When I was reading the book "FRIDAY" (Robert Heinlein) the first time, much of it seemed the stuff of fantasy, even though technically some of the things described in that book were already taking place -- in fact, I've wondered before about genetic engineering in the context of human achievement -- I've even wondered if... never mind...
..But I was walking down the street today and saw this newspaper headline, thought you guys should know: because it can and will be done to humans if it isn't already being done via Expressed Sequence Tagging.
Molecular breeding
http://union-bulletin.com/news/2014/...-improvements/
Molecular breeding speeds crop improvements
Adrian Higgins of The Washington Post
As of Saturday, April 19, 2014
WOODLAND, Calif. — Alan Krivanek, a tomato breeder for Monsanto, dons a white protective suit, wipes his feet on a mat of disinfectant and enters a greenhouse to survey 80,000 seedlings. He is armed with a spreadsheet that will tell him which ones are likely to resist a slew of diseases. The rest he will discard.
#Krivanek, 42, is part of a new generation of plant breeders who are transforming the 10,000-year history of plant selection. And their work has quietly become the cutting-edge technology among today’s major plant biotech companies.
#Instead of spending decades physically identifying plants that will bear fruits of the desired color and firmness, stand up to drought, and more, breeders are able to speed the process through DNA screening.
#When his tomato plants were just a week old, technicians manually punched a hole in each seedling to get leaf tissue that was taken to a nearby lab, converted into a chemical soup and then scanned for genetic markers linked to desired traits.
#Krivanek uses the information to keep just 3 percent of the seedlings and grow them until they produce fruit this spring, when he can evaluate fully grown plants, keep a few hundred, sow their seeds and then screen those plants.
#“I’m improving my odds. Maybe I can introduce to market a real super-hybrid in five years,” Krivanek said. “A predecessor might take a whole career.”
#The technology — called marker-assisted or molecular breeding — is far removed from the better-known and more controversial field of genetic engineering, in which a plant or animal can receive genes from a different organism.
#Marker-assisted breeding, by contrast, lays bare the inherent genetic potential of an individual plant to allow breeders to find the most promising seedling among thousands for further breeding.
#Because the plant’s natural genetic boundaries are not crossed, the resulting commercial hybrid is spared the regulatory gantlet and the public opposition focused on such plants as genetically modified Roundup Ready corn or soybeans, which are engineered to withstand herbicide sprays.
#Marker-assisted breeding has been embraced not only by the multinational biotech companies in California’s Central Valley but also by plant scientists in government, research universities and nongovernmental organizations fervently seeking new, overachieving crops. The goal is to sustainably feed an expanding global population while dealing with the extremes of climate change.
#But critics of Big Agriculture worry about the needs of small-scale farmers and breeders.
#Low-tech conventional breeding — judging plants by how they look and perform, not by their DNA — has been the lifeblood of small seed companies and local growers, often in conjunction with breeding programs at land-grant universities. But those programs have shrunk by a third in recent years, and the remaining ones are increasingly gravitating to the trendy sphere of molecular breeding.
#Organic farmers, who need crop varieties designed for specific regions and less-intensive growing methods, are not being served by the new applied science, said John Navazio, a senior scientist with the Organic Seed Alliance.
#“There used to be a significant winter spinach production area in southern Virginia and Delmarva, and that’s completely gone,” he said. The spinach-growing industry has moved to megagrowers in California and Arizona.
#Few observers, though, expect plant scientists to abandon a technology that has already yielded significant results. One of the earliest validations of marker-assisted breeding came in 2009 with the introduction of a rice variety in India that could survive complete submersion after monsoons, which earned it the nickname “scuba rice.”
#Once the genetic marker was identified, the variety was developed in just three years by scientists at the International Rice Research Institute in Los Banos, the Philippines.
#The key was to create rice that looked and performed like the existing one favored by Indian farmers — so it would be accepted — but with the flood-tolerant gene, said Glenn Gregorio, a senior rice breeder with the institute.
#The organization has since released more than 10 additional monsoon-resistant varieties to flood-prone areas of India, Bangladesh, Indonesia and the Philippines.
#The varieties would have been extremely difficult to create with conventional breeding, he said, and taken decades to achieve.
