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Science

Nanopore DNA Sequencing 51

Posted by Hemos from the everything-moves-faster-and-faster dept.
mindpixel writes: "Harvard scientists have concieved a revolutionary technology for probing, and eventually sequencing, individual DNA molecules using single-channel recording techniques. The technique essentially pulls a single strand of DNA through a nanopore, reading off the individual bases electrically. The technique could allow for decoding of a person's genome in hours instead of years." While the sequencing in hours instead of years is something that's pretty darn cool, our holdup in using this data is actually now what the genes are, and how they interact. That will still take years for us to figure out.
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Nanopore DNA Sequencing More

Nanopore DNA Sequencing

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  • Note the word "concieved" in the first line of the document...there is not much in place yet. The page sounds to me like a breathless plea for lots of venture capital funding.

    There are several companies rushing to commercialize this general way of sequencing and haplotyping. The most interesting one I've seen so far is US Genomics [usgenomics.com].

    The problem is still at the stage of "translating our pretty drawings and ideas into working hardware". There are tremendous engineering challenges both with the hardware (detection devices and materials handling) and software (algorithms etc.)

    The science is solid and the ideas are clever. Its just going to take a while to build a system that can reliably resolve single molecules as they speed down a tiny channel.

    just my $.02

  • I don't think that this is possible because of the structures involved. DNA is a long double-helix (ignoring any integral structutal proteins,so pulling it through a hole is possible. However, most proteins fold and form large structures, and unfolding these would probably be extremely difficult, never mind examining the many component amino acids. AFAIK, this is the reason the way protein folds is so important, as well as x-ray crystallography determining the structure of known proteins.
  • This will be a great boon for storage device makers! Each genome will be terabytes of data.

    To answer an earlier question, sequencing is reading the DNA and recording the base pairs in some fashon. Often this information ends up as an asci file. Because of the mechanical limits of the current sequencing technologies, chemicals called restriction enzymes are used to snip long strands of DNA at particular patterns of sequence. A sample of DNA is amplified using a technique called polymerase chain reaction ( PCR ) which gives many many copies of the precisely same sample. It is then split into multiple samples each "cut" with a different restriction enzyme each with a different "trigger sequence" so the different samples end up being cut in different places which means that the cut pieces of different samples overlap the cuts in other samples. Then all the samples are seperatly sequenced into files. The files can then be compared for overlaps and "assembled" into longer sequences until the sequence of the original sample ( which was too big for the machine ) is known. After the sequence is known, it can be converted from nucleic acid ( G A T C ) code to amino acid code ( google can probably find you the genetic code ) which is composed of 3 nucleic bases per amino acid. Because we really do not know where a given amino acid starts within the nucleic file, we often do a sliding frame translation, decoding the entire sequence for each possible starting point of amino acid translation. The proper translation is often indicated by having a minimal number of null translation frames. The decoded sequence can be compared to other previously decoded sequence which have been analyzed for function - these blocks end up being called genes. A gene from a mous which makes a particular protein is the same as that gene from a human, so by starting with simple organisims, many genes for specific proteins have been found which help decode the more complex organisims....

    hmmmmm sorry for the drif folks...

    Z

  • Yay! One step closer to Gattaca. Wheee.
  • Let's see your C.V.
  • I can't imagine this technique ultimately being implemented using only a single nanopore through which all 23 chromosomes have to be squeezed, one after the other. My guess is that a relatively large collection of nanopores would operate in parallel, as you suggested, on chromosome fragments, and the data collected would still have to be assembled into a complete genome sequence. Not unlike the shotgun sequencing technique, as someone else pointed out. With shotgun sequencing, the genome is blasted into fragments (one way of blasting it apart is to sonicate a solution of DNA, which gives a distribution of fragment sizes up to a couple of kilobases IIRC), and the fragments are sequenced by sequencing machines. The sequenced fragments are reassembled into a complete genomic sequence by a computer program which exploits redundancy in the fragments (many fragments overlap, as the original sonicated solution of DNA contains a large number of copies of the strand being sequenced). The sequence obtained from running this program is thus a "best guess", with some (hopefully small) probability of error. A good reassembly algorithm would exploit every possible aspect of the distribution of fragment sizes; e.g. certain shotgun techniques create a bimodal fragment size distribution, and the bigger fragments are "stitched together" using the smaller ones where necessary.

