Tag Archives: new technology

Frontiers in Physics: Real Time DNA Sequencing

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zmw_dna_poly_phos_nucl.jpgIt tookscientists more than twenty years after the first DNA sequencing technology wasdiscovered to sequence the entire human genome; yet our own cells complete thistask every time our bodies produces a daughter cell.  So to achieve the goal of real time DNAsequencing, Pacific Biosciences had the idea to spy on Mother Nature as shegoes to work copying DNA. Now, the company’s commercial device planned to be on the market in 2010, promises to be 20,000times faster than current second generation technology, with turn around timeof about ten minutes rather than ten days. Chief Technology Officer SteveTurner says in four to five years, new technologies promise to rocket thistechnology forward even further, making it will possible to sequence an entire humangenome in fifteen minutes, on a chip that costs less than 100 dollars.

DNA polymerase is a natural enzyme that constantly makescopies of DNA. DNA is a double stranded chain, and when the two strands areseparated, it’s possible to recreate one based on the other. That’s because DNAconsists of only four building blocks, or nucleotides. Each nucleotide onlypairs up with one other: adenine (A) pairs with thymine (T), and guanine (G)pairs with cytosine (C). Thus, if one side of the chain reads AATTGGCC, theother side reads TTAACCGG. Polymerase unzips a DNA chain and as long as thereare nucleotides to be had, it grabs them and makes a copy of the chain.

Second generation DNA sequencing techniques use polymeraseas a reagent, throwing it away after reading only a few nucleotides in thesequence. Turner says one of his company’s main objectives was to achieve what they callSingle Molecule Real Time DNA Sequencing (SMRTDNA sequencing) in which they keep the polymerase around longer. One the main problems with watching thepolymerase is knowing how to see the nucleotides. Second generationtechniques attach a different color fluorophore molecule to each type of nucleotide,lighting them up like Christmas lights. But a whole chain of these lightscreates too much background noise to see the individuals and their order on the chain.

Pacific Biosciences overcame this first challenge byattaching the fluorophores to a part of the nucleotide that is naturallycleaved off by the DNA polymerase. It diffuses away with 100% efficiency in atotally natural process, and keeps the background noise to a low minimum.

To illuminate the individual nucleotides as they areattached to the chain, the company has developed a SMRT chip- a strip of metalwith thousands of small wells in it (see image). At the bottom of each well is apolymerase, resting on a glass bottom, and latched onto a strand of DNA whichit will unzip and begin to copy. Base pairs fly around the surface of the chip,but only a few at a time dip down into the well. This immediately minimizes thebackground noise from those unattached nucleotides. Engineers shine a laser through the glass bottom, but thelight does not come up through the well. This uses the same concept found inyour microwave oven. You don’t want those microwaves flying around the kitchen,but you want to see what’s cooking. So the door of the oven has small holes cutin it, which are large enough to let visible light escape, but too small formicrowaves to pass through. Similarly, the wavelength of the laser light is toolarge to pass up through into the wells. But there is an evanescent penetrationvolume of only a few zeptoliters (10-21). This illuminates the polymerase, but not the space around it where the nucleotides are floating. And when a nucleotide is bound to the DNA cahin, it releases a burst of light.

The Pacific Biosciences technique uses no reagent, unlikesecond generation sequencing methods which use a tremendous amount of reagent(it would take two semitrailers full to sequence an entire human genome). It’s 20,000 times faster andonly takes ten minute to turn around from the time the sequencing finishes. Inaddition, the Pacific Biosciences it has three times the read time -or the length of a DNA strand that is read sequentially before the processstops. Normally this is shortened by an overwhelming background noise.

Considering that the technique utilizes a lense and asingle-photon CCD array to collect the light, Turner says he hopes DNAsequencing will come to be considered a type of medical imaging in the next tenyears.

