Scientists hope to find Life on Mars it by decoding Martian DNA

There are not enough genomes for Craig Venter to sequence here on Earth, so he's making plans to send a DNA sequencer to Mars.

"There will be life forms there," Venter said, with his usual confidence, at a Wired Health conference this week in New York.

If he can build a machine to find it, the next steps would be to decode its DNA, beam it back to Earth, put those genetic instructions into a cell and then boot up a Martian life form in a biosecure lab.

Assuming that there is DNA to be found on the Red Planet, the notion of equipping a future Mars rover to sequence the DNA isn't so crazy.

Venter has already sent his yacht around the globe to scoop up seawater and sequence whatever DNA it found in marine microbes.

He has also been working on technology to create small genomes from scratch and insert them into living cells to bring these organisms to life.

The difference now is that all of this technology would be applied to Mars. It's highly unlikely that any DNA-based life forms could survive on the Martian surface, so Venter's "biological teleporter" would dig under the surface for samples to sequence.

If they find anything, "it would take only 4.3 minutes to get the Martians back to Earth," he said. "Now we can rebuild the Martians in a P4 spacesuit lab."

Venter isn't the only one looking for Martian DNA. According to a report in the MIT Technology Review, so is Jonathan Rothberg, founder of the genome sequencing company Ion Torrent.

Rothberg is working with NASA-funded scientists from the Massachusetts Institute of Technology and Harvard to adapt his company's Personal Genome Machine for use on Mars, the report says.

It's part of a NASA astrobiology project known as the Search for Extra-Terrestrial Genomes, or SETG.

MIT research scientist Christopher Carr is part of a group that's "building a miniature RNA/DNA sequencer to search for life beyond Earth," according to his website.

"Top places to look include Mars, Enceladus (a moon of Saturn), and Europa (a moon of Jupiter)." Carr told Tech Review that one of the biggest challenges is shrinking Ion Torrent's 30-kilogram machine down to a mere 3 kg - light enough to fit on a Mars rover.

That's just one of the hurdles. NASA has no firm plans for a rover to succeed Curiosity, the lab-on-wheels that reached the Red Planet in August.

Even if a new rover gets the green light, there's no guarantee that a gene sequencer would get one of the coveted spots for research instruments.

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USB stick can sequence DNA in seconds

It may look like an ordinary USB memory stick, but a little gadget that can sequence DNA while plugged into your laptop could have far-reaching effects on medicine and genetic research.

The UK firm Oxford Nanopore built the device, called MinION, and claims it can sequence simple genomes – like those of some viruses and bacteria – in a matter of seconds.

More complex genomes would take longer, but MinION could also be useful for obtaining quick results in sequencing DNA from cells in a biopsy to look for cancer, for example, or to determine the genetic identity of bone fragments at an archaeological dig.

The company demonstrated today at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida, that MinION has sequenced a simple virus called Phi X, which contains 5000 genetic base pairs.

Proof of principle
This is merely a proof of principle – "Phi X was the first DNA genome to be sequenced ever," says Nick Loman, a bioinformatician at the Pallen research group at the University of Birmingham, UK, and author of the blog Pathogens: Genes and Genomes.

But it shows for the first time that this technology works, he says. "If you can sequence this genome you should be able to sequence larger genomes."

Oxford Nanopore is also building a larger device, GridION, for lab use. Both GridION and MinION operate using the same technology: DNA is added to a solution containing enzymes that bind to the end of each strand.

When a current is applied across the solution these enzymes and DNA are drawn to hundreds of wells in a membrane at the bottom of the solution, each just 10 micrometres in diameter.

Within each well is a modified version of the protein alpha hemolysin (AHL), which has a hollow tube just 10 nanometres wide at its core.

As the DNA is drawn to the pore the enzyme attaches itself to the AHL and begins to unzip the DNA, threading one strand of the double helix through the pore.

The unique electrical characteristics of each base disrupt the current flowing through each pore, enough to determine which of the four bases is passing through it. Each disruption is read by the device, like a tickertape reader.

Amborella: The First Genus of Flowers 130 Million Years ago

Amborella is a genus of rare understory shrubs or small trees endemic to the island of New Caledonia.

The genus consists of only a single species, Amborella trichopoda, and is the only member of the family Amborellaceae.

Wood of Amborella lacks the vessels characteristic of most flowering plants.

It is of great interest to plant systematists because molecular phylogenetic analyses consistently place it at or near the base of the flowering plant lineage.

That is, it represents a line of flowering plants that diverged very early on (about 130 million years ago) from all the other extant species of flowering plants.

Comparing characteristics of this basal angiosperm, other flowering plants and fossils may provide clues about how flowers first appeared—what Darwin called the "abominable mystery".

$1,000 dollar genome by 2012

By 2012, sequencing the human genome will be done in two hours and will cost $1,000, Ion Torrent’s Jonathan Rothberg said at a recent conference.

