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Cheap (tens of dollars) genetic lab on a chip systems could help with pandemic control

Cross posted from Next big future

Since a journal article was submitted to the Royal Society of Chemistry, the U of Alberta researchers have already made the processor and unit smaller and have brought the cost of building a portable unit for genetic testing down to about $100 Cdn. In addition, these systems are also portable and even faster (they take only minutes). Backhouse, Elliott and McMullin are now demonstrating prototypes of a USB key-like system that may ultimately be as inexpensive as standard USB memory keys that are in common use – only tens of dollars. It can help with pandemic control and detecting and control tainted water supplies.

This development fits in with my belief that there should be widespread inexpensive blood, biomarker and genetic tests to help catch disease early and to develop an understanding of biomarker changes to track disease and aging development. We can also create adaptive clinical trials to shorten the development and approval process for new medical procedures


The device is now much smaller than size of a shoe-box (USB stick size) with the optics and supporting electronics filling the space around the microchip

Canadian scientists have succeeded in building the least expensive portable device for rapid genetic testing ever made. The cost of carrying out a single genetic test currently varies from hundreds to thousands of pounds, and the wait for results can take weeks. Now a group led by Christopher Backhouse, University of Alberta, Edmonton, have developed a reusable microchip-based system that costs just 500 (pounds) to build, is small enough to be portable, and can be used for point-of-care medical testing.

To keep costs down, ‘instead of using the very expensive confocal optics systems currently used in these types of devices we used a consumer-grade digital camera’, Backhouse explained.

The device can be adapted for used in many different genetic tests. ‘By making small changes to the system you could test for a person’s predisposition to cancer, carry out pharmacogenetic tests for adverse drug reactions or even test for pathogens in a water supply,’ said Backhouse.

The heart of the unit, the ‘chip,’ looks like a standard microscope slide etched with fine silver and gold lines. That microfabricated chip applies nano-biotechnologies within tiny volumes, sometimes working with only a few molecules of sample. Because of this highly integrated chip (containing microfluidics and microscale devices), the remainder of the system is inexpensive ($1,000) and fast.

There are many possible uses for such a portable genetic testing unit:

Backhouse notes that adverse drug reactions are a major problem in health care. By running a quick genetic test on a cancer patient, for example, doctors might pinpoint the type of cancer and determine the best drug and correct dosage for the individual.

Or health-care professionals can easily look for the genetic signature for a virus or E. coli – also making it useful for testing water quality.

“From a public health point of view, it would be wonderful during an epidemic to be able to do a quick test on a patient when they walk into an emergency room and be able to say, ‘you have SARS, you need to go into that (isolation) room immediately.’ ”

A family doctor might determine a person’s genetic predisposition to an illness during an office visit and advise the patient on preventative lifestyle changes.

FURTHER READING
Microfabrication technologies research at the University of Alberta

Rapid genetic analysis

In collaboration with the Glerum Lab we have been developing microchip based implementations of genetic amplification (PCR — the polymerase chain reaction) and capillary electrophoresis (CE) that are extremely fast.

- Cancer diagnostics

- Cell manipulation on a chip

- On chip PCR (polymerase chain reaction)

- Single cell PCR

- DNA Sequencing

On the brink of Synthetic Life: DNA synthesis has increased twenty times to full bacteria size

Reposted from Next Big Future which was advancednano.

A 582,970 base pair sequence of DNA has been synthesized.

It’s the first time a genome the size of a bacterium has chemically been synthesized that’s about 20 times longer than [any DNA molecule] synthesized before.

This is a huge increase in capability. It has broad implications for DNA nanotechnology and synthetic biology.

It is particularly relevant for the lifeboat foundation bioshield project

This means that the Venter Institute is on the brink of sythesizing a new bacterial life.

The process to synthesize and assemble the synthetic version of the M. genitalium chromosome

began first by resequencing the native M. genitalium genome to ensure that the team was starting with an error free sequence. After obtaining this correct version of the native genome, the team specially designed fragments of chemically synthesized DNA to build 101 “cassettes” of 5,000 to 7,000 base pairs of genetic code. As a measure to differentiate the synthetic genome versus the native genome, the team created “watermarks” in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity. To obtain the cassettes the JCVI team worked primarily with the DNA synthesis company Blue Heron Technology, as well as DNA 2.0 and GENEART.

