Wednesday, 31 October 2007

Cat Genome Sequenced

Domestic cat genome sequenced Wednesday, 31 October 2007 A report that appears in the scientific journal Genome Research details the first assembly, annotation, and comparative analysis of the domestic cat genome (Felis catus). The DNA of a 4-year-old Abyssinian cat named Cinnamon, whose well-documented lineage can be traced back several generations to Sweden, has been sequenced. Cinnamon is one of several mammals that are currently being analyzed using “light” (two-fold) genome sequence coverage. To make sense of Cinnamon’s raw sequence data, a multi-centre collaboration of scientists leveraged information from previously sequenced mammalian genomes as well as previous gene-mapping studies in the cat. In doing so, they found that Cinnamon’s sequences spanned about 65% of the euchromatic (gene-containing) regions of the feline genome. Cinnamon DNA was sequenced about 1.9 times the length of her 2.7 billion base-pair genome. For comparison, the human genome was sequenced seven times over, and the dog’s seven and a half times. The data is presnted at the Garfield Project. The similarity between the cat genome and six recently completed mammalian genomes (human, chimpanzee, mouse, rat, dog, and cow) allowed the scientists to identify 20,285 putative genes in the cat genome. The comparison also revealed hundreds of chromosomal rearrangements that have occurred among the different lineages of mammals since they diverged from a diminutive ancestor that roamed the earth among the dinosaurs some 100 million years ago. The genome sequence analysis is certainly expected to lead to health benefits for domestic cats. But the domestic cat also serves as an excellent model for human disease, which is one reason why the National Human Genome Research Institute (NHGRI) initially authorized the Cat Genome Sequencing Project three years ago. Domestic cats possess over 250 naturally occurring hereditary disorders, many of which are similar to genetic pathologies in humans. Cats areoften used as a model to study conditions such as heart disease, blindness or HIV. For example, Cinnamon’s pedigree carries a genetic mutation that causes retinitis pigmentosa, a degenerative eye disease that can lead to blindness. In humans, retinitis pigmentosa affects 1 in 3,500 Americans. The domestic cat also serves as an excellent model for human infectious diseases, including HIV/AIDS. Feline immunodeficiency virus (FIV) is a genetic relative of human immunodeficiency virus (HIV), which causes AIDS. Using the cat genome sequence data, the researchers identified 327,000 single letter differences (known as SNPs, DIPs, and STRs), which can be used to determine the genetic basis for common hereditary diseases. The scientists have already used these variants to identify the causative gene for Cinnamon’s retinitis pigmentosa (they published a paper describing this study in the May/June, 2007 issue of the Journal of Heredity). These variants will also be useful for parentage testing, forensic analysis, and studies of evolution, including the reconstruction of domestication processes, fancy breed development, and ecological adaptation among the great roaring cats. The researchers also analyzed the feline genome for interesting features such as microRNAs, Numts (pronounced “new mights” — nuclear genomic fragments that migrated to cat chromosomes from mitochondria), and a vast sea of selfish DNA-like repetitive elements. The repetitive elements included scores of genomic stretches from historic retroviruses, some with known links to cancer. References Pontius, J. U. et al . Genome Res. 17, 1675–1689 (2007). ......... ZenMaster

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Human tests of embryonic stem cell therapies to start?

Human tests of embryonic stem cell therapies to start? Wednesday, 31 October 2007 Geron Corp. and Advanced Cell Technology Inc. are getting ready to start clinical testing of embryonic stem cells for different conditions next year, CNN reports today. Both companies are preparing to submit applications to the FDA to begin human testing of experimental treatments that are based on ESCs. If the companies get the go-ahead, they could begin tests as soon as next year. In the past, the FDA has approved human tests of products based on stem cells taken from adult tissue. But Geron and ACT would be the first to begin human testing of treatments based on the more controversial research using stem cells derived from embryos. Human tests are the most advanced form of testing and one of the final hurdles before the FDA approves a drug. Geron has already met with the FDA and will submit its plans for human testing to the agency by the end of this year, according to Sion Rogers, a spokesman for the company. "We expect to be in the clinic [for human testing] next year," said Rogers. ACT plans to submit its application for human testing to the FDA by the middle of next year, said Chief Executive Robert Lanza, who spoke at the 7th International Stem Cell Conference on Tuesday. His company is developing potential treatments for vision loss diseases, including macular degeneration and Stargardt's, based on studies involving monkeys. Geron and ACT will not compete with each other because their potential products are unrelated. "We think that it doesn't matter who gets to the clinic first, because the entire stem cell space will benefit when someone gets there," said Ren Benjamin, analyst for Rodman & Renshaw. "It will create a lot of excitement in investors, because it's a big milestone for the embryonic stem cell space." Novocell, another privately-held biotech based in San Diego, uses embryonic stem cell research in developing treatments for diabetes. Chief Executive Alan Lewis said that he is a couple of years behind Geron and ACT, and he is yet to finish studies using mice. "The study needs to be completed before we got out and bang a drum and talk about curing diabetes," said Lewis. ......... ZenMaster

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Stem cells can improve memory after brain injury