    Anyway, I see two issues. One, what size DNA strand can be sequenced using a nanopore without breaking? Two, how many nanopores can be made to operate simultaneously? With 100 nanopores operating in parallel on 10-kilobase DNA fragments at 10 seconds per nanopore per fragment, you're getting 10 kilobases per second, or a billion bases every three hours. At these speeds, the real limiting factor is probably going to be something other than raw sequencing speed. I think it's a very exciting technology.

  • why not use ATP-driven translocation of polynucleotides, single-base pairing receptors changing their fluorescence, the pores able to regulate each other so that only one is sequencing at a time, enzymes stretching out hairpins, things like this make me wish i come back to my old toys one day...

  • ... our holdup in using this data is actually now what the genes are, and how they interact. That will still take years for us to figure out.

    But it's very important empirically to have more than one dataset. Who's GNOME did we sequence anyway? And comparing the sequence of many different instances of genes from different people is not time consuming. You're talking about figuring out how the Human GNOME works. That's a completely different dicipline.

    Being able to decode strands of Nucleic Acids (and the technique might be applicatble to Poly Peptides(Protiens) as well) in a matter of minuites without the mess of Gel Electrophoresis would be HUGE.

  • Well, you couldn't sequence the entire Human GNOME in hours. The artice reads:

    Because the pore in the channel is large enough to admit only a single strand of DNA, the time it takes for the DNA to be drawn through the channel (enlarged view) effectively measures the length of the DNA molecule (here, 1,300 ms corresponding to a 1,060 nt polymer).

    So if there are 3 billion bases in the Human GNOME,

    1.3sec/1060bases*3,000,000,000bases/60sec/60min/24 hours = 42 days
    Of course if the apparatus is easy to use I supose you could have several running at the same time provided you could prepare the material fast enough.
  • Sequencing: finding out how the A, T, C, and G units are arranged in you.

    Decoding: finding out what the sequence leads to as far as expression of traits goes. Like why you have an aversion to bio-tech speak (grin).
  • What's the difference between decoding and sequencing?

    I guess I'm a little naive on the genome thing... but the way quantum computing is going, I better brush up on it, eh?



  • Well as i understand it,

    At the moment DNA gets broken up into small segments and fired at a device that can decode each of thease segments,
    The problem it you know what the segments are but not what order there in, like a big jigsaw.
    Sequencing is putting thease pieces back in the correct order.

    This new process decodes the DNA in sequence so there hard and sloq sequencing step is no longer needed
  • It could aldo make a convenient reader for a DNA based tagging system.

    Such a system could be used to trace all kinds of "things" and "substances"

  • at a probability of 16384 to one against.

  • This is very true. I can't wait to break off a little bit of a Linnean holotype for a bit of DNA , ;) . This of course will provide much more data for diagnosing new species and species relationships ultimately fueling the debate on "linnean" [phylocode.com] versus "phylogenetic" [ohiou.edu] nomenclature. Now if the zoological community would get off the a$ses and create/support a universal warehouse for all nomenclature.
  • I do believe I submitted this story over a month ago, after having seen it long before that. Glad to see things are being kept up-to date around here.
  • no equivilant to the verb "to have"
    So?
    "I have no child."
    "There's no child unto me."
    You can understand that, although we wouldn't say it that way. So, too, for other meanings of the verb "to have":

    "You have my stuff."
    "My stuff is with you."

    "I have to go."
    "I need to go."

