Category Archives: Genetic Engineering

ScienceDaily (Oct. 11, 2012) Scientists have observed the neurological mechanism behind temperature-dependent -- febrile -- seizures by genetically engineering fruit flies to harbor a mutation analogous to one that causes epileptic seizures in people. In addition to contributing the insight on epilepsy, their new study also highlights the first use of genetic engineering to swap a human genetic disease mutation into a directly analogous gene in a fly.

In a newly reported set of experiments that show the value of a particularly precise but difficult genetic engineering technique, researchers at Brown University and the University of California-Irvine have created a Drosophila fruit fly model of epilepsy to discern the mechanism by which temperature-dependent seizures happen.

The researchers used a technique called homologous recombination -- a more precise and sophisticated technique than transgenic gene engineering -- to give flies a disease-causing mutation that is a direct analogue of the mutation that leads to febrile epileptic seizures in humans. They observed the temperature-dependent seizures in whole flies and also observed the process in their brains. What they discovered is that the mutation leads to a breakdown in the ability of certain cells that normally inhibit brain overactivity to properly regulate their electrochemical behavior.

In addition to providing insight into the neurology of febrile seizures, said Robert Reenan, professor of biology at Brown and a co-corresponding author of the paper in the Journal of Neuroscience, the study establishes

"This is the first time anyone has introduced a human disease-causing mutation overtly into the same gene that flies possess," Reenan said.

Engineering seizures

Homologous recombination (HR) starts with the transgenic technique of harnessing a transposable element (jumping gene) to insert a specially mutated gene just anywhere into the fly's DNA, but then goes beyond that to ultimately place the mutated gene into exactly the same position as the natural gene on the X chromosome. HR does this by outfitting the gene to be handled by the cell's own DNA repair mechanisms, essentially tricking the cell into putting the mutant copy into exactly the right place. Reenan's success with the technique allowed him to win a special grant from the National Institutes of Health last year.

The new paper is a result of that grant and Reenan's collaboration with neurobiologist Diane O'Dowd at UC-Irvine. Reenan and undergraduate Jeff Gilligan used HR to insert a mutated version of the para gene in fruit flies that is a direct parallel of the mutation in the human gene SCN1A that causes febrile seizures in people.

When the researchers placed flies in tubes and bathed the tubes in 104-degree F water, the mutant fruit flies had seizures after 20 seconds in which their legs would begin twitching followed by wing flapping, abdominal curling, and an inability to remain standing. After that, they remained motionless for as long as half an hour before recovering. Unaltered flies, meanwhile, exhibited no temperature-dependent seizures.

The researchers also found that seizure susceptibility was dose-dependent. Female flies with mutant strains of both copies of the para gene (females have two copies of the X chromosome) were the most susceptible to seizures. Those in whom only one copy of the gene was a mutant were less likely than those with two to seize, but more likely than the controls.

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Engineered flies spill secret of seizures

Berkeley Lab Researchers Develop New Tool for Making Genetic Engineering of Microbial Circuits Reliably Predictable

Synthetic biology is the latest and most advanced phase of genetic engineering, holding great promise for helping to solve some of the world's most intractable problems, including the sustainable production of energy fuels and critical medical drugs, and the safe removal of toxic and radioactive waste from the environment. However, for synthetic biology to reach its promise, the design and construction of biological systems must be as predictable as the assembly of computer hardware.

An important step towards attaining a higher degree of predictability in synthetic biology has been taken by a group of researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) under the leadership of computational biologist Adam Arkin. Arkin and his team have developed an "adaptor" that makes the genetic engineering of microbial components substantially easier and more predictable by converting regulators of translation into regulators of transcription in Escherichia coli. Transcription and translation make up the two-step process by which the coded instructions of genes are used to synthesize proteins.

"Application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex biological circuits in microorganisms," Arkin says. "This in turn should allow for safer and more efficient constructions of increasingly complex functions in microorganisms."

Arkin is the director of Berkeley Lab's Physical Biosciences Division and the corresponding author of a paper describing this work in Nature Methods. The paper is titled "An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Co-authoring this paper were Chang Liu, Lei Qi, Julius Lucks, Thomas Segall-Shapiro, Denise Wang and Vivek Mutalik.

