Thursday, 29 November 2007

ESI generate clinical-grade hESC lines

ES Cell International generate six clinical-grade hESC lines Thursday, 29 November 2007 The use of clinical-grade human embryonic stem cells (hESCs) for cell therapy has taken an important step forward. ES Cell International (ESI) has derived the first clinical-grade hESCs by using current Good Manufacturing Practice (cGMP) and Good Tissue Practice (cGTP) respectively, according to an article in the latest issue of "Cell Stem Cell". To hasten the clinical use of hESCs, ESI and the Singapore Stem Cell Bank (SSCB) are currently working out a distribution agreement. This will provide research-grade variants of clinical-grade cell lines to academic researchers at not-for-profit institutes around the world for a fee. ESI will also provide commercial industry players and those who want to conduct clinical trials access to clinical-grade versions of hESCs, under a licence. Reference: The Generation of Six Clinical-Grade Human Embryonic Stem Cell Lines Cell Stem Cell, Vol 1, 490-494, 15 November 2007 ......... ZenMaster

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How Many Genes in the Human Genome?

New Study from Broad Institute Lowers Human Gene Count to 20,500 Thursday, 29 November 2007 A study published online this week in the Proceedings of the National Academy of Sciences indicates that the number of protein-coding genes in the human genome may be much lower than the current estimate of around 24,500 genes. According to the study, published by Michele Clamp and colleagues at the Broad Institute, human gene catalogue’s such as Ensembl, RefSeq, and Vega include many open reading frames that are actually “random occurrences” rather than protein-coding regions — a finding that cuts the number of protein-coding genes in the genome to around 20,500. The Broad team analyzed ORFs for which there is no evidence of evolutionary conservation with mouse or dog. According to the researchers, it has been “broadly suspected” that many of these ORFs are “functionally meaningless,” but there has been no scientific evidence to prove they are not valid genes. “As a result,” they note in the PNAS paper, “the human gene catalogue has remained in considerable doubt.” Clamp and colleagues developed a method to characterize the properties of putative genes that lack cross-species counterparts. By analyzing these non-conserved ORFs alongside the genomes of two primates, the researchers found that they are neither the result of gene innovation in the primate lineage nor the result of gene loss in mouse or dog. This offers “strong evidence” that these non-conserved ORFs are indeed “spurious,” and should be removed from the gene catalogue’s, according to the paper. The Broad team did acknowledge that the study has “certain limitations” that could impact the final gene count. For example, they note, they did not consider 197 putative genes that lie in regions that were omitted from the finished assembly of the human genome. They concede that it’s likely there are additional protein-coding genes yet to be found, but they believe that “the final total is likely to remain under 21,000.” Reference: Distinguishing protein-coding and noncoding genes in the human genome Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0709013104 ......... ZenMaster

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A molecular map for aging

A molecular map for aging in mice and humans Wednesday, 28 November 2007 Researchers at the National Institute of Aging and Stanford University have used gene arrays to identify genes whose activity changes with age in 16 different mouse tissues. The study, published November 30 in PLoS Genetics, uses a newly available database called AGEMAP to document the process of aging in mice at the molecular level. The work describes how aging affects different tissues in mice, and ultimately could help explain why lifespan is limited to just two years in mice. As an organism ages, most tissues change their structure (for example, muscle tissues become weaker and have slow twitch rather than fast twitch fibres), and all tissues are subject to cellular damage that accumulates with age. Both changes in tissues and cellular damage lead to changes in gene expression, and thus probing which genes change expression in old age can lead to insights about the process of aging itself. Previous studies have studied gene expression changes during aging in just one tissue. The new work stands out because it is much larger and more complete, including aging data for 16 different tissues and containing over 5.5 million expression measurements. One noteworthy result is that some tissues (such as the thymus, eyes and lung) show large changes in which genes are active in old age whereas other tissues (such as liver and cerebrum) show little or none, suggesting that different tissues may degenerate to different degrees in old mice. Another insight is that there are three distinct patterns of aging, and that tissues can be grouped according to which aging pathway they take. This result indicates that there are three different clocks for aging that may or may not change synchronously, and that an old animal may be a mixture of tissues affected by each of the different aging clocks. Finally, the report compares aging in mice to aging in humans. Several aging pathways were found to be the same, and these could be interesting because they are relevant to human aging and can also be scientifically studied in mice. Reference: AGEMAP: A gene expression database for aging in mice. PLoS Genet 3(11): e201. ......... ZenMaster

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Tuesday, 27 November 2007

Stem cell therapies for brain more complicated than thought

Stem cell therapies for brain more complicated than thought Tuesday, 27 November 2007 A team of MIT researchers suggests that stem cell therapies for the brain could be much more complicated than previously thought. In a study published in the Public Library of Science (PLoS) Biology on Nov. 13, MIT scientists report that adult stem cells produced in the brain are pre-programmed to make only certain kinds of connections — making it impossible for a neural stem cell originating in the brain to be transplanted to the spinal cord, for instance, to take over functions for damaged cells. Some researchers hope to use adult stem cells produced in the brain to replace neurons lost to damage and diseases such as Alzheimer’s. The new study calls this into question. “It is wishful thinking to hope that adult stem cells will be able to modify themselves so that they can become other types of neurons lost to injury or disease”, said Carlos E. Lois, assistant professor of neuroscience in MIT’s Picower Institute for Leaning and Memory. In developing embryos, stem cells give rise to all the different types of cells that make up the body--skin, muscle, nerve, brain, blood and more. Some of these stem cells persist in adults and give rise to new skin cells, stomach lining cells, etc. The idea behind stem-cell therapy is to use these cells to repair tissue or organs ravaged by disease. To realize this potential, the stem cells have to be “instructed” to become liver cells, heart cells or neurons. The MIT study, which looked only at adult neural stem cells, suggests it will be necessary to learn how to program any kind of stem cell — embryonic, adult or those derived through other means — to produce specific types of functioning neurons. Without this special set of instructions, a young neuron will only connect with the partners for which it was pre-programmed. The adult brain harbours its own population of stem cells that spawn new neurons for life. The MIT study shows that a neural stem cell is irreversibly committed to produce only one type of neuron with a pre-set pattern of connections. This means that a given neuronal stem cell can have only limited use in replacement therapy. “A stem cell that produces neurons that could be useful to replace neurons in the cerebral cortex (the type of neurons lost in Alzheimer's disease) will be most likely useless to replace neurons lost in the spinal cord,” said Lois, who also holds an appointment in MIT’s Department of Brain and Cognitive Sciences. “Moreover, because there are many different types of neurons in the cerebral cortex, it is likely that we will have to figure out how to program stem cells to become many different types of neurons, each of them with a different set of pre-specified connections.” “In the stem cell field, it is generally thought that the main limitation to achieve brain repair is simply for the new neurons to reach a given brain region and to ensure their survival. Once there, it has been assumed that stem cells will ‘know what to do’ and will become the type of neuron that is missing. It seems that is not the case at all. Our experiments indicate that things are much more complicated,” Lois said. Lois and colleagues from MIT’s departments of Brain and Cognitive Sciences and Biology found that the stem cells give rise to neurons that become a very specific neuronal type that is already pre-specified to make a much defined set of connections and not others. Even if the stem cells are transplanted to other parts of the brain, they do not change the type of connections they are programmed to make. “This suggests that we will have to know much more about the different types of neuronal stem cells, and to identify the characteristic features of their progeny,” Lois said. “We may need to have access to many different types of ‘tailored’ stem cells that give rise to many different types of neurons with specific connections. In addition, we may need a combination of several of these tailored stem cells to eventually be able to replace the different types of neurons lost in a given brain region.” ......... ZenMaster

