Researchers from the University of North Carolina (UNC) School of Medicine have identified the seventh and eighth bases of DNA.
For decades, scientists have known that DNA consists of four basic units — adenine, guanine, thymine, and cytosine. In recent history, scientists have expanded that list from four to six.
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, since it causes the DNA’s double helix to fold even tighter upon itself. Last year, the researchers found 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 cytosine.
However, the researchers could not continue the reaction on to the seventh and eighth bases, called 5 formylC and 5 carboxyC. The problem was that their experimental assay wasn’t sensitive enough. They redesigned it and were able to detect the seventh and eighth bases — called 5-formylcytosine (5fC) and 5 carboxylcytosine (5caC) — which 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.
The researchers then examined embryonic stem cells as well as mouse organs and found that both bases can be detected in genomic DNA.
Their findings could have important implications for stem cell research, since it could provide researchers with new tools to erase previous methylation patterns to reprogram adult cells. It could also inform cancer research by giving scientists the opportunity to reactivate tumor suppressor genes that had been silenced by DNA methylation.
Tuesday, July 26, 2011
Touchscreen keyboard morphs to fit your typing style
Typing on a touchscreen is not one of life's pleasures: the one-size-fits-all nature of most virtual keyboards is a hassle that puts many of us off using them. I've lost count of the number of times I've seen journalists put down an iPad, for instance, and pick up a laptop or netbook to do some serious notetaking or writing.
IBM, however, says it doesn't have to be that way. In a recently filed US patent application, three IBM engineers posit the notion of a virtual keyboard in which the position of the keys and the overall layout is entirely set by the user's finger anatomy. That way, they argue, people will be better able to type at speed, with all keys within comfortable range and so end up, with fewer errors.
After an initial calibration stage, in which the keyboard asks users to undertake a series of exercises to set response time, anatomical algorithms get to work, sensing through the touchscreen the finger skin touch area, finger size and finger position for the logged in user.
As this information is gathered - IBM does not say over what period this learning takes place - the virtual key buttons are automatically resized, reshaped and repositioned in response.
The patent shows a keyboard with some keys subtly higher than others, and with some fatter than others. This "adapts the keyboard to the user's unique typing motion paths" governed by their different physical finger anatomies, says IBM, which suggests the idea being used in both touchscreen and projected "surface computing" displays.
There does seem scope for such ideas. In a review of the Apple iPad, review website MacInTouch said: "A touch typist found it frustratingly glitchy versus a real keyboard, producing all sorts of ghost characters when the screen repeatedly misinterpreted his fingers' intentions."
Perhaps anatomical profiling is just what's needed.
IBM, however, says it doesn't have to be that way. In a recently filed US patent application, three IBM engineers posit the notion of a virtual keyboard in which the position of the keys and the overall layout is entirely set by the user's finger anatomy. That way, they argue, people will be better able to type at speed, with all keys within comfortable range and so end up, with fewer errors.
After an initial calibration stage, in which the keyboard asks users to undertake a series of exercises to set response time, anatomical algorithms get to work, sensing through the touchscreen the finger skin touch area, finger size and finger position for the logged in user.
As this information is gathered - IBM does not say over what period this learning takes place - the virtual key buttons are automatically resized, reshaped and repositioned in response.
The patent shows a keyboard with some keys subtly higher than others, and with some fatter than others. This "adapts the keyboard to the user's unique typing motion paths" governed by their different physical finger anatomies, says IBM, which suggests the idea being used in both touchscreen and projected "surface computing" displays.
There does seem scope for such ideas. In a review of the Apple iPad, review website MacInTouch said: "A touch typist found it frustratingly glitchy versus a real keyboard, producing all sorts of ghost characters when the screen repeatedly misinterpreted his fingers' intentions."
Perhaps anatomical profiling is just what's needed.
Wednesday, June 1, 2011
Brain scans reveal why some people feel your pain
Researchers at Monash University in Melbourne, Australia, have observed atypical neurophysiological activity in amputees who experience synesthetic pain (pain synesthetes) when observing pain in another.