    "I've never gone."
    "I never went."
    There is no particularly compelling reason that a language should use "to have". In fact, if English /does/ use the word "to have", then objectively speaking it's probably less sensible to say "That's my book" than "I have that book", since you're stressing the fact that you're the one whose it is (ie "who has it") rather than that that is a book. It doesn't really matter though -- constructs are whatever people make of them over many generations.
    ~
  • I like to think that genomics is the ultimate in the Law of Natural Selection. Every living thing wants to breed with only the healthiest and strongest of it's species. And just like Gattaca we will soon have that power. In a few hundred years this application of natural selection may breed out most genetic diseases naturally instead of having to rely on drugs.
  • here we come? I just love it when sci-fi becomes fact.
  • Mobious Genomics [mobious.com] is a British company that claims to be on the verge of offering a new machine that will revolutionize gene sequencing by combining biology "with quantum physics". The "genius" behind the company, Dan Densham used to go to Med SChool with me until he dropped out to concentrate on this breakthrough. there are various semi-sycophantic articles on the web, such as this one [mail-archive.com], about how intelligent etc. he is and what a huge breakthrough his equipment will bring. I've always been wary about claims of "giant leaps" in science, especially when they come from someone Ive seen vomiting copiously following one too many beers (i.e. two) at the medical school bar. However it looks like Doc Densham (Im assuming hes got a PhD by now, even if its honorary) is getting lots of backing for his "biochip", which is great. The actual Tech is pretty hazily described, but appears to use molecular resonance- on the basis of radiation released whern a specific enzyme (helicase/primase) interacts with the base- I assume his "biochip" senses the state of that radiation as the DNA "passes through" the enzyme. Interesting.

    P.S. if you're reading this Dan, do you need an electrophysiologist? G. (LOL)

  • DNA passwords!

  • Somewhere in a lab at Harvard University in Boston, mid 2001:

    "Professor, the computer is decoding the first base pairs right now!"

    "Record them for posterity, this is history in the making"

    "Ok... reading now... G... A... T... T... A... C... A..."


  • Not only will this allow sequencing on minute amounts of DNA but it appears to be nondestructive to the degree that one could get multiple reads, i.e reverse polarity and reread the sequence(s). Gaining the holy Felgett's advantage at the cost of a few minutes and a few microvolts. I can't help but also think of the potential this holds for data storage. An array of micopores on a chip could read massive amounts of data off a drop of liquid in minutes.
  • the next step is a DIY kit that you could do from home! That would be some funky shyte.
  • Thank you for the info! I did however find some examples (below) of how DNA folding and tangling can affect the transcription process. I vaguely remember reading something a long time ago about single proteins originating from different segments of DNA, but I may have been imagining it. It may not be a strong enough affect to be a barrier to our understanding like you say, but I don't get the idea that DNA tangling is all that well understood. Is this true?

    Here are the links along with key excerpts:

    "...It has been put forward that many of these chromosomal changes are caused by the ability of certain specific types of DNA sequences to fold into unusual structures which interfere with the faithful copying of chromosomes."

    www.cpa.ed.ac.uk/news/research/07/item3.html

    "...The knots and kinks in the DNA provide crucial topological stop-and-go signals for the enzymes."

