Cat-sanova. (via China-Place)
Because of this, virologists can directly study only the recent history of viruses like this. Older samples have reached mutation saturation, with so many accumulated spelling errors that scientists can’t account for them all. Taking the history of retroviruses back thousands or millions of years would require a different way to measure mutation rates.
Katzourakis turned to another technique. He searched for something akin to viral fossils inside the DNA of their hosts. Retroviruses often insert copies of their genetic material into their hosts’ cells. Most of the time, the information dies with the host. On rare occasions, however, a retrovirus hits the evolutionary jackpot and slips inside the genome of a sperm or egg cell. Nestled securely in its host’s DNA, the virus gets passed down through the generations.
Katzourakis used these viral relics to study the ancient origin of retroviruses. But when he did so, he got a big surprise. The rate of evolution of these retroviruses over long periods appeared to slow dramatically, nearly matching that of humans and other complex life — organisms that have proofreader machinery and thus should change at a much slower pace.
If the viruses were evolving much more slowly than scientists thought, it could imply that the viruses were much older than expected as well. After all, a slowly evolving virus will need more time to change by the same amount as a quickly evolving virus.
So he set out to find an accurate date for the origin of retroviruses. To do this, he turned to a group of the most ancient retroviruses, the so-called foamy viruses, which infect everything from monkeys to cows. This promiscuity enabled Katzourakis to calibrate his evolutionary clock to determine precisely when foamy viruses emerged. If two species shared a foamy-virus sequence, the virus must have infected their common ancestor, before the two species diverged.
“It gives us a way to date events in deep evolutionary history that’s independent of the sequences themselves,” Katzourakis said.
Researchers in labs around the world had slowly pushed back the date of origin of foamy viruses to 100 million years ago. But Katzourakis found hints that the virus had infected reptiles, amphibians and even fish far earlier than 100 million years ago. To conclusively show that retroviruses were older than the accepted date of 100 million years, however, Katzourakis would need to date the virus itself.
He dived into Ho’s papers on the time-dependent rate phenomenon, hoping to figure out how to apply it to viruses. He also wanted to create a general model that would allow researchers to input the timescale they were observing and get back details about the organism’s evolutionary rate.
Katzourakis and his student Pakorn Aiewsakun tried out four different ways to quantify how quickly the evolutionary rate appeared to change based on timescale. They found that a power law rate-decay model fit their data best and showed that evolutionary rates decrease exponentially as the timescale increases. A subsequent study of 396 different viruses revealed that the evolutionary rate slows at the same rate across almost all genome types and replication strategies. Existing evolutionary clocks, which fail to account for the time-dependent rate phenomenon, inaccurately date ancient viruses as being much younger than they really are.
Katzourakis and Aiewsakun then used the newly developed mathematical framework to recalculate the emergence of foamy viruses. Using their newly developed model, the scientists showed in a paper published in January that foamy viruses emerged somewhere between 460 and 550 million years ago. Independent work by the University of Arizona virologist Michael Worobey, published in Virus Evolution nearly simultaneously, also suggested that these viruses originated earlier than expected.These studies established the oldest date for any known group of viruses, although Katzourakis believes other viral groups may be even more ancient.
The findings have implications far beyond the earning of a trophy for the oldest virus. A convergence on the same date of origin for foamy viruses provides evidence that the time-dependent rate phenomenon isn’t just a relic of statistics or the methods researchers use to date species. Katzourakis’s model also gives researchers a tool to quantify the effects of the time-dependent rate phenomenon, which will prove key to understanding the factors that drive this phenomenon.
More broadly, the work by Katzourakis and Ho challenges the idea of a steadily ticking evolutionary clock. “This changes the way we conceive of molecular evolution,” Duchêne said. “It shows that there is no universal rate of evolution. Even the same organisms have rates that vary over time.”
It also means that scientists may need to revise the dates of evolutionary events in the deep past, as they likely underestimated how long ago they truly happened, Katzourakis said. He is trying to understand whether the pruning of mutations by natural selection and mutational saturation is the sole contributor to the time-dependent rate phenomenon, or whether other factors play a role in how and why the phenomenon emerges.
“Is it a limitation of our tools, or is there something that we’ve overlooked? If we can understand this process, it will give us some big evolutionary insights,” Katzourakis said.
This article was reprinted on Wired.com.
Happy Mother’s Day!
Cracking the case. (by Loading Artist)
The person I’m talking to in this comic is a guy I worked with at one time, but we worked at a pretty nice place. Having someone talk all the time about how good his job is doesn’t make for a very funny comic strip, so I made my fictional workplace a dysfunctional dump.
I only used use the drawings of my work friend a few times, but one of those times, I had him ask if he could “put on a Speedo and ride me to Thailand,” so I think he suffered enough.
As I’ve said a great many times, I do not deal well with heat. However, I’d rather live in a town with warm winters and unbearably hot summers than in a town with warm-ish summers and unbearably cold winters.
Either way, you end up not wanting to go outside for half of the year. In a town with the unbearably hot summers, the winters are warm, and during the summer, at least the roads are clear.
Adam Victor Brandizzi
Tirinha com political compass, eis aí um meme histórico!
Adam Victor Brandizzi
This is amazing but these pictures are not vibrant at all :P
With genetically engineered color vision, gut-dwelling bacteria transform into vibrant artists—though their work is a bit derivative.
In a study published in Nature Chemical Biology, MIT researchers wired Escherichia coli with a synthetic network of 18 genes that allows them to sense and respond to red, green, and blue. Once excited by the colors, the genetic circuitry activates and inspires the bacteria to produce corresponding pigments or fluorescent proteins. Mats of microbes then turn their petri dishes into canvases, creating vivid replicas of patterns and artwork.
Right now, the bright bacteria simply demonstrate how far synthetic biologists have come in genetic tinkering. But, in the future, the researchers, led by MIT’s Christopher Voigt, hope that the RGB microbes could find a variety of applications. “Colored light offers many channels to pattern cells to build tissues or materials, control cells at a distance, or serve as a means of communication between electronic and biological systems,” Voigt and his colleagues write.