The researchers found that reduced alpha and theta brainwaves in pain synesthetes may reflect inhibition of normal inhibitory mechanisms (neurotransmitters involved in the processing of observed pain) as well as increased synesthetic pain.
The researchers used EEG to record brain activity in eight amputees who experienced both phantom and synesthetic pain, 10 amputees who experienced just phantom pain, and 10 healthy people with no amputations while they looked at images of hands or feet in potentially painful and non-painful situations.
When viewing the images, the researchers found that the pain synesthetes exhibited decreased theta and alpha brainwaves compared with the other volunteers. The researchers said that such a decrease reflects an increase in neural activity, suggesting that their mirror systems (neurons that fire when an animal observes the same action performed by another) are activated more strongly.
They said the traumatic experience associated with losing a limb may heighten the sensitivity of pain synesthetes to others’ pain. When threatened, our body naturally becomes hypervigilant to pain: our pain threshold lowers, which can make even small triggers painful. Pain synesthesia may be a symptom of an abnormal, ongoing hypervigilance, the researchers said.
The researchers found that reduced alpha and theta brainwaves in pain synesthetes may reflect inhibition of normal inhibitory mechanisms (neurotransmitters involved in the processing of observed pain) as well as increased synesthetic pain.
The researchers used EEG to record brain activity in eight amputees who experienced both phantom and synesthetic pain, 10 amputees who experienced just phantom pain, and 10 healthy people with no amputations while they looked at images of hands or feet in potentially painful and non-painful situations.
When viewing the images, the researchers found that the pain synesthetes exhibited decreased theta and alpha brainwaves compared with the other volunteers. The researchers said that such a decrease reflects an increase in neural activity, suggesting that their mirror systems (neurons that fire when an animal observes the same action performed by another) are activated more strongly.
They said the traumatic experience associated with losing a limb may heighten the sensitivity of pain synesthetes to others’ pain. When threatened, our body naturally becomes hypervigilant to pain: our pain threshold lowers, which can make even small triggers painful. Pain synesthesia may be a symptom of an abnormal, ongoing hypervigilance, the researchers said.
Mining patterns in search data with Google Correlate
Google Correlate has been launched on Google Labs. Users can now upload their own data series and retrieve a list of search terms based on popularity to see what best corresponds with a real world trend.
In the example below, official flu activity data were uploaded from the U.S. CDC over the last several years. The data reveal that people search for terms like [cold or flu] in a pattern similar to actual flu rates. Finding these correlated terms, a Google Flu Trends graph was built.
Users can also enter search terms such as [ribosome] and find other terms with activity that correspond well over time.
A white paper describes the methodology behind Google Correlate. How can Google help with the flu? Find out here.
In the example below, official flu activity data were uploaded from the U.S. CDC over the last several years. The data reveal that people search for terms like [cold or flu] in a pattern similar to actual flu rates. Finding these correlated terms, a Google Flu Trends graph was built.
Users can also enter search terms such as [ribosome] and find other terms with activity that correspond well over time.
A white paper describes the methodology behind Google Correlate. How can Google help with the flu? Find out here.
Gestural interfaces: a step backwards in usability?
Usability researchers from the Nielsen Norman group have pointed out that well-tested and understood standards of interaction design are being “overthrown, ignored, and violated” in the rush to develop natural gestural interfaces that can lead to “usability disaster.”
“The first crop of iPad apps revived memories of Web designs from 1993, when Mosaic first introduced the image map that made it possible for any part of any picture to become a UI element,” said Norman Nielsen. “As a result, graphic designers went wild: anything they could draw could be a UI, whether it made sense or not. It’s the same with iPad apps: anything you can show and touch can be a UI on this device. There are no standards and no expectations.”
“One of the worst designs last year was USA Today‘s section navigation, which required users to touch the newspaper logo despite the complete lack of any perceived affordance that the logo would have this effect….
“I thought I’d driven a stake through splash screens many years ago and eradicated them from the Web, but apparently splash screens are super-vampires that can haunt users from beyond the grave.”
