Evolution of new genes captured
Like job-seekers searching for a new position, living things sometimes have to pick up a new skill if they are going to succeed. Researchers from the University of California, Davis, and Uppsala University, Sweden, have shown for the first time how living organisms do this.
The observation, published Oct. 19 in the journal Science, closes an important gap in the theory of natural selection.
Scientists have long wondered how living things evolve new functions from a limited set of genes. One popular explanation is that genes duplicate by accident; the duplicate undergoes mutations and picks up a new function; and, if that new function is useful, the gene spreads.
"It’s an old idea and it’s clear that this happens," said John Roth, a distinguished professor of microbiology at UC Davis and co-author of the paper.
The problem, Roth said, is that it has been hard to imagine how it occurs. Natural selection is relentlessly efficient in removing mutated genes: Genes that are not positively selected are quickly lost.
How then does a newly duplicated gene stick around long enough to pick up a useful new function that would be a target for positive selection?
Experiments in Roth’s laboratory and elsewhere led to a model for the origin of a novel gene by a process of “innovation, amplification and divergence.” This model has now been tested by Joakim Nasvall, Lei Sun and Dan Andersson at Uppsala.
Filed under genes genetics evolution natural selection mutation neuroscience science
BeerSci: What Beer’s Key Ingredient Reveals About Our Own Genomes
The yeast S. cerevisiae is instrumental in brewing ale. But did you know that it’s also instrumental in helping scientists better understand cells?
Humans have been exploiting S. cerevisiae's fermentation prowess for thousands of years. Without it we wouldn't have beer, bread or wine. In addition to its uses in food production, S. cerevisiae is also an amazing tool for molecular and cell biology, one that is helping scientists suss out the rules of how our cells work and gain clues to what happens at the molecular level when things go wrong.
That’s because S. cerevisiae is one of the simplest eukaryotic cells—cells like those that make up your dog, your houseplants or your local bartender. In fact, in 1996 S. cerevisiae became the first eukaryote to have its genome sequenced. According to the Saccharomyces Genome Database, S. cerevisiae's genome has some 12,100,000 base pairs and some 6,600 open reading frames (that is, places in the genome that could possibly contain a gene).
Most of you, I am sure, remember that there are two general kinds of cells: prokaryotic and eukaryotic. That is, “no nucleus” and “has a nucleus.” That’s all true, but the differences between the two kinds of cells are much more profound than that. Bacteria — prokaryotes — organize their genetic material in a completely different (and much simpler) way than do eukaryotes. Prokaryotes usually only have a chunk of DNA for a genome — usually circular — and a few extra chunks, called plasmids, kicking around in the cytosol. Those plasmids are really useful in doing things like sharing genes between bacteria, and its how one antibiotic-resistant strain of bacteria can pass along antibiotic resistance to a bunch of nigh-unrelated strains of bacteria in, say, your intestines. The genes in bacteria are generally read exactly as they are found in the DNA, kind of like how you’re reading this sentence. No intervening clumps of letters to clutter things up.
Eukaryotes, on the other hand, bundle up all that DNA (and they have a lot of it) into a protein-DNA complex called chromatin, then wind that chromatin into individual chromosomes. Further, the genes are constructed in such a way that they must be heavily processed before they can ever “code” for a functional protein. Much of what we understand about eukaryotic cellular processes and eukaryotic gene expression, we learned by studying the molecular mechanics of S. cerevisiae.
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Filed under S. cerevisiae biology cells cellular processes eukaryotic genomics neuroscience prokaryotic yeast genome science
Complete mitochondrial DNA genome sequences from the first New Zealanders
The dispersal of modern humans across the globe began ∼65,000 y ago when people first left Africa and culminated with the settlement of East Polynesia, which occurred in the last 1,000 y. With the arrival of Polynesian canoes only 750 y ago, Aotearoa/New Zealand became the last major landmass to be permanently settled by humans. We present here complete mitochondrial genome sequences of the likely founding population of Aotearoa/New Zealand recovered from the archaeological site of Wairau Bar. These data represent complete mitochondrial genome sequences from ancient Polynesian voyagers and provide insights into the genetic diversity of human populations in the Pacific at the time of the settlement of East Polynesia.
