Enrique Ibarra-Laclette, Claudia Anahí Pérez-Torres and Paulina Lozano-Sotomayor

The humped bladderwort plant (shown here in a scanning electron micrograph) is a voracious carnivore, with its tiny bladders leveraging vacuum pressure to suck in bitty prey at great speed.

One person's trash may be another person's treasure, but sometimes, trash is just trash.

So-called junk DNA, the vast majority of the genome that doesn't code for proteins, really isn't needed for a healthy organism, according to new research.

"At least for a plant, junk DNA really is just junk — it's not required," said study co-author Victor Albert, a molecular evolutionary biologist at the University of Buffalo in New York.

While the findings, published Sunday in the journal Nature, concern a carnivorous plant, they could have implications for the human genome as well. Genes make up only 2 percent of the human genome, and researchers have argued in recent years that the remaining 98 percent may play some hidden, useful role. [Image Gallery: Amazing Carnivorous Plants]

Trash or treasure
For decades, scientists have known that the vast majority of the genome is made up of DNA that doesn't seem to contain genes or turn genes on or off. The thinking went that most of this vast terrain of dark DNA consisted of genetic parasites that copy segments of DNA and paste themselves repeatedly in the genome, or that it consists of the fossils of once useful genes that have now been switched off. Researchers coined the term junk DNA to refer to these areas.

"Nobody's really known what junk DNA does or doesn't do," Albert told LiveScience.

But in recent years, researchers have debated whether "junk" might be a misnomer and if this mysterious DNA might play some role. A massive project called ENCODE, which aimed to uncover the role of the 3.3 billion base pairs, or letters of DNA, in the human genome that don't code for proteins, found that in test tubes, about 80 percent of the genome seemed to have some biological activity, such as affecting whether genes turn on. Whether that translated to any useful or necessary function for humans, however, wasn't resolved.

Lean genome
Albert and his colleagues sequenced the genome of the carnivorous bladderwort plant, Utricularia gibba, which lives in wet soil or fresh water throughout the world and sucks swimming microorganisms into its tiny, 1-milimeter-long bladders.

Enrique Ibarra-Laclette and Claudia Anahí Pérez-Torres

The genome of the carnivorous bladderwort plant (shown here in a light micrograph) is just 3 percent "junk DNA," suggesting such noncoding DNA is not crucial for complex life.

The genome had just 80 million base pairs. Compared with most other plant species, that genome was positively tiny, Albert said. The lily genome, for instance, can have 40 billion base pairs.

Yet the bladderwort had about 28,500 genes, not much different from plants of similar type and complexity.

The difference was in the junk: The bladderwort plant seemed to have stripped out a vast amount of noncoding DNA. Yet the plant did just fine without that material.

In fact, through a genetic quirk the bladderwort had its entire genome duplicated — meaning the plant got two full copies of the genome — three separate times since it diverged from the tomato. Yet the carnivorous plant somehow retained its tiny genome.

Unnecessary bulk
The findings suggest junk DNA really isn't needed for healthy plants — and that may also hold for other organisms, such as humans.

But it's still a mystery why some organisms have genomes bloated with junk while other genomes are studies in minimalism.

One possibility is that there was some evolutionary pressure to strip the genome of extra material. But that's unlikely given that similar plants with huge genomes don't seem to fare badly, Albert said.

It's more plausible that, by chance, the bladderwort plant has biological processes that favor stripping out extraneous DNA over adding it in, Albert said.

Follow Tia Ghose on Twitter @tiaghose. Follow LiveScience @livescience, Facebook & Google+. Original article on LiveScience.com.

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Aquamarine Fukushima

An African coelacanth, photographed using a Remotely Operated Vehicle off the coast of Tanga, Tanzania.

The genome of the coelacanth, an ancient-looking lobed-finned fish, has been sequenced and is already providing insight to the evolutionary changes that allowed the first four-limbed animals, called tetrapods, to crawl out of the water and on to land.

The sequence and preliminary analysis, reported Thursday in the journal Nature by a team spanning 40 research institutions and 12 countries, is a "massive piece of work," Xiaobo Xu, a paleontologist at Kean University who was not involved in the effort, told NBC News in an email.

"The paper really provides rare and valuable genomic data for offering heavy-weight opinions on issues bearing on the fish (to) tetrapod transition," he said.

It also settles a debate that has long raged amongst evolutionary biologists: what fish is the closest relative of tetrapods: the coelacanth or the equally odd-looking lobed-finned lungfish. The winner, according to analysis of the newly-published genome, is the lungfish.

