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21 Oct 2017 09:35

Anyone got any useful thoughts on the applications / limitations of this?

Is this the same realm as the biosensors already mentioned or are microfluidic chips a different branch of the lab-on-a-chip world?
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21 Oct 2017 10:00

Athletes and their Coaches will soon be using embedded real-time technology in their bodies for sports science anyway. We're already seeing beginnings of this with thigs like Professor Tony Purnell's Burger Van at Manchester Velodrome for example measuring all the riders data in realtime including stuff like lactate, oxygen, hydration monitoring etc. It won't be long until this is embedded under the skin and wirelessly communicates with you head unit and in turn relays everything to a main computer in the team car or track side.
samhocking
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Re:

21 Oct 2017 10:44

fmk_RoI wrote:Anyone got any useful thoughts on the applications / limitations of this?

Is this the same realm as the biosensors already mentioned or are microfluidic chips a different branch of the lab-on-a-chip world?

Microfuildics is interesting, but as Theranos has shown, it's not quite there yet. It can do things like look for biomarkers, and titrate to look for certain chemicals, etc. But as far as I know, a lot of it still requires preparation of the sample, as in you can't just put a drop of blood or urine on the chip and expect it to work well.

Basically, the whole basis of the technology is creating incredibly tiny channels in a substrate. It's then possible to manipulate fluids that are added to the channels, such as transporting into an area that contains a reactant, or has the correct conditions to crystalize a certain protein, etc. Add some smarts and you can read out the results. This makes it possible to check for certain diseases, presence of specific substances and the like. Fantastic stuff if you want to check a large, remote population for HIV at a reasonable cost.

The limitation is that it's super tough to do things like look for testosterone ratios, or do a blood profile with any kind of accuracy. It can do some things really well, but for now it'll still take a full lab to perform anti-doping controls with any accuracy.

John Swanson
ScienceIsCool
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Re: Laboratories

21 Oct 2017 20:22

The linked article, and a link in that link, note that the purpose of the technology is to identify bacteria and viruses. That can be done on microchips right now. Basically, the chip contains DNA sequences that are unique to, and therefore markers for, known bacteria and viruses. If a properly treated microsample is applied to the chip, the DNA from the sample will bind to, or hybridize with, the specific DNA sequences on the chip that correspond to what’s in the sample. Fluorescence is used to locate and identify the sequence on the chip.

This has been done routinely in labs for a long time now. As ScienceisCool notes, the sample does have to be properly prepared, but I think it’s easy enough to design a kit that allows one to do that. Where it becomes more difficult, again a nod to SiC, is if you want to detect certain substances, macromolecules like proteins, or smaller molecules like drugs. You could design chips for those, too, but they might require more elaborate steps, and if you want to be able to test for all these substances, along with DNA sequences, on a single chip, it becomes much more difficult.

But if Dr. Nash wants to have an impact right now, it would certainly be possible to test for bacteria and viruses known to infect horses with current chip technology. I don’t follow horse racing, but surely they must have vets at the track—and of course any owner/stable will have one—who could easily be trained to carry out the test. Since there are a limited number of infectious agents, diagnosis should not be that difficult—at least not at the level that concludes, there is a problem here, the horse should be removed, maybe quarantined and examined more thoroughly.

And since we’re discussing this in the Clinic, I’ll add that this kind of technology could also be used to detect some kinds of gene doping.
Merckx index
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Re: Laboratories

21 Oct 2017 21:28

Merckx index wrote:And since we’re discussing this in the Clinic, I’ll add that this kind of technology could also be used to detect some kinds of gene doping.
Excuse the ignorant question, but is this because a virus is used to introduce the edit?
User avatar fmk_RoI
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Re: Laboratories

21 Oct 2017 23:44

fmk_RoI wrote:
Merckx index wrote:And since we’re discussing this in the Clinic, I’ll add that this kind of technology could also be used to detect some kinds of gene doping.
Excuse the ignorant question, but is this because a virus is used to introduce the edit?


Well, it's more general than that. Microchips are used to identify specific sequences of DNA, whatever the source. A synthetic gene used to dope could be produced by editing a natural gene, but as far as detection goes, it doesn't matter how it's created. If some unique portion of the sequence is known, it can be identified by chip technology. A microchip is like a filter that traps certain sequences of DNA.