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Researchers find mature heart cell potential in hESCs

UC Davis researchers find evidence of mature heart cell potential in hESCs Finding advances field toward future use of stem cell treatment of end-stage heart disease Tuesday, 27 November 2007 In a new study, UC Davis researchers report the first functional evidence that heart cells derived from human embryonic stem cells exhibit one of the most critical properties of mature adult heart cells, an important biological process called excitation-contraction coupling. The finding gives scientists hope that these cells can one day be coaxed into becoming functionally viable cells safe for transplantation into the damaged hearts of patients with end-stage disease, potentially avoiding the necessity of a heart transplant. Currently, there are nearly 3,000 people on heart transplant lists around the nation, including more than 300 in California. UC Davis research scientist Ronald Li and his colleagues write in their study, “Functional Sarcoplasmic Reticulum for Calcium-Handling of Human Embryonic Stem Cell-Derived Cardiomyocytes: Insights for Driven Maturation,” that they observed cells that had begun the maturation process toward becoming heart cells. The article, available online in Stem Cell Express, will be published in the December issue of the journal Stem Cells. “Previous experiments were able to derive heart cells from human embryonic stem cells,” said Li, who is an associate professor of cell biology and human anatomy at UC Davis School of Medicine and senior author of the study. “... but those cells always remained too immature to be of any therapeutic use and actually could cause lethal arrhythmias in animal models. Now, what we’ve been able to do is push the therapeutic potential of human embryonic stem cells further so that eventually they might be used safely, and with enhanced efficacy, in transplantation cases.” The main function of the heart is to mechanically pump blood in a highly coordinated fashion throughout the body. To do this, heart cells must receive electrical signals and contract in response to those signals. This link, called the excitation-contraction coupling, is dependent on the cells’ ability to move calcium ions across an internal organelle known as sarcoplasmic reticulum, or the so-called “calcium store.” The ability to handle calcium is disrupted in the cells of patients who experience heart failure. For future stem-cell based therapies to work, scientists will need to have heart cells that exhibit mature excitation-contraction coupling. Until now, researchers studying heart cells (also called cardiomyocytes) derived from human embryonic stem cells have been unable to find evidence of functional calcium stores. Li found protein functions that are involved in the early stages of this coupling process. He and his colleagues now plan to move on and engineer the calcium-handling properties in order to enhance contractile properties in cardiomyocytes for both improved safety and functional efficacy. In the current study, Li and his colleagues took human embryonic stem cells and grew them in cultures, allowing them to differentiate, or develop, into heart cells. Once they had these tiny, pulsing masses, the investigators energized the cells with small amounts of electrical current and chemicals, including caffeine. They then measured how the amount of intracellular calcium changed and looked for the presence of proteins and cellular structures known to be involved in excitation-contraction coupling. Li and his colleagues are the first to find evidence of the functional calcium stores for excitation-contraction coupling. They also found four of the seven key proteins that play key roles in handling calcium in the cell, as well as functional sarcoplasmic reticulum. The UC Davis researchers used different cell lines than those utilized in previous studies, which they say may explain why they were able to achieve a breakthrough in their investigation where others had not. The UC Davis group also looked at a smaller number of cells during various stages of development, enabling them to more accurately dissect the different population subsets. The authors said that differences in cell culture and experimental conditions could also account for the results not seen in previous efforts. According to Li, the fact that different cell lines exhibit different potentials for differentiation and maturation underscores the need to develop new and additional stem cell lines in order to advance critical research into potential therapies for patients. “This is a good example of the type of exciting, bench-to-bedside research now under way at UC Davis and the potential it has for new treatments,” said Jan Nolta, director of the UC Davis Stem Cell Program in Sacramento. “As additional embryonic stem cell lines become available for research, we’ll be able to more fully explore the possibilities inherent in this powerful field of bioscience.” Li’s study is a first step toward deriving cardiomyocytes with fully functional contractile properties from human embryonic stem cells. With heart transplants being the current treatment of last resort due to severe shortages of donor organs and the complexity of transplantation, the long term goal of researchers like Li is to come up with alternatives that are both safe and effective. “Our latest study gives us great hope of eventually achieving a breakthrough where stem cell therapy could be used in the types of cases that today require a heart transplant,” concluded Li. Along with Li, co-authors of the paper are Jing Liu, Jidong Fu and David Siu all from UC Davis School of Medicine. The research was funded by the National Institutes of Health, California Institute of Regenerative Medicine, the Croucher Foundation and UC Davis School of Medicine. ......... ZenMaster

