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Biotech Science

Scientists Create Synthesized DNA Bases 125

Posted by ScuttleMonkey
from the and-mother-nature-is-pissed dept.
Iddo Genuth writes to tell us that researchers at the Scripps Research Institute in San Diego have created two artificial DNA bases in an effort to "expand biology's potential." "In the future, [chemist Floyd] Romesberg envisions manipulating the genetic code of bacteria in order to assemble better drugs or even man-made proteins. Until now, the bases only work in bacteria, so human augmentation is currently not possible. Another option is to use alpha and beta to help construct nanomachines to be used for drug delivery. 'This is like jumping from the Stone Age to the Bronze Age,' Romesberg says. 'It takes time to figure out how best to use metal.'" Update 18:10 GMT by SM: Roger writes to share the NewScientist link with a bit more information. There is also the original release text for consideration.
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Scientists Create Synthesized DNA Bases

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  • I want my Vitamin C! (Score:4, Interesting)

    by snowgirl (978879) * on Friday June 27, 2008 @12:48PM (#23970497) Journal

    Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

    • Re: (Score:3, Insightful)

      by twatter (867120)

      This has implications beyond the delivery of drugs. Drugs act at the protein level, but imagine a delivery mechanism that does not require a protein receptor, but instead acts at the DNA filament level.

      This is HUGE news.

    • Re: (Score:3, Funny)

      by Sir_Real (179104)

      Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

      Apparently a war has already been delcared on Scurvy, and it appears to almost be won [internetwks.com]

      • Re: (Score:3, Interesting)

        by snowgirl (978879) *

        Hahahah, it's so funny, because reading about the history of Scurvy, people actually thought this way for awhile.

        Personally, I really think it'd be awesome if we could just repair our Vitamin C gene, and generate Vitamin C ourselves again... but then we also need to fix the gene that processes uric acid, so that we don't fill up on stuff doing the job of Vitamin C... since high uric acid levels have been associated with Type II diabetes, it might just effect a reduction in diabetes in humans.

    • by jollyreaper (513215) on Friday June 27, 2008 @01:20PM (#23971003)

      Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

      Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

      • by snowgirl (978879) *

        Can we get back our Vitamin C gene again? I would love being able to eat less fruit... Scurvy sucks.

        Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

        Sorry, I prefer my alcohol in the form of Riesling wines. I haven't suffered from Scurvy yet, so I'm apparently getting enough vitamin C, but I don't really eat a lot of fruits and vegetables, so... not so sure.

        Anyways, making fruits and veggies a more optional part of our diet, since we can make our own vitamin C might have a positive impact on our quality of life. (Of course, it puts the Vitamin C Herbal Supplement people out of business, but hey, they're just the new patent medicine anyways, so...)

      • by ShieldW0lf (601553) on Friday June 27, 2008 @01:51PM (#23971545) Journal
        If it hasn't been sprayed through a pile of burning rotten vegetation from Scotland, it's shite.
      • Re: (Score:3, Funny)

        by 93,000 (150453)

        Pretty reckless with your precious fluilds, there, buddy.

        I only drink grain alcohol and rain water.

      • Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

        Just wait until he starts bitching about his liver. :P

        • Re: (Score:3, Interesting)

          by snowgirl (978879) *

          Have you ever tried coconut rum and fresh OJ? You'll never bitch about drinking your fruits again.

          Just wait until he starts bitching about his liver. :P

          Why does no one look at my name? Is it just standard presumption that everyone on slashdot is a guy, even when their login is "snowgirl"?

          • Re: (Score:1, Funny)

            by Anonymous Coward

            dude, calm down man.

          • Girls on slashdot? You must be joking! :P

          • Re: (Score:3, Funny)

            by spazdor (902907)

            Nicknames are meaningless. The big giveaway that you're a girl was that you drink Rieslings.

            That shit's for ladies and, uh, whoever plays one on the Internet.

            • by snowgirl (978879) *

              Girls can't enjoy drinking beer? :P Sometimes I do, but usually, unless it's a German light beer, it tastes so bad that I'd usually rather have something that I can stand drinking.