    www.khouse.org/articles/technical/19971201143.ht ml
  • "...our holdup in using this data is actually now what the genes are, and how they interact." One example of this, is the protein folding problem. A sequence of DNA, which corresponds to a sequence of amino acids in a protein, still leaves the problem of how the string of amino acid molecules folds up to make a 3D structure. This problem is still really really hard. What makes things harder is that DNA itself folds up and tangles upon itself, meaning that different sections of DNA on completely different ends of the long molecule can contribute to the same protein. It's going to be very difficult to make full use of knowing the sequence of a strand of DNA until problems like these are solved. I'm not an expert, does anyone out there know of any interesting advances in the protein folding problem?
  • Ok.. Count to 10 and take it easy... This forums are not for geneticists, they are for everyone. Of course that some of the ppl that have posted messages on this particular forum are ignorant, arrogant and idiotic, but since it's a democratic system they can express them selfs and say what they want, even if it's stupid. Modesty and pacience are two important virtues for a scientist, work on them. BTW: "I've been conducting genomics and proteomics-related research since before those terms and the genome sequencing projects existed". wow! 20-30 years? That's a lot of time...
  • Being able to sequence DNA quickly is only one small technological benefit from this nanopore discovery. In the '70s the McKenna brothers in their book The Invisible Landscape [amazon.com] postulated a similar mechanism in the post synaptic membrane of neurons. As virtually any technology that humans invented was invented previously by nature, I believe that this mechanism is there in neurons and that this discovery will propel research into this precise area. What we have with this nanopore discovery is conversion of DIGITAL DNA sequences into ANALOG electrical signals. Moreover this is a way for thought to be stored in DNA! As thought in our brains is electrical signals, we now have a mechanism demonstrating how instinctive behavior is passed on through DNA. I call it Meme Storage in DNA [slashdot.org].
  • Actually, I'd say "decoding" is just a journalist term. I've never heard anyone who actually does sequencing or bioinformatics refer to sequence analysis as "decoding".
  • At the moment DNA gets broken up into small segments and fired at a device that can decode each of thease segments
    It's worse than that -- the segments are thousands of base pairs long (I forget how many), but the process for reading them can only do a few hundred base pairs at a time, so it only reads the beginning and end of each segment. So you have to get segments with enough overlap that the beginning of each sequence that is actually read matches up with the end of some other sequence.
    --
  • This would make real DNA Fingerprinting a reality.
    Get arrested, give a blood sample. It'll only take a few hours to verify who you are. None of this "probably" stuff, they'll have YOUR sequence on file, and there won't be any doubt (unless you have an identical twin).
  • I think gels are used for very small samples of DNA. About 500 base pairs is the limit for a gel. With 72 channels on the gel that is nowhere near the number of base pairs in a chromisome.

    The faster better technique is electrostatically driven capliary tubes. They suck the sample through a microcapliary and shine a laser on it as it passes by. Generally the same 72 channels in parallel as the gel method - something about legacy analysis software as well as the plates that hold the samples and the robots which manipulate them. Kind of like the gauge of the railroad tracks used to carry space shuttle boosters being determined by the wheel spacing of the wheels on a roman chariot which was determined by the space required by two side by side horses.

    we have the most advanced transportation system in the world having a major design parameter determined by the width of a roman horses ass.

    Z
  • for this thing not too bad..

    The article mentions 3 billion bases in less than 2 hours. That comes to

    (3/2) x 10e9 / (3.6 x 10e3) bases/sec
    = 416667 bases/sec.

    So you would need a sustained writing speed of about 400 kilobytes/sec, or if you compress it into 4 bases per byte, say 100 kilobytes/sec. to write to about 3 GB (or 730MB compressed) of disk space.

    You could fit it onto an IBM Microdrive attached to your Palm!

  • You are both right and wrong with your post, and your enthusiasm for learning is encouraging.

    You're correct: The protein folding ploblem is is hard, in the worst (best?) sense of the word. That is to say, NO, there have been no interesting advances in the field; All that has been done so far, more or less, is to throw some processor cycles at the problem. There have some good results from this aproach, but no new insights or understanding of the problem.

    This would be a good project for an interested and motivated student looking for a trip to Stockholm.

    With an understanding of protein folding, we could rapidly discard the current: "piss on the porch, see if the cat licks it up," era of biotech, and actually do some engineering. Proteins are, to put it mildly, amazing: they are nanomachines that work, sometines with such elegance that when you see what is really going on it is enough to take your breath away as you try to yell Holly Sh*t and wonder if you are living your life right.

    Designing proteins to functional specifications would be highly interesting, i.e., one of the simplest scenarios: "Uh, how about we have it arange the glucose carbons in a cubic crystal latice and let the O and H diffuse out as water?"

    Today, we can pretty much string together any arbitrarilly long sequence of amino acids we want, but they are just so much fried egg until the folding problem is solved. When, and if, that day comes, our world is going to change in surprising ways. The implications reach far beyond medicine and agriculture.