"We think we have definitively shown it now," Jessica Alföldi, a research scientist at the Broad Institute of MIT and Harvard and co-first author of the paper, told NBC News. "They are very close, which is why it took so much data to figure it out."

Slow evolving genes
Scientists thought coelacanths went extinct about 70 million years ago, during the Late Cretaceous period. That changed when a fish trawler off the South African coast delivered a fresh-caught coelacanth to a local natural history museum in 1938, proving that the fish are alive and well.

The coelacanths' odd, ancient-looking looks raised eyebrows and earned it the nickname "living fossil" — much to the chagrin of evolutionary biologists, noted Alföldi. ("It makes people think there was no evolution," she explained.)

Analysis of the coelacanth genome reveals that the ancient fish is indeed evolving just about as quickly as all vertebrates in every aspect except one: its genes, the stretches of protein that code for specific functions.

Other aspects, such as the amount of transposable elements — so-called "junk DNA" — that jump around the genome, is about the same as other species, a sign of evolution. In addition, big chunks of DNA are constantly being rearranged. 

"But if we look at the proteins and say how much have these proteins changed in the last 400 million years, they have changed more in us than in the coelacanths, and they have changed a lot more in pretty much every other vertebrate species that we looked at," Alföldi said.

Why? 

One speculation is that coelacanths haven't needed to evolve, Alföldi said. They live in deep sea caves and appear to have few predators or competitors for food.

Fin to limb
Comparisons of the coelacanth genome with other vertebrates allows researchers to see what genes were lost and regulatory elements gained as lobed-finned fish crawled out of the sea and on to land. 

Some of the preliminary findings are expected, such as a suite of changes to regions of the genome that control limb development, for example. 

"This is consistent with the hypothesis that the autopod (the hand and digits) of land-living vertebrates is a modification of features already present in lobe-finned fishes, rather than something that arose entirely de novo," Matt Friedman, a paleobiologist at Oxford University, said in an email to NBC News.

Others, however, were unexpected, though "end up making total sense once you think about it," Alföldi said.

For example, genes related to smell exhibit a wide range of changes as vertebrates came on to land, which make sense given that smelling underwater is different than on land, she noted. Other changes are seen in sections of the genome that regulate immunity and the way fish and land animals poop.

For Friedman, who was not involved with the team, the findings are in line with decades of paleontological and anatomical studies of the coelacanths and other lobe-finned fish.

"Apart from specific genetic details — which are of course new — most of what is here seems to corroborate our current ideas about evolutionary changes associated with the origin of terrestriality," he said.

The specific genetic details will allow members of the research team and the broader scientific community to better understand what Yu called "the unique genomic features that shed light on the shared evolutionary past of lobe-finned fish and tetrapods."

John Roach is a contributing writer to NBC News. To learn more about him, visit his website. 

By Tanya Lewis
LiveScience

The transistor revolutionized electronics and computing. Now, researchers have made a biological transistor from DNA that could be used to create living computers.

A transistor is a device that controls the flow of electrons in an electrical circuit, which acts as an on-off switch. Similarly, the biological transistor— termed a transcriptor — controls the flow of an enzyme as it moves along a strand of DNA (deoxyribonucleic acid). These cellular building blocks could be used to do anything from monitoring their environment to turning processes on and off in the cells. The findings were reported Thursday in the journal Science.

"Transcriptors are the key component behind amplifying genetic logic," lead author Jerome Bonnet, a bioengineer at Stanford University, said in a statement. On their own, these devices do not represent a computer, but they allow for logical operations, such as "if this-then that" commands, one of three basic functions of computers (the other two being storing and transmitting information).

To make the transcriptors, the researchers took a group of natural proteins, the workhorses of cells, and used them to control how the enzyme known as RNA polymerase zipped along a DNA molecule. The team used these transcriptors to create the mathematical operators that perform computations using Boolean logic.

1s and 0s
Boolean logic, named for the 19th-century mathematician George Boole, refers to a branch of math in which variables can have a true or false value (a 1 or a 0). In a Boolean circuit, the logic gates are like traffic conductors, deciding which of these values gets transmitted. [Album: The World's Most Beautiful Equations]

For example, the "AND" gate takes in two values as input, and only outputs 1 (a true value) if both inputs are 1. An "OR" gate, by contrast, outputs a 1 if either of its inputs is 1. Combining these simple gates in different ways gives rise to even the most complex forms of computing.