#The big multinational companies, including Monsanto, Syngenta, DuPont Pioneer, Bayer CropScience and Dow AgroSciences, have invested heavily in the new plant-breeding programs, which will increasingly require colossal data-processing abilities.
#“In many ways, the company has gone beyond” genetic engineering, said Robert Fraley, Monsanto’s chief scientist. “The breeding technology has changed dramatically in the last few years.”
#Marker-assisted breeding won’t bring an end to GMOs, scientists say, because genetically engineered crops can achieve highly specific tasks now unobtainable through even marker-assisted breeding.
#But given the obstacles to GMO development — $100 million to create one variety, at least 10 years for regulatory approval and widespread public opposition — marker-assisted breeding has become alluring to such companies as Monsanto.
#It is attractive because it is a powerful tool to assemble an array of desirable traits in a plant. A GMO plant, by contrast, has been engineered for a specific task — such as containing a bacterium that would kill a certain pest.
#“GMO really hasn’t delivered on its promises,” said Janet Cotter, a scientist with Greenpeace’s international science unit in Exeter, England. “For more-complex traits, I think people are seeing marker-assisted selection as a lot more valuable.”
#The rice institute’s Gregorio said that about 5 percent of its breeding programs involve genetically engineered varieties, while marker-assisted varieties account for as much as 15 percent.
#In a decade, probably two-thirds of its introductions will be developed through next-generation advanced molecular breeding, he said.
#For developing nations, the technology promises to avert certain crop disasters; for the supermarket shopper in the West, it might bring a whole new experience: flavor.
#Seed companies acknowledge that in their quest to improve yield and shelf life, the taste has suffered, but they say advanced breeding is bringing heirloom flavors back to industrialized varieties.
#“This is one area where (marker-assisted) breeding begins to make an impact,” said Alexander Tokarz, head of vegetables for Syngenta, the Swiss biotech giant. “Early on, we brought shelf life into tomatoes and lost the flavor.”
#The technology has been around for about 20 years but has become much easier and less expensive to use in the past few years, and consumers are only now seeing the results.
#Precision-bred cucumbers, peppers and other vegetables are showing up in supermarkets, but the unlabeled and brandless nature of loose produce makes it difficult to distinguish them, said Carly Scaduto, a spokeswoman for Monsanto.
#Some varieties of Monsanto’s improved-nutrition broccoli — branded as Beneforté — became widely available in 2012. Last year, the company introduced Debut, an advanced hybrid tomato for growers and home gardeners. A group of blight-resistant peppers are in the final stage of testing before their commercial introduction, she said.
#Felix Serquen, who heads Syngenta’s tomato-breeding research in Woodland, this year is introducing a beefsteak for California growers that resists the nematode, a root pest.
#He is launching another variety — SevenTY III — that resists a strain of fusarium that is a major bane to growers in Florida.
#Scientists acknowledge the technology has evolved with little effort to inform the public about it. Sekhar Boddupalli, head of Monsanto’s consumer research for vegetables, wonders whether people even want to know. He pulls out his smartphone and places it on the table in front of him.
#“Are they asking how the iPhone really works? ‘Is it safe for me?’” he said. “No. But what they’re seeing is the benefit of this.”
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http://www.hindawi.com/journals/ijg/2012/373768/
Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application
Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction.
Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.
http://en.wikipedia.org/wiki/Expressed_sequence_tag
An expressed sequence tag or EST is a short sub-sequence of a cDNA sequence.[1] They may be used to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination.[2] The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases (e.g. GenBank 1 January 2013, all species).
An EST results from one-shot sequencing of a cloned cDNA. The cDNAs used for EST generation are typically individual clones from a cDNA library. The resulting sequence is a relatively low quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides. Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes. They may be represented in databases as either cDNA/mRNA sequence or as the reverse complement of the mRNA, the template strand.
ESTs can be mapped to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping, Happy mapping, or FISH. Alternatively, if the genome of the organism that originated the EST has been sequenced, one can align the EST sequence to that genome using a computer.
The current understanding of the human set of genes (as of 2006) includes the existence of thousands of genes based solely on EST evidence. In this respect, ESTs have become a tool to refine the predicted transcripts for those genes, which leads to the prediction of their protein products and ultimately their function. Moreover, the situation in which those ESTs are obtained (tissue, organ, disease state - e.g. cancer) gives information on the conditions in which the corresponding gene is acting. ESTs contain enough information to permit the design of precise probes for DNA microarrays that then can be used to determine the gene expression.