              It isn't a "girls drink wine" and "boys drink beer/hard alcohol" world. My friend refuses to drink wine anymore, because she's moved on to strictly vodka. (Personally, I find hard alcohol much too annoying to buy here in Washington what with the state-controlled liquor stores.)

              More so, the indicator that I drink Rieslings shows

              • by spazdor (902907)

                Don't get me wrong. I will get into fist fights with dudes who disagree with my many ill-informed opinions about the supremacy of Cabernet Shiraz over all other blended reds. I am a wine asshole of the highest order.

                Riesling is pretty much always way too sweet for me though, and I honestly don't know any dudes who feel differently. Same with ice wines.

                • by pjt33 (739471)
                  There are sweet Rieslings and dry Rieslings. Dry Riesling, preferably from the Moselle region, is my white wine of choice. Well, unless Champagne is on offer.
                • by snowgirl (978879) *

                  My ex-boyfriend drinks a lot of beer now, but pretty much preferred, so called "bitch beers" before being introduced to beer that actually tastes good. (Odd that it could be more acceptable for a guy to drink girlie drinks rather than drink Budweiser, Coors, Miller, et aliae ">cervissiae culae.)

                  He actually prefers Rieslings, because, well, they taste good if you don't have a distinguished palette. My palette for Rieslings is a little better than "it's sweet", I like a dry component for it to be "refres

          • by Kreigaffe (765218)

            Duh, there are no girls on the internet.

            (I for one welcome our mammary-bearing overlords?)

          • by bsDaemon (87307)

            Well, since the girls in MMORPGS usually are just fat guys with all their hair on their backs instead of their heads, it probably feeds the stereotype about slashdotters, too.

            if it makes any difference, I managed to notice.

            • by snowgirl (978879) *

              Well, since the girls in MMORPGS usually are just fat guys with all their hair on their backs instead of their heads, it probably feeds the stereotype about slashdotters, too.

              if it makes any difference, I managed to notice.

              I swear, when I started reading this I expected "in their hands" not "on their backs"... >_ lol

          • name? I have no idea what this name thing is, maybe you can explain it to me and how this denotes your gender 978879.


            838224.
            • by snowgirl (978879) *

              Duh, it's because when I am happy, I write it forwards, but when I'm angry, I write it backwards. The fact that you can't tell the difference between those two shows that you don't understand me, therefore, I must be a girl!

              978879

              • your post makes no sense, I have no idea what your point is, this makes me angry!

                422838.
                • by snowgirl (978879) *

                  SEE?! That's how you know I'm a girl >.> I make no sense.

                  (Note, before you get upset at me for being sexist to my own sex... it's entirely a joke, as I'm playing off the very stereotypes that I reject.)

    • by Hatta (162192)

      Are you serious? Could there be anything more delicious than fruit? Try growing your own strawberries some time, they're positively orgasmic. Fruit is the best.

      • Re: (Score:3, Informative)

        by snowgirl (978879) *

        I don't hate the fruit! I just hate that every other animal in the world can synthesize their own Vitamin C, but we can't!

        It's about EQUALITY, not wanting to get rid of fruit. I do like fruit; I have some cherries right now, and they're absolutely divine.

        So, in all, I love fruit, I don't want to get rid of it... I just want to get rid of Scurvy...

        • Hey, it's not just us, the guinea pigs are in the same boat, they can't synthesise vitamin C either.

          You should hate our fruit guzzling ancestors, if thier diet wasn't nice and high in vitamin C, the defective gene would have been naturaly selected out.
          • by snowgirl (978879) *

            It's not the _SAME_ boat, it's a completely part of the gene!

            It's more like they're in a different boat that just happens to be drifting the same way as ours.

            • It has the same effect, they can't synthesise vitamin C, it's the same gene just a different part, so its more like they are sat in the prow, and we are sat at the stern.
              • by snowgirl (978879) *

                But chimps and gorillas have the same genetic defect as we do, too. So, the chimps and gorillas can't be seated in the same place of the boat with us. (Matter within space is governed my mandatory mutexes.) So, it's like there is one boat with us and chimps and gorillas on it, and another boat that just happened to drift up next to us, which has guinea pigs on it. We're both going the same way, we're both just as up the creek, just in different boats.