    You're a bit wrong: DNA folding is not, by itself, a barrier to our understanding of the genome. Actually, we have a pretty good understanding of how the whole transcription translation thing works, with a pretty solid understanding of splicing, targeting, etc., even some understanding of promoters, enhancers, and so on, we just don't know, for the most part, what the hell the products of this process (proteins) are doing.

  • Usual biotech-speak is "sequencing" and "mapping," the latter being figuring out which genes are where in the raw sequence data (AGCCTGATC ...) which comes from the former.

    "Decoding" is a useful but too-broad term; it covers mapping and everything that comes afterward, such as figuring which of the mapped genes will express when, and to what degree, and how the proteins thus expressed will fold, and how they'll interact with each other. Once you've got all that, you have Mastered The Secrets Of Life Itself.

    There is, to put it mildly, a lot of work to be done here. Job security for bioinformaticians.
  • What will it be used for?

    Immortality, my friend. Immortality.

    The honolulu(sp?) technique used in cloning (done with mice - an incredibly difficult subject for cloning because the eggs cycle so quickly), unlike the faulty technique used with Dolly (which involved starving the nucleus-donor cell, and then using an electric shock to cause it to merge with the nucleus-free egg), has fertility rates that are rapidly approaching those of normal mice, and little to no genetic damage per breed. Yet, at around 5 generations of clones (cloning a clone of a clone of a clone of a clone), we start to see premature aging. Why? Because, as DNA lives, it slowly mutates. As must mutations are bad, it steadily poisons the mice's genetics.

    The key is in a DNA backup.

    Digital data doesn't corrode. It can be verified, backed up, copied, you name it. With the recent production of a completely DNA-synthesized fruit fly, the possibility approaches that we can completely re-create an individual's DNA strand. Then, when cloning organs for the individual, we use the backup DNA, not DNA from the person themself, as that DNA has become slightly corrupted overtime.

    Digitizing DNA strands is a key to immortality.
    That is why this is important.

    -= rei =-

    P.S. - I vote for genetically altered population. I certainly hope we see that day soon when people can make choices on whether or not they want their children to have to suffer.
  • DNA sequencing is already done using an extremely inexpensive and idiot-proof process. So this technology could improve that perhaps in terms of speed and cost, which is always a Good Thing if you're a researcher!

    I was thinking that this method could also be used to sequence proteins - a process which is now done using an automated process which can only produce (correct me if I'm wrong, and if I am I'll eat a bug) maybe 30 "letters" of sequence. Compare this to many hundreds at a run from DNA sequencing. If proteins could be sequenced hundreds of amino acids at a time, you could sequence a whole protein in one run. This would be better than the current method, where fragments are sequenced, and then the overlaps are compared to piece together the whole sequence.

  • It looks to me that there is a big gap between the idealized graph above, which shows clearly the different nucleotides, and the actual data they have gotten which shows blocks of 30 purines and 70 pyrimidines. Can they really distinguish between adjacent nucleotides or are they so close physically they will just crowd through and blur together?

    And will they be able to tell A from G (both purines) and C from T (both pyrimidines)? I don't have the charges handy but I think C and T are pretty close.

    Also, DNA breaks very easily. No way are you going to be able to pull a whole chromosome through at once. If they get just 100 bases at a time, will that be useful?
  • It's great the we might be able to do sequencing in a matter of hours rather than years, but the real question is, what does that get us?

    Every drug company has a Genomics division these days, to analize the existing data from the Human Genome Project [doe.gov]. Now that new data can be gathered at such increadible speeds, are we any closer to improving the quality of life based on this work. Probably not, and the cause is a double edged sword.