Neural stem cells work by protecting existing cells and promoting neuronal connections Wednesday, 31 October 2007
Neural stem cells shown in green, neurons in red.
New UC Irvine research is among the first to demonstrate that neural stem cells may help to restore memory after brain damage. In the study, mice with brain injuries experienced enhanced memory — similar to the level found in healthy mice — up to three months after receiving a stem cell treatment. Scientists believe the stem cells secreted proteins called neurotrophins that protected vulnerable cells from death and rescued memory. This creates hope that a drug to boost production of these proteins could be developed to restore the ability to remember in patients with neuronal loss. “Our research provides clear evidence that stem cells can reverse memory loss,” said Frank LaFerla, professor of neurobiology and behaviour at UCI. “This gives us hope that stem cells someday could help restore brain function in humans suffering from a wide range of diseases and injuries that impair memory formation.” The results of the study appear Oct. 31 in the Journal of Neuroscience. LaFerla, Mathew Blurton-Jones and Tritia Yamasaki performed their experiments using a new type of genetically engineered mouse that develops brain lesions in areas designated by the scientists. For this study, they destroyed cells in the hippocampus, an area of the brain vital to memory formation and where neurons often die. To test memory, the researchers gave place and object recognition tests to healthy mice and mice with brain injuries. Memories of place depend upon the hippocampus, and memories of objects depend more upon the cortex. In the place test, healthy mice remembered their surroundings about 70 percent of the time, but mice with brain injuries remembered it just 40 percent of the time. In the object test, healthy mice remembered objects about 80 percent of the time, while injured mice remembered as poorly as about 65 percent of the time. The scientists then set out to learn whether neural stem cells from a mouse could improve memory in mice with brain injuries. To test this, they injected each mouse with about 200,000 neural stem cells that were engineered to appear green under ultraviolet light. The colour allows the scientists to track the stem cells inside the mouse brain after transplantation. Three months after implanting the stem cells, the mice were tested on place recognition. The researchers found that mice with brain injuries that also received stem cells remembered their surroundings about 70 percent of the time — the same level as healthy mice. In contrast, control mice that didn’t receive stem cells still had memory impairments. Next, the scientists took a closer look at how the green-coloured stem cells behaved in the mouse brain. They found that only about 4 percent of them turned into neurons, indicating the stem cells were not improving memory simply by replacing the dead brain cells. In the healthy mice, the stem cells migrated throughout the brain, but in the mice with neuronal loss, the cells congregated in the hippocampus, the area of the injury. Interestingly, mice that had been treated with stem cells had more neurons four months after the transplantation than mice that had not been treated. “We know that very few of the cells are becoming neurons, so we think that the stem cells are instead enhancing the local brain microenvironment,” Blurton-Jones said. “We have evidence suggesting that the stem cells provide support to vulnerable and injured neurons, keeping them alive and functional by making beneficial proteins called neurotrophins.” If supplemental neurotrophins are in fact at the root of memory enhancement, scientists could try to create a drug that enhances the release or production of these proteins. Scientists then could spend less time coaxing stem cells to turn into other types of cells, at least as it relates to memory research. “Much of the focus in stem cell research has been how to turn them into different types of cells such as neurons, but maybe that is not always necessary,” Yamasaki said. “In this case, we did not have to make neurons to improve memory.” ......... ZenMaster

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Thursday, 25 October 2007

New group of tiny RNAs - the piRNAs

New group of tiny RNAs play a big role in controlling genes Thursday, 25 October 2007 A study by researchers at the Yale Stem Cell Center for the first time demonstrates that piRNAs, a recently discovered class of tiny RNAs, play an important role in controlling gene function, it was reported this week in Nature. Haifan Lin, director of the stem cell center and professor of cell biology at Yale School of Medicine, heads the laboratory that originally identified piRNAs. Derived mostly from so-called “junk DNA,” piRNAs had escaped the attention of generations of geneticists and molecular biologists until last year when Lin’s team discovered them in mammalian reproductive cells, and named them. The lab’s current work suggests that piRNAs have crucial functions in controlling stem cell fate and other processes of tissue development. In this study Lin and his Ph.D. student, Hang Yin, discovered more than 13,000 Piwi-associated piRNAs in fruit flies. One particular piRNA, they found, forms a complex with the protein known as Piwi, which then binds to chromatin, a strategic region in the genome that regulates the activity of the gene. Chromatin’s role is to package DNA so that it will fit into the cell, to strengthen the DNA to allow cell division, and to serve as a mechanism to control gene expression. “This is important in maintaining self-renewal of stem cells,” Lin said. “These small RNAs might provide new tools to harness the behaviour of stem cells and other biological processes related to diseases.” “This finding revealed a surprisingly important role for piRNAs, as well as junk DNA, in stem cell division,” Lin said. “It calls upon biologists to look for answers beyond the one percent of the genome with protein coding capacity to the vast land of junk DNA, which constitutes 99 percent of the genome.” ......... ZenMaster

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Wednesday, 24 October 2007

Differentiation in human embryonic stem cells

Important tool in understanding differentiation in hESCs Wednesday, 24 October 2007 Researchers know very little about how human embryonic stem cells (hESC) self-renew. To fully understand these cells’ self renewal capacity and pluripotency, and their regulation, it is necessary to efficiently generate genetically modified cells and analyze the consequences of elevated and reduced expression of genes. Researchers at the University of Minnesota’s Stem Cell Institute have described how an existing genetic tool can be used to study how human embryonic stem cells differentiate. The research appears in the November 2007 issue of Experimental Biology and Medicine. The research team, led by the University of Minnesota’s Meri Firpo, Ph.D., included gene therapy researchers at Los Angeles Children’s Hospital, and developmental biologists at the University of Michigan. The researchers used “knockdown” technology to reduce the expression of oct4, a gene known to be necessary for self renewal of mouse and human embryonic stem cells. As seen in work done with mouse cells by knockdown and other genetic means, they showed that reducing the amount of oct4 in human ES cells induced differentiation. The researchers then used a plasmid vector to transiently increase levels of oct4 in hESC. This also resulted in differentiation as expected, but with differentiation patterns similar to those seen with the knockdown. This was an unexpected result, because when expression of oct4 is up-regulated in mouse ES cells, they differentiate into a different type of cell than if the expression of oct4 is down-regulated. "This suggests a key difference in the regulation of early development between mouse and human embryos" Firpo said. “While animal models are clearly important, this research shows that scientists need human models to truly understand what happens in early human development.” ......... ZenMaster

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Signal that switches on eye development