As companies race to crack the $1,000 genome, contending DNA machines in the marketplace suggest an end is near.

Ion Torrent’s DNA machine reads sequences based on chemicals and electronic technology.

The technology is called the Personal Genome Machine and it has been used to determine the source of E. coli or mutations present in the genomes of patients’ cancers.

The Ion Personal Genome Machine, which is about the size of a desktop computer, uses chemistry and semiconductor technology to produce readouts of genetic information in a couple of hours.

Christopher Mims wrote in Technology Review:

“Right now don’t have very many correlations between those 3 billion base pairs [of the human genome] and outcomes or medicines,” says Rothberg.

He predicts it will take at least 10 years of clinical experiments with full genome sequencing to get us to the point where we can begin to unlock its value.

“And it will be 20 years before we understand cancer at same level as HIV and can come up with combinations of medicine [tailored] for each individual,” says Rothberg.

NASA Research Shows DNA Building Blocks in Space

NASA-funded researchers have found more evidence meteorites can carry DNA components created in space.

Scientists have detected the building blocks of DNA in meteorites since the 1960s, but were unsure whether they were created in space or resulted from contamination by terrestrial life.

The latest research indicates certain nucleobases, the building blocks of our genetic material, reach the Earth on meteorites in greater diversity and quantity than previously thought.

The discovery adds to a growing body of evidence that the chemistry inside asteroids and comets is capable of making building blocks of essential biological molecules.

Previously, scientists found amino acids in samples of comet Wild 2 from NASA’s Stardust mission and in various carbon-rich meteorites.

Amino acids are used to make proteins, the workhorse molecules of life. Proteins are used in everything from structures such as hair to enzymes, which are the catalysts that speed up or regulate chemical reactions.

The findings will be published in the online edition of the Proceedings of the National Academy of Sciences. In the new work, scientists analyzed samples of 12 carbon-rich meteorites, nine of which were recovered from Antarctica. The team found adenine and guanine, which are components of DNA nucleobases.

Also, in two of the meteorites, the team discovered for the first time trace amounts of three molecules related to nucleobases that almost never are used in biology. These nucleobase-related molecules, called nucleobase analogs, provide the first evidence that the compounds in the meteorites came from space and not terrestrial contamination.

“You would not expect to see these nucleobase analogs if contamination from terrestrial life was the source, because they’re not used in biology,” said Michael Callahan, astrobiologist and lead author of the paper from NASA’s Goddard Space Flight Center in Greenbelt, Md.

“However, if asteroids are behaving like chemical ‘factories’ cranking out prebiotic material, you would expect them to produce many variants of nucleobases, not just the biological ones, because of the wide variety of ingredients and conditions in each asteroid.”

Additional evidence came from research to further rule out the possibility of terrestrial contamination as a source of these molecules. The team analyzed an eight-kilogram (17.6-pound) sample of ice from Antarctica, where most of the meteorites in the study were found.

The amounts of nucleobases found in the ice were much lower than in the meteorites. More significantly, none of the nucleobase analogs were detected in the ice sample. The team also analyzed a soil sample collected near one of the non-Antarctic meteorite’s fall site.

As with the ice sample, the soil sample had none of the nucleobase analogue molecules present in the meteorite.

Launched in Feb. 7, 1999, Stardust flew past an asteroid and traveled halfway to Jupiter to collect particle samples from the comet Wild 2. The spacecraft returned to Earth’s vicinity to drop off a sample-return capsule on January 15, 2006.

The research was funded by NASA’s Astrobiology Institute at the agency’s Ames Research Laboratory in Moffett Field Calif., and the Goddard Center for Astrobiology in Greenbelt, Md.; the NASA Astrobiology Exobiology and Evolutionary Biology Program and the NASA Postdoctoral Program at the agency’s Headquarters in Washington.

Additional information and images are available at: NASA DNA Study

Caltech Researchers Create the First Artificial Neural Network Out of DNA

Artificial intelligence has been the inspiration for countless books and movies, as well as the aspiration of countless scientists and engineers.

Researchers at the California Institute of Technology (Caltech) have now taken a major step toward creating artificial intelligence-not in a robot or a silicon chip, but in a test tube.

The researchers are the first to have made an artificial neural network out of DNA, creating a circuit of interacting molecules that can recall memories based on incomplete patterns, just as a brain can.

"The brain is incredible," says Lulu Qian, a Caltech senior postdoctoral scholar in bioengineering and lead author on the paper describing this work, published in the July 21 issue of the journal Nature.

"It allows us to recognize patterns of events, form memories, make decisions, and take actions. So we asked, instead of having a physically connected network of neural cells, can a soup of interacting molecules exhibit brainlike behavior?"

The answer, as the researchers show, is yes.

