One species' entire genome discovered inside another's

Whole-genome transfer raises questions about evolution, sequencing Friday, 31 August 2007 Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the entire genome of a bacterial parasite residing inside the genome of its host species. The finding, reported in today’s Science, suggests that lateral gene transfer — the movement of genes between unrelated species — may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution. Such large — scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. The results also have serious repercussions for genome — sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits. “This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.” “It didn’t seem possible at first,” says Werren, professor of biology at the University of Rochester and a world — leading authority on the parasite, called Wolbachia. “This parasite has implanted itself inside the cells of 70 percent of the world’s invertebrates, coevolving with them. And now, we’ve found at least one species where the parasite’s entire or nearly entire genome has been absorbed and integrated into the host’s. The host’s genes actually hold the coding information for a completely separate species.” Wolbachia may be the most prolific parasite in the world — a “pandemic,” as Werren calls it. The bacterium invades a member of a species, most often an insect, and eventually makes its way into the host’s eggs or sperm. Once there, the Wolbachia is ensured passage to the next generation of its host, and any genetic exchanges between it and the host also are much more likely to be passed on. Since Wolbachia typically live within the reproductive organs of their hosts, Werren reasoned that gene exchanges between the two would frequently pass on to subsequent generations. Based on this and an earlier discovery of a Wolbachia gene in a beetle by the Fukatsu team at the University of Tokyo, Japan, the researchers in Werren’s lab and collaborators at J. Craig Venter Institute (JCVI) decided to systematically screen invertebrates. Julie Dunning-Hotopp at JCVI found evidence that some of the Wolbachia genes seemed to be fused to the genes of the fruit fly, Drosophila ananassae, as if they were part of the same genome. Michael Clark, a research associate at Rochester then brought a colony of ananassae into Werren’s lab to look into the mystery. To isolate the fly’s genome from the parasite’s, Clark fed the flies a simple antibiotic, killing the Wolbachia. To confirm the ananassae flies were indeed cured of the Wolbachia, Clark tested a few samples of DNA for the presence of several Wolbachia genes. To his dismay, he found them. “For several months, I thought I was just failing,” says Clark. “I kept administering antibiotics, but every single Wolbachia gene I tested for was still there. I started thinking maybe the strain had grown antibiotic resistance. After months of this I finally went back and looked at the tissue again, and there was no Wolbachia there at all.” Clark had cured the fly of the parasite, but a copy of the parasite’s genome was still present in the fly’s genome. Clark was able to see that Wolbachia genes were present on the second chromosome of the insect. Clark confirmed that the Wolbachia genes are inherited like “normal” insect genes in the chromosomes, and Dunning-Hotopp showed that some of the genes are “transcribed” in uninfected flies, meaning that copies of the gene sequence are made in cells that could be used to make Wolbachia proteins. Werren doesn’t believe that the Wolbachia “intentionally” insert their genes into the hosts. Rather, it is a consequence of cells routinely repairing their damaged DNA. As cells go about their regular business, they can accidentally absorb bits of DNA into their nuclei, often sewing those foreign genes into their own DNA. But integrating an entire genome was definitely an unexpected find. Werren and Clark are now looking further into the huge insert found in the fruit fly, and whether it is providing a benefit. “The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host,” says Werren. “The question is, are these foreign genes providing new functions for the host? This is something we need to figure out.” Evolutionary biologists will certainly take note of this discovery, but scientists conducting genome — sequencing projects around the world also may have to readjust their thinking. Before this study, geneticists knew of examples where genes from a parasite had crossed into the host, but such an event was considered a rare anomaly except in very simple organisms. Bacterial DNA is very conspicuous in its structure, so if scientists sequencing a nematode genome, for example, come across bacterial DNA, they would likely discard it, reasonably assuming that it was merely contamination — perhaps a bit of bacteria in the gut of the animal, or on its skin. But those genes may not be contamination. They may very well be in the host’s own genome. This is exactly what happened with the original sequencing of the genome of the ananassae fruit fly — the huge Wolbachia insert was discarded from the final assembly, despite the fact that it is part of the fly’s genome. In the early days of the Human Genome Project, some studies appeared to show bacterial DNA residing in our own genome, but those were shown indeed to be caused by contamination. Wolbachia is not known to infect any vertebrates such as humans. “Such transfers have happened before in the distant past” notes Werren. “In our very own cells and those of nearly all plants and animals are mitochondria, special structures responsible for generating most of our cells’ supply of chemical energy. These were once bacteria that lived inside cells, much like Wolbachia does today. Mitochondria still retain their own, albeit tiny, DNA, and most of the genes moved into the nucleus in the very distant past. Like Wolbachia, they have passively exchanged DNA with their host cells. It’s possible Wolbachia may follow in the path of mitochondria, eventually becoming a necessary and useful part of a cell.” “In a way, Wolbachia could be the next mitochondria,” says Werren. “A hundred million years from now, everyone may have a Wolbachia organelle.” “Well, not us,” he laughs. “We’ll be long gone, but Wolbachia will still be around.” ......... ZenMaster

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Over-sized mice get even bigger!

'Mighty mice' made mightier Wednesday, 29 August 2007 The Johns Hopkins scientist who first showed that the absence of the protein myostatin leads to oversized muscles in mice and men has now found a second protein, follistatin, whose overproduction in mice lacking myostatin doubles the muscle-building effect. Results of Se-Jin Lee’s new study, appearing on August 29 in the online, open-access journal PLoS ONE, show that while mice that lack the gene that makes myostatin have roughly twice the amount of body muscle as normal, mice without myostatin that also overproduce follistatin have about four times as much muscle as normal mice. Lee, M.D., Ph.D., a professor of molecular biology and genetics, says that this added muscle increase could significantly boost research efforts to “beef up” livestock or promote muscle growth in patients with muscular dystrophy and other wasting diseases. Specifically, Lee first discovered that follistatin was capable of blocking myostatin activity in muscle cells grown under lab conditions. When he gave it to normal mice, the rodents bulked up, just as would happen if the myostatin gene in these animals was turned off. He then genetically engineered a mouse that both lacked myostatin and made extra follistatin. If follistatin was increasing muscle growth solely by blocking myostatin, then Lee surmised that follistatin would have no added effect in the absence of myostatin. “To my surprise and delight, there was an additive effect,” said Lee, who notes these muscular mice averaged a 117 percent increase in muscle fibre size and a 73 percent increase in total muscle fibres compared to normal mice. “These findings show that the capacity for increasing muscle growth by targeting these pathways is much more extensive than we have appreciated,” adds Lee. “Now we’ll search for other players that cooperate with myostatin, so we can tap the full potential for enhancing muscle growth for clinical applications.” Lee adds that this issue is of particular significance, as most agents targeting this pathway, including one drug being currently tested in a muscular dystrophy clinical trial, have been designed to block only myostatin and not other related proteins. ......... ZenMaster