Filed under mitochondrial genomes Polynesians New Zealand DNA mtDNA evolution science
Neuroscientists propose a revolutionary DNA-based approach to map wiring of the whole brain
A team of neuroscientists have proposed a new and potentially revolutionary way of obtaining a neuronal connectivity map (the “connectome”) of the whole brain of the mouse. The details are set forth in an essay published October 23 in the open-access journal PLOS Biology.
The team, led by Professor Anthony Zador, Ph.D., of Cold Spring Harbor Laboratory, aims to provide a comprehensive account of neural connectivity. At present the only method for obtaining this information with high precision relies on examining individual cell-to-cell contacts (synapses) in electron microscopes. But such methods are slow, expensive and labor-intensive.
Zador and colleagues instead propose to exploit high-throughput DNA sequencing to probe the connectivity of neural circuits at the resolution of single neurons.
“Our method renders the connectivity problem in a format in which the data are readable by currently available high-throughput genome sequencing machines,” says Zador. “We propose to do this via a process we’re now developing, called BOINC: the barcoding of individual neuronal connections.”
The proposal comes at a time when a number of scientific teams in the U.S. are progressing in their efforts to map connections in the mammalian brain. These efforts use injections of tracer dyes or viruses to map neuronal connectivity at a “mesoscopic” scale—a mid-range resolution that makes it possible to follow neural fibers between brain regions. Other groups are scaling up approaches based on electron microscopy.
Filed under brain connectome BOINC barcoding technique DNA neuron neuroscience science
The Fabric for Weaving Memory
The details of memory formation are still largely unknown. It has, however, been established that the two kinds of memory – long term and short term – use different mechanisms. When short-term memory is formed, certain proteins in the nerve cells (neurons) of the brain are transiently modified. To establish long-term memory, the cells have to synthesize new protein molecules. This has been shown in experiments with animals. When drugs were used to block protein synthesis, the treated animals were not able to form long-term memory.
The precise mechanism by which the newly synthesized proteins regulate memory formation is still poorly understood. They are thought to strengthen existing connections between neurons, as well as establish new connections. Both processes are required for long-term memory formation.
A nerve cell in the brain makes connections with tens of thousands of other nerve cells through so-called synapses. When memory is formed, only specific synapses, which are activated by a specific experience are modified. The mechanism of how the synthesis of new proteins can be restricted to these activated synapses has been unclear. Neurobiologists have postulated the existence of “synaptic tags”. One of the candidates is a family of proteins known to regulate local protein synthesis, the CPEB family of proteins. These proteins have been known for some time to perform important tasks during embryonic development, and recently have been identified in neuronal synapses.
In 2007, Krystyna Keleman, a neuroscientist at the Research Institute of Molecular Pathology (IMP) in Vienna, was able to show that fruit flies require CPEB proteins for long-term memory formation.
To study memory formation, the researchers at the IMP looked at the sexual behavior of flies. After copulation, female flies loose interest in the courtship advances of males. Male flies must learn – by trial and error – that only virgin females are receptive. The key to telling them apart is their smell.
Filed under drosophila memory LTM STM protein synthesis memory formation neuroscience science
Why Some People See Sound
Some people may actually see sounds, say researchers who found this odd ability is possible when the parts of the brain devoted to vision are small.
These findings points to a clever strategy the brain might use when vision is unreliable, investigators added.
Scientists took a closer look at the sound-induced flash illusion. When a single flash is followed by two bleeps, people sometimes also see two illusory consecutive flashes.
Past experiments revealed there are strong differences between individuals when it comes to how prone they are to this illusion. “Some would experience it almost every time a flash was accompanied by two bleeps, others would almost never see the second flash,” said researcher Benjamin de Haas, a neuroscientist at University College London.
These differences suggested to de Haas and his colleagues that maybe variations in brain anatomy were behind who saw the illusion and who did not. To find out, the researchers analyzed the brains of 29 volunteers with magnetic resonance imaging (MRI) and tested them with flashes and bleeps.
On average, the volunteers saw the illusion 62 percent of the time, although some saw it only 2 percent of the time while others saw it 100 percent of the time. They found the smaller a person’s visual cortex was — the part of the brain linked with vision —the more likely he or she experienced the illusion.
"If we both look at the same thing, we would expect our perception to be identical," de Haas told LiveScience. "Our results demonstrate that this not quite true in every situation — sometimes what you perceive depends on your individual brain anatomy."