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Wednesday, 21 November 2007

Reprogramming of human fibroblasts to ESCs achieved

Reprogramming of human fibroblasts to ESCs achieved Tuesday, 20 November 2007 Scientists have managed to reprogram human skin cells directly into cells that look and act like embryonic stem (ES) cells. The technique makes it possible to generate patient-specific stem cells to study or treat disease without using embryos or oocytes – and therefore could bypass the ethical debates that have plagued the field. The new discovery is being published online today in Cell, in a paper by Shinya Yamanaka of Kyoto University and the Gladstone Institute for Cardiovascular Disease in San Francisco, and in Science, in a paper by James Thomson and his colleagues at the University of Wisconsin. While both groups used just four genes to reprogram human skin cells, two of the four genes (Oct3/4, Sox2, c-Myc, and Klf4) used by the Japanese scientists were different from two of the four used by the American group (Oct4, Sox2, Nanog, and Lin28). All the genes in question, though, act in a similar way – they are master regulator genes whose role is to turn other genes on or off. A limitation is that the scientists use a retrovirus to insert the genes into the cells’ chromosomes. Retroviruses slip genes into chromosomes at random, and sometimes cause mutations that can make normal cells turn into cancers during this process. In addition, one of the genes that the Japanese scientists insert, the c-Myc gene, in fact is a cancer gene. “It is only a matter of time until retroviruses are not needed,” Dr. Douglas Melton, co-director of the Stem Cell Institute at Harvard University predicted. “Anyone who is going to suggest that this is just a side show and that it won’t work is wrong,” Dr. Melton said. The new discovery was preceded by work in mice. Last year, Dr. Yamanaka published a paper showing that he could add four genes to mouse cells and turn them into mouse embryonic stem cells (see Turning Adult Cells Embryonic). This publication last year set off what became an international race to repeat the work with human cells. “Dozens, if not hundreds of labs, have been attempting to do this,” said Dr. George Daley, associate director of the stem cell program at Children’s Hospital in Boston. In this new work, Yamanaka and his colleagues used a retrovirus to ferry into adult cells the same four genes they had previously employed to reprogram mouse cells: Oct3/4, Sox2, Klf4, and c-Myc. They reprogrammed cells taken from the facial skin of a 36-year-old woman and connective tissue from a 69-year-old man. Roughly one iPS (induced pluripotent stem) cell line was produced for every 5000 cells the researchers treated with the technique, an efficiency that enabled them to produce several cell lines from each experiment. Thomson's team started from scratch, identifying its own list of 14 candidate reprogramming genes. The team used a systematic process of elimination to identify four factors: Oct3 and Sox2, as Yamanaka used, and two different genes, Nanog and Lin28. The group reprogrammed cells from foetal skin and from the foreskin of a newborn boy. The researchers were able to transform about one in 10,000 cells, but still enough to create several cell lines from a single experiment. Although promising, both techniques share a downside. The retroviruses used to insert the genes could cause tumours in tissues grown from the cells. The crucial next step, everyone agrees, is to find a way to reprogram cells by switching on the genes rather than inserting new copies. The field is moving quickly toward that goal. "It is not hard to imagine a time when you could add small molecules that would tickle the same networks as these genes" and produce reprogrammed cells without genetic alterations, said Dr. Douglas Melton of Harvard University. Once the kinks are worked out, "the whole field is going to completely change," said stem cell researcher Jose Cibelli of Michigan State University in East Lansing. "People working on ethics will have to find something new to worry about." See also: UW-Madison scientists also guide human skin cells to embryonic like state Yamanaka Turns Human Fibroblasts to ESC-like Cells Turning Adult Cells Embryonic How to Make Stem Cells Stay Growing ......... ZenMaster

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Tuesday, 20 November 2007

UW-Madison scientists also guide human skin cells to embryonic like state

UW-Madison scientists guide human skin cells to embryonic state Tuesday, 20 November 2007 In a paper published in the online edition of the journal Science, a team of University of Wisconsin-Madison researchers reports the genetic reprogramming of human skin cells to create cells indistinguishable from embryonic stem cells. The finding is not only a critical scientific accomplishment, but potentially remakes the tumultuous political and ethical landscape of stem cell biology as human embryos may no longer be needed to obtain the blank slate stem cells capable of becoming any of the 220 types of cells in the human body. Perfected, the new technique would bring stem cells within easy reach of many more scientists as they could be easily made in labs of moderate sophistication, and without the ethical and legal constraints that now hamper their use by scientists. The new study was conducted in the laboratory of UW-Madison biologist James Thomson, the scientist who first coaxed stem cells from human embryos in 1998. It was led by Junying Yu of the Genome Center of Wisconsin and the Wisconsin National Primate Research Center. "The induced cells do all the things embryonic stem cells do," explains Thomson, a professor of anatomy in the University of Wisconsin School of Medicine and Public Health. "It's going to completely change the field." In addition to exorcising the ethical and political dimensions of the stem cell debate, the advantage of using reprogrammed skin cells is that any cells developed for therapeutic purposes can be customized to the patient. "They are probably more clinically relevant than embryonic stem cells," Thomson explains. "Immune rejection should not be a problem using these cells." An important caveat, Thomson notes, is that more study of the newly-made cells is required to ensure that the "cells do not differ from embryonic stem cells in a clinically significant or unexpected way, so it is hardly time to discontinue embryonic stem cell research." The successful isolation and culturing of human embryonic stem cells in 1998 sparked a huge amount of scientific and public interest, as stem cells are capable of becoming any of the cells or tissues that make up the human body. The potential for transplant medicine was immediately recognized, as was their promise as a window to the earliest stages of human development, and for novel drug discovery schemes. The capacity to generate cells that could be used to treat diseases such as Parkinson's, diabetes and spinal cord injuries, among others, garnered much interest by patients and patient advocacy groups. But embryonic stem cells also sparked significant controversy as embryos were destroyed in the process of obtaining them, and they became a potent national political issue beginning with the 2000 presidential campaign. Since 2001, a national policy has permitted only limited use of some embryonic stem cell lines by scientists receiving public funding. In the new study, to induce the skin cells to what scientists call a pluripotent state, a condition that is essentially the same as that of embryonic stem cells, Yu, Thomson and their colleagues introduced a set of four genes,Oct4, Sox2, NANOG, and LIN28, into human fibroblasts, skin cells that are easy to obtain and grow in culture. Finding a combination of genes capable of transforming differentiated skin cells to undifferentiated stem cells helps resolve a critical question posed by Dolly, the famous sheep cloned in 1996. Dolly was the result of the nucleus of an adult cell transferred to an oocyte, an unfertilized egg. An unknown combination of factors in the egg caused the adult cell nucleus to be reprogrammed and, when implanted in a surrogate mother, develop into a fully formed animal. The new study by Yu and Thomson reveal some of those genetic factors. The ability to reprogram human cells through well defined factors would permit the generation of patient-specific stem cell lines without use of the cloning techniques employed by the creators of Dolly. "These are embryonic stem cell-specific genes which we identified through a combinatorial screen," Thomson says. "Getting rid of the oocyte means that any lab with standard molecular biology can do reprogramming without difficulty to obtain oocytes." Although Thomson is encouraged that the new cells will speed new cell-based therapies to treat disease, more work is required, he says, to refine the techniques through which the cells were generated to prevent the incorporation of the introduced genes into the genome of the cells. In addition, to ensure their safety for therapy, methods to remove the vectors, the viruses used to ferry the genes into the skin cells, need to be developed. Using the new reprogramming techniques, the Wisconsin group has developed eight new stem cell lines. As of the writing of the new Science paper, which will appear in the Dec. 21, 2007 print edition of the journal Science, some of the new cell lines have been growing continuously in culture for as long as 22 weeks. Reference: Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells In addition to Yu and Thomson, authors of the new study include Maxim A. Vodyanik, Kim Smuga-Otto, Jessica Antosiewicz-Bourget, Jennifer L. Frane and Igor I. Slukvin, all of UW-Madison; and Shulan Tian, Jeff Nie, Gudrun A. Jonsdottir, Victor Ruotti and Ron Stewart, all of the WiCell Research Institute. See also: Yamanaka Turns Human Fibroblasts to ESC-like Cells Turning Adult Cells Embryonic How to Make Stem Cells Stay Growing ......... ZenMaster