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hESC help rat hearts repair

Human derived stem cells can repair rat hearts damaged by heart attack Monday, 27 August 2007 When human heart muscle cells derived from embryonic stem cells are implanted into a rat after a heart attack, they can help rebuild the animal's heart muscle and improve function of the organ, scientists report in the September issue of Nature Biotechnology. The researchers also developed a new process that greatly improves how stem cells are turned into heart muscle cells and then survive after being implanted in the damaged rat heart. The findings suggest that stem-cell-based treatments might one day help people suffering from heart disease, the leading cause of death in most of the world. The study was conducted by researchers at the University of Washington School of Medicine in Seattle and at Geron Corp. in Menlo Park, California. The scientists set out to tackle two of the main challenges to treating damaged hearts with stem cells: the creation of cardiac cells from embryonic stem cells, and the survival of those cells once they are implanted in a damaged heart. "Past attempts at treating infarcted hearts with stem cells have shown promise, but they have really been hampered by these challenges," explained Dr. Chuck Murry, director of the Center for Cardiovascular Biology in the UW Institute for Stem Cell and Regenerative Medicine, and corresponding author on the study. "This method we developed goes a long way towards solving both of those problems. We got stem cells to differentiate into mostly cardiac muscle cells, and then got those cardiac cells to survive and thrive in the damaged rat heart." Embryonic stem cells can differentiate, or turn into, any type of cell found in the body. But researchers had struggled to get stem cells to differentiate into just cardiomyocytes, or heart muscle cells — most previous efforts resulted in cell preparations in which only a fraction of 1 percent of the differentiated cells were cardiac muscle cells. By treating the stem cells with two growth factors, or growth-encouraging proteins, and then purifying the cells, they were able to turn about 90 percent of stem cells into cardiomyocytes. The researchers dealt with the other big challenge of stem cell death by implanting the cells along with a cocktail of compounds aimed at helping them grow. The cocktail included a growth "matrix" — a sort of scaffolding for the cells to latch on to as they grow — and drugs that block processes related to cell death. When using the pro-growth cocktail, the success rate of heart muscle grafts improved drastically: 100 percent of rat hearts showed successful tissue grafts, compared to only 18 percent in grafts without the cocktail. "The problem of cell death is pretty common in stem-cell treatments," Murry explained. "When we try to regenerate with liquid tissues, like blood or bone marrow, we're pretty good at it, but we haven't been very successful with solid tissues like skeletal muscle, brain tissue, or heart muscle. This is one of the most successful attempts so far using cells to repair solid tissues — every one of the treated hearts had a well-developed tissue graft." When the researchers followed up on the stem-cell treatment by taking images of the rat hearts, they found that the grafts helped thicken the walls that normally stretch out after a heart attack and cause the heart to weaken. The thickened walls were also associated with more vigorous contraction. "We found that the grafts didn't just survive in the rat hearts — they also helped improve the function of the damaged heart," said Dr. Michael Laflamme, UW assistant professor of pathology and the lead author of the study. "That's very important, because one of the major problems for people suffering a myocardial infarction is that the heart is damaged and doesn't pump blood nearly as well. This sort of treatment could help the heart rebound from an infarction and retain more of its function afterwards." The next step in studying stem-cell treatments for the heart is to conduct similar experiments in large animals, like pigs or sheep, while further refining the treatment in rats. Early human clinical trials could begin in about two years, Murry said. ......... ZenMaster

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British scientists in hybrid embryo plea

British scientists in hybrid embryo plea Sunday, 26 August 2007 Last year, British scientists applied for licence to create human-cow hybrid embryos, to isolate stem cells from the resulting blastocysts. Now, the Human Fertilisation and Embryology Authority is expected to announce its decision next week on whether to give permission to the UK laboratories to create the hybrid embryos to advance the understanding of genetic diseases. Dr Stephen Minger from King's College London is one of the researchers that has applied for a licence to do work using such hybrids. Another is Dr Lyle Armstrong, who is based at the North East England Stem Cell Institute (NESCI ) at the International Centre for Life in Newcastle. Dr. Minger said in an interview with The Observer, that: “I'm cautiously optimistic that the authority will allow us a licence. I hope we have made the case that by doing this research; we can study a number of genetic diseases far more clearly. The cell discoveries we make could then be used to develop therapies for diseases such as Alzheimer's which affect so many people, but for which we now have almost no therapy to offer.” To do this work they would need a large number of embryos to make stem cells, far more than could be achieved by asking women to donate their eggs for research. Instead of using human eggs and sperm for these experiments, Dr. Minger thinks it makes far more sense to use cow eggs, since these can be taken from ovaries of thousands of cows that are slaughtered every day anyway. To do this work they would need a large number of embryos to make stem cells, far more than could be achieved by asking women to donate their eggs for research. The British government this spring shifted its position on animal-human hybrid embryos: having been initially against the concept, it is now proposing to allow partial hybrids, where a complete set of human genes is inserted into an animal's egg cell, for research purposes only, through a new Human Tissue and Embryo Bill aimed at overhauling the laws surrounding fertility treatment. The move has prompted strong protests from some religious and anti-abortion groups that oppose any such research. ......... ZenMaster