                It's called parallel evolutionary convergence... it's

                • My analogy requires it to be the same boat, but we boarded it at different places along the river.

                  The advantage of my analogy is being in the same boat as the guinea pigs, we can easily catch and eat them, and they are very tasty.
  • by Sir_Real (179104) on Friday June 27, 2008 @12:51PM (#23970561)

    There is a more technical explanation in the link [scripps.edu] at the end of the article.

  • by NFN_NLN (633283) on Friday June 27, 2008 @12:53PM (#23970597)

    He's adding new bases which have no coding to amino acids. I don't see the purpose of this. Is it just for adding a trace or marker in DNA?

    All the bases do are code for amino acids and it's the amino acid sequence which accounts for a protein's shape. In the end it's the protein's shape that matters for chemical interactions.

    • by olyar (591892) on Friday June 27, 2008 @12:58PM (#23970669) Homepage Journal
      Mostly they just want to be able to write a technical paper called "All your base (pairs) are belong to us".
    • by Robert1 (513674) on Friday June 27, 2008 @01:03PM (#23970763) Homepage

      You're totally right. This is such a non-story and frankly mildly offensive in how full of himself the scientist is with sweeping comments like that.

      As it stands currently, the amount of genetic degenerecy in amino acid coding means that they would easily have those double and tripled coded amino acids switched to something else. They could potentially add another 20-30 new amino acids with absolutely no change in the number or form of the base pairs used.

      Its like finding a solution to a problem that doesn't exist, will never exist, and serves no purpose even if it was found. But apparently its equivalent from going to the iron age from the bronze age. Ha!

      • Re: (Score:3, Interesting)

        by Gat0r30y (957941)
        ahh, come on - this is exactly like the transition from the stone age to the bronze age. If bronze had no additional useful function other than to help keep track of who made a stone.
        I'm pretty sure the only use for this is going to be marking genes, probably just to keep track of who owns the patents.
        The first genetic DRM?
      • You mean like lasers were (a solution to a problem that didn't exist)?

      • Re: (Score:2, Interesting)

        by ViperOrel (1286864)
        Actually, even though you have redundancies in the current set, with this new pair you could code for new amino acids (or anything else you wanted to stick in there) without having to worry about disrupting other things those redundancies were already coding for.

        My 2c.
      • Re: (Score:3, Insightful)

        by Anonymous Coward

        Yeah, while the science here is kind of neat, it's not the biggest news in the world. The article title does not at all reflect what's newsworthy here, anyway. Scientists have been creating synthetic and/or modified nucleotides for decades and successfully incorporating them in to DNA and RNA. The news is that they found a synthetic base that can be copied by DNA polymerase. This is the enzyme that copies your DNA, putting an A next to a T on the opposite strand, a C opposite a G, a T opposite an A, and

      • by redxxx (1194349)

        Seriously, who would ever going to need more than 4 base pairs?

      • I haven't read *extensively* about this but I have read some stuff, including articles about this research in other places.
        The goal is to be able to integrate other amino acids -- or just other stuff -- to the standard rna->protein translation so you can put heavier tools in your proteins.
        One way to do this is to hijack a current codon. This is being done by a group who are trying to use one of the three 'stop' codons. The problem with this approach is that, while there is redundancy, that redundancy i

        • ...either way you have to build your own new tRNA's with your new weird amino acids or whatever ready to be linked into your protein, but this guy's approach might mean that's *all* you have to do (plus use his patented system) rather than also having to proofread the whole genome repeatedly.

          Here's a list of what you'd have to add to the organism (it's a little complicated, but you've definitely grasped the essentials):

          1. A gene using codons incorporating one or both of these new bases to encode your novel protein of interest containing something beyond the standard 20 amino acids.
          2. tRNA genes that have the reverse compliment of any new codons you've introduced (otherwise the sequence functions like a stop codon).
          3. Gene encoding an amyl transferase protein that binds your novel anim

      • by Randseed (132501)

        You're totally right. This is such a non-story and frankly mildly offensive in how full of himself the scientist is with sweeping comments like that.

        As it stands currently, the amount of genetic degenerecy in amino acid coding means that they would easily have those double and tripled coded amino acids switched to something else. They could potentially add another 20-30 new amino acids with absolutely no change in the number or form of the base pairs used.