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Yamanaka Turns Human Fibroblasts to ESC-like Cells

Simple recipe turns human skin cells into embryonic stem cell-like cells Tuesday, 20 November 2007 A simple recipe — including just four ingredients — can transform adult human skin cells into cells that resemble embryonic stem cells, researchers report in an immediate early publication of the journal Cell, a publication of Cell Press. The converted cells have many of the physical, growth and genetic features typically found in embryonic stem cells and can differentiate to produce other tissue types, including neurons and heart tissue, according to the researchers. They added, however, that a comprehensive screen of the activity of more than 30,000 genes showed that the so — called “induced pluripotent stem (iPS) cells” are similar, not identical, to embryonic stem cells. "Pluripotent" refers to the ability to differentiate into most other cell types. The chemical cocktail used in the new study is identical to one the team showed could produce iPS cells from adult mouse cells in another Cell report last year. That came as a surprise, said Shinya Yamanaka of Kyoto University in Japan, because human embryonic stem cells differ from those in mice. Those differences had led them to suspect "that some other factors might be required to generate human iPS cells,” he said. The findings are an important step forward in the quest for embryonic stem cell — like cells that might sidestep the ethical stumbling blocks of stem cells obtained from human embryos. He emphasized, however, that it would be “premature to conclude that iPS cells can replace embryonic stem cells.” Embryonic stem cells, derived from the inner cell mass of mammalian blastocysts — balls of cells that develop after fertilization and go on to form a developing embryo — have the ability to grow indefinitely while maintaining pluripotency, the researchers explained. Those properties have led to expectations that human embryonic stem cells might have many scientific and clinical applications, most notably the potential to treat patients with various diseases and injuries, such as juvenile diabetes and spinal cord injury. The use of human embryos, however, faces ethical controversies that hinder the applications of human embryonic stem cells, they continued. In addition, it is difficult to generate patient or disease — specific embryonic stem cells, which are required for their effective application. One way to circumvent these issues is to induce pluripotent status in other cells of the body by direct reprogramming, Yamanaka said. Last year, his team found that four factors, known as Oct3/4, Sox2, c-Myc, and Klf4, could lend differentiated fibroblast cells taken from embryonic or adult mice the pluripotency normally reserved for embryonic stem cells. Fibroblasts make up structural fibers found in connective tissue. Those four factors are “transcription factors,” meaning that they control the activity of other genes. They were also known to play a role in early embryos and embryonic stem cell identity. The researchers have now shown that the same four factors can generate iPS cells from fibroblasts taken from human skin. “From about 50,000 transfected human cells, we obtained approximately 10 iPS cell clones,” Yamanaka said. “This efficiency may sound very low, but it means that from one experiment, with a single ten centimetre dish, you can get multiple iPS cell lines.” The iPS cells were indistinguishable from embryonic stem cells in terms of their appearance and behaviour in cell culture, they found. They also express genetic markers that are used by scientists to identify embryonic stem cells. Human embryonic stem cells and iPS cells display similar patterns of global gene activity. They showed that the converted human cells could differentiate to form three “germ layers” in cell culture. Those primary germ layers in embryos eventually give rise to all the body’s tissues and organs. They further showed that the human iPS cells could give rise to neurons using a method earlier demonstrated for human embryonic stem cells. The iPS cells could also be made to produce cardiac muscle cells, they found. Indeed, after 12 days of differentiation, clumps of cells in the laboratory dishes started beating. The human iPS cells injected under the skin of mice produced tumours after nine weeks. Those tumours contained various tissues including gut — like epithelial tissue, striated muscle, cartilage and neural tissue. They finally showed that iPS cells can also be generated in the same way from other human cells. “We should now be able to generate patient — and disease — specific iPS cells, and then make various cells, such as cardiac cells, liver cells and neural cells,” Yamanaka said. “These cells should be extremely useful in understanding disease mechanisms and screening effective and safe drugs. If we can overcome safety issues, we may be able to use human iPS cells in cell transplantation therapies.” Shinya Yamanaka is also a senior investigator at the Gladstone Institute of Cardiovascular Disease (GICD), an independent, non-profit biomedical research organization affiliated with the University of California, San Francisco. “The rapid application of this approach to human cells has dramatically changed the landscape of stem cell science,” said GICD Director Deepak Srivastava, MD. “Dr. Yamanaka’s work is monumental in its importance to the field of stem cell science and its potential impact on our ability to accelerate the benefits of this technology to the bedside. Not only does this discovery enable more research, it offers a new pathway to apply the benefits of stem cells to human disease.” “Dr. Yamanaka and his group have made yet another extremely important contribution to the stem cell field,” said Richard Murphy, interim president of the California Institute for Regenerative Medicine (CIRM). “Their results open the door to generating alternative sources of pluripotent cells from patients, which is a major step forward. However, much work still needs to be done to fully characterize and understand the capacity of these induced pluripotent cells to study and to treat human diseases.” CIRM’s Murphy added, “Dr. Yamanaka’s work, which uses viral vectors to introduce into cells pluripotency-associated genes, further emphasizes the critical need we have to continue working with naturally occurring human embryonic stem cells, which remain the gold standard against which all alternative sources of human pluripotent stem cells must be tested.” Reference: Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors The researchers include Kazutoshi Takahashi, Kyoto University, in Kyoto, Japan; Koji Tanabe, of Kyoto University, in Kyoto, Japan; Mari Ohnuki, of Kyoto University, in Kyoto, Japan; Megumi Narita, of Kyoto University, in Kyoto, Japan, and the Japan Science and Technology Agency, in Kawaguchi, Japan; Tomoko Ichisaka, of Kyoto University, in Kyoto, Japan, and the Japan Science and Technology Agency, in Kawaguchi, Japan; Kiichiro Tomoda, of the Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA; and Shinya Yamanaka, of Kyoto University, in Kyoto, Japan, the Japan Science and Technology Agency, in Kawaguchi, Japan; and the Gladstone Institute of Cardiovascular Disease, in San Francisco, CA, USA See also: UW-Madison scientists also guide human skin cells to embryonic like state Turning Adult Cells Embryonic How to Make Stem Cells Stay Growing ......... ZenMaster