Signal that switches on eye development - could lead to 'eye in a dish' Wednesday, 24 October 2007 Researchers at the University of Warwick, funded by Wellcome Trust, have uncovered a crucial signal that switches on eye development. This discovery will greatly assist researchers looking at stem cells connected to eye development and opens up an avenue of research that could eventually lead to an “eye in a dish”. The University of Warwick research team led by Professor Nick Dale and Professor Elizabeth Jones from the University of Warwick’s Biological Sciences Department have published their work today, 25th October 2007, in Nature in a paper entitled Purine-mediated signalling triggers eye development. The researchers were exploring whether release of ATP (an important signalling and energy carrying molecule) influenced the development of locomotion in frogs. Their experiment introduced molecules called ectoenzymes (normally found on the outside surface of cells) into frog embryos at one of the earliest stages when the frogs-to-be were just 8 cells in size. Three ectoenzymes were used: E-NTPDase1, E-NTPDase2 and E-NTPDase3. These ectoenzymes degrade ATP following its release from cells, however each version of the ectoenzyme has slightly different effects on this degradation. The Warwick research team’s interest in locomotion was quickly eclipsed when they were amazed to find that the introduction of just one of the ectoenzymes (E-NTPDase2) had a dramatic affect on eye development in the tadpoles grown from these embryos. When introduced in cells that would form the head area of the tadpole multiple eyes appeared to be created. That was not the only surprise. When it was introduced in some cells that formed body parts outside the head area it could still produce an additional “ectopic” eye leading to tadpoles with an additional eye in their side, abdomen or even along their tail. E-NTPDase2 quickly latches on to ATP converting it to ADP. This meant that where and when the researchers introduced E-NTPDase2 it led to nearby cells experiencing much higher levels of ADP. The Warwick team hypothesized that ATP must be released in a short burst from the location where the eye will develop so that it can be converted to ADP by E-NTPDase2, thereby providing the trigger for eye development. They were able to measure these short bursts of ATP using ATP sensors specially developed by Professor Dale. This is the first time researchers have been able to see and measure bursts of ATP so early in the development of living creatures. The genes that initiate and direct eye development are well known and are collectively termed the “Eye Field Transcription Factors” (EFTFs). One of the mysteries of the field is how these genes get turned on in the correct location and at the correct time to initiate eye development. The Warwick research shows that this short burst of ATP followed by accumulation of ADP is a key signal for initiating expression of the EFTFs and hence the development of the eye. The discovery of this surprising new signal that literally switches on eye development it is not restricted to frogs. Mutations to the E-NTPDase2 gene on the human 9th chromosome are already known to cause severe head and eye defects. This suggests that this newly discovered mechanism for triggering eye development applies across a wide range of species. This new understanding of how eye development is triggered will greatly assist researchers exploring stem cells connected to eye development and opens up an avenue of a research that could in just a few decades lead to the ability to produce an “eye in a dish”. ......... ZenMaster

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Friday, 19 October 2007

Interspecies Chimeric Mice Using ESCs Created

Scientists create 'interspecies' rodent using embryonic stem cells Friday, 19 October 2007
From left: Mus musculus (house mouse); chimera, a genetic fusion of a house and wood mouse; and Apodemus sylvaticus (wood mouse). Photo courtesy of Bruce Lahn.
By injecting embryonic stem (ES) cells from a wood mouse into the early embryo of a house mouse, an international team of scientists has produced normal healthy animals made up of a mixture of cells from each of the two distantly related species. This is the first time that stem cells from one mammalian species have been shown to contribute extensively to development when introduced into the embryo of another, very different species. In an advanced online posting on Oct. 3, 2007, in the journal Human Molecular Genetics, scientists from the University of Chicago, Sun Yat-sen University, China, and the University of Liverpool, U.K., describe how they produced a viable "chimera" – a single organism with traits from two different species. Although both are rodents, the wood mouse (Apodemus sylvaticus) and the house mouse (Mus musculus) have evolved separately for up to 20 million years. Their genes differ by as much as 18 percent, about 12 times the difference between human and chimpanzee. Before now, scientists have used ES cells to make chimeras within the same species or with closely related species. "There are surprisingly high degrees of conservation in developmental programs between at least some distantly related mammalian species," said study co-author Bruce Lahn, a Howard Hughes investigator and professor of human genetics at Chicago. "When early embryonic cells from two divergent species are mixed together, they can communicate with each other properly and develop into one seamless, functional organism." "These results demonstrate the feasibility of differentiating ES cells into a wide range of cell types in vivo by introducing them into an evolutionary divergent host," the authors wrote. "This interspecies approach may be the only way to study ES cells of some species, such as human ES cells, in an in vivo context." The scientists extracted wood mouse ES cells and introduced a gene that produced a fluorescent protein, which enabled them to visually track the descendents of the stem cells in the chimeric organisms. They then injected about 15 wood mouse ES cells into each of the 1,250 house mouse blastocysts and transferred the viable embryos into 44 surrogate house mouse mothers. From these, 220 pups were born, 16 of them (7.3 percent) showed chimerism based on their appearance. In those 16 chimeras, up to 40 percent of the cells in some organs were wood mouse cells. These cells were integrated into all of the tissues at various levels. The chimeras appeared healthy and had no apparent defects. They did demonstrate some behavioural differences. They were less "jumpy" than a typical wood mouse but more so than a typical, much tamer, house mouse. Although genetically different (the wood mouse has 48 chromosomes, the house mouse, 40), both of these species have similar developmental schedules. The gestation period for a wood mouse is 23 days; the gestation time for a house mouse is 19 days. They also have approximately the same body size. The chimeras varied in terms of how much and where the injected ES cells generated tissue. "It's completely random where the cells will develop and grow tissue," Lahn said, adding that more studies are planned. "We're going to continue with these animals for a while to see if we can understand the developmental cues and learn how to manipulate the system," Lahn said. "For example, could injected wood mouse embryonic stem cells contribute more extensively to the liver in a house mouse that carries a genetic defect that prevents it from growing its own liver? Or, could we alter the stem cells in ways that could prevent them from contributing brain tissue?" The researchers also plan to merge mouse and rat, which have vastly different body sizes, as well as 20 percent genetic difference. Key Scientific and Technological Projects of Guangdong Province and of Guangzhou, and the National Natural Science Foundation of China funded this project. Other authors of the paper are:
Jaehyun Lee, Donghyun Park, Eric Vallender, Tammy Vallender and Li Zhang, of the University of Chicago; Shu-Nong Li, Wei-Qiang Li, Bao-Feng Ma, Tao Wang, Xin-Bing Yu and Xiu-Ming Zhang, of Sun Yat-sen University in Gaungzhou, China; Lahn, Frank Fuxiang Mao and Andy Peng Xiang, affiliated with both institutions; and John Waters of the University of Liverpool, U.K.

