Tag Archives: RNA

EteRNA

EteRNA logoEteRNA, developed by Carnegie Mellon University and Stanford University is a Flash-based folding game, like Fold It, that enlists users to fold RNA for optimized versions, which can then be tested in the lab. Citizen science!

You can participate by signing up directly at the site or linking through facebook (and setting your profile on the EteRNA site).

The game comes with a tutorial to get you familiar with the building blocks of RNA and how to manipulate them to get the desired folding shape. After the tutorial one can try to solve a number of increasingly difficult puzzles.

Scores are kept and displayed in a leaderboard. The game auto-saves the progress on the latest puzzle you might have been working on.

For more expert knowledge on how to solve the puzzles, a number of strategy guides can be found through the community which help in solving and further optimizing the RNA folds.

Scoring 10,000 points or more, by solving the tutorials and a bunch of the challenges, gives you access to the RNA Lab where a real version of some version of RNA can be designed and proposed, which after voting, will then be tested in the real lab.

You can get an idea of what it looks like through an embedded version, as below:

For more detailed info on how the folding of RNA is used, see their information page.

Some media links:
RNA Game Lets Players Help Find a Biological Prize (NY Times)
Online game helps predict how RNA folds (New Scientist)
New video game makes game players Stanford professor’s virtual lab assistants (Stanford)

And finally a short video from Carnegie Mellon that explains EteRNA:

Science Shorts 20100514

scienceFindings weaken autism theory
The mirror neuron system, which is thought to play a central role in social communications, appears to respond normally in individuals with autism. The finding counters theories suggesting that a mirror system dysfunction causes the social difficulties related to the disorder.

Earliest birds didn’t make a flap
Archaeopteryx, Confuciusornis plumage probably not strong enough to support sustained flight

Physics of gene transcription unveiled
A research team has made precise measurements of where and how RNA polymerase encounters obstacles while it reads nucleosomal DNA.

New water-splitting catalyst found
Expanding on work published two years ago, MIT’s Daniel Nocera and his associates have found yet another formulation, based on inexpensive and widely available materials, that can efficiently catalyze the splitting of water molecules using electricity. This could ultimately form the basis for new storage systems that would allow buildings to be completely independent and self-sustaining in terms of energy: The systems would use energy from intermittent sources like sunlight or wind to create hydrogen fuel, which could then be used in fuel cells or other devices to produce electricity or transportation fuels as needed.

Scientists Listen to Faint Sounds Inside Insects [2]
A team of Clarkson University scientists led by Prof. Igor Sokolov are using atomic force microscopy (AFM) to record sounds emanating from inside living insects like flies, mosquitoes and ladybugs.

New information on the development of the brain
With their French colleagues, researchers at the University of Helsinki have found a mechanism in the memory centre of newborn that adjusts the maturation of the brain for the information processing required later in life. The study was published this week in an American science magazine The Journal of Neuroscience.

Insects Not ‘Hard-Wired’: Young Male Crickets Grow Larger in the Presence of Abundant Male Song
In the animal kingdom, sexual signals often are manifested as displays of bright coloration or, in the case of crickets, as loud song.

Sun’s constant size surprises scientists
A group of astronomers led by the University of Hawaii’s Dr. Jeff Kuhn has found that in recent times the sun’s size has been remarkably constant. Its diameter has changed by less than one part in a million over the last 12 years.

Supermassive Black Hole Kicked Out of Galaxy
Big black holes aren’t known for budging, which is why the new finding is so unusual.

A plant virus that switched to vertebrates

From: A plant virus that switched to vertebrates (Virology Blog)

Viruses can be transmitted to completely new host species that they have not previously infected. Usually host defenses stop the infection before any replication and adaptation can take place. On rare occasions, a novel population of viruses arises in the new host. These interspecies infections can sometimes be deduced by sequence analyses, providing a glimpse of the amazing and unpredictable paths of virus evolution. One example is a plant virus that switched hosts and infected vertebrates.

Circoviruses infect vertebrates and have small, circular, single-stranded DNA genomes. Nanoviruses have the same genome structure, but infect plants. The genes encoding one of the viral proteins – called the Rep protein – appear to be hybrids, and share significant sequence similarity. They also exhibit homology with a protein encoded by caliciviruses, which are RNA viruses that infect many different vertebrates.

Analysis of the viral DNA sequences suggests that two remarkable events occurred during the evolution of circoviruses and nanoviruses. Not long ago, a nanovirus was transmitted from a plant to a vertebrate. This event might have occurred when a vertebrate fed on an infected plant. The virus adapted to vertebrates, and the circovirus family was established. After the host switch from plants to vertebrates, recombination took place between the circovirus and a vertebrate calicivirus. A reverse transcriptase probably converted the circovirus RNA genome to DNA to allow recombination to occur. (…)