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Sunday, 18 November 2007

Genetic Testing: Customer DNA analyses

Genetic Testing: Customer DNA Analyses Sunday, 18 November 2007 Three companies have started or are planning services to test customers’ DNA at nearly one million locations (SNP’s) where the human genome is known to vary between individuals. All are offering services to help consumers interpret the information contained in their own genomes. Would you subscribe to such a service? 23andMe Mountain View, Calif. Available now for $999 Services: genotyping 580,000 SNPs using Illumina technology; Gene Journals reporting risk for 20 diseases and physical traits; tools for tracing ancestry and DNA similarity with family and friends; Genome Explorer to provide access to all data to allow customers to compare any published study with their own genotype; will provide referrals to genetic counsellors. Online: deCODE Genetics Reykjavik, Iceland Available now for $985 Services: genotyping one million SNPs using Illumina technology; deCODEme will provide risk reports for about 20 diseases and physical traits; tools for tracing ancestry and DNA similarity with family and friends; genetic counsellors available for consultations. Online: Navigenics Redwood Shores, Calif. Available in 2008 for $2,500 Services: will genotype one million SNPs using Affymetrix technology; health Compass will provide risk reports for about a dozen diseases; results relayed by genetic counsellor. Online: Read more at: My Genome, Myself: Seeking Clues in DNA NY Times - November 17, 2007 ......... ZenMaster

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Dolly Professor Abandons Human Cloning

Dolly Professor Abandons Human Cloning Attempts Sunday, 18 November 2007 The Scottish scientist who created Dolly the sheep more than a decade ago said he is abandoning the cloning technique that he pioneered, according to an interview published Saturday. Professor Ian Wilmut of Edinburgh University, who led the team that created Dolly in 1996, told The Daily Telegraph that he is abandoning cloning to pursue a new technique that can create stem cells without an embryo. He has now embraced a technique developed by Prof Shinya Yamanaka of Kyoto University, Japan, that involves genetically modifying adult cells to make them almost as flexible as stem cells. The research has been conducted on mice. He said: “The work which was described from Japan of using a technique to change cells from a patient directly into stem cells without making an embryo has got so much more potential.” “Even though it's only been described for the mouse, when we were considering which option to pursue, whether to clone or whether to copy the work in Japan, we decided to copy the work in Japan.” Speaking to the Daily Telegraph, Prof Wilmut said: “Before too long we will be able to use the Yamanaka approach to achieve the same, without making embryos. In the long term, direct reprogramming will be more productive.” “I decided a few weeks ago not to pursue nuclear transfer [the method used to create Dolly the sheep]," and he admitted the new method "was easier to accept socially”. Professor Wilmut believes that within five years the new technique could provide a better and ethically more acceptable alternative to cloning embryos for medical research. Now, when Professor Wilmut has decided not to pursue his licence to clone human embryos, an award he was granted just two years ago, one can wonder about some recent actions in his career. A few years ago he was involved in and made plans to collaborate with Hwang Woo-suk on therapeutic cloning before the Korean work was uncovered to be fraudulent. Together with the American Gerald Schatten, they set up The International Stem Cell Bank in Seoul, which became nothing when the fraud was unveiled. None of these experts in cloning realized by themselves that something was wrong with the Korean results. Does he have the technical ability to make human cloning possible? Or does he lack people in his present group who would do the actual cloning work? I doubt he, Professor Wilmut, have the molecular biology expertise needed to be able to repeat Prof Yamanaka experiments on mouse fibroblasts in human counterpart. Only time will tell if this also will be another attempt to ‘build a castles in Spain’ by the Scottish professor. See also: Turning Adult Cells Embryonic ......... ZenMaster

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Thursday, 15 November 2007

‘Stem Cells to Cure Parkinson's in 5 Years’

‘Stem Cells to Cure Parkinson's in 5 Years’ Thursday, 15 November 2007 An international symposium on advanced stem cell research is held in Seoul, S. Korea, this week to develop a roadmap for developments in the vital scientific field. The 2007 Seoul Symposium on Stem Cell Research is held at Korea University on Thursday and Friday (Nov. 15-16) with about 1,000 experts in attendance, the organizers said. Nineteen speakers from six countries are scheduled to outline future trends in stem cell research, applications of stem cells and the control of cell growth to facilitate the use of cells for medical treatments. The event was first held in October 2003. ‘Stem Cells to Cure Parkinson's in 5 Years’ Olle Lindvall, a professor at the Wallenberg Neuroscience Center, Lund University Hospital in Sweden, said that the cure for the Parkinson's disease is likely to be one of the first and most effective applications of human stem cell research, though the field in general has many obstacles to overcome. “I think that Parkinson's disease is one of the diseases where we will be able to do the first clinical test,” Lindvall told The Korea Times on Thursday. Lindvall is one of the main players in the field of regenerative neurology, and a 25-year veteran in restoring brain function with cell therapies. “With the stem cell approach, though I cannot guarantee, scientifically-based clinical trials will be carried out within five years. When it comes to the other diseases, it is less sure.” “We have transplanted dopamine cells from foetuses into the brain and saw they can survive. I think that there are many attempts to produce this type of cell from different types of stem cells,” he said, adding that animal tests are already underway in many institutions around the world. “I think that it can realistically happen within the next five years.” ......... ZenMaster