The scientists created biological versions of these logic gates, by carefully calibrating the flow of enzymes along the DNA (just like electrons inside a wire). They chose enzymes that would be able to function in bacteria, fungi, plants and animals, so that biological computers might be made with a wide variety of organisms, Bonnet said.

Living Computers
Like the transistor, one main function of the transcriptor is to amplify signals. Just as transistor radios amplify weak radio waves into audible sound, transcriptors can amplify a very small change in the production of an enzyme to produce large changes in the production of other proteins. Amplification allows signals to be carried over large distances, such as between a group of cells.

The new technology offers some electric possibilities: sensing when a cell has been exposed to sugar or caffeine, for example, and storing that information like a value in computer memory. Or telling cells to start or stop dividing depending on stimuli in their environment.

The researchers have made their biological logic gates available to the public to encourage people to use and improve them.

Follow Tanya Lewis on Twitter and Google+. Follow us @livescience, Facebook and Google+. Original article on LiveScience.com.

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F. Demeter

A new genetic analysis suggests that humans left Africa no earlier than 95,000 years ago, pushing the date of that migration back more than 100,000 years.

By Tia Ghose
LiveScience

Our early human ancestors may have left Africa more recently than thought, between 62,000 and 95,000 years ago, suggests a new analysis of genetic material from fossil skeletons.

The new findings are in line with earlier estimates, but contradict a more recent study that put humans' first exodus from Africa at least 200,000 years ago.

The new results "agree with what we know from archaeology," said study co-author Alissa Mittnik, a biologist at University of Tübingen, in Germany.

Hot debate
Exactly when the first humans emerged from Africa to colonize the world has been a topic of heated debate. [Photos: Our Closest Human Ancestor]

All of the estimates hinge on one number: the gene mutation rates. By knowing how often genes change, and then counting up the number of genetic differences between different species or groups of people, scientists can create a "molecular clock" to decipher how long ago they shared a common ancestor.

Early studies used genetic differences in mitochondrial DNA — genetic material inside the cells' energy-making structures that gets passed on from mother to child — between chimpanzees and humans.

But since that technique is based on the number of mutations divided by the time since the two shared a common ancestor, it requires an estimate of when the common ancestor of chimpanzees and humans lived.

Newer research estimated the mutation rate in modern human families based on DNA from the nucleus, which involved another way of getting at the common ancestor timing. That method suggested humans were racking up genetic mutations at half the rate — meaning to reach the genetic differences we see today humans would've had to leave Africa more than 200,000 years ago.

Fossil DNA dated
But that didn't jive with archaeological and other evidence, Mittnik told LiveScience.

For instance, the slower mutation rates that were previously reported had several implications, including "much earlier dates for the separation of the lineages of chimps and humans, and of Neanderthals and Homo sapiens, and earlier dates for so-called "African Eve" and the exit of modern humans from Africa," Chris Stringer, an paleobiologist at the Natural History Museum in London, who was not involved in the study, wrote in an email.

It seems unlikely that all of those dates are wrong. To sort out the problem, the researchers extracted mitochondrial DNA from 11 ancient human fossil skeletons from Europe and Asia. Using radioactive carbon dating, the oldest was estimated to be 40,000 years old, while the most recent came from medieval times.

The team found a mutation rate suggesting that humans left Africa between 62,000 and 95,000 years ago.

Method questioned
The researchers estimate that in its effort to avoid false positives (mutations that weren't really mutations), the nuclear DNA method missed quite a few real mutations. That would lead to an underestimate of the mutation rate and a longer estimate for when humans left Africa, diverged from Neanderthals, and other things.

Right now, it's not clear which method is most reliable, Peter Visscher, a quantitative geneticist at the University of Queensland, who was not involved in the study, wrote in an email to LiveScience.

"This debate will continue a bit longer, but soon there is likely to be a consensus on what mutation rates are in the present, because there is so much sequencing being done around the world," Visscher wrote.

The findings were published Thursday in the journal Current Biology.

Follow Tia Ghose on Twitter @tiaghose. Follow LiveScience @livescience, Facebook and Google+. Original article on LiveScience.com.

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By Stephanie Pappas
LiveScience

Though they roam the deep sea around the globe, enigmatic giant squid are all part of the same species, new research finds.

The new study reveals that the genetic diversity of giant squid (Architeuthis) is remarkably low — far lower than that of other marine species examined, said study researcher Tom Gilbert of the University of Copenhagen. The findings suggest that the squid intermingle and mate across the globe.

"The results are extremely surprising," Gilbert told LiveScience.