        Its like finding a solution to a problem that doesn't exist, will never exist, and serves no purpose even if it was found. But apparently its equivalent from going to the iron age from the bronze age. Ha!

        Yeah, he just synthesized two new DNA base pairs with no corresponding tRNA, meaning that they'll just function as stop codons, which makes them worthless for now. That's in addition to your point. The thing that kills me is that he first article makes the guy just look like a raging buffoon. The New

    • Re: (Score:3, Informative)

      TFA's TFA mentions information storage in DNA, which makes sense as this basically moves from base-4 to base-5 (The base pairs up with itself, so it's only one new base) thereby improving storage density. They also did some work to evolve a polymerase that replicates the DNA with the new base.

      DNA (single strands) and RNA also fold into themselves, and there is some evidence that the folding affects some mechanisms in the cell. Modifying them with these self-binding pairs could probably be hacked up to chang

      • Re: (Score:2, Informative)

        by ZackZero (1271592)
        Actually, if you read the second article (or the first link in the updated story), you'll see that the first base would pair up with itself instead of the second synthetic base - its intended pair. They "tweaked" it and it now pairs correctly... supposedly.

        However, this makes it base-6 instead of base-5 or the current base-4. If you recall your high-school biology class, the base pairs only exist in two combinations, but in a total of four permutations. There's adenine-thymine, thymine-adenine, cytosine
        • Yeah, I read it before the update was posted so didn't see the extra article. I wrote base-5 because the first article made it out to be symmetric, so it was only one extra permutation.

    • Re: (Score:3, Informative)

      by Edward Kmett (123105)

      Grossly simplifying, you read off codons (via mRNA, etc.) generating peptides so that you can build up proteins, etc. Some of those codons turn on or off transcription to amino acids.

      As noted in the article the fidelity of transcription of these is lower than conventional DNA. So perhaps they could make perfectly suitable markers for areas you want to provoke a mutation at a higher rate, perhaps dropping them into large introns to encourage mutation in those areas.

      The 3FB self-pair also expands the vocabula

    • Re: (Score:3, Insightful)

      by tempest69 (572798)
      aarrgggg.... intergenic regions of bacteria are reasonably important.. regulation of the production of proteins is a really important process. being able to add an artificial control mechanism to genes that are guaranteed not to exist in nature is a powerful tool.. While temperature sensitive promoters are impressive, they still have some problems. But having a fully artificial promoter sequence should allow for some really impressive experiments once a bit more technology is added to the system. Plus
    • Both protein and DNA are partially self assembling polymers, and their purposes can in theory be completely interchangeable. A lot of the most basic functions of metabolism are carried out by RNA-based structures as well as proteins.

      I think that what they are proposing is to create a DNA structure that can be replicated when kept artifially fed with these new bases, but which can then be used as a drug in its own right when introduced into humans. Presumably the most common use of it would be to interact
    • by Atmchicago (555403) on Friday June 27, 2008 @03:05PM (#23972867) Homepage

      All the bases do are code for amino acids

      That's actually not true. A lot of DNA bases are important in mediating binding to proteins, such as RNA or DNA polymerase, histones, etc. Other bases are important in RNA-based regulator mechanisms, such as anti-terminators.

      So the truth is that although we can't really say what we can do with these extra bases right now, the possibilities extend way beyond making new proteins and have many implications for regulation. Why is regulation important? Because differential gene expression is the fundamental principle that allows for cell differentiation and mediating responses to external change.

      And for the record, IAAB (I am a biologist).

    • Well the next step is to invent new amino acids. Then we can umm... write papers about that too..
  • Now they can get to work on making me a hot Draenei chick with a proper ghetto booty.

    • by Kingrames (858416)

      You want to BE one? okay.
      But you can already do that, the surgery's just a bit expensive.

      • by kwabbles (259554)

        You know that's now what I meant, but now that you mentioned it - I had about a 5 second sick visual that I found strangely exciting, and now I have to go wash my disturbed mind out with soap.

        • by Kingrames (858416)

          You know that's now what I meant...

          See? it was such a good idea, you decided that was what you meant in the first place after all.