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Stem cells extracted from cloned macaque embryos

Stem cells extracted from cloned macaque embryos Thursday, 15 November 2007 Producing primate embryonic stem cells by somatic cell nuclear transfer J Byrne, D Pedersen, L Clepper, M Nelson, W Sanger, S Gokhale, D Wolf & S Mitalipov Nature advance online publication 14 November 2007 doi:10.1038/nature06357; Published online 14 This work was previously reported early this summer: Monkey cloning Wednesday, 20 June 2007 ......... ZenMaster

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Wednesday, 14 November 2007

Human ESC's derived from PGD embryos with Fragile X

hESCs derived from PGD embryos with Fragile X Wednesday, 14 November 2007 A human stem cell line derived from embryos that were identified by preimplantation genetic diagnosis (PGD) to carry the mutation for fragile X syndrome has provided an unprecedented view of early events associated with this disease. In addition to giving scientists fresh insight into fragile X, results from this unique model system have emphasized the value of this new source of embryonic stem cells and may have a significant impact on the way that genetic diseases are studied in the future. The research is published in the November issue of the journal Cell Stem Cell, published by Cell Press. Fragile X syndrome, the most common cause of inherited mental impairment and of autism, is caused by the absence of the fragile X mental retardation protein (FMRP). Most individuals with fragile X exhibit a specific mutation in the fragile X mental retardation 1 (FMR1) gene that usually coincides with epigenetic DNA modifications. However, the developmental timing and mechanisms associated with acquisition of these characteristics are not clear due to the absence of appropriate cellular and animal models. To examine developmentally regulated events involved in fragile X pathogenesis, Dr. Nissim Benvenisty and Dr. Rachel Eiges from the Hebrew University Department of Genetics in Jerusalem, Israel, together with Dr. Dalit Ben-Yosef from the IVF unit at the Tel-Aviv Sourasky Medical Center, established a human embryonic stem cell (hESC) line from a preimplantation fragile X-affected embryo identified by PGD. The fragile X cell line, called HEFX, displayed all characteristics typical of an hESC line and possessed the full genetic mutation observed in fragile X patients. The work "highlights the value of [human embryonic stem cells] as a model system for early human embryo development," the study's co-author, Rachel Eiges, told The Scientist. "We show that it can be used as a powerful tool to analyze the effect of a specific mutation on particular developmental events, allowing exploring processes which are otherwise inaccessible for research." The researchers found that undifferentiated HEFX cells transcribed FMR1 and expressed FMRP, suggesting that the fragile X mutation by itself is not sufficient to cause FMR1 inactivation. The research team went on to show that differentiated derivatives of HEFX cells exhibited a decrease in FMRI transcription and FMRP expression along with an increase in epigenetic modifications associated with fragile X syndrome. “The fact that FMR1 inactivation and other modifications take place after differentiation suggests that it might be possible to prevent some of these events as an attempt to rescue the abnormal phenotype in cells with the full fragile X mutation,” suggests Dr. Benvenisty. HEFX cells represent an excellent model for examination of early embryogenesis and will contribute to a clearer understanding of the molecular mechanisms underlying fragile X pathogenesis. This research is also compelling on a more general level in that it validates the usefulness of hESCs derived from embryos that have been screened for specific mutations with PGD. hESC lines derived in this manner represent a potent tool for the study of a variety of human diseases and the development of new therapeutic strategies.

"Certainly, stem cell lines such as this will help science unravel the mechanisms associated with human genetic disorders, and hopefully lead to new therapeutic treatments and interventions in the future," said Robert Lanza of Advanced Cell Technology in Los Angeles, CA, who was not involved in the research. Such an approach has been overshadowed by the focus on developing stem cells as treatments for various disorders, he noted. ......... ZenMaster

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Retroviruses spurred evolution of gene regulatory networks

Ancient retroviruses spurred evolution of gene regulatory networks in humans and other primates Wednesday, 14 November 2007 When ancient retroviruses slipped bits of their DNA into the primate genome millions of years ago, they successfully preserved their own genetic legacy. Today an estimated 8 percent of the human genetic code consists of endogenous retroviruses (ERVs) — the DNA remnants from these so-called "selfish parasites." Surprisingly, the infected hosts and their primate descendants also appear to have benefited from this genetic invasion, new evidence suggests. The ancient retroviruses — distant relatives of the human immunodeficiency virus (HIV) — helped a gene called p53 become an important "master gene regulator" in primates, according to a study published this week in the online early edition of Proceedings of the National Academy of Sciences. The study, led by researchers at the University of California, Santa Cruz, offers an explanation for how regulatory networks of genes evolved. Not all genes are created equal; some are masters that can selectively turn on and off many other genes. The advent of gene regulatory networks allowed for greater control over gene expression in higher vertebrates. With tightly controlled variations in gene expression, species that had very similar genetic codes — for instance, humans and chimpanzees — could nevertheless exhibit striking differences. Scientists have long wondered how a master regulator such as p53 gained the ability to turn on and off a broad range of other genes related to cell division, DNA repair, and programmed cell death. How did p53 build its complex and powerful empire, so to speak? Using the tools of computational genomics, the UCSC team gathered compelling evidence that retroviruses helped out. ERVs jumped into new positions throughout the human genome and spread numerous copies of repetitive DNA sequences that allowed p53 to regulate many other genes, the team contends. "This would have provided a mechanism to quickly establish a gene regulatory network in a very short evolutionary time frame," said Ting Wang, a post-doctoral researcher at UCSC and lead author of the paper. Thus, p53 was crowned "guardian of the genome," as biologists now call it. Its job is to coordinate the surveillance system that monitors the well-being of cells. Indeed, p53 is so important that when it fails, cancer often results. About half of all human tumours contain a mutated or defective p53 gene. "Our work provides a new window on the complex biology of p53," said co-author David Haussler, a professor of biomolecular engineering at UCSC and a Howard Hughes Medical Institute Investigator. "From a biomedical standpoint, it's important because these changes only occurred in the primate lineage, not in mice." By analyzing and comparing genetic data from different species, the team estimated that certain ERVs entered the genome about 40 million years ago, and spread rapidly in primates about 25 million years ago. Scientists have long suspected that retroviral elements could play a role in gene regulation. More than 50 years ago, Nobel Laureate Barbara McClintock observed that transposable elements — or "jumping genes" — altered gene expression in maize. In 1971, Roy Britten and Eric Davidson theorized that commonly observed repetitive DNA sequences actually served as codes for gene regulatory networks. The DNA remnants of retroviruses tend to be repetitive sequences and can jump around, when active. The UCSC team finally gathered concrete evidence to support Britten and Davidson's hypothesis. The group trolled the human genome for ERVs, identified p53 binding sites in them, and tested their ability to activate genes regulated by p53. More than one-third of all known p53-binding sites turned out to be associated with ERVs, they discovered. These results raise new questions about the role of so-called "junk DNA," the vast regions of the genome that don't code for proteins. ERVs fall into that category. Many scientists once believed that such DNA served no purpose, but new data from the Haussler lab and other labs are challenging that view. "We're starting to uncover the treasure in this junk," said Wang. Moreover, the team has proposed a new mechanism for evolutionary change. Conventional wisdom says that evolution is driven by small changes — point mutations — to the genetic code. If a change is beneficial, the mutation is passed onto future generations. Now it appears that another level of evolution occurs that is not driven by point mutations. Instead, retroviruses insert DNA sequences and rearrange the genome, which leads to changes in gene regulation and expression. If such a change in gene regulation is beneficial, it is passed onto future generations. This research should have broad implications, according to Wang. "Our prediction is that this is a general mechanism that has been around ever since viruses," Wang said. "ERV-mediated expansion of a gene regulatory network probably happened more than once and not just in primates. We predict it led to other master gene regulators, not just p53." ......... ZenMaster

