Tag: dna

Christians block US DNA work

godThe US is falling behind the rest of the world when it comes to DNA research because fundementalist Christians believe that Jesus would not want them doing that sort of thing.

The problem is that Congress has been listening to Christian lobby groups and banned human germline modification mostly on the basis that God saw his creation was good and therefore humans should not tinker.

However a paper published today in Science by Harvard law and bioethics professor I. Glenn Cohen and leading biologist Eli Adashi of Brown University say that without a course correction, “the United States is ceding its leadership in this arena to other nations”.

True, they might be godless heathens who believe in things like evolution and global warming but there is a possibily that they will sort out the world’s health crisis while the US is having to deal with biblical plagues.

Germline gene modification is the act of making heritable changes to early stage human embryos or sex cells that can be passed down to the next generation, and it will be banned in the US. This is different from somatic gene editing, which is editing cells of humans that have already been born.

The ban, added by the House of Representatives as a rider to the fiscal year 2016 budget, could have far-reaching implications if it continues to be annually renewed, according to the authors.

What will be “amusing” is when Congressmen start telling American parents that their precious little snowflakes will not be allowed treatments for life threatening conditions which are available overseas. It is unlikely that such parents will see it as a wonderful thing that their child is going to get to see Jesus before his classmates.

James Hughes, executive director of the Institute for Ethics and Emerging Technologies added that boffins were on the cusp of being able to do [gene editing] safely, and the prospect of a telling a parent that they won’t have access to these therapies is morally untenable. Up to 4,000 children a year are diagnosed with some form of mitochondrial disorder

In the UK, which some in the field see as being more liberal than the US in gene editing legislation, MRT was approved by both houses of Parliament last year, following a robust period of investigation, public debate, and multiple rounds of parliamentary review.

Congress began looking into gene editing last year with hearings led by House Science, Space and Technology committee Chair Lamar Smith (R-TX), who believes that the US should proceed with severe caution when it comes to genetically altering embryos with heritable changes, even if it means putting off curing diseases.



DNA could be your new hard-drive

DNADNA could be used to store digital information and preserve essential knowledge for thousands of years.

Scientists exploring the archiving DNA conducted a test in which error-free data was downloaded after the equivalent of 2,000 years.

The next challenge is to find a way of searching for information encoded in strands of DNA floating in a drop of liquid.

Lead researcher Dr Robert Grass, from the Swiss Federal Institute of Technology (ETH), said: “If you go back to medieval times in Europe, we had monks writing in books to transmit information for the future, and some of those books still exist. Now, we save information on hard drives, which wear out in a few decades.”

DNA has a “language” not unlike the binary code used in computers, said Dr Grass. While a hard drive uses zeros and ones to represent data, the DNA code is written in sequences of four chemical nucleotides, known as A,C,T and G.

DNA can pack more information into a smaller space, and also has the advantage of durability.

In theory, a fraction of an ounce of DNA could store more than 300,000 terabytes of data, said Dr Grass. And archaeological finds had shown that DNA dating back hundreds of thousands of years can still be sequenced today.

Grass’s team managed to encode DNA with 83 kilobytes of text from the 1921 Swiss Federal Charter, and a copy of Archimedes’ famous work The Method dating from the 10th century.

The DNA was encapsulated in silica spheres and warmed to nearly 71C for a week – the equivalent of keeping it for 2,000 years at 10C. When decoded, it was found to be error-free.

The scientists are now working on ways to label specific pieces of information on DNA strands to make them searchable.

DNA storage could be used to preserve troves of historical texts, government documents or entire archives of private companies – all in a single drop.

Currently, though, the technology is pricy. Encoding a few megabytes of data in DNA would set you back “thousands of dollars” and personal drives are a long way off.

There’s power in touch

Fingers crossedScientists have created a biodegradable nanogenerator fashioned out of DNA that will take energy from everyday movements and turn it into electricity.

According to the American Chemical Society a number of scientists all over the world are building prototypes of nanogenerators that take movement like walking and covert it into power.

The dream is that one day we won’t have to run for the electricity socket but our mobile devices will be powered by the things that we do, whether energetic or not.

The scientists build their nanogenerator using a flexible biocompatible polymer film using polyvinylidene fluoride. They improved the material’s energy harvesting functions by adding DNA.

DNA, apparently, has good electrical properties and is both biodegradable and biocompatible, just by tapping their were able to light up 22 to 55 LEDs, as this video shows.

FDA guns for Google boss's missus

The outfit which borught the psychological genius Wilhelm Reich to an early grave, is now gunning for the estranged wife of Google boss Sergey Brin.

According to Bloomberg, the Food and Drug Administration, which shut down Reich just in case he put big pharm out of business by coming up with a cure for cancer, has ordered 23andMe, the Google-backed DNA analysis company co-founded by Anne Wojcicki to stop selling its products.

Wojcicki was given the company which makes a Saliva Collection Kit and Personal Genome Service, which tells users whether they carry a disease, are at risk of a disease and would respond to a drug.

Most of the uses fall into the category of a medical device and require Food and Drug Administration approval, the agency told the company.