Some authors use the term "EST" to describe genes for which little or no further information exists besides the tag.[3]
The significance of ESTs, their properties, methods to analyze EST dataset and their applications in different areas of biology have been reviewed by Nagaraj et al. (2007).[4]
Hacking the Genome
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James D. Watson, co-discoverer of DNA double helix, calls Craig Venter “Hitler”: * Watson also had quite a few disagreements with Craig Venter regarding his use of EST fragments while Venter worked at NIH. Venter went on to found Celera genomics and continued his feud with Watson. Watson was even quoted as calling Venter “Hitler”.[53]
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J. Craig Venter Institute(Rockville)
Bohra, A and Dubey, A and Saxena, R K and Penmetsa, R V and Poornima, K N and Kumar, N and Farmer, A D and Srivani, G and Upadhyaya, H D and Gothalwal, R and Ramesh, S and Singh, Dhiraj and Saxena, K B and Kavi Kishor, P B and Singh, N K and Town, C D and May, G D and Cook, D R and Varshney, R K (2011) Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.). BMC Plant Biology, 11 (1). pp. 56-70. ISSN 14712229
Dubey, A and Farmer, A and Schlueter, J and Cannon, S B and Abernathy, B and Tuteja, R and Woodward, J and Shah, T and Mulasmanovic, B and Kudapa, H and Raju, N L and Gothalwal, R and Pande, S and Xiao, Y and Town, C D and Singh, N K and May, G D and Jackson, S and Varshney, R K (2011) Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Research, 18 (3). pp. 153-164. ISSN 1340-2838, 1756-1663
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http://www.blueheronbio.com/
Overview
The latest tool in genome editing – CRISPR/Cas9 – allows for specific genome disruption and replacement in a flexible and simple system resulting in high specificity and low cell toxicity. The CRISPR/Cas9 genome editing system requires the co- expression of a Cas9 protein with a guide RNA vector expressed from the human U6 polymerase III promoter. With the protospacer-adjacent motif (PAM - the sequence NGG) present at the 3′ end, Cas9 will unwind the DNA duplex and cleave both strands upon recognition of a target sequence by the guide RNA. The functional cassette synthesized by Blue Heron in the rescue donor vector can then be inserted into the unwound DNA. The repaired genome will now express your desired sequence with or without tags.
Cas9 Further Reading
Genome editing of human pluripotent stem cells to generatehuman cellular disease models. Dis Model Mech. 2013 Jun 10
Biotechnology: Rewriting a genome. Nature 2013 Mar 7;495(7439):50-1
RNA-Guided Human Genome Engineering via Cas9. Science 2013 Feb 15;339(6121):823-6
Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 2013 Feb 15;339(6121):819-23
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This is reality. This is now:
.......................................................A bacterial enzyme that uses guide RNA molecules to target DNA for cleavage has been adopted as a programmable tool to site-specifically modify genomes of cells and organisms, from bacteria and human cells to whole zebrafish.
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http://en.wikipedia.org/wiki/Friday_%28novel%29
Friday is a 1982 science fiction novel by Robert A. Heinlein. It is the story of a female "artificial person," the eponymous Friday, genetically engineered to be stronger, faster, smarter, and generally better than normal humans. Artificial humans are widely resented, and much of the story deals with Friday's struggle both against prejudice and to conceal her enhanced attributes from other humans. The story is set in a Balkanized world, in which the nations of the North American continent have been split up into a number of smaller states.
Friday was nominated for the Nebula Award for Best Novel in 1982,[1] and the Hugo Award for Best Novel in 1983.[2]
The book's protagonist is Friday Baldwin, an artificial person both mentally and physically superior in many ways to an ordinary human, but she faces great prejudice and will most likely be killed if her "non-human" status is discovered. Employed as a highly self-sufficient combat courier, her various missions take her throughout the globe and also to some of the near-Earth space colonies. The novel is set in a complex, Balkanized world, and Friday is caught up in several civil disturbances during the course of her travels. She reaches her employer's home base safely but is soon displaced. Sent on a space journey as a courier, she realizes that the journey is likely to end with her death, evades the ship's authorities, and settles on a pioneer world with friends made earlier in the narrative.
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