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Tuesday, 13 November 2007

Steps towards spinal cord reconstruction

Steps towards spinal cord reconstruction Tuesday, 13 November 2007 A new study has identified what may be a pivotal first step towards the regeneration of nerve cells following spinal cord injury, using the body’s own stem cells. This seminal study, published in this week’s Proceedings of the National Academy of Science, identifies key elements in the body’s reaction to spinal injury, critical information that could lead to novel therapies for repairing previously irreversible nerve damage in the injured spinal cord. Very little is known about why, unlike a wound to the skin for example, the adult nervous system is unable to repair itself following spinal injury. This is in contrast to the developing brain and non-mammals which can repair and regenerate after severe injuries. One clue from these systems has been the role of stem cells and their potential to develop into different cell types. “Because of their regenerative role, it is crucial to understand the movements of stem cells following brain or spinal cord injury,” says Dr. Philip Horner, co-lead investigator and neuroscientist at the University of Washington. “We know that stem cells are present within the spinal cord, but it was not known why they could not function to repair the damage. Surprisingly, we discovered that they actually migrate away from the lesion and the question became why – what signal is telling the stem cells to move.” The researchers then tested numerous proteins and identified netrin-1 as the key molecule responsible for this migratory pattern of stem cells following injury. In the developing nervous system, netrin-1 acts as a repulsive or attractive signal, guiding nerve cells to their proper targets. In the adult spinal cord, the researchers found that netrin-1 specifically repels stem cells away from the injury site, thereby preventing stem cells from replenishing nerve cells. “When we block netrin-1 function, the adult stem cells remain at the injury site,” says Dr. Tim Kennedy, co-lead investigator and neuroscientist at the Montreal Neurological Institute of McGill University. “This is a critical first step towards understanding the molecular events needed to repair the injured spinal cord and provides us with new targets for potential therapies.” ......... ZenMaster

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Sunday, 11 November 2007

UN Analysis on Human Cloning

Ban human reproductive cloning, or prepare for human rights for clones, says UN study. Sunday, 11 November 2007 A report by the United Nations University's Institute of Advanced Studies (UNU-IAS) on the advances on human cloning comes to the conclusion that the international community faces a stark choice: outlaw human reproductive cloning or prepare for the creation of cloned humans. In the second case global leaders need to be prepared to protect the rights of cloned individuals from potential abuse, prejudice and discrimination. The report by the UNU-IAS says a ban on human reproductive cloning, coupled with freedom for nations to permit controlled therapeutic research, is the global community's best option. The report is entitled “Is Human Reproductive Cloning Inevitable: Future Options for UN Governance”. Virtually every nation opposes human reproductive cloning and more than 50 countries have legislated bans on such efforts. However, attempts to reach a binding worldwide treaty failed at the UN in 2005, over divisions on whether to outlaw all cloning or permit cloning of human cells for research. Only a minority of countries supported a non-binding Declaration on Human Cloning to outlaw all types of cloning. At present, another 140 members of the UN have no laws regulating human cloning efforts, therefore providing loopholes for unscrupulous scientists. “Human reproductive cloning could profoundly impact humanity,” says UN Under-Secretary-General Konrad Osterwalder, Rector of UNU. “This report offers a plain language analysis of the opportunities, challenges and options before us – a firm and thoughtful base from which the international community can revisit the issue before science overtakes policy.” Without an international prohibition, human reproductive cloning accomplished in certain countries could be judged perfectly legal by the International Court of Justice, warn UNU-IAS co-authors Brendan Tobin, Chamundeeswari Kuppuswamy, Darryl Macer and Mihaela Serbulea. “Failure to outlaw reproductive cloning means it is just a matter of time until cloned individuals share the planet,” says barrister Mr. Tobin of the Irish Centre for Human Rights, National University of Ireland, at Galway. “If failure to compromise continues, the world community must accept responsibility and ensure that any cloned individual receives full human rights protection. It will also need to embark on an extensive awareness building and sensitivity program to ensure that the wider society treats clones with respect and ensure they are protected against prejudice, abuse or discrimination.” Presently “there is almost universal international consensus on the desirability of banning reproductive cloning based in part on religious and moral grounds, but mostly on concerns about underdeveloped technologies producing clones with serious deformities or degenerative diseases,” Mr. Tobin adds. “The failure to adopt an international convention on therapeutic cloning means that reproductive cloning is inadequately controlled. There are maverick scientists who are continuing with experimentation.” “As technologies advance and possibilities of success increase, the current consensus is likely to erode and with it the possibility of securing a ban on reproductive cloning.” “... but will the world be ready to accept cloned individuals?” “Whichever path the international community chooses it will need to act soon – either to prevent reproductive cloning or to defend the human rights of cloned individuals,” says Dr. A.H. Zakri, Director of UNU-IAS, based in Yokohama, Japan. The report calls the prospect of human cloning “one of the most emotive and divisive issues to face UN negotiators and the international community in recent years.” There have been no substantiated claims of cloned human embryos grown into foetal stages and beyond but such an historic event is not far off, most experts agree. Chamundeeswari Kuppuswamy, one of the co-authors of the report and law lecturer at Sheffield University, said: "China has guidelines on human reproductive cloning but no law as such, while there are many African countries that don't have any legislation in place." "It is not terribly expensive to set up the experiments, process the eggs and get the raw materials needed to perform cloning and as research in the area continues, someone is going to manage it." "The state of the science at the present time, however, means that there are going to be a lot of failures and deformities in any clones produced, which is one of the major concerns if it goes on unregulated." “Licences are being granted for therapeutic cloning, which means in time scientists will perfect the technique for human reproductive cloning.” Cloning have been achieved with many mammals like mice, sheep, pigs, cows, horses and dogs and US researchers last summer accomplished the first cloning of a primate – a rhesus monkey embryo cloned from adult cells and then grown to generate stem cells. Reproductive cloning is, for examples, banned in the UK but scientists are allowed to clone embryos for therapeutic research. Two years ago, a team at Newcastle University managed to create the country's first cloned human embryo, which survived for five days in a laboratory. Prof Alison Murdoch, who led the Newcastle team, said: "We shouldn't be afraid of the idea of having two individuals with genetically identical material, although I cannot see a good clinical need for that." "The risk you run by trying to ban cloning outright is that it may send those scientists who want to do that kind of research to countries where it is completely unregulated." Prof. Ian Wilmut, who led the team that cloned Dolly the sheep, welcomed the UN report, insisting that it would be "dangerous and ethically inappropriate" to clone a child. “By contrast, a method for the production of embryo stem cells would provide important new opportunities to study inherited diseases.” Reference: Is Human Reproductive Cloning Inevitable: Future Options for UN Governance ......... ZenMaster