Consisting of four artificial neurons made from 112 distinct DNA strands, the researchers' neural network plays a mind-reading game in which it tries to identify a mystery scientist.

The researchers "trained" the neural network to "know" four scientists, whose identities are each represented by a specific, unique set of answers to four yes-or-no questions, such as whether the scientist was British.

After thinking of a scientist, a human player provides an incomplete subset of answers that partially identifies the scientist. The player then conveys those clues to the network by dropping DNA strands that correspond to those answers into the test tube.

Communicating via fluorescent signals, the network then identifies which scientist the player has in mind. Or, the network can "say" that it has insufficient information to pick just one of the scientists in its memory or that the clues contradict what it has remembered. The researchers played this game with the network using 27 different ways of answering the questions (out of 81 total combinations), and it responded correctly each time.

This DNA-based neural network demonstrates the ability to take an incomplete pattern and figure out what it might represent-one of the brain's unique features.

"What we are good at is recognizing things," says coauthor Jehoshua "Shuki" Bruck, the Gordon and Betty Moore Professor of Computation and Neural Systems and Electrical Engineering. "We can recognize things based on looking only at a subset of features." The DNA neural network does just that, albeit in a rudimentary way.

Biochemical systems with artificial intelligence-or at least some basic, decision-making capabilities-could have powerful applications in medicine, chemistry, and biological research, the researchers say.

In the future, such systems could operate within cells, helping to answer fundamental biological questions or diagnose a disease. Biochemical processes that can intelligently respond to the presence of other molecules could allow engineers to produce increasingly complex chemicals or build new kinds of structures, molecule by molecule.

Researchers identify seventh and eighth bases of DNA

For decades, scientists have known that DNA consists of four basic units -- adenine, guanine, thymine and cytosine. Those four bases have been taught in science textbooks and have formed the basis of the growing knowledge regarding how genes code for life. Yet in recent history, scientists have expanded that list from four to six.

Now, with a finding published online in the July 21, 2011, issue of the journal Science, researchers from the UNC School of Medicine have discovered the seventh and eighth bases of DNA.

These last two bases -- called 5-formylcytosine and 5 carboxylcytosine -- are actually versions of cytosine that have been modified by Tet proteins, molecular entities thought to play a role in DNA demethylation and stem cell reprogramming.

Thus, the discovery could advance stem cell research by giving a glimpse into the DNA changes -- such as the removal of chemical groups through demethylation -- that could reprogram adult cells to make them act like stem cells.

"Before we can grasp the magnitude of this discovery, we have to figure out the function of these new bases," said senior study author Yi Zhang, Ph.D., Kenan Distinguished Professor of biochemistry and biophysics at UNC and an Investigator of the Howard Hughes Medical Institute. "Because these bases represent an intermediate state in the demethylation process, they could be important for cell fate reprogramming and cancer, both of which involve DNA demethylation."

Much is known about the "fifth base," 5-methylcytosine, which arises when a chemical tag or methyl group is tacked onto a cytosine. This methylation is associated with gene silencing, as it causes the DNA's double helix to fold even tighter upon itself.

Last year, Zhang's group reported that Tet proteins can convert 5 methylC (the fifth base) to 5 hydroxymethylC (the sixth base) in the first of a four step reaction leading back to bare-boned cytosine. But try as they might, the researchers could not continue the reaction on to the seventh and eighth bases, called 5 formylC and 5 carboxyC.

The problem, they eventually found, was not that Tet wasn't taking that second and third step, it was that their experimental assay wasn't sensitive enough to detect it. Once they realized the limitations of the assay, they redesigned it and were in fact able to detect the two newest bases of DNA. The researchers then examined embryonic stem cells as well as mouse organs and found that both bases can be detected in genomic DNA.

The finding could have important implications for stem cell research, as it could provide researchers with new tools to erase previous methylation patterns to reprogram adult cells.

It could also inform cancer research, as it could give scientists the opportunity to reactivate tumor suppressor genes that had been silenced by DNA methylation.

Telomere Nobelist: Selling a 'biological age' DNA test for ageing

Elizabeth Blackburn is launching a commercial genetic test that measures DNA markers of ageing – what can we learn from it?

Your test measures telomere shortening, a marker of biological ageing. What can this tell us?
Telomeres are stretches of DNA at the ends of chromosomes that protect them against degradation. 

Checking your telomere length is a bit like weighing yourself: you get this single number which depends on a lot of factors. Telomere length gives a sense of your underlying health. We see telomere shortening in diseases of ageing - like heart disease and cancer.

What evidence is there to support health predictions based on telomere length?
In 2004, results from a study that I worked on with colleagues at the University of California, San Francisco, linked chronic stress to shortening of telomeres. 

Chronic stress is also associated with a higher risk of heart disease. Bone marrow failure is also associated with short telomeres. If a test showed you had telomere shortening, it would be a red flag suggesting you should take a look at possible risk factors.