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Out-of-body experiences

Scientists propose explanation for out-of-body experiences 23-Aug-2007 Using virtual reality goggles to mix up the sensory signals reaching the brain, scientists have induced out-of-body-like experiences in healthy people, suggesting a scientific explanation for a phenomenon often thought to be a figment of the imagination. The sight of their bodies located somewhere else — thanks to the goggles — plus the feel of their real bodies being touched simultaneously made volunteers sense that they had moved outside of their physical bodies, according to a pair of studies in the 24 August 2007 issue of the journal Science, published by AAAS, the non-profit science society. A disconnect between the brain circuits that process both these types of sensory information may thus be responsible for some out-of-body experiences, the researchers say. Out-of-body experiences, which generally involve the feeling of disembodiment and seeing one’s own body from a location outside the body, can occur in part through drug use, epileptic seizures and other types of brain disturbances. By projecting a person’s awareness into a virtual body, the techniques used in these studies may be useful for training people to do delicate “tele-operating” tasks, such as performing surgeries remotely. The findings may also remove some of the stigma that patients with neurological disorders may feel about having these experiences, which are frequently attributed to an active imagination or some sort of paranormal phenomenon. The studies also help solve the age-old question of how we perceive our own bodies. “I’m interested in why we feel that our selves are inside our bodies — why we have an ‘in-body experience,’ if you like. This has been discussed for centuries in philosophy, but it’s hard to tackle experimentally,” said Science Brevium author Henrik Ehrsson of University College London, in London, and the Karolinska Institute in Stockholm. Both Ehrsson and another research team, led by Olaf Blanke of the Ecole Polytechique Fédérale de Lausanne (EPFL) and the University Hospital in Geneva, Switzerland, used video cameras and virtual reality goggles to show volunteers images of their own bodies from the perspective of someone behind them. The researchers also touched the volunteers’ bodies, both physically and virtually. The volunteers in Ehrsson’s study viewed images recorded by the cameras through their headsets. In Blanke and colleagues’ study, the video was converted into holograph-like computer simulations. Ehrsson had the volunteers watch a plastic rod moving toward a location just below the cameras while their real chests were simultaneously touched in the corresponding spot. Questionnaire responses afterwards indicated that the volunteers felt they were located back where the cameras were placed, watching a dummy or a body that belonged to someone else. “This experiment suggests that the first-person visual perspective is critically important for the in-body experience. In other words, we feel that our self is located where the eyes are,” Ehrsson said. Ehrsson also had the volunteers watch a hammer swing down to a point below the camera, as though it were going to “hurt” an unseen portion of the virtual body. Measurements of skin conductance, which reflects emotional responses such as fear, indicated that the volunteers sensed their “selves” had left their physical bodies and moved to the virtual bodies. Blanke’s team used a similar setup to create out-of-body-like experiences (which they cautioned lacked some aspects of full-blown out-of-body experiences). After the virtual reality exercise, a researcher would blindfold the volunteers and guide them backward. When the volunteers were asked to return to their original position, they tended to drift toward where they had seen their virtual bodies standing. Both studies conclude that “multisensory conflict” is a key mechanism underlying out-of-body experiences. “Brain dysfunctions that interfere with interpreting sensory signals may be responsible for some clinical cases of out-of-body experiences,” Ehrsson said. “Though, whether all out-of-body experiences arise from the same causes is still an open question.” Bodily self-consciousness may also involve a cognitive dimension – the ability to distinguish between one’s own body and other objects – in addition to sensory signals, Blanke and his co-authors propose. Supporting this idea, Blanke’s team reports that when the volunteers viewed a human-sized block instead of an image of a human body, they successfully returned to their original standing place, indicating that no out-of-body-like illusion had occurred. “Full-body consciousness seems to require not just the ‘bottom up’ process of correlating sensory information but also the ‘top down’ knowledge about human bodies,” Blanke said. Some of the out-of-body experiences that have previously eluded scientific explanation may be related to distorted “full-body perception,” according to Blanke. Virtual reality systems may provide further answers. “We have decades of intense research on visual perception, but not very much yet on body perception. But that may change, now virtual reality offers a way to manipulate full body perception more systematically and probe out-of-body experiences and bodily self consciousness in a new way,” Blanke said. “The Experimental Induction of Out-of-Body Experiences,” by H. Henrik Ehrsson of University College London, in London, UK and Karolinska Institute in Stockholm, Sweden. This research was supported by the Wellcome Trust, the PRESENCCIA project, an EU-funded project under the IST programme, the Human Frontier Science Program, the Swedish Medical Research Council and the Swedish Foundation for Strategic Research. “Video Ergo Sum: Manipulating Bodily Self-Consciousness,” by Bigna Lenggenhager and Tej Tadi at Ecole Polytechique Fédérale de Lausanne (EPFL), Switzerland; Thomas Metzinger at Johannes Gutenberg-Universität Mainz in Mainz, Germany; and Olaf Blanke at Ecole Polytechique Fédérale de Lausanne (EPFL), Switzerland and University Hospital in Geneva, Switzerland. This research was supported by the Cogito Foundation, the Fondation de Famille Shandoz, the Fondation Odier and the Swiss National Science Foundation. See the journal Science www.sciencemag.org. More on these studies: First out-of-body experience induced in laboratory setting EurekAlert - 23-Aug-2007 The embodied self: Using virtual reality to study the foundations of bodily self-consciousness EurekAlert - 23-Aug-2007 ......... ZenMaster

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Isolation of a new gene family essential for early development

Isolation of a new gene family essential for early development Wednesday, 22 August 2007

Researchers at the newly established Centre for Epigenetics at Biotech Research and Innovation Centre (BRIC), University of Copenhagen, have identified a new gene family (UTX/JMJD3) essential for embryonic development. The family controls the expression of genes crucial for stem cell maintenance and differentiation, and the results may contribute significantly to the understanding of the development of cancer.

How embryonic stem cells work All organisms consist of a number of different cell types each producing different proteins. The nerve cells produce proteins necessary for the nerve cell function; the muscle cells proteins necessary for the muscle function and so on. All these specialised cells originate from the same cell type – the embryonic stem cells. In a highly controlled process called differentiation, the stem cells are induced to become specialised cells.