    The problem is the restrictions through international treadies and government regulation, on gentic engineering of humans. Don't get me wrong, I'm not in favor of such modification of the human genome, howeer, this leaves only one recourse. They can create medications that the sufferer of a genetic defect can take every day for their entire lives to prevent the ocurrance of an illness that they are genetically predisposed to. This is a boon for drug companies. If they can generate long term revenue streams by creating medications which reduce the chances of developing illnesses to which certain people are genetically predisposed to, and clain that they are doing this, instead of developing ways to repair a gene at birth - not because it's more proficable to do it this way but - because this is the only avenue they're allowed to pursue due to federal and international regulations against messing with the human genome; then who are the regulations truly serving? the population, or the drug companies?

    Along the same lines, there will always be countries which are not signatories to the afore mentioned international regulations - in which drug companies can deelop the gene theropies which could truly benefit sufferers of gentic diseases and defects. That said, there will always be a black market for these theropies, once deeloped.

    The question becomes which is a better world to live in: one where we have a drug dependant population, or one where we have a genetically altered population.

    At this point I'll conclude my analysis because any further speculation will lead to the realm of Gattica style science-fiction. There is, however a great deal to consider...

    --CTH

    --
  • Note the word "concieved" in the first line of the document...there is not much in place yet.

    That was my first take as well, but then when I looked through the references, I found that many feasibility questions seem to be resolved already. For instance, I read the main page [harvard.edu] and thought, "Sure, but how do you transport the strand through the nanopore?" Then I checked the first reference listed [pnas.org], and what do you know: "We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane."

    The final system may still be largely conceptual, but it's by no means blue sky. I tend to be a techno-skeptic but this work impresses me.

    The page sounds to me like a breathless plea for lots of venture capital funding.

    This is grossly unfair. The language and style are well within the normal bounds for scientific papers. The word "revolutionary" is appropriate for a technology that would do years of work in hours. And in case you didn't notice, it's not private research -- it's being done at The Department of Molecular and Cellular Biology, The Biological Laboratories, Harvard University [harvard.edu]. What interest would a university laboratory have in "venture capital"? If they later spin it off into private industry for product development, then they might go for venture funding, but it simply makes no sense to do so now. There's a big difference between research sponsorship and venture funding.

    Tim

  • ... some folk come out with a device that can do the whole job in a day.

    It must be a bit like climbing mount Everest the hard way and while you are sitting at the top eating your Kendal Mint Cake, someone rides up the access road on a bicycle.

    So what was the point of spending several hundred million doing the job the hard way? Oh they filled a gazillion patents on the sequences the read out. And there I thought you had to invent something to get a patent.

  • Celera Genomics, using modern technology (and alot of financial backing, and the fact they are a subsidiary of the people who make sequencing machines,) competed the genome in a matter of months.

    Just to correct a few inaccuracies. Firstly it hasn't been completed yet. Celera Genomics decided to claim they'd finished it, which spurred the public project to also claim the same. In reality both had only 90 - 95% of the consensus sequence and only then at "draft" quality.

    Secondly, I feel it's wrong to claim that Celera were the people to "complete" it. Celera used their own data in conjunction with the public data, and yet they have (more or less) comparable results in terms of coverage, number of contigs, quality and so on. Personally I feel that this is like admitting that their own work doesn't add anything new to the public effort - ie they failed.

    The bottleneck with sequencing at the moment is in the "finishing" process - tidying up the results to produce highly accurate answers. This is largely caused due to the randomness of the shotgun sequencing approach. As it's effectively solving a jigsaw puzzle from lots of randomly cut pieces of DNA, in some places you'll get lots stacking up and in others you'll find none. It is unrealistic (not to mention expensive) to keep increasing the coverage so that everywhere gets covered by the random shotgun process.

    Instead a fixed depth (only 3 or 4 fold in the draft sequences) is used followed by directed sequencing where the user, or an automatic program, analyses the data set and chooses experiments to perform (primer walking typically). The graphs I've seen of draft vs finished data show quite well how the finishing is lagging behind.

    However this new strategy, not being random, will greatly reduce the amount of finishing needed. However note that at present they are using it for probes rather than full scale sequencing. It has great potential, but looks to be years away from replacing the current work.