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Thursday, 8 November 2007

Draft Guidelines for Stem Cell Research in India

Draft Guidelines for Stem Cell Research in India Thursday, 08 November 2007 After five years of consultation, a panel of Indian experts has at last devised a set of guidelines to regulate stem cell research and its use in India. The Indian Council of Medical Research (ICMR) and the Department of Biotechnology (DBT) will submit the final guidelines to the Union Health Ministry on November 8. The guidelines on stem cell research and its use will be enforced after the government gives its consent. The committee has decided that human cloning should not be allowed in India. The regulations say that embryonic stem cell research can be executed, but the donor’s consent will be mandatory. All cord blood banks would have to be registered with the Drug Controller-General of India (DCGI). Research or therapy using foetal stem cells / placenta will be allowed but those who fail to follow the rules will face a heavy penalty, in the form of monetary fine as well as jail term. The road map also specifies that termination of pregnancy can’t be attempted for donating foetal tissue for any possible financial or therapeutic profit. The medical person entrusted with the care of the woman planning to undergo termination of pregnancy and the person who will use the foetal material can’t be the same. The identity of the donor and the recipient will have to be kept secret. Two committees are being planned to oversee and regulate the area: A National Apex Committee for Stem Cell Research and Therapy (NAC-SCRT) and an Institutional Committee for Stem Cell Research and Therapy (IC-SCRT). They will analyze the scientific, technical, ethical, legal and social issues in embryonic stem cell research. All institutions and investigators carrying out research on human stem cells must be registered with NACSCRT through IC-SCRT. All research studies and clinical trials will have to obtain the prior approval of IC-SCRT for permissive research and NACSCRT for restricted research. At the same time India’s first Clinical Research Facility (CRF) for Stem Cells and Regenerative Medicine (CRF) will open in Hyderabad by the Centre for Cellular and Molecular Biology (CCMB) along with Nizam’s Institute of Medical Sciences. It will be completed by the year 2009. Union Minister for Science & Technology Kapil Sibal laid the foundation stone for the project last week, on a five-acre site at Uppal at CCMB. He said that the DBT in association with ICMR had formulated draft guidelines for stem cell research and placed them for public debate. Sibal also said that more than 40 institutions and hospitals in country are involved in different aspects of embryonic and adult stem cell research. Many programmes are unveiled to encourage the basic researchers, clinicians and industry to come together to share information. Sibal said a Bill in Parliament will soon be introduced to provide incentives and/or up to 30 per cent of the license fee’s as royalty to scientists to encourage them for their research. Sibal said, “We do not have many experts hence the need for having a public debate on the issue, with a view to incorporating divergent points.” See also: India’s First Institute of Regenerative Medicine ......... ZenMaster

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Tuesday, 6 November 2007

New Jersey Voters Defeat Stem Cell Measure

New Jersey Voters Defeat Stem Cell Measure Wednesday, 07 November 2007 In a stunning defeat for Gov. Jon S. Corzine, New Jersey voters on Tuesday rejected a ballot measure that would have permitted the state to borrow $450 million for stem cell research. The defeat of the stem cell measure by a resounding 53-47 percent margin dealt a sharp blow to Mr. Corzine, who had campaigned heavily for it and had contributed $200,000 to the effort. But at midnight, Mr. Corzine’s press secretary said the governor was not ready to concede. “Regardless of the outcome, New Jersey will continue to create a climate where stem cell research can thrive,” said the spokeswoman, Lilo Stainton. ......... ZenMaster

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NJ to vote on stem cell bond act The state decides on $450 million for research Tuesday, 06 November 2007 New Jersey residents will vote today (November 6) whether to devote $450 million to stem cell research over the next ten years. The referendum, introduced by state Governor Jon Corzine in July, would, if passed, put New Jersey among a group of states, including California, New York and Massachusetts, that have devoted extensive funds to stem cell research. According to the Governor's press release, this act "authorizes the sale of state general obligation funds in the amount of $450 million over 10 years" to be given to stem cell researchers. Last year, Corzine signed into law a bill that provided $270 million for new research facilities — $150 million of which will go to the New Jersey Stem Cell Institute. Recently, New Jersey has allocated smaller grants to support stem cell research, but on the whole the state has been somewhat behind other states. ......... ZenMaster
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