The Food and Drug Administration has to decide if the product will cause any harm to patents, or Big Pharm generally. After all if people know what is making them sick, Big Pharm can not make a lot of money a range of expensive quack cures.

Wojcicki, who recently separated from her husband, Google co-founder Sergey Brin, started 23andMe about six years ago to help people assess their risk of cancer, heart disease and other medical conditions. Brin used the saliva kit and discovered that he had a gene that makes him susceptible to Parkinson’s.

However, the FDA is concerned about the public health consequences of inaccurate results from the PGS device. It just wants to make sure that the tests work.

“Even after these many interactions with 23andMe, we still do not have any assurance that the firm has analytically or clinically validated the PGS for its intended uses, which have expanded from the uses that the firm identified in its submissions,” the FDA wrote.

It was concerned that 23andMe plans to expand the device’s use without obtaining FDA approval.

A spokeswoman for 23andMe, Catherine Afarian, said in an e-mail that the company’s relationship with the FDA is extremely important and it will attempt to address its concerns.

In this case, the sticking point appears to be UnitedHealth Group, the largest publicly traded U.S. health insurer, which raised concern in a March 2012 report about the accuracy and affordability of the tests.

It thinks that while 23andMe might be on the right path to provide such types of genetic tests within the next 10 years there was a need to identify which work best. 

Intel wants to examine your DNA

Fashion bag maker Intel is sprucing up supercomputer design so that some top boffins can have half a chance to understand DNA codes.

Chipzilla has signed a deal with imec and five Flemish universities to set up the ExaScience Life Lab on the imec campus in Leuven.

The objective of the collaboration is to come up with new supercomputer ideas that will generate breakthroughs in life sciences and biotechnology.

The supercomputers will be designed to accelerate the processing of entire genome sequences. At the moment an analysis takes approximately 48 hours and the thought is that computer design is falling behind. There will also be an expected explosion of genome data becoming available in the coming years.

According to Intel, the lab will examine the use of computer simulations in the life sciences. Testing hypotheses through computer simulation both cells and tissues instead of through wet-lab testing saves considerable amounts of time and cost associated to lab tests

Intel lab manager Luc Provoost said that Chipzilla has an extensive network of research labs in Europe. Once operational, the ExaScience Life Lab will be our European centre of excellence for high performance computing in the life sciences..

Later the plan is to collaborate with Janssen Pharmaceuticals to build even more powerful DNA supercomputers. 

Researchers build bio-computer

Israeli scientists have built a computer using only biomolecules such as DNA and enzymes.

Researchers at the Technion-Israel Institute of Technology have created an advanced biological transducer.

The machine can manipulate genetic codes, and use the output as new input for subsequent computations. The idea is that it will be used in gene therapy and cloning.

Biomolecular computing devices could be crucial to developing computers that can interact directly with biological systems and even living organisms.

We would have thought that the downside was the lack of a decent QWERTY keyboard but the researchers are quite excited by the fact that no interface is required.

According to  Science Daily, all components of molecular computers, including hardware, software, input and output, are molecules that interact in solution along a cascade of programmable chemical events.

Ehud Keinan of the Technion Schulich Faculty of Chemistry said that the early results show a novel, synthetic designed computing machine that computes iteratively and produces biologically relevant results,

In addition to enhanced computation power, this DNA-based transducer offers multiple benefits, including the ability to read and transform genetic information, miniaturisation to the molecular scale, and the aptitude to produce computational results that interact directly with living organisms.

This particular transducer is designed to be used on genetic material to evaluate and detect specific sequences, and to alter and algorithmically process genetic code. Similar devices could be applied for other computational problems.

It is probably only a matter of time before you can increase your computer power by sneezing on your PC. 

Scientists prove learning hurts your brain

A team of scientists based at UCSF has established a link between learning and brain damage. Researchers found that brain activity could lead to DNA damage within brain cells, and although the damage is repaired quickly, it might explain the mechanism behind some neurological diseases. So thanks a lot, mum, I told you nothing good would come of law school.

The DNA damage is negligible and it is quickly repaired, but in theory at least it is possible that too much brain activity could result in some physical damage to the nerve cells in your brain. Alcohol and drugs tend to kill brain cells faster than watching a political debate, so the learned among us are safe. Probably.

The researchers used genetically modified mice that were tailored made to mimic some mutations associated with early onset Alzheimer’s disease. They found indications of brain damage went up when the brains of the mice were active, when they were given a new environment to explore. The control group of mice also showed signs of DNA damage, but at somewhat lower levels.

The scientists then tried to figure out whether the damage was caused solely be neural activity, by shining a bright light into the mice while they were anesthetised. That also worked and it seems the DNA damage is inflicted by neural activity. Then they tried using a range of inhibitors and found that the damage is caused by a single neural signalling molecule – glutamate.

Fortunately the researchers found that the damage usually repairs within a single day. However, if you want to stay on the safe side, we recommend watching a few extra hours of reality TV or joining the Tea Party. 

Retail banks “will be dead in 15 years”

An analyst at the White Bull conference here in Barcelona said that in his view, retail banks will disappear over the next 15 years.

The reason for that is that quite a few of the top 100 multinationals have financial services arms where they can make value add on transactions.