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Xenotransplanting embryonic pig pancreatic cells

Cross-species transplant in rhesus macaques is step toward diabetes cure for humans Friday, 19 October 2007 With an eye on curing diabetes, scientists at Washington University School of Medicine in St. Louis have successfully transplanted embryonic pig pancreatic cells destined to produce insulin into diabetic macaque monkeys – all without the need for risky immune suppression drugs that prevent rejection. The transplanted cells, known as primordia, are in the earliest stages of developing into pancreatic tissues. Within several weeks of the transplants, the cells became engrafted, or established, within the three rhesus macaque monkeys that received them. The cells also released pig insulin in response to rising blood glucose levels, as would be expected in healthy animals and humans. "The approach reduced the animals' need for insulin injections and has promise for curing diabetes in humans," says senior investigator Marc Hammerman, M.D., the Chromalloy Professor of Renal Diseases in Medicine. "The transplants worked without a need for immune suppression and that is a major obstacle we have overcome." Although the transplants fell short of producing sufficient insulin to cure the macaques' diabetes, Hammerman predicts that with additional research, including the transplantation of additional embryonic pig cells into the animals, he will be able to reduce their need for insulin injections entirely. The new research follows on the heels of reports by Hammerman and his colleagues demonstrating that transplanted pig pancreatic primordia can cure both type 1 and type 2 diabetes in rats, without using immune suppression drugs. Other scientists have tried different types of pancreatic cell transplants – in animals and humans – as a stepping stone to curing diabetes, but they all require anti-rejection drugs. These drugs must be taken daily to stave off rejection and have adverse effects of their own that limit the success of the transplants. As a treatment for diabetes in people, pig insulin typically works as well as the human form. Before recombinant DNA technology enabled pharmaceutical companies to manufacture human insulin in the 1980s, pig and cow insulin were routinely given to diabetic patients. The primates in the current study had type 1 diabetes, the form that occurs when islet cells in the pancreas stop producing insulin all together. The Washington University researchers transplanted 19 embryonic pig pancreatic primordia into each diabetic monkey. Each primordia is smaller than the diameter of a period that ends a sentence and is transplanted into a membrane that envelops the intestines and other digestive organs. The transplanted cells were retrieved from the pig embryos early in their development, which is believed to render them "invisible" to the primates' immune system or induce a state of tolerance, either of which eliminates the need for immune suppression. The researchers determined by multiple methods that the transplanted cells became established within the primates. And as the cells matured, they began to release pig insulin. "We found using every method that the cells engraft long-term and, thus, are not rejected by the animals' immune systems," Hammerman says. "It's been more than two years since our first transplant was carried out. That particular primate doesn't produce any primate insulin, but has pig insulin circulating in its bloodstream that has reduced by more than 50 percent the amount of injected insulin the animal needs, compared to levels before the transplant. The animals have never received immune suppression drugs." Two of the macaques remain healthy. One, however, became anaemic about six weeks post-transplant and was euthanized a month later after developing acute respiratory distress. The researchers could not find a link between this animal's illness and the pancreatic cell transplants. The two remaining macaques have each received two transplants of embryonic pancreatic cells. One of the animals has been followed for 23 months after his first transplant, and the amount of insulin he needs to have injected has declined by some 55 percent over baseline levels. The other macaque has been followed for 10 months after his initial transplant, and his need for injected insulin continues to decline over time. Hammerman and his colleague Sharon Rogers, research instructor in medicine, are leaders in the emerging field of organogenesis, which focuses on growing organs from transplanted embryonic organ precursors known as primordia. Unlike embryonic stem cells, which can become virtually any cell type, primordia are locked into becoming cells of a particular organ. "We are encouraged by these results," Rogers says. "The absence of a need for immune suppression in diabetic rats gave us hope that we were on the right track. But many findings in rats do not hold true for species that are more closely related to humans, such as non-human primates. This one did." The team will now determine how best to eliminate the need for injected insulin in the diabetic macaques that receive transplants, thus demonstrating long-term effectiveness of the technique, and establish the absolute safety of pancreatic primordia transplants. If these experiments succeed, the researchers plan to conduct clinical trials in humans with diabetes. "We hope to find out how to apply our findings to human type 1 and type 2 diabetics because the embryonic pig primordia would represent an unlimited source of tissue for transplantation," Hammerman says. ......... ZenMaster

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Thursday, 18 October 2007

Zerhouni again urges more stem cell research

NIH director Zerhouni again urges more stem cell research Thursday, 18 October 2007 In a magazine interview in Medline Plus this week, National Institutes of Health Director Elias Zerhouni says that human embryonic stem cell research should be expanded. "All avenues of research need to be pursued," Zerhouni says. “Unfortunately, the scientific foundation of stem cell research is sometimes lost in the societal, moral, and ethical battle between hype and hope. But our job at NIH is to push the science forward to serve our patients.” He adds: "We must continue the research at all levels, or there will be no progress." “So I think it’s a multi-pronged attack, both from the point of basic understanding and continually improving what we do. Finally, it’s important to emphasize that science evolves with strong ethics.” “Good science is good ethics.” Zerhouni in March during a Senate Appropriations Committee subcommittee hearing on NIH funding for fiscal year 2008 said that he supports lifting restrictions on federal funding for embryonic stem cell research A Congressional Quarterly health-care reporter wrote at the time that Zerhouni "perhaps put himself on a path toward unemployment." Those views put Zerhouni, who serves at the pleasure of President Bush, at odds with his boss. Bush has twice vetoed legislation to do what Zerhouni wants. Bush "has to draw the line in a different place than Dr. Zerhouni" and come from a "broader" view than that of a scientist, White House spokesperson Tony Fratto said in a comment. He added that Bush's policy accounts for "moral and religious views." Zerhouni spokesperson John Burklow commented this controversy: "As the director of the country's primary biomedical research agency, Dr. Zerhouni believes that he serves the president, and the American people, best by providing candid scientific expertise and perspective" ......... ZenMaster