Synthetic biology combines modern principles of science and engineering to develop novel biological functions and systems that can tackle problems natural systems cannot. The focus is on bacteria and other microbes that can metabolize a wide variety of valuable chemicals and molecules, and play a critical role in the global cycles of carbon and other important elements. One of the keys to success in synthetic biology is the design and construction of customized genetic switches in microbes that can control the expression of both coding and non-coding RNA, act on operons (small groups of genes with related functions that are co-transcribed in a single strand of messenger RNA), and be tethered to higher-order regulatory functions (a property called composability).

"Much of the regulatory potential of a bacterium is contained in the five-prime untranslated regions (UTRs), which control the expression of physically adjacent downstream genes and have become attractive platforms for a parts-based approach to synthetic biology," Arkin says. "This approach, in which integrated engineered regulatory parts respond to custom inputs by changing the expression of desired genes, must satisfy two criteria if it is to have long-term success. First, the regulatory parts must be easily engineered in a way that yields large homogenous sets of variants that respond to different custom inputs, and second, the parts must be composable such that they can be easily and predictably assembled into useful higher-order functions."

In the five prime UTRs of bacteria, two primary types of regulators can serve as starting points for designing new parts - those that regulate transcriptional elongation, in which cellular inputs are linked to the process by which a sequence of DNA nucleotides is transcribed into a complementary sequence of RNA; and those that regulate translation, in which a ribosome translates the RNA message into a protein. Transcriptional elongation regulators meet the second criterion by featuring versatility and composability that makes them ideal for building custom regulatory functions. Translational regulators meet the first criterion by being easier to engineer and relatively common to all bacteria.

"Our solution for meeting both criteria was to develop an adaptor based on tryptophanase, the catabolic operon for tryptophan that converts regulators of translational initiation into regulators of transcriptional elongation," Arkin says. "Because our adaptor strategy bypasses the otherwise restrictive tradeoff between criterion one and criterion two, we believe it will have a crucial role in the long-term development of five prime UTRs as platforms for the design and integration of custom regulatory parts."

When an E.coli translational regulator was fused to the adaptor created by Arkin and his colleagues, it was also able to control transcriptional elongation. The team applied their adaptor to the construction of several transcriptional elongation regulators that respond to RNA and small-molecule inputs. Included were five mutually orthogonal RNA-triggered attenuators (meaning they can terminate transcription), which the team assembled into logic gates driven by two, three or four RNA inputs that linked to ribosome binding sites. Because their adaptor is so easily linked to ribosome binding sites, a common mechanism in bacteria, the team believes the adaptor will be widely applicable.

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A Welcome Predictability

Fluorescence microscopy images of cells containing various plasmid pairs which were constructed with the help of a tna element adaptor and logic gates driven by two, three or four RNA inputs that linked to ribosome binding sites.

(Phys.org)Synthetic biology is the latest and most advanced phase of genetic engineering, holding great promise for helping to solve some of the world's most intractable problems, including the sustainable production of energy fuels and critical medical drugs, and the safe removal of toxic and radioactive waste from the environment. However, for synthetic biology to reach its promise, the design and construction of biological systems must be as predictable as the assembly of computer hardware.

An important step towards attaining a higher degree of predictability in synthetic biology has been taken by a group of researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) under the leadership of computational biologist Adam Arkin. Arkin and his team have developed an "adaptor" that makes the genetic engineering of microbial components substantially easier and more predictable by converting regulators of translation into regulators of transcription in Escherichia coli. Transcription and translation make up the two-step process by which the coded instructions of genes are used to synthesize proteins.

"Application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex biological circuits in microorganisms," Arkin says. "This in turn should allow for safer and more efficient constructions of increasingly complex functions in microorganisms."

Arkin is the director of Berkeley Lab's Physical Biosciences Division and the corresponding author of a paper describing this work in Nature Methods. The paper is titled "An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Co-authoring this paper were Chang Liu, Lei Qi, Julius Lucks, Thomas Segall-Shapiro, Denise Wang and Vivek Mutalik.

Enlarge

When a bacterial translational regulator is fused to a tna element adaptor, it is able to also regulate transcriptional elongation.

"Much of the regulatory potential of a bacterium is contained in the five-prime untranslated regions (UTRs), which control the expression of physically adjacent downstream genes and have become attractive platforms for a parts-based approach to synthetic biology," Arkin says. "This approach, in which integrated engineered regulatory parts respond to custom inputs by changing the expression of desired genes, must satisfy two criteria if it is to have long-term success. First, the regulatory parts must be easily engineered in a way that yields large homogenous sets of variants that respond to different custom inputs, and second, the parts must be composable such that they can be easily and predictably assembled into useful higher-order functions."