          Now I just need a couple more, and a videocamera. PROFIT!

  • Interesting, but I'd rather we have a better understanding of current genetic material and manipulation thereof before we go creating new bases that don't exist in nature.

    This might just be an approrpiate time for the 'whatcouldpossiblygowrong' tag.

  • We'll get beyond DNA (Score:1, Informative)

    by Anonymous Coward
    Further on, I don't think we'll want to be shackled by our past at all. At some point in posthumanity, you'll just be able to comprehend better systems and think of the DNA-based life as just outdated. We already have far better information density in more stable forms. DNA does happen to do a good job in making use of its own information, but that is not nearly as efficient a process. Think of the early sound and graphics chips that were soldered onto NES cartridges. It did its job, but something else came
  • by Raul654 (453029) on Friday June 27, 2008 @01:01PM (#23970725) Homepage

    For those of you who forgot your biology, 3 DNA consecutive DNA base pairs (called a codon) are translated into a single amino acid. (Khorana, Holley and Nirenberg won the 1968 Noble prize in medicine for figuring this out and determining the mapping [codondevices.com] from base pairs to amino acids)

    So, after reading the technical article [scripps.edu], it says that DNA polymerase can bind to the new base pairs (allowing it to replicate), but it doesn't say what amino acids (if any) these new base pairs code for. That's important information because this alleged breakthrough is useless if it doesn't so something useful where proteins are concerned.

    • Also keep in mind that the coding for base triplets into amino acids is governed by tRNA, which are short segments of RNA that conform to provide one end that holds an amino acid and the other end (actually the middle, but folded over) that has a three-base segment that binds to mRNA during translation. tRNA are coded in the cell's DNA, so if you really wanted to change the translation table, you would just change the genes that produce tRNA in the first place.

      It is possible, however, that the idea here is

    • Woah nelly! :)
      They can't code for anything, yet.
      The point of the article (and the 3 year old link) seemed to be that these base pairs can be built into the DNA as it replicates by standard enzymes. What this means is that we can now build the blueprints, and guarantee a level of control for any new amino acids that are to be produced. That, however, will take a hell of a lot more work.
  • Two new DNA bases? In terms of potential gene expression - this is like the art world getting two new visible base colors, which can mix with the usual red, green, blue, black and white in new ways to create further complex colors... oh, yes it'll take a very long time to figure out what they mean in all these contexts, but the potential there is absolutely huge.

    We're still limited to the same physical limits we've ever had - but the potential for efficient complexity and new expressions using genetic syst

    • What a shitty article. The reference it links claims there's only one new base that pairs with itself, 3-flourobenzene. "Alpha" and "beta", my ass.

      assuming that these bases will self-replicate in the wild,

      Since (I think it's safe to assume, based on the use of "unnatural") current organisms do not have a metabolic pathway for synthesizing the artificial base, unless it's bacteria grown in media supplied with some there's no way for a replicating genome to conserve the altered structure.

      Two new DNA bases? In terms of potential gene expression - this is like the art world getting two new visible base colors, which can mix with the usual red, green, blue, black and white in new ways to create further complex colors... oh, yes it'll take a very long time to figure out what they mean in all these contexts, but the potential there is absolutely huge.

      Colors? No. As other people have mentioned, the article says nothing about what

      • Cool - If that's all that is, then yeah, not quite the potential I thought it could be.

        Ryan Fenton

    • Except it would be like 2 new colors that no one could see. There would have to be significant amounts present as rNTPs to transcribe it, and it would have to bond to specific tRNAs It would, in computer terms, be like adding two instructions, but the processor can't quite handle them.
  • They should have just gone ahead and called them ADAM and EVE :)
  • If we're synthesizing bases you'd think that we could come up with better names than Alpha and Beta. If you work in biology at all you know that these designations are already overused. If you don't, this is essentially naming the bases "one" and "two". BwwaaahhhhH!! Hopefully these are on
  • Old News (Score:4, Interesting)

    by dwye (1127395) on Friday June 27, 2008 @01:14PM (#23970903)
    We have seen this before. The new bases just make new STOP codons, until someone creates new types of MRNA and/or TRNA to let the mitochondria process them to add a matching amino acid.

