Posts tagged biology
Articles and news from the latest research reports.
A glance at a star-nosed mole (Condylura cristata) is enough to convince most people that something very strange has evolved in the bogs and wetlands of North America. There’s nothing else on the planet quite like this little palm-sized mammal. Its nose is ringed by 22 fleshy appendages, called rays, which are engorged with blood and in a constant flurry of motion when the animal searches for food.
What is this star? How did it evolve and what is it for? What advantage would be worth sporting such an ungainly structure? To a neuroscientist interested in sensory systems, this kind of biological anomaly represents an irresistible mystery. I first began studying star-nosed moles in the early ’90s in an attempt to answer some of these basic questions. But I soon discovered that this unusual animal, like many other specialized species, could reveal general principles about how brains process and represent sensory information. In fact, star-nosed moles have been a gold mine for discoveries about brains and behavior in general—and an unending source of surprises. The most obvious place to start the investigation was with that bizarre star.
(Source: the-scientist.com)
![According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”.
Scientists have long recognised that some non-coding DNA has a function, and more and more solid examples have come to light [edited for clarity - Ed]. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.
And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”
That the genome is complex will come as no surprise to scientists, but ENCODE does two fresh things: it catalogues the DNA elements for scientists to pore over; and it reveals just how many there are. “The genome is no longer an empty vastness – it is densely packed with peaks and wiggles of biochemical activity,” says Shyam Prabhakar from the Genome Institute of Singapore. “There are nuggets for everyone here. No matter which piece of the genome we happen to be studying in any particular project, we will benefit from looking up the corresponding ENCODE tracks.”](http://41.media.tumblr.com/tumblr_m9y0xaewSN1rog5d1o1_500.jpg)
According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”.
Scientists have long recognised that some non-coding DNA has a function, and more and more solid examples have come to light [edited for clarity - Ed]. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.
And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”
That the genome is complex will come as no surprise to scientists, but ENCODE does two fresh things: it catalogues the DNA elements for scientists to pore over; and it reveals just how many there are. “The genome is no longer an empty vastness – it is densely packed with peaks and wiggles of biochemical activity,” says Shyam Prabhakar from the Genome Institute of Singapore. “There are nuggets for everyone here. No matter which piece of the genome we happen to be studying in any particular project, we will benefit from looking up the corresponding ENCODE tracks.”
On the surface, ants and the Internet don’t seem to have much in common. But two Stanford researchers have discovered that a species of harvester ants determine how many foragers to send out of the nest in much the same way that Internet protocols discover how much bandwidth is available for the transfer of data. The researchers are calling it the “anternet.”
For 25 years, the rhesus monkeys were kept semi-starved, lean and hungry. The males’ weights were so low they were the equivalent of a 6-foot-tall man who tipped the scales at just 120 to 133 pounds. The hope was that if the monkeys lived longer, healthier lives by eating a lot less, then maybe people, their evolutionary cousins, would, too. Some scientists, anticipating such benefits, began severely restricting their own diets.
The results of this major, long-awaited study, which began in 1987, are finally in. But it did not bring the vindication calorie restriction enthusiasts had anticipated. It turns out the skinny monkeys did not live any longer than those kept at more normal weights. Some lab test results improved, but only in monkeys put on the when they were old. The causes of death — , heart disease — were the same in both the underfed and the normally fed monkeys.
Boo! Robots learn to jump like frightened mammals
ROBOTS developed in the safety of a laboratory can be too slow to react to the dangers of the real world. But software inspired by biology promises to give robots the equivalent of the mammalian amygdala, a part of the brain that responds quickly to threats.
(Image: SuperStock)
STARTLE, developed by Mike Hook and colleagues at Roke Manor Research of Romsey in Hampshire, UK, employs an artificial neural network to look out for abnormal or inconsistent data. Once it has been taught what is out of the ordinary, it can recognise dangers in the environment.
For instance, from data fed by a robotic vehicle’s on-board sensors, STARTLE could notice a pothole and pass a warning to the vehicle’s control system to focus more computing resources on that part of the road.
"If it sees something anomalous then investigative processing is cued; this allows us to use computationally expensive algorithms only when needed for assessing possible threats, rather than responding equally to everything," says Hook.
This design mimics the amygdala, which provides a rapid response to threats. The amygdala helps small animals to deal with complex, fast-changing surroundings, allowing them to ignore most sensory stimuli. “The key is that it’s for spotting anomalous conditions,” says Hook, “not routine ones.”
STARTLE has been tested in both vehicle navigation and robot health monitoring. In the latter, it can be trained to respond to danger signs, such as sudden changes in battery power or temperature. It has also been tested in computer networks, as a way to detect security threats, having been trained to identify the pattern of activity associated with an attack.
"A robot amygdala network could be useful," says neuroscientist Keith Kendrick of the University of Electronic Science and Technology of China in Chengdu. "Such a low-resolution analysis will sometimes make mistakes, and you will avoid something needlessly." But a slower, high-resolution analysis is also carried out, he says, which can override the mistakes.
Hooks says that STARTLE could be useful for any robots in complex environments. For example, a robot vehicle would be able to spot other drivers behaving erratically, a major challenge for conventional computing.
Source: NewScientist
Proteins adorning the surfaces of human cells perform an array of essential functions, including cell signaling, communication and the transport of vital substances into and out of cells. They are critical targets for drug delivery and many proteins are now being identified as disease biomarkers—early warning beacons announcing the pre-symptomatic presence of cancers and other diseases.