Gene family helps regulate stem cell differentiation The BRIC researchers have now identified a new gene family, which by modifying gene expression is essential for the regulation of the differentiation process. The UTX and JMJD3 proteins demethylate tri-methylated Lys-27 on histone H3. These results have been obtained by using both human and mouse stem cells, as well as by studying the development of the round worm, C. elegans. Taken together, the results suggest that histone H3 demethylation as regulated by UTX/JMJD3 proteins is essential for proper development.

Perspectives The new findings are in line with a number of recent publications that support the idea that differentiation may not entirely be a “one-way process”, and may have impact on the therapeutic use of stem cells for the treatment of various genetic diseases such as cancer and Alzheimer’s disease.

Epigenetics Epigenetics is a relatively new field of research but nonetheless “hot” within biotechnological and biomedical research now. With the opening of Centre for Epigenetics University of Copenhagen joins the re-search front internationally, e.g. the EU has initiated a research net work for epigenetics – see http://epigenome.eu

Reference: UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development Nature advance online publication 22 August 2007 doi:10.1038/nature06145 .........

ZenMaster

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India’s First Institute of Regenerative Medicine

India’s First Institute of Regenerative Medicine Tuesday, 21 August 2007 Read at: http://www.geocities.com/giantfideli/art/CellNEWS_India_MIRM.html ......... ZenMaster

Milestone in the regeneration of brain cells

Milestone in the regeneration of brain cells Supportive cells generate new nerve cells Monday, 20 August 2007

The majority of cells in the human brain are not nerve cells but star-shaped glia cells, the so called ‘astroglia’.

“Glia means ‘glue’,” explains Götz.

As befits their name, until now these cells have been regarded merely as a kind of “putty” keeping the nerve cells together.

A couple of years ago, the research group had been already able to prove that these glia cells function as stem cells during development. This means that they are able to differentiate into functional nerve cells. However, this ability gets lost in later phases of development, so that even after an injury to the adult brain glial cells are unable to generate any more nerve cells.

In order to be able to reverse this development, the team studied what molecular switches are essential for the creation of nerve cells from glial cells during development. These regulator proteins are introduced into glial cells from the postnatal brain, which indeed respond by switching on the expression of neuronal proteins.

In his current work, Dr. Benedikt Berninger, was now able to show that single regulator proteins are quite sufficient to generate new functional nerve cells from glia cells. The transition from glia-to-neuron could be followed live at a time-lapse microscope. It was shown that glia cells need some days for the reprogramming until they take the normal shape of a nerve cell.

“These new nerve cells then have also the typical electrical properties of normal nerve cells”, emphasises Berninger.

“We could show this by means of electrical recordings”.

“Our results are very encouraging, because the generation of correctly functional nerve cells from postnatal glia cells is an important step on the way to be able to replace functional nerve cells also after injuries in the brain,” underlines Magdalena Götz.

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ZenMaster

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Conquest of land began in shark genome

Conquest of land began in shark genome Ancient genetic toolkit primed escape from aquatic life Wednesday, 15 August 2007

When the first four-legged animals sprouted fingers and toes, they took an ancient genetic recipe and simply extended the cooking time, say University of Florida scientists writing in Wednesday’s issue of the journal PLoS ONE.

Even sharks — which have existed for more than half a billion years— have the recipe for fingers in their genetic cookbook — not to eat them, but to grow them.

While studying the mechanisms of development in shark embryos, UF scientists identified a spurt of genetic activity that is required for digit development in limbed animals.

Previous work suggested that the transition from fins to limbs involved the addition of a late phase of gene activity during embryonic development, something thought to be absent during the development of fish fins.

The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.

“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute.

“Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”

Researchers say the same genes that produced ancient fins likely enlarged their role about 365 million years ago in amphibians struggling to adapt to swamps and terrestrial living, creating a distinct burst of development and more versatile appendages.

Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted cat shark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.

They discovered a phase of gene expression in sharks that was thought until recently to occur only when digits began to form in limbed animals.

Why, then, don’t sharks have fingers? Renata Freitas and GuangJun Zhang, co-authors of the paper and graduate students in the zoology department of the College of Liberal Arts and Sciences, speculate that sharks and many other types of fish do not form more dramatic appendages during this late phase of Hox gene expression because it occurs briefly and only in a narrow band of cells, compared with the more extended time frame and larger anatomical area needed to prefigure the hand and foot in limbed animals.

“We know when this particular Hox gene is mutated in humans, it results in malformations of fingers and toes,” Cohn said.

“Until now it was thought these mutations were affecting a relatively recent innovation in the genetic process of limb development. Our results show that this phase of Hox expression is much more ancient and suggest that if the origin of digits involved a prolonged activity of Hox genes, a truncated period could result in defective digits.”

In a parallel study, researchers at the University of Chicago found this second phase of gene expression in paddlefish, a primitive living descendant of early fish with the first bony skeletons.

Finding the second phase in sharks, which have skeletons consisting not of bone but of cartilage, means the genetic processes necessary to muster fingers and toes existed more than 500 million years ago in the common ancestor of fish with cartilaginous skeletons and bony fish — more than 135 million years before digits debuted in the earliest limbed animals.

“The leap from aquatic life to terrestrial life is an extremely dramatic, important point in evolution that has captured the interest of many,” said Marie Kmita, Ph.D., director of the Genetics and Development Research Unit at the Institut de Recherches Cliniques de Montréal who was not involved in the research.

“Understanding how changes in gene regulation modify the body architecture is of extreme interest to scientists who are trying to find ways to improve human health by learning from developmental processes. This work shows a late phase of gene regulation seems fated to the emergence of digits.” ......... ZenMaster

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Unravelling new complexity in the genome

Unravelling new complexity in the genome Tuesday, 14 August 2007

A major surprise emerging from genome sequencing projects is that humans have a comparable number of protein-coding genes as significantly less complex organisms such as the minute nematode worm Caenorhabditis elegans. Clearly something other than gene count is behind the genetic differences between simpler and more complex life forms.

Increased functional and cellular complexity can be explained, in large part, by how genes and the products of genes are regulated. A University of Toronto-led study published in the latest issue of Genome Biology reveals that a step in gene expression (referred to as alternative splicing) is more highly regulated in a cell and tissue-specific manner than previously appreciated and much of this additional regulation occurs in the nervous system. The alternative splicing step allows a single gene to specify multiple protein products by processing the RNA transcripts made from genes (which are translated to make protein).