From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation.

The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome.

At this stage the team could not obtain half genome clones in E. coli, so the team experimented with yeast and found that it tolerated the large foreign DNA molecules well, and that they were able to assemble the fragments together by homologous recombination. This process was used to assemble the last cassettes, from 1/4 genome fragments to the final genome of more than 580,000 base pairs. The final chromosome was again sequenced in order to validate the complete accurate chemical structure.

The synthetic M. genitalium has a molecular weight of 360,110 kilodaltons (kDa). Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages.

Is 2007 TU24 A Wake Up Call?

On January 29th, 2008, Near Earth Object 2007 TU24 will intersect Earth’s orbit at the startling proximity of only 0.0038AU — or 1.4 lunar distances from our planet. According to the resources I reviewed, this NEO represents the closest known approach to Earth until 2027, assuming no more surprises like the 2007 TU24, which was discovered on October 11th, 2007.

That an asteroid won’t strike is an assumption we can’t afford to make. 2007 TU24 will not impact the planet but may pass through a portion of Earth’s magnetosphere. We can’t predict the repercussions of this transit with any certainty at this time. However, the possibilities range from no effect to potentially catastrophic changes to weather, tectonic plate movement, the oceans, and more.

Some might say that we do not need to be concerned — that this kind of near miss (and let’s be frank here — in the vastness of even our solar system, 1.4 lunar distances from Earth is a near miss) is a freak occurrence. Don’t be so sure. One day later — that’s right, on January 30th, it was thought possible — one might even say reasonably likely — that another asteroid would strike our second nearest celestial neighbor, Mars.

Recent updates based upon more detailed information about the path of asteroid 2007 WD5 have concluded that the odds of an impact occurring have now dropped to one in ten thousand, making an impact exceptionally unlikely. However, our ability to identify objects less than 100 meters across is insufficient to provide us with enough time to do anything aside from evacuating the regions likely to be impacted by a collision with an incoming NEO.

More than one expert has stated that NEOs represent one of the most pressing potential mega-disasters threatening human — or even all — life on Earth. Yet, solving this problem is within the capabilities of our technology. Between better early detection and developing a meaningful defensive strategy, protecting humanity from this threat is possible. All we need is the funding and the mandate from the people to secure the required resources.

Cell phone sensors detect radiation to thwart nuclear terrorism

PhysOrg.com is reporting that researchers at Purdue University are working to develop a system that would use a network of cell phones to track radiation in an effort to prevent terrorist attacks with dirty bombs or nuclear weapons. Tiny solid-state radiation sensors are already commercially available and the additional circuitry would not add significant bulk to portable electronic products.

The researchers tested the system and demonstrated that it is capable of detecting a weak radiation source 15 feet from the sensors. A fully developed system could cover a nation with millions of cell phones equipped with radiation sensors able to detect even light residues of radioactive material. Because cell phones already contain global positioning locators, the network of phones would serve as a large scale tracking system that would require no intervention from individual users.

Poll: Top 10 Existential Risks

How would you allocate a hypothetical $100 million budget for a Lifeboat Foundation study of the top 10 existential risks… risks that are both global and terminal?

$?? Biological viruses…
$?? Environmental global warming…
$?? Extraterrestrial invasion…
$?? Governments abusive power…
$?? Nanotechnology gray goo…
$?? Nuclear holocaust…
$?? Simulation Shut Down if we live in one…
$?? Space Threats asteroids…
$?? Superintelligent AI un-friendly…
$?? Other
$100 million total

To vote, please reply below.