Monster of the deep
Giant squid are mysterious creatures. They dwell in the deep ocean, making them difficult to observe in their natural habitats. In fact, no one had observed a live giant squid in the wild until 2004. The first video of a live giant squid wasn't released until this year. The animals appear to grow as long as 60 feet (18 meters) and are carnivores that prey on fish and other squid.

Mark Norman

Scientists say giant squid can grow up to about 60 feet (18 meters) long, including their massive tentacles.

Most of what scientists know about the creatures comes from corpses found washed up on beaches or in sperm whale stomachs (the giant squid are apparently a common whale meal). Once in a while, a fishing trawler will entangle a giant squid in its nets. No one had ever published data on giant squid genetics before now.

Gilbert and his colleagues wanted to know if genetics could open any windows into giant squid life, particularly the size and diversity of their populations. No one even knew for sure how many giant squid species might be out there. Estimates ranged from one all the way up to 21, though the highest numbers were unlikely. [Release the Kraken! Giant Squid Photos]

Squid genes
The researchers extracted DNA from 43 soft-tissue samples from giant squid. Some of the samples came from squid found in whale stomachs or washed ashore, whereas others were frozen samples from giant squid dredged up by fishing trawlers. The scientists analyzed mitochondrial DNA, or mDNA, which is found in tiny cell structures called mitochondria. These structures help cells convert energy into a usable form, and their DNA is separate from the DNA in a cell's nucleus; mDNA is inherited from the maternal line.

The mDNA sequences were extremely similar among all samples, the researchers found. The samples exhibited more than 20 times less genetic diversity than other local squid populations, Gilbert said, and there was no population structure. The results suggest that giant squid are all one species. Even more, they're all part of the same big population, meaning there don't seem to be groups of giant squid that interact only with one another. Geography doesn't seem to be a barrier to their breeding, to the extent that any giant squid in the world is a potential partner for any other giant squid in the global oceans.

That's amazing, Gilbert said, given that giant squid vary substantially in body form and live everywhere except at the poles.

"It's very, very hard to explain," he said.

The researchers are now working to confirm the results using nuclear DNA from the giant squid, in order to rule out that possibility that the similarities in mDNA could be some quirk of evolution. If the results hold, they suggest the giant squid may have undergone a recent population expansion and that the young squid larvae disperse over massive distances, traveling randomly across the globe.

"There are huge unexplored questions," Gilbert said.

The researchers report their findings Tuesday in the journal Proceedings of the Royal Society B.

Follow Stephanie Pappas on Twitter and Google+. Follow us @livescience, Facebook and Google+. Original article on LiveScience.com

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Nicolle Rager Fuller / NSF

An artist's conception shows an RNA molecule, which may have served as an early form of life on Earth.

By Charles Choi
LiveScience

The human genome can generate molecular hoops similar in makeup to DNA that could potently interfere with genetic activity, researchers say.

These findings reveal there are secrets within the genomes of humans and other animals that scientists are still uncovering, and the old belief that life has useless junk DNA is more false than ever, scientists added.

Discovering more about circular versions of RNA (a molecule similar to DNA that can carry genetic information) could also lead to new ways of fighting diseases such as diabetes, brain tumors and Parkinson's disease, investigators added.

The human genome — the blueprint for human life — is made of DNA. From the genome, intermediate molecules known as RNA are created that help manufacture key biomolecules such as proteins, which then carry out cellular processes.

After international teams of researchers completely sequenced the human genome, they found about 95 percent of it unexpectedly did not code for proteins. Since this noncoding DNA initially seemed to have no known biological function, some scientists referred to it as junk DNA. [Unraveling the Human Genome: 6 Molecular Milestones]

However, over time, researchers have discovered this noncoding DNA can serve a wide variety of vital purposes. For instance, noncoding DNA can give rise to snippets of RNA known as micro-RNA that can suppress the so-called messenger RNA that normally helps manufacture proteins. This micro-RNA serves a key role in controlling genetic activity, and scientists are developing therapies based on micro-RNA to dampen harmful, malfunctioning genes.

Now researchers find the genomes of humans and other animals can generate circular RNA, highly stable rings that can sponge up micro-RNA, apparently keeping them from interfering with genetic activity if necessary.

"There seems to be a whole new layer of gene regulation," researcher Jørgen Kjems, a molecular biologist at Aarhus University in Denmark, told LiveScience.

For instance, Kjems and his colleagues found high levels of a circular RNA they dubbed ciRS-7 in the human and mouse brain. This molecule potently suppresses a micro-RNA named miR-7, which is found in everything from worms to humans. They also found a circular RNA known as Sry that is specific to testicles and targets a micro-RNA known as miR-138, suggesting that circular RNA might play a role in sex development.