“We are finding that a significant number of genes operating in the same biological processes and pathways are regulated by alternative splicing differently in nervous system tissues compared to other mammalian tissues,” says lead investigator Professor Benjamin Blencowe of the Banting and Best Department of Medical Research and Centre for Cellular and Biomolecular Research (CCBR) at the University of Toronto

According to Blencowe, it is particularly interesting that many of the genes have important and specific functions in the nervous system, including roles associated with memory and learning. However, in most cases the investigators working on these genes were not aware that their favourite genes are regulated at the level of splicing. Blencowe believes that the data his group has generated provides a valuable basis for understanding molecular mechanisms by which genes can function differently in different parts of the body.

Blencowe attributes these new findings in part to the power of a new tool that he, together with his colleagues including Profs. Brendan Frey (Department of Electrical and Computer Engineering) and Timothy Hughes (Banting and Best, CCBR), developed a few years ago. This tool, which comprises tailored designed microarrays or “gene chips” and computer algorithms, allows the simultaneous measurement of thousands of alternative splicing events in cells and tissues.

“Until recently researchers studied splicing regulation on a gene by gene basis. Now we can obtain a picture of what is happening on a global scale, which provides a fascinating new perspective on how genes are regulated,” Blencowe explains.

A challenge now is to figure out how the alternative splicing process is regulated in a cell and tissue-specific manner. In their new paper in Genome Biology, Dr. Yoseph Barash, a postdoctoral fellow working jointly with Blencowe and Frey, has provided what is likely part of the answer. By applying computational methods to the gene chip data generated by Matthew Fagnani (an MSc student) and other members of the Blencowe lab, Barash has uncovered what appears to be part of a “regulatory code” that controls alternative splicing patterns in the brain.

One outcome of these new studies is that the alternative splicing process appears to provide a largely separate layer of gene regulation that works in parallel with other important steps in gene regulation.

“The number of genes and coordinated regulatory events involved in specifying cell and tissue type characteristics appear to be considerably more extensive than appreciated in previous studies,” says Blencowe.

“These findings also have implications for understanding human diseases such as cancers, since we can anticipate a more extensive role for altered regulation of splicing events that similarly went unnoticed due to the lack of the appropriate technology allowing their detection.” .........

ZenMaster

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Gene regulation, not just genes, is what sets humans apart from monkeys

Gene regulation, not just genes, is what sets humans apart from our cousins Monday, 13 August 2007

The striking differences between humans and chimps aren’t so much in the genes we have, which are 99 percent the same, but in the way those genes are used, according to new research from a Duke University team.

It’s rather like the same set of notes being played in very different ways.

In two major traits that set humans apart from chimps and other primates – those involving brains and diet – gene regulation, the complex cross-talk that governs when genes are turned on and off, appears to be significantly different.

“Positive selection, the process by which genetic changes that aid survival and reproduction spread throughout a species, has targeted the regulation of many genes known to be involved in the brain and nervous system and in nutrition,” said Ralph Haygood, a post-doctoral fellow in the laboratory of Duke biology professor Gregory Wray.

Haygood is lead author in a report on the research to be published online on Sunday, Aug. 12, in the research journal Nature Genetics.

His group looked at the regulatory sequences immediately adjacent to 6,280 genes on the DNA of chimps, humans and the rhesus macaque, a more distant primate relative that has 88 percent the same genes as humans. These regulatory stretches of DNA are where proteins bind to the genome to initiate a gene’s function. And it is here that evolution has apparently fine-tuned the performance of genes, Wray said, resulting in the dramatic differences in the human brain.

Though many studies have looked for significant differences in the coding regions of genes relating to neural system development and failed to find any, the Duke team believes this is the first study to take a genome-wide look at the evolution of regulatory sequences in different organisms.

Other studies have found significant differences between these species in the coding regions that govern the immune system, the sense of smell and the manufacture of sperm, but the coding regions of neural-related genes had shown very little sign of positive selection in these studies. Yet, as far back as 1975 when Mary-Claire King and Allan Wilson first said humans and chimps were 99 percent the same genetically, they had offered the suggestion that greater differences might be found in the regulatory regions.

The type of analysis performed by the Duke team couldn’t be done until the macaque genome was published in 2005 because they needed a third, closely related relative to compare the regulatory sequences.

The mouse genome had been used as a reference point for comparing the coding sequences of humans and chimps, but the non-coding sequences have generally evolved much faster.

“Mice wouldn’t work for analyzing the non-coding sequences, because they’re too different from humans and chimps,” Haygood said.

While the biochemistry that cells use to turn food into energy is essentially the same across most animal species, the fine-tuning of how an organism deals with the different sorts of sugars and complex carbohydrates in its diet lies in the regulatory sequences, Wray said.

Chimps are fruit-eaters, for the most part, and would not last long away from their fruit-rich forest. The sugars in their diet are relatively simple to break down and convert to cellular fuel. Humans, on the other hand, eat a wider array of foods, including many the chimps would simply not be able to digest like starchy root crops. The researchers found dramatic differences in the regulatory regions of their genes for breaking down more complex carbohydrates. It may be that parts of the human metabolism are cranked up to digest carbohydrates down to simpler sugars.

“Regulatory changes have adapted to changing circumstances without changing the essential chemistry of metabolism,” Wray said.

“This may set the stage for a more focused analysis of the human diet.”

Much is being written and hypothesized about how dietary changes have contributed to the current human pandemics of obesity and diabetes, and perhaps there will be some insights from understanding how these regulatory sequences have evolved, he said.

To do a genome-wide analysis of regulatory regions, Haygood and post-doctoral fellow Olivier Fedrigo had to adapt some of the statistical tools used for genome-wide analysis of coding regions. To be sure their results would be robust, they focused on just the most reliably accurate published DNA sequences in common between the three animals, discarding two-thirds of the genome to ensure accuracy.

“With only three species, we had to be very stringent about quality,” Fedrigo said.

