Brain Network Connections Revealed

ScienceDaily (July 13, 2011) — Research conducted by Maria Ercsey-Ravasz and Zoltan Toroczkai of the University of Notre Dame's Interdisciplinary Center for Network Science and Applications (iCeNSA), along with the Department of Physics and a group of neuroanatomists in France, has revealed previously unknown information about the primate brain.

New research has shown that the brain is characterized by a highly consistent, weighted network among the functional areas of the cortex, which are responsible for such functions as vision, hearing, touch, movement control and complex associations. The study revealed that such cortical networks and their properties are reproducible from individual to individual.

The researchers published an article in the journal Cerebral Cortexshowing that the brain is characterized by a highly consistent, weighted network among the functional areas of the cortex, which are responsible for such functions as vision, hearing, touch, movement control and complex associations. The study revealed that such cortical networks and their properties are reproducible from individual to individual.

Ercsey-Ravasz, a postdoctoral associate, and Toroczkai, professor of physics, analyzed 70 man-years' worth of data on macaque brains collected by a large group led by Henry Kennedy in Lyon, France. The Kennedy team injected ink tracers into a portion of the brain and scanned thin brain slices to track the movement of the chemical through the nerve cells' branches, called axons, to the soma of the cells. Kennedy enlisted iCeNSA for its expertise at analyzing networks, which has also been applied to fields as diverse as the spread of disease and the social networks. Their analysis identified the consistency of connectivity among the areas of the brain.

Ercsey-Ravasz, in a study of the data that will be included in a later paper, also has demonstrated that the number of connections is greatest between areas that are closest, and the number declines in a consistent pattern as distance increases. The regularity of the patterns from animal to animal suggests that the connections are necessary, and the fewer long-distance connections likely are control switches that coordinate or modulate information exchange amongst the brain areas.

The study is part of a broader investigation of brain function and intelligence that has accelerated in recent years as researchers abandoned the once-promising analogy between computer circuitry and human intelligence, a project that stalled in the 1970s. "It turns out the brain is not just this beautiful circuitry you could just back-engineer," Toroczkai says. "It is an amazingly complex system, and this is why it is very hard to understand why it works."

The adult primate brain contains 100 billion neurons with branches that connect at more than 100 trillion points. A top-down approach called functional decomposition, identifying bundles within the brain, helps overcome the sheer data volume. The macaque brain has 83 such areas; the human brain more than 120. "What we find is a network of connections between the functional areas," Toroczkai says. "That's important because we now have more detailed information about how the brain is wired on a large-scale, functional level."

Toroczkai and Ercsey-Ravasz will continue research in the field with US and international collaborators, aimed at understanding how information received through the senses and converted to electric pulses is processed in the brain. "It looks like there is some sort of general algorithm that is being run in this brain network," he says. "The wiring is very strange. It is not something you would expect. It constitutes one of the major motivations for this study."

New Means of Overcoming Antiviral Resistance in Influenza

ScienceDaily (July 13, 2011) — Researchers from the University of California, Irvine, with assistance from the San Diego Supercomputer Center at UC San Diego, have found a new approach to the creation of customized therapies for virulent flu strains that resist current antiviral drugs.

The 150- and 430-loop structures are shown for 09N1 crystal structure (purple), 09N1 second most dominant molecular dynamics (MD) cluster representative structure (green backbone) and VN04N1 crystal structure (orange), indicating that the pandemic N1 adopts an open 150-loop conformation. Gly147, Ile149, Lys150 and Pro431 are shown in stick representation. This simulation was conducted on SDSC's Trestles supercomputer. 

The findings, published online this week in Nature Communications, could aid development of new drugs that exploit so-called flu protein 'pockets.'

Using powerful computer simulations on SDSC's new Trestles system, launched earlier this year under a $2.8 million National Science Foundation (NSF) award, UCI's Rommie Amaro and Robin Bush together with SDSC's Ross Walkercreated a method to predict how pocket structures on the surface of influenza proteins promoting viral replication can be identified as these proteins evolve, allowing for possible pharmaceutical exploitation.

"Our results can influence the development of new drugs taking advantage of this unique feature," said Amaro, an assistant professor of pharmaceutical sciences and computer science at UCI. Prior to joining UCI in 2009, Amaro was a postdoctoral fellow in chemistry at UC San Diego.