  • A similar technique is DNA sequencing using scanning-tunneling microscopes and atomic force microscopes. Here is a Google search [google.com], and here is an article from 1992 [the-scientist.com].
  • Harvard scientists have concieved a revolutionary technology

    This sounds exactly like late-night infomercials that invariably say things like "our scientists [actors in white lab coats conspicuously walking around behind the one being interviewed] have devised a revolutionary new formula that will make you lose weight without dieting or exercising!"

    That is, if the people selling something describe it as "revolutionary" themselves, it isn't. If it really is revolutionary, we'll hear about it in other places. The HP-35 from the slide rule article -- that's revolutionary.

    So while this may be a significant improvement, I'd change the prose if I was them.
  • More often than not, doing things the "hard way" is an essential first step in figuring out how to do it the "easy way". I can think of innumerable examples where people have worked hard to accomplish something significant only to have someone come out with an easier way to do it. But this is crucial to the development of science and technology. Take for example PCR used in genetic analysis. One of the guys down the hall used to spend hours and hours and hours leading to days just getting the reaction products to the point where he can analyze them. Now we can accomplish this in just a couple of hours. Or what about something a little closer to home for the Slashdot crowd? I can remember my father having to program the mainframe system at the university using paper tape and punch cards. God forbid if you got anything out of order or misplaced a few paper punches. There was a logic to programming those things, but trouble shooting could be much more complex than it is now with automated trouble screening for code in development applications. Additionally, the same program my father took several weeks to write I can now write in a couple of hours with current development tools and I get visualization tools that could not even be dreamed of when my father was in graduate school. Additionally, we have the luxury of unbelievable speed of analysis on a Powerbook I can tote around in a backpack rather than trying to get time on the campus mainframe at 3:00 in the morning.

    My point is that all this pain grief and expense was absolutely required to get where we are today and in most fields this will continue to be the way things are as we have no way of knowing what is hard and how it can be easy if what we are doing is new and innovative.

  • A genome a day.... (Score:3)

    by Marcus Brody ( 320463 ) on Sunday July 08, 2001 @06:02AM (#100626) Homepage
    Firstly, this idea has been around a while (i.e. check the references on the article), but it does appear to be getting there now. Perhaps 5-10 years before we start seeing commercial sequencing machines based on this technology???

    It will not replace conventional sequencing technology, unless it can beat the now pretty cheap cost. Conventional sequencing is based on labelling the individual DNA bases with a different flourescent dye, and running the DNA through a gel which seperates the DNA according to size: As each base runs through the gel, it goes past a laser/detector which can detect the specific DNA base (A,T,C or G) at that position. Due to gradual impovements to this technique over the last 20 or so years (originally it employed radiation, rather then flourescence) the speed, sensitivity and cost has decreased dramatically. For example, the human genome project started in ernest about 10 yrs ago. Celera Genomics, using modern technology (and alot of financial backing, and the fact they are a subsidiary of the people who make sequencing machines, [appliedbiosystems.com]) competed the genome in a matter of months. The increase in DNA sequencing capacity puts moore's law to shame.

    For example, our lab could process around 100kb (thats KiloBases guys!) of data a day, but we never even touch this with our machine [appliedbiosystems.com]. No need, and the same stands for many small-medium research labs. Alot of people like us will probably stick with conventional sequencing technology for a long time (it works well, is high enough throuput, cheap & easy).

    However, the are some exciting applications with single strand sequencing. For example forensics. Also, it allows the oppotunirty of sequencing RNA (this is the "messenger" which passes the "important" part of the DNA message to the ribosomes, which then "compile" a protein - the stuff which actually does things, like an enzyme or structural component). Sequencing RNA is exciting, as currently you have to convert the RNA back to DNA (which can cause problems) and then sequence that.