The researchers don’t think these findings will be of any help resolving questions about how and when the ancestors of humans and chimps diverged on the tree of life, but it’s safe to say that “most of this is ancient history,” Wray said. ......... ZenMaster

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Scientists produce functioning neurons from human embryonic stem cells

Scientists produce functioning neurons from human embryonic stem cells Neurons will be used to create models of neurological diseases. Thursday, 09 August 2007 Scientists with the Institute of Stem Cell Biology and Medicine at UCLA were able to produce from human embryonic stem cells a highly pure, large quantity of functioning neurons that will allow them to create models of and study diseases such as Alzheimer’s, Parkinson’s, prefrontal dementia and schizophrenia. Researchers previously had been able to produce neurons – the impulse-conducting cells in the brain and spinal cord - from human embryonic stem cells. However, the percentage of neurons in the cell culture was not high and the neurons were difficult to isolate from the other cells. UCLA’s Yi Sun, an associate professor of psychiatry and biobehavioral sciences, and Howard Hughes Medical Institute investigator Thomas Südhof at the University of Texas Southwestern Medical Center were able to produce 70 to 80 percent of neurons in cell culture. Sun and Südhof also were able to isolate the neurons and determine that they had a functional synaptic network, which the neurons use to communicate. Because they were functional, the neurons can be used to create a variety of human neurological disease models. The study results are published today in an early online edition of the peer-reviewed journal Proceedings of the National Academy of Sciences. “Previously, the system to grow and isolate neurons was very messy and it was unknown whether those neurons were functioning,” Sun said. “We’re excited because we have been able to purify so many more neurons out of the cell culture and they were, surprisingly, healthy enough to form synapses. These cells will be excellent for doing gene expression studies and biochemical and protein analyses.” Sun’s method prodded human embryonic stem cells to differentiate into neural stem cells, the cells that give rise to neurons. When the time was right, Sun’s team added protein growth factors into the cell culture that stopped the neural stem cells from self-renewing and prodded them into differentiating into neurons. To isolate the cells, Sun and her team added an enzyme that digests a sort of protein matrix that holds cells in culture together. The neurons could then be separated from the neural stem cells that had not yet differentiated, a sort of chemical round-up that isolated the neurons. The cells were then put into a cell strainer that allowed passage through of the isolated neurons. The large number of pure neurons produced will allow Sun and her team to study their biological form and structure, the genes they express, the development of synapses and the electric and chemical communication activities within the synapse network. “We will be able to study the cellular properties of neurons in a very defined way that will maybe tell us what goes wrong in diseases such as Alzheimer’s and Parkinson’s,” Sun said. “We’re currently creating many models of human neurological diseases that may provide the answers we’re looking for. We don’t know what causes prefrontal dementia, Huntington’s disease or schizophrenia. The key is likely in the quality of neuronal communications. By studying the chemical and electrical transmissions, we may be able to determine what goes wrong that leads to these debilitating diseases and find a way to stop or treat it.” Sun will be among the first researchers to be able to study true neuron function. A second important discovery in Sun’s study showed that two embryonic stem cells lines derived in similar manners, and therefore expected to behave similarly when differentiating, did not. Using the same techniques to prod the two embryonic stem cells lines to differentiate, Sun found that one line had a bias to become neurons that are found in the forebrain. The other line differentiated into neurons found in rear portions of the brain and spinal cord. The finding was surprising, and significant, Sun said. “The realization that not all human embryonic stem cell lines are born equal is critical,” Sun said. “If you’re studying a disease found in a certain part of the brain, you should use a human embryonic stem cell line that produces the neurons from that region of the brain to get the most accurate results from your study. Huntington’s disease, for example, is a forebrain disease, so the neurons should be differentiated from a cell line that is biased to produce neurons from the forebrain.” Sun said there are ways to prod an embryonic stem cell line biased to become neurons found in the rear brain to become neurons found in the forebrain. However, there are limits to how much prodding can be done. Sun and her team confirmed that the two embryonic stem cell lines were different through gene expression analysis – neurons that perform different functions in different parts of the brain express different genes. The cell line prone to becoming neurons found in the forebrain expressed genes typically found those neurons, while the other line expressed genes found in the rear brain and spinal cord. Sun and her team now are studying why the two human embryonic stem cell lines have biases to become different types of neurons. “If we knew that, we might be able to tweak or alter whatever is driving the bias so that limitation in the stem cell line could be bypassed,” Sun said. ......... ZenMaster

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A unique arrangement for egg cell division

A unique arrangement for egg cell division Thursday, 09 August 2007 Researchers uncover how the molecular machinery functions that mediates cell division in developing egg cells. Which genes are passed on from mother to child is decided very early on during the maturation of the egg cell in the ovary. In a cell division process that is unique to egg cells, half of the chromosomes are eliminated from the egg before it is fertilised. Using a powerful microscope, researchers from the European Molecular Biology Laboratory (EMBL) have now revealed how the molecular machinery functions that is responsible for chromosome reduction of egg cells in mice. In the current issue of Cell they report the assembly of this machinery, which is very different from what happens in all other cells in the body. The process is likely conserved across species and the new insights might help shed light on defects occurring in human egg cell development. The first step in the development of an egg cell is the division of its progenitor cell, the oocyte. Unlike other cells in the body, an oocyte does not divide equally to produce two identical daughter cells. Instead, it undergoes a reducing division, which halves its genetic material to generate a single egg cell with 23 instead of the normal 46 chromosomes in humans. It is crucial that the egg has half the normal set of chromosomes, because the second half is brought in by the sperm cell during fertilisation. The molecular apparatus that makes sure that the egg ends up with the correct number of chromosomes is a bipolar spindle consisting of protein filaments, called microtubules that are part of the cell’s skeleton. Spindle microtubules attach themselves to the chromosomes, separate them and pull one half out of the oocyte into a small polar body that is later discarded. “Microtubule spindles are found in all dividing cells. What is special about oocytes is that they lack specialised spindle-forming organelles, called centrosomes,” says Jan Ellenberg, Coordinator of the Gene Expression Unit at EMBL, “all other cells contain two centrosomes from where the microtubules originate. They predetermine the bipolar structure of the spindle that is essential to extrude exactly half of the chromosomes outside of the egg. For a long time we did not understand how mammalian oocytes could assemble a bipolar spindle without such centrosomes.” Tracking spindle assembly over time with a high resolution microscope in live mouse oocytes, Ellenberg and his PhD student Melina Schuh found that the missing centrosomes are replaced by a flexible system of many small microtubule organising centres (MTOCs) in oocytes. Like centrosomes, these MTOCs serve as platforms from which microtubules grow, but they are not permanent structures. MTOCs only form when the division is about to start and accumulate in the cell’s centre. There, the around 80 individual MTOCs start interacting in a tug-of-war of pulling and pushing each other. This ultimately leads to a self-organized spindle with two poles in which all chromosomes are accurately aligned for the subsequent chromosome elimination. “Assembling a spindle from so many centres takes very long and involves a lot of coordination in space and time,” says Melina Schuh, who carried out the research in Ellenberg’s lab, “if the spindle fails to accurately segregate the chromosomes this results in diseases like Down syndrome and infertility. It is therefore very important that we now understand how this crucial division at the beginning of life is orchestrated.” ......... ZenMaster