The search for effective flu drugs has always been hampered by the influenza virus itself, which mutates from strain to strain, making it difficult to target with a specific pharmaceutical approach. The most common clinical flu treatments are broad-based and only partially effective. They work by interrupting the action of an enzyme in the virus called neuraminidase, which plays a critical role in viral replication.

In 2006, scientists discovered that avian influenza neuraminidase (N1) exhibited a distinctive, pocket-shaped feature in the area pinpointed by clinically used drugs. They named it the 150-cavity.

Amaro and Bush, associate professor of ecology and evolutionary biology, conducted research using resources at the San Diego Supercomputer Center, as well as the National Institute for Computational Sciences (NICS) to learn the conditions under which the pockets form. They created molecular simulations of flu proteins to predict how these dynamic structures move and change, as well as and where and when the 150-cavity pockets will appear on the protein surface.

This sequence analysis method could be utilized on evolving flu strains, providing vital information for drug design, Amaro said. "Having additional antivirals in our treatment arsenal would be advantageous and potentially critical if a highly virulent strain, for example, H5N1, evolved to undergo rapid transmission among humans or if the already highly transmissible H1N1 pandemic virus was to develop resistance to existing antiviral drugs," she added.

Walker, an assistant research professor who runs the Walker Molecular Dynamics Lab at SDSC, developed a customized version of the AMBER software, a widely used package of molecular simulation codes, to run these specific simulations on Trestles under the NSF's TeraGrid Advanced User Support System. That included detailed performance tuning including hard-coding atom counts, atom types and parameters, and being able to use Trestles for uninterrupted two-week runs that together consumed more than one million SUs (single processor hours).

"We initially used the Athena supercomputer at NICS, which provided us with all the initial comparison data before Trestles came online earlier this year," said Walker, who is also an adjunct assistant professor in UC San Diego's Department of Chemistry and Biochemistry. "We had Trestles all ready to go as soon as the first H1N1 protein structure was available, and using the earlier work we did on Athena, we were able to putTrestles immediately to work to conduct simulations of the structure as part of this research."

Skin. The addition of two particular gene snippets to a skin cell's usual genetic material is enough to turn that cell into a fully functional neuron, report researchers from the Stanford University School of Medicine.

ScienceDaily (July 13, 2011) — High doses of the hormone progesterone can kill neuroblastoma cells while leaving healthy cells unscathed, scientists at Emory University School of Medicine have found in laboratory research.

The results, published in the journalMolecular Medicine, suggest that progesterone could be used to fight neuroblastoma, the most common form of cancer affecting small children.

More research is necessary to determine the optimal dose, how long progesterone treatment should last and if it should be used alone or in combination with radiation or chemotherapy. Emory scientists are also exploring whether it can stop the growth of other brain cancer types such as glioblastoma and astrocytoma. Progesterone has also been reported to slow growth of several other types of cancers in the laboratory, but has not been used clinically against neuroblastoma.

The first author in the team of researchers is Fahim Atif, PhD, instructor in emergency medicine, with senior author Donald G. Stein, PhD, Asa G. Candler professor of emergency medicine and director of Emory's Department of Emergency Medicine Brain Research Laboratory. Daniel Brat, MD, PhD, professor of pathology and laboratory medicine in Emory School of Medicine was a collaborator on the research team.

The discovery grew out of studies of progesterone's protective effects in brain injury. Based on Stein's pioneering work, medical centers across the country are now testing progesterone in the setting of acute traumatic brain injury in a phase III clinical trial. While investigating how to enhance progesterone's effectiveness, Atif and his colleagues observed that it could protect healthy neurons from stress but caused cells from a tumor cell line to die.

In a mouse model, progesterone treatment cut tumor growth in half over eight days, while no drug toxicity was seen with healthy neurons or in live animals. The researchers showed that progesterone can decrease the levels of proteins produced by tumor cells that attract new blood vessel growth and help tumor cells invade other tissues.

"This fits with what we know about one of progesterone's roles during pregnancy, which is to regulate the growth of placenta," Atif says. "Placental cells behave in a way that resembles tumor cells, invading the uterine wall and tapping into the mother's blood vessels."

In studies performed elsewhere, doses of progesterone that were lower than the most effective dose in the Emory study actually accelerated cancer growth. Based on their results, the Emory researchers propose that for fighting certain types of cancer, high doses of progesterone may be better than low doses.