Carbon Nanotubes Help Cook Cancer

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MWNT.jpgIt seems that one out of every few fictional villains ends up resorting to the same method for destroying the earth: hitting it with a giant laser. Although these fictional plans never elaborate on the real world physics, in some ways the villains have the right idea. Lasers are powerful tools and simply used as a heating device, they can kill cells. Thermal therapy is being used to kill cancer cells in tumors that other methods fail to eliminate, but as with radiation therapy there is a risk of overheating healthy cells, or not heating the tumor cells enough.  

A new idea for improving thermal therapy was recently published in PNAS and presented at the AAPM session “Frontiers in Medical Physics,” by the young research assistant Xuangfang (Leo) Ding from Wake Forest University. Using multi-walled carbon nanotubes (MWCN’s – shown above) Ding and his collaborators hope to make guided laser cancer removal safer and more effective.

The treatment injects cancer tumors with MWCN’s,  and uses a guided near infrared laser to heat them up and deliver a fatal temperature rise to the cancer cells.  The laser pulse is low energy (3 W/cm2) and fast (30 seconds per dose). The team uses Magnetic Resonance Temperature Imaging, MRTI, to identify the tumor and then to monitor the tumor’s temperature as well as the temperature of the surrounding tissue. Trials with mice showed a significant rise in the temperature of the cancer cells injected with the MWCN’s, compared to without. And, the tumors were far less likely to come back.

The treatment can be used non-invasively on superficial tumors like skin cancer, and with minimal invasivity to deeper tumors by inserting a small laser optic fiber into the target as well as the MWCN’s. The exception is lung cancer, where the motion of the tumor would cause too great an error in the MRTI.

Since carbon nanotubes are not approved by the FDA, it’s uncertain when the team can begin clinical trials, and they are still investigating any potential side effects of the MWCN’s.

New Ideas for New Accelerators

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One of the largest disadvantages of therapies that require accelerators is the size and cost of the accelerators themselves. These factors limit who can receive care and where. So for medicine and the future of accelerators in general, the community is pushing for smaller and more affordable (but of course, that’s the case with all technology isn’t it?). At a very intriguing session I got to hear about an approach that a group of scientists at Stanford University and Fluence LLC are developing to make smaller particle accelerators for medical applications.  They are also collaborating with the Stanford medical school and SLAC National Accelerator Laboratory, who are contributing expertise in Monte Carlo simulations for beam transport and dose calculations.

Their technique is called electromagnetic plasma acceleration (not to be confused with other plasma accelerators that use lasers) and it goes something like this: get a neutral gas in-between two electrodes and let it break down into electrons and ions. The currents that flow through the plasma then generate  their own magnetic field (this is a big advantage because no magnets are needed); this exerts a force to the right, and the electrons start to move.

This alone is not a new approach.  But normally the ions upstream form a wall, sort of like a piston, and push the other particles forward.  This works for lower energies, but when one tries to accelerate the piston faster it starts to tilt and downstream gas can blow by it without being accelerated. This is like a piston with a hole in it, which doesn’t push anything. So there’s a definite limit to how fast you can get those particles to move.

But new research has shown that you can make tweaks to the system and cause the piston wall to disappear. Early work performed on this topic by Dah Yu Cheng in the 1970′s already showed that there are two ways to accelerate these particles. One (the piston) moves the particles like an explosion. The other moves them the way a jet engine does, in a more jet or bullet-like shape that is also more efficient. The Stanford team is now trying to understand this second mode of acceleration. While there was previously a limit on how fast you could accelerate the particles until the piston tipped, this limitation does not apply to the second mode.  They’ve got particles moving at around 100 keV, which is still far short of the 100 MeV’s needed for proton accelerators, but that’s what the Stanford team is dedicated to reaching. They’ll have other challenges as well, including reducing the wide energy distribution that the particle jets tend to have.

Flavio Poehlmann, who delivered the talk in place of professor Mark Cappelli who was unable to attend, said the team expects another ten years of work before they reach their energy goal. They’re currently in the process of submitting patents before they publish any papers on the subject.