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Researchers find culprit in aging muscles that heal poorly

Researchers find culprit in aging muscles that heal poorly Thursday, 09 August 2007 Communication is critical. Garbled in, garbled out, so to (mis-)speak. Workers who get incomplete instructions produce an incomplete product, and that's exactly what happens with the stem cells in our aging muscles, according to researchers from the Stanford University School of Medicine. Their study found that, as we age, the lines of communication to the stem cells of our muscles deteriorate and, without the full instructions, it takes longer for injured muscles to heal. Even then, the repairs aren't as good. But now that the researchers have uncovered the conduit that conveys the work orders to muscle stem cells, that knowledge could open the door to new therapies for injuries in a host of different tissues. The key to the whole process is Wnt, a protein traditionally thought to help promote maintenance and proliferation of stem cells in many tissues. But in this instance, Wnt appears to block proper communication. "That was a total surprise," said Thomas Rando, MD, PhD, associate professor of neurology and neurological sciences. "We had no idea that the Wnt signalling pathway would have a negative effect on stem cell function." Rando, who also does research and clinical work at the Veterans Affairs Palo Alto Health Care System, is senior author of the research that will be published in the Aug. 10 issue of Science. Rando said many drugs can block Wnt signalling. "Theoretically, given the number of ways to block Wnt and Wnt signalling, one could envision this becoming a therapeutic," he said. "You could potentially enhance the healing of aged tissues by reducing this effect of Wnt signalling on the resident stem cells." In addition to helping the elderly heal faster and better from muscle injuries, Rando said, the potential benefits could include tissues such as skin, gut and bone marrow, or for that matter, potentially any tissue, such as liver and brain, in which stem cells contribute to normal cellular turnover. Rando and his colleagues made the discovery while studying the effect of environment on muscle stem cell activity in mice. Rando had already discovered that old muscle stem cells, if placed in a youthful environment, had just as great a capacity for repairing acutely damaged tissue as do young cells. It was while the researchers were testing the opposite situation - how the repair capabilities of young muscle stem cells were affected by being placed in an aged environment – which the Wnt pathway came to light. The work was done with live mice whose circulatory systems were joined and in lab dishes with young cells immersed in serum from old blood. As expected, the young muscle stem cells were influenced negatively by the aged environment, repairing damaged muscle tissue just as slowly and poorly as old stem cells in the same surroundings. This confirmed their earlier research showing that the ability of muscle stem cells to regenerate tissue depends on the age of the cells' environment (including the age of the blood supplying the tissue), not the age of the stem cell. Although Rando's research focused on the repair of acute trauma to muscles, he suspects that the same sort of problem arises on a lesser scale in repairing damage that results from the normal wear and tear of aging. Rando also found that the misdirected stem cells – the ones that failed to generate new muscle cells in the old environment - were instead differentiating into scar-tissue-producing cells called fibroblasts. The stem cells weren't just failing to respond to the garbled instructions; they were actually giving rise to daughter cells that turned into the wrong thing. The consequence of muscle stem cells producing fewer muscle cells (myoblasts) and more fibroblasts is that the healing muscle had more scar tissue, also known as fibrosis. "That says something about how cells decide who they're going to be. Even if they start off knowing they're supposed to be a muscle cell, they can change," said Rando. "If you're exposed to the wrong environment, it will change your fate." Rando said the type of fibrosis that occurs in the aging muscle tissue is the same type seen in muscular dystrophy. He is already exploring how inhibiting Wnt signalling might help provide therapy for that disease. Wnt has also popped up unexpectedly in work by researchers at the National Institutes of Health, published in the same issue of Science, who were studying the effects of a deficiency of a hormone called klotho. Klotho deficiency causes a syndrome that resembles extremely rapid aging in mice, which end up dying very young compared with normal mice. In seeking to understand why that happens, the NIH researchers discovered that klotho inhibits Wnt activity. The hypothesis is that klotho production declines with age, and thus its effectiveness against Wnt decreases, allowing Wnt activity to pick up and disrupt the normal signalling to the stem cells in a variety of tissues studied. Rando said that, although the work of his team and the NIH researchers is different in terms of the techniques used and the questions being studied, "...what's surprising is how supportive of each other the fundamental conclusions (of the two papers) are about Wnt signalling and aging." ......... ZenMaster

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Evolution is driven by gene regulation

