stem cell gene delivery costs to milliseconds instead of years
Like a magician who says, "Pick a Card, Any Card", the scientist from the Stanford University team Debashis Sahoo, PhD, appeared to offer some kind of trick when asked researchers Stanford Institute for Stem Cell Biology and Regenerative Medicine to choose any two genes already known to be involved in the development of stem cells. Finding these genes may take years and hundreds of thousands of dollars, but was skeptical scientists promising Sahoo stem cell in a split second and almost zero cost, we could find new genes involved in the same development path as the two genes that provide. Sahoo
came to demonstrate that this amazing feat can actually be done. The proof of principle for the idea, published online March 15 in the Proceedings of the National Academy of Sciences, opening a powerful way to carry out mathematical research with stem cells and shows the power of interdisciplinary collaboration in science. Also shows that computers using existing databases to mine radical can accelerate research in the laboratory. Ultimately can lead to progress in various areas of medicine as the diagnosis of disease or cancer treatment.
Biologists have long used the mathematics and statistics in their work. In the simplest case, when looking for genes involved in particular biological process, looking for genes that have a symmetrical relationship. For example, if you know A gene is involved in a particular process, trying to determine if the C gene is related to the gene, during the same process.
four years ago, while studying for his doctorate in electrical engineering consultant David Dill, PhD, professor of computer science and co-director Sylvia Plevritis, PhD, associate professor radiology, Sahoo took a class inmunologíay realized that many of the relationships in biology are not symmetrical, but asymmetrical. As an analogy, Sahoo observed that fruit trees will almost certainly be gone, but the trees outside the fruiting season may or may not have leaves, depending on the season. Dill
Sahoo and realized that these asymmetrical relations can be found through the application of Boolean logic, in which the researchers established a series of if / then rules and then recorded the data of candidates that meet all standards. For example, scientists may know that a gene is active early in the development of cells and the C gene is active much later. By detecting large public databases, Sahoo can find the genes that are rarely active when one is active, and almost always active when C is active in many other cell types. Then, researchers can test to determine whether these genes are activated between early and late stages of development.
The paper, lead author Sahoo looked at gene expression patterns in the development of an immune cell called B cell Using two B-genes de las células conocidas, sahoo buscado a través de bases de datos con miles de productos de los genes en milisegundos y encontraron 62 genes que coincidían con los patrones que él espera ver los genes que se enciende en medio de la activación de los dos genes que comenzó con . Luego examinó bases de datos de participación de 41 cepas de ratones de laboratorio que había sido diseñada para ser deficiente en uno o más de los 62 genes. De los 41 cepas, 26 tenían defectos en el desarrollo de las células B.
"Esta fue la validación method "Sahoo said. "Biologists are really surprised that with only a computer algorithm, in milliseconds I can find the genes that it takes a very long time to isolate in the laboratory." He added that I was particularly pleased that the information comes from databases that are widely available and other scientists have already sacrificed the information. Sahoo
now using the technique to find new genes that play a role in the development of cancers.
"This shows that the computational analysis of existing data may provide clues about which researchers must look ahead," he said. "This is something that could have an impact on cancer. It's exciting. "
interdisciplinary team that contributed to the results of the collaboration of researchers, both in the School of the Faculty of Medicine Ingenieríay. In addition to dill (the main author of the document) and Plevritis, the co-authors include Irving Weissman, MD, director of the Institute of Stanford stem cells, and postdoctoral scholars in June Seita, PhD, Matthew Inlay, PhD, and Deepto Bhattacharya, PhD, who recently moved to Stanford School of Medicine at Washington University in St. Louis.
Funding for this research came from the National Institutes of Health, Stem Cell Institute Siebel, at the Thomas and Stacey Siebel Foundation, the Cancer Research Institute, the Institute National Cancer Institute of Regenerative Medicine in California. Contribute to Better translation
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Find shipping genes to milliseconds instead of years:
Like a magician who says, "Pick a Card, Any Card" scientist Stanford University team Debashis Sahoo, PhD, appeared to offer some kind of trick when asked researchers at the Stanford Institute for Stem Cell Biology and Regenerative Medicine to choose any two genes already known to be involved in the development of stem cells. Finding these genes may last years and hundreds of thousands of dollars, but was skeptical scientists Sahoo promising stem cell in a split second and almost zero cost, we could find new genes involved in the same development path as the two genes that provide. Sahoo
came to demonstrate that this amazing feat can actually be done. The proof of principle for the idea, published online March 15 in the Proceedings of the National Academy of Sciences, opening a powerful way to carry out mathematical investigations stem cell and shows the power of interdisciplinary collaboration in science. It also shows that computers using existing databases to mine radical can accelerate research in the laboratory. Ultimately can lead to progress in various areas of medicine as the diagnosis of disease or cancer treatment.
Biologists have long used the mathematics and statistics in their work. In the simplest case, when looking for genes involved in a biological process particular, are looking for genes that have a symmetrical relationship. For example, if you know that a gene is involved in a particular process, trying to determine if the C gene is related to the gene, during the same process.
four years ago, while studying for his doctorate in electrical engineering consultant David Dill, PhD, professor of computer science and co-director Sylvia Plevritis, PhD, associate professor radiology, Sahoo took a class inmunologíay realized that many of the relationships in biology are not symmetrical, but asymmetrical. As an analogy, Sahoo observed that fruit trees will almost certainly be gone, but the trees outside the fruiting season may or may not have leaves, depending on the season . Dill
Sahoo and realized that these asymmetrical relations can be found through the application of Boolean logic, in which the researchers established a series of if / then rules and then recorded the data of candidates that meet all standards. For example, scientists could know that a gene is active early in the development of cells, and gene C is active much later. By detecting large public databases, Sahoo can find the genes that are rarely active when one is active, and almost always active when C is active in many other cell types. Then, researchers can test to determine whether these genes are activated between early and late stages of development.
The paper, lead author Sahoo looked at gene expression patterns in developing immune cell called a B cell Using two B-cell genes known Sahoo searched through databases of thousands of gene products in milliseconds and found 62 genes that matched the patterns he expects to see genes that are turned in through the activation of the two genes that started with. Then examined databases involving 41 strains of laboratory mice that had been designed to be deficient in one or more of the 62 genes. Of the 41 strains, 26 had defects in the development of B cells
"This was the validation of the method," Sahoo said. "Biologists are really surprised that with only a computer algorithm, in milliseconds I can find the genes that it takes a very long time to isolate in the laboratory." He added that I was particularly pleased that the information comes from databases that are widely available and other scientists have already sacrificed the information. Sahoo
now are using technology to find new genes that play a role in cancer development.
"This shows that the computational analysis of existing data may provide clues about which researchers must look ahead," he said. "This is something that could have an impact on cancer. It's exciting. "
interdisciplinary team that contributed to the results of the collaboration of researchers, both in the School of the Faculty of Medicine Ingenieríay. In addition to dill (the main author of the document) and Plevritis, the co-authors include Irving Weissman, MD, director of the Stem Cell Institute at Stanford, and postdoctoral scholars in June Seita, PhD, Matthew Inlay, PhD, and Deepto Bhattacharya, PhD, who recently moved to Stanford School of Medicine at Washington University in St. Louis.
Funding for this research came from the National Institutes of Health, Stem Cell Institute Siebel, at the Thomas and Stacey Siebel Foundation, the Cancer Research Institute, the Institute National Cancer Institute and the Institute of Medicine Regenerative California. Related article
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