While study of the binding properties of membrane proteins is essential, detailed analysis of these complex entities is tricky. Now, Nongjian (NJ) Tao, Professor of Electrical Engineering, and director of the Center for Bioelectronics and Biosensors at Arizona State University’s Biodesign Institute has devised a new technique for examining the binding kinetics of membrane proteins.
“This is a very important but very difficult problem to solve,” Tao notes. “We demonstrate a new method of approaching the issue, which provides a quantitative analysis of protein interactions on the surface of a cell.”
The technique—known as SPR microscopy—holds the potential to simplify the study of membrane proteins, thereby streamlining the development of new drugs, aiding the identification of diagnostic biomarkers and improving the understanding of cell-pathogen interactions.
The group’s results appear in this week’s advanced online issue of the journal Nature Chemistry.
What Time Is It on Your Circadian Clock?
Are you a morning lark or a night owl? Scientists use that simplified categorization to explain that different people have different internal body clocks, commonly called circadian clocks. Sleep-wake cycles, digestive activities, and many other physiological processes are controlled by these clocks. In recent years, researchers have found that internal body clocks can also affect how patients react to drugs. For example, timing a course of chemotherapy to the internal body time of cancer patients can improve treatment efficacy and reduce side effects.
Round the clock. Tracking the levels of 50 hormones and amino acids in blood samples (shown by ribbons) reveals a body’s internal time. Credit: PNAS
But physicians have not been able to exploit these findings because determining internal body time is, well, time consuming. It’s also cumbersome. The most established and reliable method requires taking blood samples from a patient hourly and tracking levels of the hormone melatonin, which previous research has tied closely to internal body time.
Now a Japanese group has come up with an alternative method of determining internal body time by constructing what it calls a molecular timetable based on levels in blood samples of more than 50 metabolites—hormones and amino acids—that result from biological activity. The researchers established a molecular timetable based on samples from three subjects and validated it using the conventional melatonin measurement. They then used that timetable to determine the internal body times of other subjects by checking the levels of the metabolites in just two blood samples from each subject per day.
Having such a timetable could allow doctors to synchronize drug delivery to internal body time, the team reports online today in the Proceedings of the National Academy of Sciences. “Usually personalized medicine is focusing on genetic differences, but there are also temporal differences [among patients]. That will be the next step in personalized medicine,” says systems biologist Hiroki Ueda of the RIKEN Center for Developmental Biology in Kobe, Japan, who heads the research group.
"In principle, the method holds great promise as a way of replacing the cumbersome melatonin assay," says Steven Brown, a molecular biologist at the University of Zurich in Switzerland. "The authors show in a small-scale, well-controlled experiment that they are able to predict internal body time within a precision frame of 3 hours," says Urs Albrecht of the University of Fribourg in Switzerland. Both researchers say further work will be necessary to make the technique more practical and more widely applicable, and Ueda agrees. The experimental subjects were all young men, and different molecular timetables are likely needed for women and for people of different ages. He would also like to improve the precision and make it reliable with just one blood sample per day.
Source: ScienceNOW
DNA could have existed long before life itself
24 August 2012 by Michael Marshall
THE latest twist in the origin-of-life tale is double helical. Chemists are close to demonstrating that the building blocks of DNA can form spontaneously from chemicals thought to be present on the primordial Earth. If they succeed, their work would suggest that DNA could have predated the birth of life.
Lurking at the dawn of time (Image: Snorri Gunnarsson/Flickr/Getty)
DNA is essential to almost all life on Earth, yet most biologists think that life began with RNA. Just like DNA, it stores genetic information. What’s more, RNA can fold into complex shapes that can clamp onto other molecules and speed up chemical reactions, just like a protein, and it is structurally simpler than DNA, so might be easier to make.
After decades of trying, in 2009 researchers finally managed to generate RNA using chemicals that probably existed on the early Earth. Matthew Powner, now at University College London, and his colleagues synthesised two of the four nucleotides that make up RNA. Their achievement suggested that RNA may have formed spontaneously - powerful support for the idea that life began in an “RNA world”.
Researchers from the University of York are fitting one thousand northern hairy wood ants with tiny radio receivers in a world first experiment at the National Trust’s Longshaw Estate in Derbyshire to find out how they communicate and travel between their complex nests.
Early fruits of the collaboration between the Genome 10K project and Beijing Genomics Institute (BGI) to sequence 100 vertebrate species have resulted in the sequencing and release of the genome of one of naturalist Charles Darwin’s Galápagos finches, the medium ground finch Geospiza fortis.
This finch genome, the first of the BGI-Genome 10K collaboration to be made available through the UCSC Genome Browser, represents both a scientific and a symbolic advancement, according to Erich Jarvis, Duke University associate professor who studies the neurobiology of vocal learning in songbirds.
Endemic to the subtropical or tropical dry forests and shrublands of the Galápagos Islands this species evolves rapidly in response to environmental changes. ”These finches are of great historical significance, but when Darwin first studied these birds, he was unlikely to have envisioned how this species would become a perfect model to study evolution in action,” said Goujie Zhang, BGI’s associate director of research. “Having the reference genome of this species has opened the door for carrying out studies that can look at real-time evolutionary changes on a genomic level of all of these enigmatic species.”
(Image by: Petr Baum)