“The first crop of iPad apps revived memories of Web designs from 1993, when Mosaic first introduced the image map that made it possible for any part of any picture to become a UI element,” said Norman Nielsen. “As a result, graphic designers went wild: anything they could draw could be a UI, whether it made sense or not. It’s the same with iPad apps: anything you can show and touch can be a UI on this device. There are no standards and no expectations.”
“One of the worst designs last year was USA Today‘s section navigation, which required users to touch the newspaper logo despite the complete lack of any perceived affordance that the logo would have this effect….
“I thought I’d driven a stake through splash screens many years ago and eradicated them from the Web, but apparently splash screens are super-vampires that can haunt users from beyond the grave.”
Thursday, May 26, 2011
Transformer robot turns into a helicopter
A transformer robot that turns into a helicopter has been developed by researchers at the University of Minnesota’s Center for Distributed Robotics.
The robot uses separate motors to run the wheels and the rotors rather than a complex system. Although the first prototype is fragile, future designs will have simpler and more robust folding mechanisms, according to the researchers, including an extendable boom with a tail rotor, similar to those used by helicopters, to provide more stability in flight.
The robot uses separate motors to run the wheels and the rotors rather than a complex system. Although the first prototype is fragile, future designs will have simpler and more robust folding mechanisms, according to the researchers, including an extendable boom with a tail rotor, similar to those used by helicopters, to provide more stability in flight.
Wednesday, May 25, 2011
‘Survival protein’ protects the brain against effects of stroke
A “survival protein” that protects the brain against the effects of stroke in rodent brain tissue has been discovered by scientists at Johns Hopkins University. The finding has implications for treating stroke as well as Parkinson’s Disease, diabetes, and heart attack.
When brain tissue is subjected to a stressful but not lethal insult, a defense response occurs that protects cells from subsequent insult. The scientists dissected this preconditioning pathway to identify the most critical molecular players, including the Iduna protein. This protein increased three- to four-fold in preconditioned mouse brain tissue following an insult to the tissue, the scientists said.
The team exposed mouse brain cells to short bursts of a toxic chemical, and then screened these “preconditioned” cells for genes that turned on as a result of the insult. Focusing on Iduna, the researchers turned up the gene’s activity in the cells during exposure to the toxic chemical, which induced preconditioning. Cells deficient in Iduna did not survive, but those with more Iduna did.
The scientists found that the Iduna protein interferes with a particular kind of cell death that’s implicated in complications from diabetes and heart attack as well as stroke. By binding with a molecule known as PAR polymer, Iduna prevents the movement of cell-death-inducing factor (AIF) into a cell’s nucleus.
“Apparently, what doesn’t kill you makes you stronger,” says Valina Dawson, Ph.D. “This protective response was broad in its defense of neurons and glia and blood vessels — the entire brain. It’s not just a delay of death, but real protection that lasts for about 72 hours.”
When brain tissue is subjected to a stressful but not lethal insult, a defense response occurs that protects cells from subsequent insult. The scientists dissected this preconditioning pathway to identify the most critical molecular players, including the Iduna protein. This protein increased three- to four-fold in preconditioned mouse brain tissue following an insult to the tissue, the scientists said.
The team exposed mouse brain cells to short bursts of a toxic chemical, and then screened these “preconditioned” cells for genes that turned on as a result of the insult. Focusing on Iduna, the researchers turned up the gene’s activity in the cells during exposure to the toxic chemical, which induced preconditioning. Cells deficient in Iduna did not survive, but those with more Iduna did.
The scientists found that the Iduna protein interferes with a particular kind of cell death that’s implicated in complications from diabetes and heart attack as well as stroke. By binding with a molecule known as PAR polymer, Iduna prevents the movement of cell-death-inducing factor (AIF) into a cell’s nucleus.
“Apparently, what doesn’t kill you makes you stronger,” says Valina Dawson, Ph.D. “This protective response was broad in its defense of neurons and glia and blood vessels — the entire brain. It’s not just a delay of death, but real protection that lasts for about 72 hours.”
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