In the five prime UTRs of bacteria, two primary types of regulators can serve as starting points for designing new parts those that regulate transcriptional elongation, in which cellular inputs are linked to the process by which a sequence of DNA nucleotides is transcribed into a complementary sequence of RNA; and those that regulate translation, in which a ribosome translates the RNA message into a protein. Transcriptional elongation regulators meet the second criterion by featuring versatility and composability that makes them ideal for building custom regulatory functions. Translational regulators meet the first criterion by being easier to engineer and relatively common to all bacteria.

"Our solution for meeting both criteria was to develop an adaptor based on tryptophanase, the catabolic operon for tryptophan that converts regulators of translational initiation into regulators of transcriptional elongation," Arkin says. "Because our adaptor strategy bypasses the otherwise restrictive tradeoff between criterion one and criterion two, we believe it will have a crucial role in the long-term development of five prime UTRs as platforms for the design and integration of custom regulatory parts."

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Researchers develop new tool for making genetic engineering of microbial circuits reliably predictable

ScienceDaily (Oct. 8, 2012) Synthetic biology is the latest and most advanced phase of genetic engineering, holding great promise for helping to solve some of the world's most intractable problems, including the sustainable production of energy fuels and critical medical drugs, and the safe removal of toxic and radioactive waste from the environment. However, for synthetic biology to reach its promise, the design and construction of biological systems must be as predictable as the assembly of computer hardware.

An important step towards attaining a higher degree of predictability in synthetic biology has been taken by a group of researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) under the leadership of computational biologist Adam Arkin. Arkin and his team have developed an "adaptor" that makes the genetic engineering of microbial components substantially easier and more predictable by converting regulators of translation into regulators of transcription in Escherichia coli. Transcription and translation make up the two-step process by which the coded instructions of genes are used to synthesize proteins.

"Application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex biological circuits in microorganisms," Arkin says. "This in turn should allow for safer and more efficient constructions of increasingly complex functions in microorganisms."

Arkin is the director of Berkeley Lab's Physical Biosciences Division and the corresponding author of a paper describing this work in Nature Methods. The paper is titled "An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Co-authoring this paper were Chang Liu, Lei Qi, Julius Lucks, Thomas Segall-Shapiro, Denise Wang and Vivek Mutalik.

Synthetic biology combines modern principles of science and engineering to develop novel biological functions and systems that can tackle problems natural systems cannot. The focus is on bacteria and other microbes that can metabolize a wide variety of valuable chemicals and molecules, and play a critical role in the global cycles of carbon and other important elements. One of the keys to success in synthetic biology is the design and construction of customized genetic switches in microbes that can control the expression of both coding and non-coding RNA, act on operons (small groups of genes with related functions that are co-transcribed in a single strand of messenger RNA), and be tethered to higher-order regulatory functions (a property called composability).

"Much of the regulatory potential of a bacterium is contained in the five-prime untranslated regions (UTRs), which control the expression of physically adjacent downstream genes and have become attractive platforms for a parts-based approach to synthetic biology," Arkin says. "This approach, in which integrated engineered regulatory parts respond to custom inputs by changing the expression of desired genes, must satisfy two criteria if it is to have long-term success. First, the regulatory parts must be easily engineered in a way that yields large homogenous sets of variants that respond to different custom inputs, and second, the parts must be composable such that they can be easily and predictably assembled into useful higher-order functions."

In the five prime UTRs of bacteria, two primary types of regulators can serve as starting points for designing new parts -- those that regulate transcriptional elongation, in which cellular inputs are linked to the process by which a sequence of DNA nucleotides is transcribed into a complementary sequence of RNA; and those that regulate translation, in which a ribosome translates the RNA message into a protein. Transcriptional elongation regulators meet the second criterion by featuring versatility and composability that makes them ideal for building custom regulatory functions. Translational regulators meet the first criterion by being easier to engineer and relatively common to all bacteria.

"Our solution for meeting both criteria was to develop an adaptor based on tryptophanase, the catabolic operon for tryptophan that converts regulators of translational initiation into regulators of transcriptional elongation," Arkin says. "Because our adaptor strategy bypasses the otherwise restrictive tradeoff between criterion one and criterion two, we believe it will have a crucial role in the long-term development of five prime UTRs as platforms for the design and integration of custom regulatory parts."