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microRNA scan uncovers reasons behind muscle dystrophies

Massive microRNA scan uncovers leads to treating muscle degeneration Thursday, 18 October 2007 Researchers have discovered the first microRNAs – tiny bits of code that regulate gene activity – linked to each of 10 major degenerative muscular disorders, opening doors to new treatments and a better biological understanding of these debilitating, poorly understood, often untreatable diseases. The study, to be published online this week by the Proceedings of the National Academy of Sciences, was led by Iris Eisenberg, PhD, of the Program in Genomics at Children’s Hospital Boston. Louis Kunkel, PhD, director of the Program in Genomics and an investigator with the Howard Hughes Medical Institute, was senior investigator. The disorders include the muscular dystrophies (Duchenne muscular dystrophy, Becker muscular dystrophy, limb girdle muscular dystrophies, Miyoshi myopathy, and fascioscapulohumeral muscular dystrophy); the congenital myopathies (nemaline myopathy); and the inflammatory myopathies (polymyositis, dermatomyositis, and inclusion body myositis). While past studies have linked them with an increasing number of genes, it's still largely unknown how these genes cause muscle weakness and wasting, and, more importantly, how to translate the discoveries into treatments. For instance, most muscular dystrophies begin with a known mutation in a “master gene”, leading to damaged or absent proteins in muscle cells. In Duchenne and Becker muscular dystrophies, the absent protein is dystrophin, as Kunkel himself discovered in 1987. Its absence causes muscle tissue to weaken and rupture, and the tissue becomes progressively non-functional through inflammatory attacks and other damaging events that aren’t fully understood. “The initial mutations do not explain why patients are losing their muscle so fast,” says Eisenberg. “There are still many unknown genes involved in these processes, as well as in the inflammatory processes taking place in the damaged muscle tissue.” She and Kunkel believe microRNAs may help provide the missing genetic links. Their team analyzed muscle tissue from patients with each of the ten muscular disorders, discovering that 185 microRNAs are either too abundant or too scarce in wasting muscle, compared with healthy muscle. Discovered in humans only in the past decade, microRNAs are already known to regulate major processes in the body. Therefore, Eisenberg believes microRNAs may be involved in orchestrating the tissue death, inflammatory response and other major degenerative processes in the affected muscle tissue. The researchers used bioinformatics to uncover a list of genes the microRNAs may act on, and now plan to find which microRNAs and genes actually underlie these processes. The findings raise the possibility of slowing muscle loss by targeting the microRNAs that control these “cascades” of damaging events. This approach is more efficient than targeting individual genes. The team also defined the abnormal microRNA “signatures” that correspond to each of the ten wasting diseases. They hope these will shed light on the genes and disease mechanisms involved in the most poorly understood and least treatable of the degenerative disorders, such as inclusion body myositis. “At this point, it’s very theoretical, but it’s possible,” says Eisenberg. Article: Distinctive patterns of microRNA expression in primary muscular disorders Iris Eisenberg et al. Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0708115104 ......... ZenMaster

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Friday, 12 October 2007

First Complete Asian Genome

Chinese Scientists Map Out First Asian Genome Friday, 12 October 2007 Chinese scientists have successfully completed the first sequence map of the diploid genome of an Asian individual, China Daily report. The Chinese project was undertaken by the Shenzhen branch of the Beijing Genomics Institute (BGI), along with the National Engineering Research Center of Systematic Bioinformatics and the Chinese Academy of Sciences and is now on display at the Ninth Annual China Hi-Tech Fair in the city. The results, based on a normal Chinese man of Han nationality, represent only the third human genome to have been sequenced in the world. It took only six months to analyzing his genome sequence with the advanced techniques used.

American scientists earlier this year created the first two genome sequence maps, that of James Watson and Craig Venter respectively. "We can never change our genes, but we can understand our genetic structure better by creating a fine map of our genome sequence. This is very helpful in preventing or controlling diseases, such as cancers," Wang Jun, the leader of the project and vice-director of BGI's Shenzhen branch, said. The next step of the project will be to sequence the genomes of more individuals to identify genetic variations in Asian populations and explore the essential mechanisms behind many diseases. Wang said the researchers would soon select 99 Chinese people for the project. The number of research subjects will be expanded to 10,000 in the following couple of years. "Everyone will have his genome sequenced in the near future for better healthcare," he said. At the same time, the project is trying to lower the cost to popularize the technology, Yang Huanming, director of the Beijing Institute of Genomics of the Chinese Academy of Sciences, said. The project in Shenzhen has lowered the cost to US$5 million. It is expected that the cost will drop to 200,000 yuan (US$26,300) by 2010. "Our final goal is to reduce the cost to less than 10,000 yuan, so that the technology will benefit more people," Yang said. He said he hoped that in the near future genome sequencing for patients would become as common as a physical examination. .........

See also: First Asian genome sequenced Nature 12 October 2007 doi:10.1038/news.2007.161

Reference to the published result (added 5 November, 2008): The diploid genome sequence of an Asian individual Jun Wang, Wei Wang, Ruiqiang Li, Yingrui Li, Geng Tian, Laurie Goodman, Wei Fan, Junqing Zhang, Jun Li, Juanbin Zhang, Yiran Guo, Binxiao Feng, Heng Li, Yao Lu, Xiaodong Fang, Huiqing Liang, Zhenglin Du, Dong Li, Yiqing Zhao, Yujie Hu, Zhenzhen Yang, Hancheng Zheng, Ines Hellmann, Michael Inouye, John Pool, Xin Yi, Jing Zhao, Jinjie Duan, Yan Zhou, Junjie Qin, Lijia Ma, Guoqing Li, Zhentao Yang, Guojie Zhang, Bin Yang, Chang Yu, Fang Liang, Wenjie Li, Shaochuan Li, Dawei Li, Peixiang Ni, Jue Ruan, Qibin Li, Hongmei Zhu, Dongyuan Liu, Zhike Lu, Ning Li, Guangwu Guo, Jianguo Zhang, Jia Ye, Lin Fang, Qin Hao, Quan Chen, Yu Liang, Yeyang Su, A. san, Cuo Ping, Shuang Yang, Fang Chen, Li Li, Ke Zhou, Hongkun Zheng, Yuanyuan Ren, Ling Yang, Yang Gao, Guohua Yang, Zhuo Li, Xiaoli Feng, Karsten Kristiansen, Gane Ka-Shu Wong, Rasmus Nielsen, Richard Durbin, Lars Bolund, Xiuqing Zhang, Songgang Li, Huanming Yang & Jian Wang Nature 456, 60-65, 6 November 2008, doi:10.1038/nature07484