Evolution is driven by gene regulation Thursday, 09 August 2007 It is not just what’s in your genes, it’s how you turn them on that accounts for the difference between species — at least in yeast — according to a report by Yale researchers in this week’s issue of Science. “We’ve known for a while that the protein coding genes of humans and chimpanzees are about 99 percent the same,” said senior author Michael Snyder, the Cullman Professor of Molecular Cellular and Developmental Biology at Yale. “The challenge for biologists is accounting for what causes the substantial difference between the person and the chimp.” Conventional wisdom has been that if the difference is not the gene content, the difference must be in the way regulation of genes produces their protein products. Comparing gene regulation across similar organisms has been difficult because the nucleotide sequence of DNA regulatory regions, or promoters, are more variable than the sequences of their corresponding protein-coding regions, making them harder to identify by standard computer comparisons. “While many molecules that bind DNA regulatory regions have been identified as transcription factors mediating gene regulation, we have now shown that we can functionally map these interactions and identify the specific targeted promoters,” said Snyder. “We were startled to find that even the closely related species of yeast had extensively differing patterns of regulation.” In this study, the authors found the DNA binding sites by aiming at their function, rather than their sequence. First, they isolated transcription factors that were specifically bound to DNA at their promoter sites. Then, they analyzed the sequences that were isolated to determine the similarities and differences in regulatory regions between the different species. “By using a group of closely and more distantly related yeast whose sequences were well documented, we were able to see functional differences that had been invisible to researchers before,” said Snyder. “We expect that this approach will get us closer to understanding the balance between gene content and gene regulation in the question of human-chimp diversity.” Science 317: 815-819 (August 10, 2007). ......... ZenMaster

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Not All Embryonic Stem Cell Lines Are Created Equal

Not All Embryonic Stem Cell Lines Are Created Equal Monday, 06 August 2007 When it comes to generating neurons, researchers have found that not all embryonic stem (ES) cell lines are equal. In comparing neurons generated from two NIH-approved embryonic stem cell lines, scientists have uncovered significant differences in the mature, functioning neurons generated from each line. The discovery implies that culture conditions during ES cell generation – which have yet to be identified – can influence the developmental properties of ES cells. Research published in the August 06, 2007, issue of Proceedings of the National Academy of Sciences. Thomas C. Südhof, M.D., HHMI investigator University of Texas Southwestern Medical Center at Dallas For the full story, go to: http://www.hhmi.org/news/sudhof20070806.html ......... ZenMaster

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Was Hwang’s Stem Cells Parthenogenetic?

Was Hwang’s Stem Cells Parthenogenetic? Friday, 03 August 2007 Researchers say they have confirmed suspicions that embryonic stem cells claimed to be extracted from the first cloned human embryo by discredited South Korean scientist Woo Suk Hwang actually owe their existence to parthenogenesis, a process in which egg cells give rise to embryos without being fertilized by sperm. Read the whole article here: Was Hwang’s Stem Cells Parthenogenetic? ZenMaster

Stem cell therapy rescues motor neurons in ALS model

Stem cell therapy rescues motor neurons in ALS model August 1, 2007

In a study that demonstrates the promise of cell-based therapies for diseases that have proved intractable to modern medicine, a team of scientists from the University of Wisconsin-Madison has shown it is possible to rescue the dying neurons characteristic of amyotrophic lateral sclerosis (ALS), a fatal neuromuscular disorder also known as Lou Gehrig's disease.

The new work, conducted in a rat model and reported today (July 31) in the online, open-access journal from the Public Library of Science, PLoS ONE, shows that stem cells engineered to secrete a key growth factor can protect the motor neurons that waste away as a result of ALS. An important caveat, however, is that while the motor neurons within the spinal cord are protected by the growth factor, their ability to maintain connections with the muscles they control was not observed.

"At the early stages of disease, we saw almost 100 percent protection of motor neurons," explains Clive Svendsen, a neuroscientist who, with colleague Masatoshi Suzuki, led the study at UW-Madison's Waisman Center.

"But when we looked at the function of these animals, we saw no improvement. The muscles aren't responding."

At present, there are no effective treatments for ALS, which afflicts roughly 40,000 people in the United States and which is almost always fatal within three to five years of diagnosis. Patients gradually experience progressive muscle weakness and paralysis as the motor neurons that control muscles are destroyed by the disease. The cause of ALS is unknown.

In the new Wisconsin study, nascent brain cells known as neural progenitor cells derived from human fetal tissue were engineered to secrete a chemical known as glial cell line derived neurotrophic factor (GDNF), an agent that has been shown to protect neurons but that is very difficult to deliver to specific regions of the brain. The engineered cells were then implanted in the spinal cords of rats afflicted with a form of ALS.

"GDNF has a very high affinity for motor neurons in the spinal cord," says Svendsen. When implanted, "the (GDNF secreting) cells survive beautifully. In 80 percent of the animals, we saw nice maturing transplants."

The implanted cells, in fact, demonstrated an affinity for the areas of the spinal cord where motor neurons were dying. According to Svendsen, the cells migrate to the area of damage where they "just sit and release GDNF."

The Wisconsin team transplanted the cells on one side of the spinal cord and used the untreated side to compare the affects of the transplanted cells and their chemical secretions.

"We only put the transplant in one small area of the spinal cord and only on one side," Suzuki says.

"The areas where we saw the human cells were the only areas where we saw protection of motor neurons."

But while the motor neurons exposed to GDNF were protected, the Wisconsin team was unable to detect the connections between the neurons and the muscles they govern.

"Even in animals that had lots of motor neurons surviving, we didn't see the (muscle) connection, which explained why we didn't see functional recovery," says Suzuki.

Although the obvious next step in the research is to try and ferret out the reasons the protected motor neurons are unable to hook up with muscles, Svendsen suggests the work further supports movement toward clinical trials in humans.

"We think the cells are safe, and they do increase the survival of the motor neurons," Svendsen argues.

"This may be very important for patients that lose neurons every day. However, it's not a trivial intervention - you have to drill a hole in the spinal cord to get the cells releasing GDNF in. But there are few options for these patients and we will continue to move forward with this approach." .........

ZenMaster

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Leave UK hybrid embryo decisions to experts

Leave UK hybrid embryo decisions to experts, panel says August 1, 2007

Experts, not government ministers, should decide what kind of hybrid animal-human embryo experiments to allow in Britain, a parliamentary panel said in a report issued on Wednesday.

Parliamentarian Phil Willis, who led the committee, said the government should leave the decision to regulators with the expertise to weigh potential scientific benefits.

"On the question of research using inter-species embryos, the committee is quite clear that it wishes to see a greater role for the regulator within a broad permissive framework set out by Parliament," Willis told a news conference before the release of the report. ..........

What do you think? Is it good or bad to keep politicians out of scientific decisions? .........

ZenMaster

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