    Where is the whatcanpossiblygowrong tag, like last time? Have the Luddites left, already?

  • Bronze Age (Score:4, Insightful)

    by wcrowe (94389) on Friday June 27, 2008 @01:17PM (#23970953)

    'It takes time to figure out how best to use metal.'

    I don't think it took too much time to figure out that the best use of bronze was to make it sharp and run someone through with it.

    • by dotmax (642602)
      mod parent up insightful
    • by oodaloop (1229816)
      Boy, hindsight sure is great isn't it?

      When you're used to working with just stone, how to make stuff with metal would not neccessarily be intuitively obvious.
  • ... all your base are belong to us.
  • Welcome our new genetically modified bacterial overlords...

    (sorry... I had to...)

  • "It takes time to figure out how best to use metal."
    to figure out how long you can stretch out your research funding so you can keep your plush job. Usually this is accomplished by publishing just enough of your findings every few years so that it impresses the prols and convinces the patrons to keep funding you because a 'breakthrough' is RSN.
  • otherwise evolution would already be using them. After all nature has already produced uracil [wikipedia.org] but does not use it in DNA. I don't see why it would not have produced and used these bases as well if they were useful.

    So I don't think that there will be any breakthroughs in producing new proteins the classical way (DNA->RNA->mitochondria->proteins).

    The sources also mention nanotech. This could be more promising, as the standard rules don't apply and any new material would multiply the available op

    • Re: (Score:3, Insightful)

      I would suggest your logic here is flawed or at the very least belies a bit of a gap in understanding how evolution works.

      All the other folk who have commented that this is like giving artists new colors nobody can see are perhaps a bit closer.

      Once we got started with anything even close to DNA, I would imagine we were more or less locked into that pattern. Evolution branches more so than tries all permutations and possibilities. It seems far more likely that once life got going with all the support syste

      • by naoursla (99850)

        I theorize that the processed that built up the RNA/DNA/tRNA/etc systems were highly optimized in their developmental stages. This new base pair is certainly less efficient than what we have. Any lifeforms that depend on it will likely be less stable than natural life. This could be a good thing. It could prevent then from outcompeting native lifeforms.

  • The use of four base sequences probably optimizes the generation complexity to the coding/mainentance complexity. Six or eight base sequences are probably less energy efficient or less stable or something.

    Although that might be a good approach for making new life forms that don't escape and outcompete native lifeforms.

  • Something similar has already been done as early as 2001. A team of researchers in Japan was able to demonstrate that artificial amino acids (instead of nucleotides) could be incorporated into the yeast translational machinery using five-base codons (instead of three). http://nar.oxfordjournals.org/cgi/reprint/29/17/3646 [oxfordjournals.org]
  • "DNA Origami" (Score:3, Informative)

    by peter303 (12292) on Friday June 27, 2008 @02:40PM (#23972415)
    Nanotechnology can coerce the DNA sugar (ribose) into exotic chapes like tri-helicies, platonic solids, etc. However there are no known biological applications of these exotic molecules. They mainly demonstrate the increasing skill of nanotechnology.
  • ...alphabeta never left- they've continued to offer the same great service and selection at every day affordable prices!
  • From the scripps article: While the polymerase does not replicate the unnatural DNA with the same fidelity observed in nature, (roughly one mistake for every 10 million bases of DNA copied), its fidelity is reasonable (typically making only one mistake for every 1000 base pairs).

    Fidelity is reasonable? Maybe for bacteria, but not in my body! You'd get this in you in the morning and you'd probably have cancer before dinner. Okay, maybe that's a bit of an exaggeration... Still, they ever get this thing worki

    • Even if I transformed a new gene incorporating these bases into cells in your body, the higher mutation rate is only going to affect the specific positions where the new bases are present. It wouldn't do anything to change the mutant rates of the proto-oncogenes and cancer-suppresser genes that are still encoded with normal As Cs Ts and Gs.

      And this doesn't even get into the complication that sequences with the new bases could only be replicated in vivo as long as there's a supply of the new bases being sy
  • Another option is to use alpha and beta to help construct nanomachines to be used for drug delivery.

    What about Gamma?

That does not compute.

Working...