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Thursday, 11 October 2007

Stem cell nuclei are soft and plastic

Stem cell nuclei are soft 'hard drives' Thursday, 11 October 2007 Biophysicists at the University of Pennsylvania have discovered that the nuclei of human stem cells are particularly soft and flexible, rather than hard, making it easier for stem cells to migrate through the body and to adopt different shapes, but ultimately to put human genes in the correct nuclear ”sector” for proper access and expression. Researchers pulled cell nuclei into microscopic glass tubes under controlled pressures and visualized the shear of the DNA and associated proteins by fluorescence microscopy. The study showed that nuclei in human embryonic stem cells were the most deformable, followed by hematopoietic stem cells, HSCs, that generate a wide range of blood and tissue cells. Both types of stem cells lack lamins A and C, two filamentous proteins that interact to stabilize the inner lining of the nucleus of most tissue cells. Lamins A and C stiffen cell nuclei and are expressed in cells only after gastrulation, when most stem cells generate the specific tissues of complex organisms. The fluid-like character of the nucleus is shown to be set largely by the DNA and the DNA-attached proteins that form chromatin. The extent of deformation of the nucleus is further modulated by the lamina. ”Understanding the sensitivity of stem cells and their nuclei to external stresses has very practical implications in handling these cells as well as in technologies such as cloning in which nuclei are manipulated,” said Dennis Discher, a professor in Penn’s School of Engineering and Applied Science and the Penn School of Medicine’s Cell and Molecular Biology Graduate Group. The study, published in the Oct. 2 issue of the Proceedings of the National Academy of Sciences, supports the theory that lamin proteins are responsible for much of the genomic ”lock-down” within differentiated cells. Differentiated cells, typified by muscle cells, fat cells and bone cells, all arise from stem cells that have committed to these specialized cell types by locking the DNA into a set pattern of gene expression. To verify that lamin proteins were responsible for nuclear stiffness, the authors created a line of epithelial cells in which lamin filaments had been almost eliminated. Once as stiff as any other differentiated tissue cell derived from stem cells, the cell became as pliable as HSCs. ”Controlling structural proteins within the nucleus might lead to new means for controlling genomic regulatory factors and for generating stem cells from adult tissue cells,” J. David Pajerowski, lead author and a graduate student in Penn’s School of Engineering and Applied Science, said. Researchers also found that over time nuclear deformations in stem cells and hematopoietic cells became resistant to returning to their original shape, which provides evidence of plastic flow similar to that of wet clay in the hands of a sculptor. Continued application of force eventually pulled nuclei into irreversible forms in which genes were re-arranged and massaged into new nuclear locations. Researchers literally visualized the flow of chromatin, the structure that carries DNA, and found irreversible distortions occurring on a timescale of minutes, a long time compared to many other cell processes but short compared to the lifetimes of nuclei in our tissue cells. ......... ZenMaster

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Adult stem cells not equal to ESCs

Adult stem cells lack key pluripotency regulator Thursday, 11 October 2007 The protein Oct4 plays a major role in embryonic stem cells, acting as a master regulator of the genes that keep the cells in an undifferentiated state. Unsurprisingly, researchers studying adult stem cells have long suspected that Oct4 also is critical in allowing these cells to remain undifferentiated. Indeed, more than 50 studies have reported finding Oct4 activity in adult stem cells. But those findings are misleading, according to research in the lab of Whitehead Member Rudolf Jaenisch. In a paper published online in Cell Stem Cells on October 10, postdoctoral fellow Christopher Lengner has shown that Oct4 is not required to maintain adult stem cells in their undifferentiated state in mice, and that adult tissues function normally in the absence of Oct4. Furthermore, using three independent detection methods in several tissue types in which Oct4-positive adult stem cells had been reported, Lengner found either no trace of Oct4, or so little Oct4 as to be indistinguishable from background readings. This means that pluripotency, the ability of stem cells to change into any kind of cell, is regulated differently in adult and embryonic stem cells. “This is the definitive survey of Oct4,” says Jaenisch, who is also an MIT professor of biology. “It puts all those claims of pluripotent adult stem cells into perspective.” Oct4 is essential in maintaining the pluripotency of embryonic stem cells, but only for a short time before the embryo implants in the uterine wall. After implantation Oct4 is turned off, and the cells differentiate into all of the 200-plus cell types in the body. “We have convincingly shown that Oct4 has no role in adult stem cells,” says Lengner. He initially set out to determine how tissues previously shown to express Oct4 (the intestinal lining, brain, bone marrow, and hair follicle) functioned without the protein. To do so, he bred mice in which the Oct4 gene had been deleted from a given tissue type. Next, Lengner stressed the tissue in several ways, forcing the adult stem cells within to regenerate the tissue. All regenerated normally. Lengner and his fellow researchers then tested to confirm that Oct4 had indeed been deleted from these cells. Finally, the researchers set out to validate the previously published reports claiming Oct4 was expressed in these adult stem cell types. Using highly sensitive assays that could detect Oct4 at the single cell level, they were unable to confirm the earlier reports. “This is a cautionary tale of believing what you read in the literature,” says Lengner, who suggests that earlier studies may have misapplied tricky analytical techniques or worked with cell cultures that had spent too much time in an incubator. “We now know that adult stem cells regulate their pluripotency, or ‘stemness’, using different mechanisms from embryonic stem cells, and we’re studying these mechanisms,” he says. “Is there a common pathway that governs stemness in different adult stem cells, or does each stem cell have its own pathway. We don’t yet know.” Reference: Oct4 is dispensable for somatic stem cell self-renewal Christopher J. Lengner, Fernando D. Camargo, Konrad Hochedlinger, G. Grant Welstead, Samir Zaidi, Sumita Gokhale, Hans R. Scholer, Alexey Tomilin and Rudolf Jaenisch Cell Stem Cell, Vol 1, 403-415, 11 October 2007 ......... ZenMaster