When an E.coli translational regulator was fused to the adaptor created by Arkin and his colleagues, it was also able to control transcriptional elongation. The team applied their adaptor to the construction of several transcriptional elongation regulators that respond to RNA and small-molecule inputs. Included were five mutually orthogonal RNA-triggered attenuators (meaning they can terminate transcription), which the team assembled into logic gates driven by two, three or four RNA inputs that linked to ribosome binding sites. Because their adaptor is so easily linked to ribosome binding sites, a common mechanism in bacteria, the team believes the adaptor will be widely applicable.

"Continued application of our adaptor should produce large collections of transcriptional regulators whose inherent composability can facilitate the predictable engineering of complex synthetic circuits," Arkin says.

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New tool for making genetic engineering of microbial circuits reliably predictable

The Associated Press Published Sunday, Oct. 7, 2012 10:03AM EDT

LOS ANGELES -- Calories. Nutrients. Serving size. How about "produced with genetic engineering?"

California voters will soon decide whether to require certain raw and processed foods to carry such a label.

In a closely watched test of consumers' appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods are safe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the food supply.

International food and chemical conglomerates, including Monsanto Co. and DuPont Co., have contributed about $35 million to defeat Proposition 37 on the November ballot. It also would ban labeling or advertising genetically altered food as "natural." Its supporters have raised just about one-tenth of that amount.

If voters approve the initiative, California would become the first state to require disclosure of a broad range of foods containing genetically modified organisms, or GMOs. Food makers would have to add a label or reformulate their products to avoid it. Supermarkets would be charged with making sure their shelves are stocked with correctly labeled items.

Genetically altered plants grown from seeds engineered in the laboratory have been a mainstay for more than a decade. Much of the corn, soybean, sugar beets and cotton cultivated in the United States today have been tweaked to resist pesticides or insects. Most of the biotech crops are used for animal feed or as ingredients in processed foods including cookies, cereal, potato chips and salad dressing.

Proponents say explicit labeling gives consumers information about how a product is made and allows them to decide whether to choose foods with genetically modified ingredients.

"They're fed up. They want to know what's in their food," said Stacy Malkan, spokeswoman for the California Right to Know campaign.

Read this article:
California initiative to test appetite for 'genetically engineered' food

By Alicia Chang

Calories. Nutrients. Serving size. How about "produced with genetic engineering"?

California voters will soon decide whether to require certain raw and processed foods to carry such a label.

In a closely watched test of consumers' appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods are safe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the food supply.

International food and chemical conglomerates, including Monsanto and DuPont, have contributed about US$35 million to defeat Proposition 37 on the November ballot. It also would ban labelling or advertising genetically altered food as "natural". Its supporters have raised just about one-tenth of that amount.

If voters approve the initiative, California would become the first state to require disclosure of a broad range of foods containing genetically modified organisms, or GMOs. Food makers would have to add a label or reformulate their products to avoid it. Supermarkets would be charged with making sure their shelves are stocked with correctly labelled items.

Genetically altered plants grown from seeds engineered in the laboratory have been a mainstay for more than a decade. Much of the corn, soybean, sugar beets and cotton cultivated in the United States today have been tweaked to resist pesticides or insects. Most of the biotech crops are used for animal feed or as ingredients in processed foods including cookies, cereal, potato chips and salad dressing.

Proponents say explicit labelling gives consumers information about how a product is made and allows them to decide whether to choose foods with genetically modified ingredients.

"They're fed up. They want to know what's in their food," said Stacy Malkan, spokeswoman for the California Right to Know campaign.

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Genetic labelling mooted in California

1:00 AM A highly contested California vote over specialized labeling could have implications for U.S. agribusinesses.

By ALICIA CHANG/The Associated Press

LOS ANGELES Calories. Nutrients. Serving size. How about "produced with genetic engineering?"

click image to enlarge

A corn-based food product carrying a label identifying it as not containing genetically modified organisms, or GMOs, is sold at the Lassens Natural Foods & Vitamins store in the Los Feliz district of Los Angeles on Friday.

The Associated Press

California voters will soon decide whether to require certain raw and processed foods to carry such a label.

In a closely watched test of consumers' appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods are safe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the food supply.

International food and chemical conglomerates, including Monsanto Co. and DuPont Co., have contributed about $35 million to defeat Proposition 37 on the November ballot. It also would ban labeling or advertising genetically altered food as "natural." Its supporters have raised just about one-tenth of that amount.

Original post:
Do we have an appetite for genetically modified food?

LOS ANGELES -- Calories. Nutrients. Serving size. How about produced with genetic engineering?