The researchers suggest this illusion could reveal a way the brain compensates for imperfect visual circuitry.
Filed under brain illusion sound-induced flash illusion vision perception neuroscience psychology science
A new study shows that electrical stimulation of a small patch of the brain causes illusions that only affect the perception of faces. (Matt Cardy/Getty Images)
Ron Blackwell didn’t enter the hospital expecting to see his doctor’s face melt before his eyes. But that’s exactly what happened when researchers electrically stimulated a small part of his brain, according to a study published Tuesday in the Journal of Neuroscience.
The doctor’s face did not actually melt, of course. Instead, the researchers argue, the stimulation short-circuited a brain area called the fusiform gyrus. Previous studies have linked a part of that area to face processing by showing that it becomes active when people perceive faces. But it’s hard to know just how important the area is for facial processing unless you can actually change its activity level while someone views faces.
Blackwell, an epileptic, turned out to be the perfect test case. He was in Stanford’s hospital so that doctors — including the study author, Dr. Josef Parvizi — could study his epilepsy and decide whether they could perform surgery to remove the part of the brain responsible for his seizures. As part of that procedure, Parvizi laid down a strip of electrodes on the surface of the brain. That gave him the capacity to painlessly and harmlessly stimulate the part of the brain they covered, and one of those electrodes was right over the fusiform gyrus.
Along with collaborators led by Stanford psychologist Kalanit Grill-Spector, Parvizi stimulated the area to see whether it would affect Blackwell’s perception of the doctor’s face. When he performed a sham stimulation — counting down from three and pressing a button that did nothing — Blackwell reported no change.
But when Parvizi applied voltage, strange things suddenly began to happen to Blackwell’s face perception. “You just turned into somebody else,” Blackwell said in a video that was recorded as part of the experiment. “Your face metamorphosed. Your nose got saggy, went to the left. You almost looked like somebody I’d seen before, but somebody different. That was a trip.” As soon as the electricity was turned off, Blackwell’s visualization of Parvizi’s face returned to normal.
Later, Blackwell confirmed that it was only the doctor’s face that changed — his body and hands remained the same.
Though only a single case, the experiment provides strong confirmatory evidence that the fusiform gyrus is indeed directly involved in processing face perception, and that the area is specialized for doing so.
(Source: Los Angeles Times)
Filed under brain brain stimulation fusiform gyrus face perception face recognition neuroscience psychology science
New hope for the blind from neuroscientists?
Scientists in the Texas Medical Center believe that there may be a way to use mental images to help some of the estimated 39 million people worldwide who are blind.
Scientists in the laboratories of Michael Beauchamp, Ph.D., an associate professor of neurobiology and anatomy at the The University of Texas Health Science Center at Houston (UTHealth) Medical School, and Daniel Yoshor, M.D., an associate professor of neurosurgery and neuroscience at Baylor College of Medicine, have discovered a neural mechanism for conscious perception that could use the brain’s image-generating ability.
“While much work remains to be done, the possibilities are exciting,” said Beauchamp, the study’s lead author. “If successful, we would in essence bypass eyes that no longer work and stimulate the brain to generate mental images. This type of device is known as a visual prosthetic.”
Filed under vision mental images prosthetics phosphene blindness neuroscience science
"Blue" Light Could Help Teenagers Combat Stress
Adolescents can be chronically sleep deprived because of their inability to fall asleep early in combination with fixed wakeup times on school days. According to the CDC, almost 70 percent of school children get insufficient sleep—less than 8 hours on school nights. This type of restricted sleep schedule has been linked with depression, behavior problems, poor performance at school, drug use, and automobile accidents. A new study from the Lighting Research Center (LRC) at Rensselaer Polytechnic Institute shows that exposure to morning short-wavelength “blue” light has the potential to help sleep-deprived adolescents prepare for the challenges of the day and deal with stress, more so than dim light.
The study was a collaboration between Associate Professor and Director of the LRC Light and Health Program Mariana Figueiro and LRC Director and Professor Mark S. Rea. Results of the study titled “Short-Wavelength Light Enhances Cortisol Awakening Response in Sleep-Restricted Adolescents,” were recently published in the open access International Journal of Endocrinology. The full text is available at http://www.hindawi.com/journals/ije/2012/301935/.
(Image credit)
Filed under sleep sleep deprivation adolescents adulthood circadian rhythms neuroscience psychology science