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Wednesday, 10 October 2007

Endogenous retrovirus in humans and monkeys

Spread of endogenous retrovirus K is similar in the DNA of humans and rhesus monkeys Wednesday, 10 October 2007 According to palaeontology and molecular studies, the chimpanzee (Pan Troglodytes) is the closer relative to the humans (Homo Sapiens) and that both lineages had a common ancestor at 5 to 7 million years ago. Moreover, the human-chimp lineage split from that of the rhesus monkey (Macaca Mulatta) around 25 million years ago. However, by studying the population dynamics of complete copies of primate endogenous retrovirus family K (ERV-K) in the genomes of humans, chimpanzee and rhesus monkey, a surprising pattern was observed. The study by Romano and colleagues being published this week on PLoS ONE revealed that human ERV-K had a similar demographic signature to that of the rhesus monkey, both differing greatly from that of the chimpanzee. The data suggested that the humans and rhesus have been purging ERV-K copies from their genomes while the chimpanzee ERV-K population kept the signature of increasing numbers of ERV-K amplification in the genome of ancestral primates during the last 20 million years. Hominids have been moving out of Africa for the last 2 million years and the modern humans (Homo Sapiens) spread around almost the entire globe during the last 100 thousand years. Moreover, Macaca is the most specious primate genus and it is believed to have originated around 2.5 million years ago and became widely dispersed within a short period of time, from the West in Afghanistan to the Eastern coast of China. It is also known that speciation events partition and restrict flow among genetic pools. As a consequence, both Homo and Macaca by colonizing new environments and undergoing successive population fluctuations that caused severe genetic bottlenecks, possible purged ERV-K from their genomes in a similar fashion. On the other hand, populations chimpanzee have been restricted to Eastern and Central Sub-Saharan Africa, ever since and crucially, are also known to have a greater genetic diversity than humans (due to a greater effective population number Ne), even when humans have a far greater census population. While the population size fluctuations due to dispersal or speciation may have had impact on genome architecture, the several expansion and bottlenecks experienced by Homo and Macaca may have played an important role in shaping ERV-K dynamics. Because Pan did not suffer severe bottlenecks since their separation from the Pan – Homo (human) common ancestor, they not only show a greater genetic diversity but also they preserved a greater number of complete ERV-K copies in their genomes. The most remarkable result was that for the first time it could be observed that genetic fluctuations caused by bottlenecks and expansion in host species play a fundamental role not only in their genetic diversity but also in the interaction with latent parasites that leave their genome copies in our DNA. Citation: Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys Romano CM, de Melo FL, Corsini MAB, Holmes EC, Zanotto PM PLoS ONE 2007, 2(10): e1026. doi:10.1371/journal.pone.0001026 ......... ZenMaster

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Tuesday, 9 October 2007

Back to the question: How much is a human egg worth?

Back to the question: How much is a human egg worth? Tuesday, 09 October 2007 Massachusetts regulations prohibit researchers from paying women for their eggs when donated for research. Similar regulations exist in California, and guidelines from both the National Academy of Sciences and the International Society for Stem Cell Research permit only limited compensation for egg donors. The law is meant to prevent coercion of poor women who might undergo the procedure out of financial need. But women who undergo the same procedure to donate eggs for assisted reproductive technology (ART), in which infertile women use another woman's eggs to get pregnant, are paid anywhere from $3,000 to $10,000. The United Kingdom has taken a different approach. Last year, the regulatory board that oversees embryonic stem-cell research in the United Kingdom (HFEA) approved an "egg sharing" program, something that some scientists and ethicists want to see adopted in the United States too. Women who plan to undergo in vitro fertilization (IVF) agree to donate to research any excess eggs gathered during the procedure in exchange for subsidized medical costs. See also: Human Ovulation Caught on Camera What is a human egg worth - £15 or US$10,000? How much is a human egg worth? Back to the question: How much is a human egg worth? Human Therapeutic Cloning at a Standstill ......... ZenMaster

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Therapeutic Cloning at a Standstill

Human Therapeutic Cloning at a Standstill Tuesday, 09 October 2007 It's rare for a scientist to take the mike at a prominent conference, face his peers, and plaintively announce that he has made absolutely no progress on an important research project. But that's exactly what Kevin Eggan, a biologist at the Harvard Stem Cell Institute, did last week at the Stem Cell Summit, in Boston. A year and a half after a highly publicized approval to start human therapeutic-cloning research at Harvard, Eggan and his collaborators have gotten nowhere. Despite extensive outreach, they still lack a crucial resource for their experiments: human eggs. "We've spent $100,000 on advertising, but we have yet to have a single woman donate eggs," says Eggan.

............................. Human Therapeutic Cloning at a Standstill A lack of human eggs has created a major roadblock in one of the most promising areas of stem-cell research. Technology Review - Tuesday, October 09, 2007 .........

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Venter makes synthetic life... or not yet?

Venter makes synthetic life... or not yet? Tuesday, 09 October 2007 Rumours of J. Craig Venter's achievements in creating artificial life are again circulating in the press – Ed Pilkington in the Guardian reported this weekend that Venter has successfully made a fully synthetic chromosome, dubbed Mycoplasma laboratorium. The chromosome reportedly consists of 381 genes, and in total contains 580,000 nucleotide base pairs. In a study published this June, Venter and colleagues switched two closely related species of bacteria by transplanting their genomes. This transplantation step would be needed to activate synthetic chromosomes as well. So far, however, the new work is not accompanied by a peer-reviewed publication. Venter "is poised to announce" the discovery in the next couple weeks, according to the Guardian article, and possibly even today, at the J. Craig Venter Institute's annual meeting. Nature's news blog, The Great Beyond points to a report in AFP, in which Heather Kowalski, the J. Craig Venter Institute's media contact, declined to confirm the breakthrough. "We have not achieved what some have speculated we have in synthetic life," Kowalski apparently told AFP. "When we do so there will be a scientific publication and we are likely months away from that." .........


