recall saying I was able, capable or willing to engage in serious discussions. Can you show me that text where I said so? If I did, I will correct it. But first, show it to me.
Ah, yes, when you write that "Your interlocutor along with his comrades and fellow travelers don’t seem interested in any serious discussion." and "Their motivations are not clear, but they don’t seem to be serious." you were clearly just talking about Box and his discussion with a single person and not really comparing two groups of people and classifying one as being all for serious discussion and the other not.
Currently, I’m a student (autodidact), hence my opinion here, where so many folks know much more than I do, would not make any difference. Perhaps one thing I can do is to read what others write and ask questions in order to learn more. Also I like to post here some of the materials I’m reviewing lately, in order to share them with other people who might be interested in the given subjects.
Ah, now I get it. You really are interested in becoming the second BA77 of this board. I have to say, you are well on your way. Throw in a couple of bible quotes and youtube videos every now and then and people will not know the difference. Thank you for clarifying this point though. I am certain it is quite useful for others on the board. Cheers.hrun0815
December 23, 2014
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#116 hrun0815
Oh, and re your post 57: it is an iPhone.
FYI - just looked at this in my wife's iPhone and confirmed what you wrote: don't see the post #s if one uses the app for the blog. However, if one looks at the blog directly on the safari browser the post #s do appear. In my Nokia Lumia the post #s show up because I look at the blog directly on the browser, not through an app. The problem with the post #s not showing has to do with the app settings or a bug in that app. Did I get this right?Dionisio
December 23, 2014
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Now, like I stated before, the mystery is how Drad lines them up in the correct sequence Why would it need to? When molecular biologists run a PCR they don't need to have the the primers line up with the target. The specific enzymes that catalyze priming in D. rad. are not entirely known, but I do see why the process needs oversight (any more than PCR does).wd400
December 23, 2014
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