Results after 80 votes updated: Jan 13, 2008 11 AM EST

$23.9 Biological viruses…
$17.9 Space Threats asteroids…
$13.9 Governments abusive power…
$10.2 Nuclear holocaust…
$8.8 Nanotechnology gray goo…
$8.6 Other
$8.5 Superintelligent AI un-friendly…
$7.2 Environmental global warming…
$0.7 Extraterrestrial invasion…
$0.4 Simulation Shut Down if we live in one…
$100 million total

Planning for First Lifeboat Foundation Conference Underway

Planning for the first Lifeboat Foundation conference has begun. This FREE conference will be held in Second Life to keep costs down and ensure that you won’t have to worry about missing work or school.

While an exact date has not yet been set, we intend to offer you an exciting line up of speakers on a day in the late spring or early summer of 2008.

Several members of Lifeboat’s Scientific Advisory Board (SAB) have already expressed interest in presenting. However, potential speakers need not be Lifeboat Foundation members.

If you’re interested in speaking, want to help, or you just want to learn more, please contact me at [email protected].

Help Develop the NanoShield

What’s the NanoShield you ask? It’s a long-term scientific research project aimed at creating a nanotechnoloigical immune system. You can learn more about it here.

Facebook users — please come join the cause and help fund the Lifeboat Foundation’s NanoShield project.

Not a Facebook user? No worries. By joining the Lifeboat Foundation and making even a small donation you can have a hugely positive impact on humanity’s future well being.

So why not join us?

Helphookup.com internet empowered volunteers against disasters

The inspiration of Help Hookup is actually a comic book called Global Frequency by Warren Ellis. My brother, Alvin Wang, took the idea to startup weekend and they launched the idea this past weekend for hooking up volunteers. It is similar to the concepts of David Brin’s “empowered citizens” and Glenn Reynolds “an army of Davids”. The concepts are compatible with the ideas and causes of the Lifeboat foundation.

Global Frequency was a network of 1,001 people that handled the jobs that the governments did not have the will to handle. I thought that it was a great idea and it would be more powerful with 1,000,001 people or 100,000,001 people. We would have to leave out the killing that was in the comic.

Typhoons, earthquakes, and improperly funded education could all be handled. If there is a disaster, doctors could volunteer. Airlines could provide tickets. Corporations could provide supples. Trucking companies could provide transportation. Etc. State a need, meet the need. No overhead. No waste.

The main site is here it is a way for volunteers to hookup

The helphookup blog is tracking the progress.

Yellowstone Caldera Rising

The Yellowstone caldera has moved upwards nine inches over the last three years, a record rate since geologists first began taking measurements in the 1920s. This is the result of a Los Angeles-sized blob of magma that recently rose up into the chamber only six miles below the surface. The Yellowstone caldera is an ancient supervolcano. Last time it erupted, 642,000 years ago, it ejected 1,000 cubic kilometers of magma into the air. If this happened in today’s world, it would kill millions and cover most of the United States in a layer of ash at least a centimeter thick. The lighter ash would rise up into the atmosphere, initiating a volcanic winter and ruining crops worldwide.

Calderas rise and fall worldwide all the time without erupting. But the activity in Yellowstone is still concerning. Like a reckless teenager in a sports car, it seems as if our civilization laughs off the possibility of its own demise like a complete joke. Yet the right sort of event, and we could be knocked flat. Instead of waiting for a disaster to happen, we should prepare in advance to minimize its probability.

I would like to see scientists do a study on the feasibility of using nuclear weapons to initiate a supervolcano eruption. If it looks feasible, then park security in Yellowstone should be increased.

One shot Gene therapy protection from radiation

University of Pittsburgh researchers injected a therapy previously found to protect cells from radiation damage into the bone marrow of mice, then dosed them with some 950 roentgens of radiation — nearly twice the amount needed to kill a person in just five hours. Nine in 10 of the therapy-receiving mice survived, compared to 58 percent of the control group.

Between 30 and 330 days, there were no differences in survival rates between experiment and control group mice, indicating that systemic MnSOD-PL treatment was not harmful to survival.

The researchers will need to verify whether this treatment would work in humans.

This is part of the early development in the use of genetic modification to increase the biological defences (shields) of people against nuclear, biological and chemical threats. We may not be able to prevent all attacks, so we should improve our toughness and survivability. We should still try to stop the attacks and create the conditions for less attacks.

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