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Read more: Creating life in the laboratory BBC - 2007/10/19 RELATED INTERNET LINKS: J Craig Venter Institute Massachusetts Institute of Technology Vanderbilt University Medical Center Harvard Medical School University of Rome Three Princeton University Los Alamos National Laboratory Southampton University Biobricks

Which came first, the chicken genome or the egg genome?

New insights into the evolution of the human genome Tuesday, 09 October 2007 Which came first, the chicken genome or the egg genome? Researchers have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates? The answers, published online by Nature Genetics on October 7, 2007, provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations. This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations.

Which came first, the chicken genome or the egg genome? Researchers from UC San Diego, U. of Washington School of Medicine and elsewhere have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates? This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations. The chicken shape in the image is actual segmental duplication data from figure 2 of the Nature Genetics paper. The egg was created with graphics editing software. Image Credit: Daniel Kane/ UC San Diego. Genomes have a remarkable ability to copy a long stretch of DNA from one chromosome and insert it into another region of the genome. The resulting chunks of repeated DNA – called “segmental duplications” – hold many evolutionary secrets and uncovering them is a difficult biological and computational challenge with implications for both medicine and our understanding of evolution. The new evolutionary history, published in Nature Genetics, is from an interdisciplinary team led by biologist Evan Eichler from the University of Washington School of Medicine and computer scientists Pavel Pevzner from University of California, San Diego. In the past, the highly complex patterns of DNA duplication – including duplications within duplications – have prevented the construction of an evolutionary history of these long DNA duplications.

Non-random distribution of sequence divergence. The distribution of sequence divergence between ancestral and derivative loci is shown as a function of the location of duplication blocks in the human genome. The authors found 20 of 437 duplication blocks that significantly depart from a continuous genomic duplication model. Eighteen blocks suggest a preponderance of evolutionary younger events (red) and two duplication blocks suggest that duplication activity occurred and then ceased; (green) The effect predominates for particular chromosomes (for example, chr2, chr4, chr5, chr9, chr16 and chrY). The researchers, including UC San Diego’s Pavel Pevzner, tracked down the ancestral origin of more than two thirds of the long DNA duplications in the human genome known as “segmental duplications” and published their results in Nature Genetics. To crack the duplication code and determine which of the DNA segments are originals (ancestral duplications) and which are copies (derivative duplications), the researchers looked to both algorithmic biology and comparative genomics. “Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable,” said Pavel Pevzner a UCSD computer science professor who modified an algorithmic genome assembly technique in order to deconstruct the mosaics of repeated stretches of DNA and identify the original sequences. “Maybe there is something special about the originals, some clue or insight into what causes this colonization of the human genome,” said Pevzner. “This is the first time that we have a global view of the evolutionary origin of some of the most complicated regions of the human genome,” said paper author Evan Eichler, a professor from the University of Washington School of Medicine and the Howard Hughes Medical Institute. The researchers tracked down the ancestral origin of more than two thirds of these long DNA duplications. In the Nature Genetics paper they highlight two big picture findings. First, the researchers suggest that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications. Second, the researchers show that a large fraction of the recent duplication architecture centres around a rather small subset of “core duplicons” – short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations. “We found that not all of the duplications in the human genome are created equal. Some of them – the core duplicons – appear to be responsible for recent genetic innovations the in human genome,” explained Pevzner, who is the director of the UCSD Center for Algorithmic and Systems Biology, located at the UCSD division of Calit2.

The researchers, including UC San Diego’s Pavel Pevzner, tracked down the ancestral origin of more than two thirds of the long DNA duplications in the human genome known as “segmental duplications” and published their results in Nature Genetics. This colourful image (figure 2 in the paper) illustrates the process of ancestral-state determination for one 750-kb duplication block on human chromosome 2p11. In this example, 15 of 16 ancestral loci were accurately predicted by the computational method. The authors uncovered 14 such core duplicons. “We note that in 4 of the 14 cases, there is compelling evidence that genes embedded within the cores are associated with novel human gene innovations. In two cases the core duplicons has been part of novel fusion genes whose functions appear to be radically different from their antecedents,” the authors write in their Nature Genetics paper. “The results suggest that the high rate of disease caused by these duplications in the normal population – estimated at 1/500 and 1/1000 events per birth – may be offset by the emergence of newly minted human/great-ape specific genes embedded within the duplications. The next challenge will be determining the function of these novel genes," said Eichler. To reach these insights, the researchers worked to systematically pinpoint the ancestral origin of each human segmental duplication and organized duplication blocks based on their shared evolutionary history. Pevzner and his associate Haixu Tang (now professor at University of Indiana) applied their expertise in assembling genomes from millions of small fragments – a problem that is not unlike the “mosaic decomposition” problem in analyzing duplications that the team faced. Over the years, Pevzner has applied the 250-year old algorithmic idea first proposed by 18th century mathematician Leonhard Euler (of the fame of pi) to a variety of problems and demonstrated that it works equally well for a set of seemingly unrelated biological problems including DNA fragment assembly, reconstructing snake venoms, and now dissecting the mosaic structure of segmental duplications. In the future, the researchers plan to continue their exploration of evolution. “We want to figure out how the human genome evolved. In the future, we will combine what we know about the evolution within genomes with comparative genomics in order to extend our view of evolution,” said Pevzner. ......... ZenMaster

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Thursday, 4 October 2007

Clinton Would Fund Stem Cell Research

Clinton Would Fund Stem Cell Research AP - October 4, 2007

NEW YORK — If elected president, Democrat Hillary Rodham Clinton says she would sign an executive order rescinding President Bush's restrictions on federal funding for embryonic stem cell research.

She says she also would bar political appointees from altering or removing scientific conclusions from government research without a legitimate reason for doing so.

The New York senator was to announce these and other proposals of her science agenda in a speech in Washington on Thursday. ......... ZenMaster

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