Progesterone's effects on cancer are known to be complex. There may be differences between progesterone, the natural hormone, and synthetic progestins. The National Institutes of Health's Women's Health Initiative study showed that women who received hormone replacement therapy with combined estrogen and progestins had an increased risk of heart disease and breast cancer, although some studies have identified a potential "safe period" if hormone replacement therapy lasts less than two years.

Progesterone has a long history as a treatment designed to prevent preterm birth. If progesterone is to be used with small children, any potential effects on development must be weighed against the risks of standard treatments.

Efficient Process Using microRNA Converts Human Skin Cells Into Neurons

ScienceDaily (July 13, 2011) — The addition of two particular gene snippets to a skin cell's usual genetic material is enough to turn that cell into a fully functional neuron, report researchers from the Stanford University School of Medicine. The finding, to be published online July 13 in Nature, is one of just a few recent reports of ways to create human neurons in a lab dish.

Skin. The addition of two particular gene snippets to a skin cell's usual genetic material is enough to turn that cell into a fully functional neuron, report researchers from the Stanford University School of Medicine.

The new capability to essentially grow neurons from scratch is a big step for neuroscience research, which has been stymied by the lack of human neurons for study. Unlike skin cells or blood cells, neurons are not something that's easy for a living human to donate for research.

"A major problem in neurobiology has been the lack of a good human model," said senior author Gerald Crabtree, MD, professor of pathology and of developmental biology. "Neurons aren't like blood. They're not something people want to give up."

Generating neurons from easily accessible cells, such as skin cells, makes possible new ways to study neuronal development, model disease processes and test treatments.

It also helps advance the effort, still in its infancy, to replace damaged or dead neurons with new ones.

Before succeeding at turning skin cells straight into neurons, scientists had discovered two years ago that they could get similar results if they transformed the skin cell first into a stem cell and then coaxed the stem cell into becoming a neuron. But Crabtree's new study and two studies by others show it's possible to go straight from skin cell to neuron without the stem-cell pit stop.

Crabtree's study is unique among the efforts because of the surprising identity of the molecules that nudged the cells to switch -- short chains of genetic material called microRNA, best known for their ability to bind to specific genetic transcripts to turn off their activity.

"In this case, though, they're playing an instructive role," Crabtree said.

The discovery of the microRNAs' ability to switch the cells came to light when Andrew Yoo, PhD, then a postdoctoral researcher in Crabtree's lab (now on the faculty of Washington University in St. Louis), was trying to better understand what makes neural stem cells move on to become mature neurons. He found that two microRNAs, miR-9/9* and miR-124, trigger it by controlling a molecular machine (called the BAF chromatin remodeling complex) that shapes chromosomes so they'll direct the cell to remain a stem cell.

"When the microRNAs bind to one subunit of this 13-membered complex they turn this function off, and the cells begin to grow up and connect to one another -- that is, they become mature, functioning neurons," said Crabtree. After they published this in Nature in 2009, Yoo went on to try to understand how the two microRNAs functioned. One way he did this was to watch what happened when he introduced them into cells that normally lacked them.

At first he didn't believe what he was seeing through the microscope: The cells with the additional microRNAs had started to look like neurons. "It was very weird. We were astounded," said Crabtree, who is also the David Korn, MD, Professor of Pathology.

Yoo, one of the new report's lead authors, continued to study the phenomenon with others at Stanford. They used a virus to carry the snippets into skin cells and investigated whether the resulting cells really were neurons. They found that 2 to 3 percent of the skin cells reliably converted to neurons: The cells generated the electrical signals neurons use to communicate with one another, and they budded off small globules, called synaptic vesicles, just as the adult neurons ordinarily do.

"What we made are neurons that are characteristic of the frontal cortex -- actually what you'd imagine would be the most difficult to make. They're the ones we think with, that we use to put two things together and see connections, not the ones involved in evolutionarily older emotional responses," said Crabtree. "We also find inhibitory neurons among the converted cells, whose role is to keep the activity of other neurons at a resting, controlled state."

The team improved the efficiency of the transformation to 20 percent by adding two of the factors used in a similar experiment by colleague Marius Wernig, MD, assistant professor of pathology, in the first published account of converting a human skin cell directly to a neuron. In May this year, Wernig reported in Nature that the combination of four particular proteins can convert skin cells directly into functional neurons with 2 to 4 percent efficiency. (Even more recently, on July 3, Nature published a study led by a researcher at the San Raffaele Scientific Institute in Milan, Italy, showing a mix of three other proteins can set off the conversion.)