In addition, when Nikolaus Rajewsky at the Max Delbrück Center for Molecular Medicine in Berlin and his colleagues analyzed human, mouse and nematode worm RNA, they detected thousands of circular RNAs. These were often linked with specific tissues or developmental stages.

The micro-RNA miR-7 regulates a number of disease genes, including Parkinson's disease, brain tumors and diabetes. As such, learning more about circular RNAs "may provide a new treatment strategy for these diseases," Kjems said. Regulating the activity of miR-7 could reduce the activity of the genes causing these diseases, he explained.

Altogether, these findings suggest that circular RNAs form a large class of genetic regulators. It remains uncertain whether these molecules work alone or whether they act by combining with other compounds, such as RNA-binding proteins.

The researchers next plan to introduce these circular molecules in animals "to see their effect on disease development, and from there, design drugs towards the diseases," Kjems said.

The scientists detailed their findings in Thursday's issue of the journal Nature.

Follow LiveScience on Twitter @livescience. We're also on Facebook and Google+. 

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By Jennifer Viegas
DiscoveryNews

Viruses can acquire fully functional immune systems, according to new research that bolsters the controversial theory that viruses are living creatures.

Until now, scientists thought that viruses existed only as primitive particles of DNA or RNA, and therefore lacked the sophistication of an immune system.

The study, published in the journal Nature, is the first to show that a virus can indeed possess an immune system, not to mention other qualities commonly associated with complex life forms.

The belief that viruses are living creatures “stems from the fact that viruses have their own complex genome, they replicate to make more of themselves, and they are evolving,” co-author Andrew Camilli of the Tufts University School of Medicine told Discovery News.

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The use of a complex immune system “doesn’t prove” that viruses are living beings, “but it does add to the argument,” he said.

Living organisms are typically defined as being capable of vital functions, such as the ability to grow and adapt to the environment over successive generations. Viruses are now on the fence between being considered a biological entity and an actual living creature.

Camilli and his colleagues focused their investigation on a viral predator of cholera bacteria. This type of virus is known as a bacteriophage (“phage” for short).

Lead author Kimberley Seed, a postdoctoral fellow in Camilli’s lab, was analyzing DNA sequences of phages taken from stool samples of Bangladesh cholera patients. She was surprised to find genes for a functional immune system previously only found in some types of bacteria.

To verify the discovery, she and her colleagues used phages both with and without the immune system to infect a new strain of cholera bacteria. Only the virus harboring the immune system readily killed the cholera bacteria.

Not only can some viruses have an immune system, some also can steal them from bacteria.

The scientists found that viruses can capture immunity genes from bacteria during a phase when “the viral genome is being replicated into dozens of copies within the infected host cell,” Camilli explained. The virus therefore steals an immune system from the bacteria. This benefits the phage virus.

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“The immune system allows the phage to target and destroy specific inhibitory genes of the host cell by literally cutting the target genes into pieces,” Seed told Discovery News. By disarming these genes, “the phage essentially disarms the host cell, and can then proceed with the infection and kill the host cell.”

While we tend to associate both viruses and bacteria with health threats, that is not always the case. In this instance, the virus winds up on the side of humans.

Camilli explained that “phages are killers of bacteria. If the species of bacteria they happen to kill is a human pathogen, then the phage is doing us a favor.”

The researchers hope that this activity could battle “superbugs,” which are bacteria with a resistance to most are all current antibiotics.

Contagion: Is a Killer Virus Out There?

Mammals, including humans, possess immune systems that, unlike those of bacteria, are encoded on much larger pieces of DNA.

“It would be very difficult, if not impossible, for a virus to capture (such an immune system),” Camilli said.

“A second consideration is that the virus has to have a good use for the captured immune system in order to hang onto it,” he added. “In the case of a phage, we have shown that it can use the captured immune system to good effect. This may or may not be true for another type of immune system, should a virus be able to capture it.”

Sylvain Moineau, a professor in the Department of Biochemistry, Microbiology and Bioinformatics at Université Laval, is one of the world's leading experts on bacteriophages. Moineau told Discovery News that the discovery of a phage with an immune system "is a remarkable finding. Phages always seem to find a way to impress us."

Moineau and colleague Manuela Villion remind that phages are among the most abundant biological entities on the planet, outnumbering their bacterial hosts tenfold. Whether they and other viruses represent living organisms, however, is still up for debate.