California voters will soon decide whether to require certain raw and processed foods to carry such a label.

In a closely watched test of consumers appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods are safe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the food supply.

International food and chemical conglomerates, including Monsanto Co. and DuPont Co., have contributed about $35 million to defeat Proposition 37 on the November ballot. It also would ban labeling or advertising genetically altered food as natural. Its supporters have raised just about one-tenth of that amount.

If voters approve the initiative, California would become the first state to require disclosure of a broad range of foods containing genetically modified organisms, or GMOs. Food makers would have to add a label or reformulate their products to avoid it. Supermarkets would be charged with making sure their shelves are stocked with correctly labeled items.

Genetically altered plants grown from seeds engineered in the laboratory have been a mainstay for more than a decade. Much of the corn, soybean, sugar beets and cotton cultivated in the United States today have been tweaked to resist pesticides or insects. Most of the biotech crops are used for animal feed or as ingredients in processed foods including cookies, cereal, potato chips and salad dressing.

Proponents say explicit labeling gives consumers information about how a product is made and allows them to decide whether to choose foods with genetically modified ingredients.

Theyre fed up. They want to know whats in their food, said Stacy Malkan, spokeswoman for the California Right to Know campaign.

Agribusiness, farmers and retailers oppose the initiative, claiming it would lead to higher grocery bills and leave the state open to frivolous lawsuits. Kathy Fairbanks, spokeswoman for the No on 37 campaign, said labels would be interpreted as a warning and confuse shoppers.

Continued here:
California to vote on 'genetically modified' labels

LOS ANGELES (AP) -- Calories. Nutrients. Serving size. How about "produced with genetic engineering?"

California voters will soon decide whether to require certain raw and processed foods to carry such a label.

In a closely watched test of consumers' appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods are safe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the food supply.

International food and chemical conglomerates, including Monsanto Co. and DuPont Co., have contributed about $35 million to defeat Proposition 37 on the November ballot. It also would ban labeling or advertising genetically altered food as "natural." Its supporters have raised just about one-tenth of that amount.

If voters approve the initiative, California would become the first state to require disclosure of a broad range of foods containing genetically modified organisms, or GMOs. Food makers would have to add a label or reformulate their products to avoid it. Supermarkets would be charged with making sure their shelves are stocked with correctly labeled items.

Genetically altered plants grown from seeds engineered in the laboratory have been a mainstay for

Proponents say explicit labeling gives consumers information about how a product is made and allows them to decide whether to choose foods with genetically modified ingredients.

"They're fed up. They want to know what's in their food," said Stacy Malkan, spokeswoman for the California Right to Know campaign.

Agribusiness, farmers and retailers oppose the initiative, claiming it would lead to higher grocery bills and leave the state open to frivolous lawsuits. Kathy Fairbanks, spokeswoman for the No on 37 campaign, said labels would be interpreted as a warning and confuse shoppers.

See original here:
California initiative will test appetite for genetically modified foods

October 6, 2012 in Nation/World

Alicia Chang Associated Press

LOS ANGELES (AP) Calories. Nutrients. Serving size. How about produced with geneticengineering?

California voters will soon decide whether to require certain raw and processed foods to carry such alabel.

In a closely watched test of consumers appetite for genetically modified foods, the special label is being pushed by organic farmers and advocates who are concerned about what people eat even though the federal government and many scientists contend such foods aresafe.

More than just food packaging is at stake. The outcome could reverberate through American agriculture, which has long tinkered with the genes of plants to reduce disease, ward off insects and boost the foodsupply.

International food and chemical conglomerates, including Monsanto Co. and DuPont Co., have contributed about $35 million to defeat Proposition 37 on the November ballot. It also would ban labeling or advertising genetically altered food as natural. Its supporters have raised just about one-tenth of thatamount.

If voters approve the initiative, California would become the first state to require disclosure of a broad range of foods containing genetically modified organisms, or GMOs. Food makers would have to add a label or reformulate their products to avoid it. Supermarkets would be charged with making sure their shelves are stocked with correctly labeleditems.

Genetically altered plants grown from seeds engineered in the laboratory have been a mainstay for more than a decade. Much of the corn, soybean, sugar beets and cotton cultivated in the United States today have been tweaked to resist pesticides or insects. Most of the biotech crops are used for animal feed or as ingredients in processed foods including cookies, cereal, potato chips and saladdressing.

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Calif. initiative will test appetite for GMO food - Sat, 06 Oct 2012 PST