"It's been a long time in coming to this," said Crabtree. "But science often progresses in leaps and starts, and then all of a sudden many scientists come to the same position at the same time. Now these studies have come out, and more will be coming, all of which are going to say that not only can you can make neurons different ways, but also you can make neurons of different types."

Wernig's study produced the same "thinking" neurons as Crabtree's did, but did not find inhibitory neurons. The Italian study produced neurons that release dopamine, a chemical that affects many behaviors, from moving, to learning, to sleeping.

Among the projects taking off from this finding is an effort to set up a model for Down syndrome. Stanford graduate student Alfred Sun, a co-leader of the study, has obtained skin cells from patients and converted them to neurons. Now he can try to see what's different about them.

"Our belief is there are certain biochemical abnormalities that might be correctable," Crabtree said.

The other researchers involved in the newly published study are the two additional co-lead authors, postdoctoral researcher Alex Shcheglovitov, PhD, and medical student Li Li; postdoctoral researchers Thomas Portmann, PhD, and Yulong Li, PhD; MD/PhD student Chris Lee-Messer; associate professor of neurobiology Ricardo Dolmetsch, PhD; and professor of molecular and cellular physiology Richard Tsien, PhD.

New Understandings of Circadian Rhythms

ScienceDaily (July 13, 2011) — A tiny plant calledArabidopsis thaliana just helped scientists unearth new clues about the daily cycles of many organisms, including humans. This is the latest in a long line of research, much of it supported by the National Institutes of Health, that uses plants to solve puzzles in human health.

Soybeans grow in spurts just before dawn.

While other model organisms may seem to have more in common with us, greens like Arabidopsis provide an important view into genetics, cell division and especially light sensing, which drives 24-hour behavioral cycles called circadian rhythms.

Some human cells, including cancer cells, divide with a 24-hour rhythm. One of the main human circadian rhythm genes, cryptochrome, has been associated with diabetes and depression. Both of these discoveries grew from work with plants.

"We don't have stems and we don't flower, but our body parts, like those of plants, are controlled by circadian clocks," says NIH geneticist Laurie Tompkins. "Clocks operate more or less the same way in all organisms, but some aspects of clock function are easier to study in plants."

The new work, released this week in the early online publication of Nature, investigated why Arabidopsis does its major stem-growing in the dark -- a pattern common to most plants. Biologist Steve Kay and colleagues at the University of California, San Diego, report that a specific trio of proteins regulates the rhythm in Arabidopsis stems.

The group of proteins, called the evening complex, interacts in the early evening to silence two genes that usually promote plant growth. When the evening complex's activity trails off a few hours before dawn, proteins release the brakes on growth and plants enter their nightly phase of rapid stem elongation.

When Kay's team mutated the three genes that code for the evening complex, they noticed that this made the Arabidopsisbiological clock run out of sync -- stems grew unusually long and flowered early.

Scientists aren't yet certain why night is the best time for stems to grow, but Kay speculates it has to do with using resources efficiently. Plants pick up carbon and nitrogen during the day, then store these essential nutrients as starch and proteins. "In the later night, they can release these resources in a coordinated fashion to provide the building blocks for stem growth," says Kay.

"Our understanding of human health and the role of clocks in health and disease can greatly benefit from studying how clocks work in plants," he adds.

Kay's work could also shed light on how clock genes regulate cell division in human embryos.

From Crops to Cures

Scientists like Kay are interested in answering basic biological questions, but others who work with plants have their eyes on future disease therapies.

Plant-based molecules, for instance, are being used to target reservoirs of HIV that hide out in their hosts. At the University of California, Berkeley, chemist Jay Keasling is looking for simple ways to get microbes to produce greater quantities of these plant-based molecules at lower cost.

How plants like Arabidopsis suppress harmful genes may also help improve HIV therapies. A team of biologists led by Craig Pikaard at Washington University in St. Louis is investigating RNA polymerases, chemicals important in determining which genes get switched on, to learn how plants silence harmful virus-derived genes. Similar silencing pathways could be harnessed for HIV therapies.

More generally, scientists are looking toward plants as a medicinal source. Chemist Sarah O'Connor at MIT is genetically engineering periwinkle plants, the natural source of the anticancer drug vinblastine, to produce variations of the drug with halogens attached. Halogens make some medicines last longer in the body, meaning that probing periwinkle's capabilities could make cancer treatments more effective