The problem is that one generally isn't going to know in advance the sequence of a gene used for doping, and even if one does, the gene may be injected directly where it's needed, like the muscles, where getting a sample for analysis is going to be difficult.
Merckx index
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Re: Laboratories

22 Oct 2017 11:00

Merckx index wrote:
fmk_RoI wrote:
Merckx index wrote:And since we’re discussing this in the Clinic, I’ll add that this kind of technology could also be used to detect some kinds of gene doping.
Excuse the ignorant question, but is this because a virus is used to introduce the edit?


Well, it's more general than that. Microchips are used to identify specific sequences of DNA, whatever the source. A synthetic gene used to dope could be produced by editing a natural gene, but as far as detection goes, it doesn't matter how it's created. If some unique portion of the sequence is known, it can be identified by chip technology. A microchip is like a filter that traps certain sequences of DNA.

The problem is that one generally isn't going to know in advance the sequence of a gene used for doping, and even if one does, the gene may be injected directly where it's needed, like the muscles, where getting a sample for analysis is going to be difficult.
So rather than the two part test allegedly used on the Rio samples, this technology, if developed, could could straight to the chase and need only look at the genes?
Until now, WADA officials have been quiet about the details of the new EPO gene-doping test, which was developed by Anna Baoutina, a molecular biologist at Australia’s National Measurement Institute who used to work in Russia (a country with systemic doping problems). Her test has two parts: One checks for the virus a scientist would use to deliver the new DNA to the body. Viruses are a good vector for gene delivery; that’s already how they work, so it’s just a matter of replacing the viral genetic material with whatever you want to insert.

The second part of the test sequences a person’s EPO genes. A normal stretch of DNA in the body has sequences called introns between the genes that produce the EPO protein. But an artificial DNA sequence has all the genes right next to each other—no introns. “This sequence that you introduce in gene therapy looks different than the one in your body,” Sundberg says.
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Re: Laboratories

22 Oct 2017 15:57

fmk_RoI wrote:
So rather than the two part test allegedly used on the Rio samples, this technology, if developed, could could straight to the chase and need only look at the genes?


The two part test is just looking at the gene sequences. The two parts just look at different sequences. I would think only one of the parts has to work for the test to be successful, though if both come up positive that is even better evidence, would provide statistically higher reliability. No doubt WADA is working on setting the criteria for a positive that can hold up under challenge.

As I said before, one needs to identify a marker sequence, something that unequivocally identifies the gene as exogenous, not native. Viral sequence generally works. The viruses used for vectors, to introduce new genes into the genome, are well characterized, as are the sequences within them that can be used to identify them uniquely.

But there are many possible viral vectors, and doping might use one that the test is not designed to detect. This part of the test can only, at best, rule out the presence of certain viral sequences, probably not all of them (I would have to know more about the details of the test to comment further; with that chip technology we were discussing upthread, one could be pretty exhaustive. Still, absence of evidence is not, as the saying goes, evidence, or at least proof, of absence). Also, there are other ways to gene dope that don't require the use of viruses, though I don't know how likely it would be that an athlete would try this. In any case, then testing for introns is like a backup plan. It's the opposite of looking for a viral sequence, in that now you're trying to confirm the absence, rather than the presence, of something.

This part of the test, though, sounds difficult to me. Many if not most natural genes have introns, so the test would have to demonstrate the absence of the intron in a gene of interest. If you know what the gene is, EPO, then you can just isolate that sequence, and determine whether it has intronic sequences. But if you don't know what the gene being used for doping is, this won't work, and you're left with just the viral sequence test. Though even as I write this, it occurs to me that if you locate the viral sequence, you would locate the gene, so I guess if the viral part of the test is successful, you could go on to the intronic sequence. But if you don't detect viral sequence, and don't know what the gene you're looking for is, there is a problem.

The bottom line is that no test for gene doping that I'm aware of is foolproof. One ought to be able to detect gene doping of EPO, and perhaps some other likely substances, that's attempted through the relatively simplest and most available technology, but as usual with doping, one can ratchet up the arms race, and find ways to evade the tests.

This is where the passport can be very helpful. Even if an athlete is successful in boosting his production of EPO or some other performance-enhancing hormone through gene doping, and even if he avoids testing positive, he should trip signals in the passport test. Indeed, the passport test may help testers decide what genes might have been used for doping, which makes it more likely they will be able to detect them.
Merckx index
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