    Another obvious application for this would be very high throuput sequencing which would be employed by the major sequencing centres. Yes, i know we already have the Human Genome, but a fashionable idea at the moment is comparative genomics. This is very much taking biology back to its roots (i.e. like Darwin and Wallace comparing the morphological characteristics of certain species and infering adaption), but at a molecular level. This will yield amazing insights with discoveries having important implications from medicine to evolution. In fact I think the general public & media will soon be bored of this. Each week it will be a new genome being announced; mouse, chicken, rat, pufferfish, rice, corn, dog, cat, cow, chimp......

  • Re:Huge! (Score:3)

    by Marcus Brody ( 320463 ) on Sunday July 08, 2001 @12:59PM (#100627) Homepage
    without the mess of Gel Electrophoresis would be HUGE

    Hey, dont knock electrophoresis mate. It is the basis of PCR resolution, Southerns, Northens, SSCP, conventional sequencing methods plus a multitude of other applications. Furthermore, refinements to this approach (read: capillary electrophoresis) have supplied one of the major advances to sequencing methodology in recent years, unlike the technology we are (were?) discussing.

    Who's GNOME did we sequence anyway

    Good Question. Apparantly, they took DNA from around 100 (i forget the exact figures here) US citizens of various sex/ethnicity, picked 7 out of the hat, and sequenced portions of each (most from a single, unidentified individual - although if nanopore technology comes to fruition, i reckons we can track him) down

    p.s. thats one of my favourite all-time techno-typo's: the Human Gnome Project. Almost as good as sequencing my ARS (a yeast thang....)

  • DNA Code (Score:4)

    by Alien54 ( 180860 ) on Sunday July 08, 2001 @04:35AM (#100628) Journal
    We now get to the point of where this is sort of link looking at the source of the Linux kernel, if it all was written entirely in Finnish [clinet.fi] in the first place, and we knew almost nothing about Finnish [finland.fi] (which is not an IndoEuropean Language [malibutelecom.fi]) and almost nothing about any kind of programming.

    But it is a place to start.

    Side note:

    while looking up the Finnish Language pages for this comment, I came across this tidbit: That Finnish has "no equivalent of the verb to have [finland.fi]". This has interesting philosophic implications in the history of open source, etc.

    Check out the Vinny the Vampire [eplugz.com] comic strip

  • Re:A genome a day.... (Score:4)

    by Marcus Brody ( 320463 ) on Sunday July 08, 2001 @07:42AM (#100629) Homepage
    Also, DNA breaks very easily. No way are you going to be able to pull a whole chromosome through at once

    Yeah. Sure, i agree with you. Once youve taken DNA out of the nucleus and stripped out the protein complement of chromatin, it is darn hard to get high-quality genomic DNA (for PFGE or whatever). Furthermore, yanking the DNA through that little hole is gonna probably cause problems.

    However, you dont need unfragmented DNA. For example, you could fragment genomic DNA, and pieces of this would randomly pass through the pore - essentially a shotgun approach. This wouldn't be a bad way of doing it. This would also get round problems with the detection mechanism. For example, if they could only disringuish between C/T with 80% accuracy, multiple reads of the same sequence could clear this up.

    The technology could also overcome problems such as cloning bias, problems with sequencing microsats (e.g. (AT)n), GC rich regions etc. Which the HGMP is still having problems with.

  • I am a zoological systematist, working in entomology.

    The human genomes was sequenced by taking lots of DNA, cutting it up randomly sequencing the random pieces of cut up DNA.

    In my field, we work with much smaller amounts of DNA. Sometimes I only have a single specimen of a tiny insect, or unique material (from rare or extinct species) to try and get some DNA out of. In older material, DNA is usually degraded and many times we end up with nothing but a destroyed or damaged specimen.

    With small amounts of DNA to begin with, we have to amplify (PCR) single genes or regions by using general primers, which means that they don't only fit on the insect DNA, but fungi and human DNA too, making contamination of your material very real risk.

    If this technology turns out to work on a larger scale, it's amazing news for me and my collegues.

    The nanopore technolgy sequences single moleculer, which means the PCR step becomes unneccesary! This means that we can get sequences from specimens with severely degrades DNA, and we don't have to be as afraid of grinding up rare material in hope of getting sequences.

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