Magical Truthsaying Bastard Shadesong (shadesong) wrote,
Magical Truthsaying Bastard Shadesong
shadesong

Odin's Day

Administration
Happy birthday to techempage!

Medical
Still with the ouch. I really am going to have to schedule a massage. :(

Bid on The Stepsister Scheme!
A reminder: jimhines is auctioning off an ARC of his new book, The Stepsister Scheme. All proceeds go to the National Coalition Against Domestic Violence. Elayna's most of the way through her ARC (if you saw her immersed in her book at Diesel last night, that was it) and is loving it (and is very happy to learn that there will be sequels). Bid now!

Facebook
I am now on Facebook. If I haven't already found you via the e-mail search thingie and you haven't found me because a friend added me, um, find me. If you want. I'm not quite sure what one does with a Facebook, beyond playing with games and apps and whatnot, which I lack the time for. Find me via shadesong AT gmail.com.

So um yeah. Yesterday was a big social networky day. It's research. (NO REALLY.)

If you add me, please tell me who you are! I know rather a lot of people, and sitting here going "Which Kat is that?" drives me bonkers.

It's interesting. My LJ friends are mostly people I've met on LJ or recently in Boston, or people I've known for years on Tamson House or the Bordertown BBS. People from other corners of my world don't show up here. But they do on Facebook. I've added my first crush (from age 4), the guys I based Napalm and Shawn on, friends from my brief life in Utah...

Babysitting
Those of you who've babysat recently (I know I have some college students on here) - how much do you charge? Elayna needs to set rates.

Free Will Astrology
Uncle Rob says: "Uranus symbolizes your instinct for freedom, your drive to express your dormant genius, and your attunement with your intuition. Saturn represents structure and responsibility; when it's prominent, it's time to get back to basics and cut down on distractions and excesses. So what should you do when these two planets are in exact opposition, as they are now? Here's one hint: We're all being squeezed between a mandate to head toward the frontier and the pressure to play it safe. To keep from being paralyzed, some of us may have to choose one way over the other. In my opinion, you Pisceans are likely to profit by choosing the Uranian path. "

Daily Science
THE desk in Gordon Sanghera’s office at Oxford Nanopore proudly displays a piece of knobbly plastic. It has a hole running through it and looks rather like a cruller doughnut, though with grey icing. In fact, it is a model of a protein molecule called alpha-hemolysin. Dr Sanghera, the firm’s boss, believes this molecule will revolutionise the sequencing of DNA.

In nature, alpha-hemolysin is used by Staphylococcus aureus, a disease-causing bacterium, to punch holes in cells’ outer membranes. The cell contents, particularly its ions (electrically charged atoms) then leak through the hole and it dies. Pushing a DNA molecule through the hole changes the speed at which ions pass. That will, in turn, be registered as a change in electrical current. The exact change varies with the bit of the DNA molecule that is passing through. So, in principle, the protein can record the order of the bases (the chemical “letters” that carry the genetic code) which make up the molecule.

If that idea can be put into practice it will, indeed, be a revolution. At the moment, sequencing DNA is slow and expensive. The molecule must be replicated many times (a step called amplification) and also labelled with fluorescent tags. These processes introduce errors and mean that a gene has to be sequenced several times to ensure a reliable result. Moreover, the cost of buying and operating the sequencing equipment is high. The result is that sequencing an entire genome costs hundreds of thousands of dollars.



In 2004 America’s National Institutes of Health (NIH) challenged researchers to work out a way of sequencing a genome for $1,000. Many of the responses involve running strands of DNA through tiny pores of one sort or another and Jeff Schloss, a programme director at the National Human Genome Research Institute (which is part of the NIH), reckons this is a particularly fruitful approach.

These “nanopore” techniques, originally proposed by Hagan Bayley, a professor of chemistry at Oxford, in 1992, are simple, at least in principle. They do not need fluorescent labels and will probably not require amplification, either. They can “read” DNA directly and rapidly, and are cheap enough to replicate in vast numbers.

In the case of Oxford Nanopore’s technology, the DNA molecule is fed through the hole one base at a time by a second protein, an enzyme called an exonuclease. This can clearly distinguish the four DNA letters, A, C, G and T. It may also be able to detect whether a letter is methylated, though this has not yet been independently verified.

Methylation, the addition to a base of a group of three hydrogens and a carbon atom, is one way in which genes are regulated. It seems to be important in some sorts of cancer, and there is also evidence that regulation by methylation can be passed from parent to offspring, meaning that characteristics acquired by one generation may be inherited by the next. The importance of such “epigenetic” inheritance is controversial; some researchers reckon it trivial while others think its role is underestimated. The ability to track methylation is thus scientifically important.

Though the firm has proved the principle, a single pore would take about 70 days to sequence an entire human genome (which has roughly the same number of letters as 1,000 Russian novels). So, in another laboratory on the other side of the science park, its researchers are working on ways of integrating the thousands of nanopores needed to read a genome in a day. Their working model is a shoebox-sized package of electronics and liquid-filled tubes, with a silicon chip at its core. The chip has 128 tiny wells, and inside each of these wells are the nanopores.

Dr Sanghera is unwilling to say how soon he will have a product, but other firms are breathing down his neck. Pacific Biosciences of Menlo Park, California, for example, eschews nanopores in favour of a technique that uses fluorescence to watch DNA molecules being built up, base by base, though it reckons it will not have a product until 2010. Which all bodes well for the NIH’s challenge. The next, far bigger question, is—when this era of cheap, personalised genomics finally does arrive, what will be done with all the data?


Plans
This is a week of everything shifting. I think I can get us out to the mall to shop for wedding shoes today. I'm still deciding what to do tonight. For now, I must pack up the imp pack for sageautumn (sorry, Sage, my for-sale box was away for a while!) and my switch-witch gifties and run them to the post office, and hit the usual library-PO-bank triangle. I will hypothetically have writing time sometime today. Which I *need*.
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