Can people do anything to prevent telomere shortening?
It looks like you can, by changing your lifestyle. Observational studies show that exercise, nutritional supplements and reducing psychological stress can help. Chronic high stress and smoking can lead to accelerated telomere shortening.

What made you decide to help launch the company Telome Health, which is selling a test for telomere length?
There was a lot of interest from the research community and also from individuals. We had a cost-effective assay in our lab which we transferred to a company to provide as a service. We are running a study called "Know your telomeres". 

The goal is to learn more about telomere length and other markers of ageing, how best to measure these markers, how they are related to health and lifestyle, and how people respond to learning their own telomere length results. People were pounding down the doors to enrol.

Is this another step on the road to commercialised personal genetic testing?
Right now, the company only offers the tests as a part of research studies. Tests for the public, through their physician, will go on sale later in the year, costing under $200.

What exactly does the telomere test entail?
It is like a cholesterol test. We can take a measurement from blood samples, cheek swabs or saliva. Specifically, we measure the telomere length in white blood cells. Cells from the immune system act a bit like a report card, an indicator for all kinds of conditions.

Have you made any lifestyle changes based on the results of your research?
I've learned a meditation technique. I exercise as often as I can. Walking is good too.

Gene responsible for severe Osteoporosis disorder discovered

Scientists have identified a single mutated gene that causes Hajdu-Cheney syndrome, a disorder of the bones causing progressive bone loss and osteoporosis (fragile bones).

The study, published in Nature Genetics today, gives vital insight into possible causes of osteoporosis and highlights the gene as a potential target for treating the condition.

There are only 50 reported cases of Hajdu-Cheney syndrome (HCS), of which severe osteoporosis is a main feature. Osteoporosis is a condition leading to reduction in bone strength and susceptibility to fractures.

It is the most common bone disease, with one in two women and one in five men over 50 in the UK fracturing a bone because of the condition. This represents a major public health problem yet, until this study, possible genetic causes of osteoporosis were poorly understood.

The team of scientists, led by the National Institute for Health Research (NIHR) comprehensive Biomedical Research Centre (BRC) at King’s College London and Guy’s and St Thomas’, set out to investigate the genetic cause of HCS in order to detect clues to the role genes might play in triggering osteoporosis.

Using a cutting edge technique for identifying disease-causing genes, known as exome sequencing, the team were able to identify NOTCH2 as the causative gene using DNA from just three unrelated HCS patients.

The team then confirmed their findings in an additional 12 affected families, 11 of whom had an alteration in the identical portion of the same gene.

Professor Richard Trembath, Head of King’s College London’s Division of Genetics and Molecular Medicine and Medicine Director of the NIHR BRC, said: “Up until now, we knew very little about the genetic mechanisms of severe bone disease but these findings add to our understanding of the uncommon condition of HCS and provide an important basis to develop future studies in more common forms of osteoporosis, including the development of potential new therapies.”

Zeros to heroes: The tragic fate of a genetic pioneer

WHEN Paul Kammerer shot himself on an Austrian hillside in 1926, he seemed destined to be remembered only as a scientific fraudster who had faked his results to prove a controversial theory. In fact, he might well have glimpsed epigenetics, influential changes in gene activity that do not involve alterations to the DNA sequence.

Kammerer was infamous for his experiments on the midwife toad, Alytes obstetricans (pictured above), an unusual amphibian which mates and raises its eggs on dry land. By keeping toads in unusually hot, dry conditions, he drove them to breed and raise their eggs in water.

Only a few eggs hatched, but the offspring of these aquatic unions also bred in water. Kammerer claimed this as proof of Lamarckian inheritance - the idea (now known to be wrong) that traits acquired during an individual's lifetime can be passed on to its offspring.

In August 1926, Kammerer was condemned as a fraud in the pages of Nature (vol 118, p 518). He killed himself six weeks later. The sad story was largely forgotten until 1971, when Arthur Koestler published a book claiming that the biologist's experiments may have been tampered with by a Nazi sympathiser. Kammerer was a socialist who was planning to build an institute in the Soviet Union, which would have made him a target of Vienna's burgeoning Nazi movement.

Then, last year, biologist Alex Vargas of the University of Chile in Santiago re-examined Kammerer's work. He was not a fraud, Vargas suggests, but had inadvertently discovered epigenetics (Journal of Experimental Zoology B, vol 312, p 667). "Kammerer had the right approach," says Vargas, who hopes that the toad experiments will one day be repeated.

We now know that the patterns of inheritance of the kind Kammerer claimed to have seen can be due to epigenetics. This process is central to molecular biology, and numerous drugs based on it are in development. It would have been discovered regardless of Kammerer - but perhaps we would not still be waiting for those drugs if he had been taken seriously.