Ralph Silva, of SRN, gave an example where he was going to buy a BMW car and before he knew where he was, BMW was selling him home insurance, car insurance and even pet insurance too.

BMW’s financial services arm knew the name of his dog, Jazz because he had visited the car showroom earlier with the mutt, and a salesman asked the name of his pet. That eliminated the need for him to go anywhere near a bank. Dozens of other companies are also plotting similar plans.

Silva also predicted that an IBM funded research programme was making headway with a CPU based not on CMOS, but on elements of DNA.  There are working chips already in the IBM labs, he said.

He also said that in future, every child will be fitted with two embedded chips which will contain healthcare information and other ID. The identity of the individual will be verified by a person putting her or his hand – with one chip in it, to his or her arm, with another chip fitted there.

Other future innovations include a single cable sending multiple signals, eliminating the need for miles and miles of cables in aircraft.

Nvidia GPUs becomes DNA star

Nvidia GPUs have sped up the number crunching at the world’s largest genome sequencing centre.

Once, the BGI in China needed four days to analyse data describing a human genome. Now it needs just six hours.

That is thanks to the fact that it upgraded the servers to use Nvidia GPUs instead of conventional chips.

Over recent years, the cost of sequencing genomes by mapping out an organism’s entire genetic code has dropped about five-fold each year. But according to Gregg TeHennepe, a senior manager and research liaison in the IT department at The Jackson Laboratory in Bar Harbor, Maine the GPU breakthrough at BGI is shrinking the gap.

This is good news for the medical world. Biological exploration, the study of diseases, and efforts to tailor drugs and other treatments based on an individual’s genetic makeup could be sped up.

According to TeHennepe, the feat BGI and Nvidia pulled off was porting key genome analysis tools to the GPU architecture, an accomplishment that the open source community and others have been working toward.

TeHennepe’s Jackson Laboratory has been conducting high-throughput sequencing for more than a year, and it has been looking into GPU computing to inprove the lab’s ability to look at the data.

The Chinese lab and Nvidia’s accomplishment is an important step forward in the effort to apply the promise of GPU computing to the challenge of scaling the mountain of high-throughput sequencing data, he said.

If BGI had used traditional CPUs, it would have needed 15 times more computer nodes, with an equivalent increase in power and air conditioning.

Another advantage of BGI’s GPU initiative is the likelihood that other institutions will be able to use BGI’s GPU-enabled applications. 

Government does double u-turn on DNA database

The government seems to have performed what looks to be a double U-Turn when it comes to the DNA database.

Privacy groups this morning kicked off about what looked to be the first backtrack when it came to the controversial database. Home Office minister James Brokenshire wrote a letter to MPs confirming  that the DNA profiles of those arrested, but never charged or found guilty of a crime would be retained by forensic science laboratories in an anonymised form.  This was a U-turn from previous promises that these records would be completely deleted.

It is thought that under this new rule, the DNA of more than one million innocent people would not be wiped from police records.

According to privacy group Big Brother Watch, the admission broke the Coalition commitment to delete all innocent profiles, apart from those accused of violent or sex crimes, from police databases.

Maria Fort, research director at the organisation, told TechEye: “This decision represents a shameful about-face from statements made by both the Prime Minister and his deputy.

“Despite promising that DNA samples would be destroyed, forensic science laboratories will still be able to retain the DNA profile record.”

She said that this meant it would still be possible to make identifications based on the barcode associated with each profile.

 “The Government claims that in some cases these DNA profiles cannot be deleted without also affecting those of convicted offenders.

 “This weak reasoning shows a distinct lack of concern for Coalition promises and for the innocent despite repeated words by the Prime Minister last week that this country maintains the value of ‘innocent until proven guilty’.”

Mr Brokenshire said he had won agreement from the information watchdog that the DNA profiles could be retained by forensic science laboratories.

However, it looks like the government has now performed another U-turn. When we contacted the Home Office to see what it had to say, we were told that profiles would be completely deleted from the national DNA database.

A spokesman said: “Our position has not changed at all. We will retain the DNA of the guilty, not the innocent.

“That means DNA records of the innocent will come off the database and physical samples will be deleted.”

However, Big Brother Watch isn’t convinced, with Ms Fort claiming that the latest statement from the Home Office is “in fact a backtrack.”

She told TechEye: “ Despite deleting the actual DNA samples of the innocent the electronic profiles are retained, merely anonymising the samples, not destroying or deleting them.  This is a technicality allowing the government to use loose language to claim they are not breaking any promises.  It is also in direct conflict with statements made before and after the election by coalition Party Leaders.”

The Information Commissioner’s Office said: ““The Information Commissioner welcomed the more proportionate approach to the retention of unconvicted individuals’ biometric data proposed in the Protection of Freedoms Bill as introduced to Parliament in February. The Information Commissioner’s evidence on the Protection of Freedoms Bill makes clear that the deletion of all DNA profile should be the norm and retention in an anonymised form the exception. In these circumstances there must be no practical way of linking back to an individual. Anything that falls short of this in practice would be unacceptable.”

We went back to the Home Office to see what it had to say but at the time of going to press it had not responded. The