Wednesday, January 31, 2007

Nutrigenomics - Eat according to your genome

If you knew that you were especially susceptible to heart disease when you gained weight, would it increase your motivation to diet? How much would you be willing to pay to find out if you are one of the lucky people who can eat as much fat as you want and not have an increased risk of heart disease? Such tests are the goal of nutrigenomics, which seeks to identify the links between nutrition and disease based on an individual's genome.

While the field is still too young to offer personal dietary advice for the average consumer, research has uncovered links among genes, diet, and heart disease. Jose Ordovas, director of the Nutrition and Genomics Laboratory at Tufts University, has spent years studying the link between metabolism of dietary fats and risk of cardiovascular disease. After analyzing data from the Framingham Heart Study, a large-scale study that has traced the health of some 5,000 people since 1948, his team has found that certain genetic variants can protect people from diet-induced cardiovascular disease--or put them at increased risk. Ordovas spoke with Technology Review about his research and the future of the field.

Is It Anthrax or Just White Powder?

A good article about A microfluidic chip that rapidly identifies pathogens by scanning their genomes.

From the article :

When a patient is admitted to the hospital with signs of a dangerous systemic bacterial infection, or when a post-office worker finds white powder in a suspicious-looking envelope, the ability to quickly identify potential pathogens is important. To accomplish that, a team of Massachusetts researchers is developing a microfluidic chip that performs fast DNA sequencing to rapidly identify bacteria. The goal is a device simple enough to use in airport and other security screening.

In order to identify the bacteria in a blood sample or in a building's ventilation system, researchers or clinicians usually must start by coaxing it to grow in culture in the lab. This takes about 14 to 48 hours. In the meantime, a patient with a drug-resistant infection may be given the wrong antibiotic, or emergency medical workers may miss the signs of a potential bioterror attack.

Click here to read the full story

Monday, January 29, 2007

RNA used to turn on genes to alleviate disease

The gene-activating method, which is being developed by UT Southwestern scientists, also is providing researchers with a novel research tool to investigate the role that genes play in human health.

In a paper appearing online at Nature Chemical Biology and in an upcoming edition of the journal, lead author Dr. Bethany Janowski, assistant professor of pharmacology at UT Southwestern, and her colleagues describe how they activated certain genes in cultured cells using strands of RNA to perturb the delicately balanced mixture of proteins that surround chromosomal DNA, proteins that control whether genes are turned on or off.

Dr. David Corey, professor of pharmacology and the paper's senior author, said the results are significant because they demonstrate the most effective and consistent method to date for coaxing genes into making the proteins that carry out all of life's functions - a process formally called gene expression.

In any medical specialty, Dr. Janowski said, there are conditions where increased gene expression would prove beneficial.

"In some disease states, it's not that gene expression is completely turned off, but rather, the levels of expression are lower than they should be," she said. As a result, there is an inadequate amount of a particular protein in the body. "If we can bring the level up a few notches, we might actually treat or cure the disease," Dr. Janowski said.

For example, some genes are natural tumor suppressors, and using this method to selectively activate those genes might help the body fend off cancer, Dr. Janowski said.

Genes are segments of DNA housed in chromosomes in the nucleus of every cell and they carry instructions for making proteins. Faulty or mutated genes lead to malfunctioning, missing or over-abundant proteins, and any of those conditions can result in disease.

Surrounding the chromosome is a cloud of proteins that helps determine whether or not a particular gene's instructions are "read" and "copied" to strands of messenger RNA, which then ferry the plans to protein-making "factories" in the cell.

In its experiments, the UT Southwestern team used strands of RNA that were tailor-made to complement the DNA sequence of a specific gene in isolated breast cancer cells. Once the RNA was introduced into the protein mix, the gene was activated, ultimately resulting in a reduced rate of growth in the cancer cells.

Dr. Corey said that while it's clear the activating effects of the new technique are occurring at the chromosome level, and not at the messenger RNA level, more research is needed to understand the exact mechanism.

Although the RNA strands the researchers introduced - dubbed antigene RNA - were manufactured, Dr. Corey said the process by which they interact with the chromosome appears to mimic what naturally happens in the body.

"One of the reasons why these synthetic strands work so well is that we're just adapting a natural mechanism to help deliver a man-made molecule," Dr. Corey said. "We're working with nature, rather than against it."

Drs. Corey's and Janowski's current results are built on previous work, published in 2005 in Nature Chemical Biology, in which they found that RNA strands could turn off gene expression at the chromosome level.

The new UT Southwestern research, coupled with that from 2005, demonstrates a shift away from conventional thinking about how gene expression is naturally controlled, as well as how scientists might be able to exploit the process to develop new drug targets, Dr. Corey said.

For example, current methods to block gene expression, such as RNA interference, rely on using RNA strands to intercept and bind with messenger RNA. While RNA interference is an effective tool for studying gene expression, Dr. Janowski said, it's more efficient to use RNA to control both activation and de-activation at the level of the chromosome.

"It goes right to the source, right to the faucet to turn the genes on or off," she said.

Dr. Corey said many researchers have the ingrained idea that RNA only targets other RNA - such as what occurs when messenger RNA is targeted during RNA interference. "That's what everyone is familiar with," he said. "But the idea of RNA being used as a sort of nucleic acid modulator of chromosomes, at the level of the chromosome itself, is novel and unexpected, and it's going to take some getting used to."

Saturday, January 27, 2007

Synthetic Biology 3.0

oiy! it's almost wierd that everything is being tagged as a number, web 2.0, synthetic bio 2.0, blog 2.0, whew! what next???

yep.. Synthetic Biology 3.0!!

The conference is gonna be held on the 24th to 27th June 2007, at Zurich Switzerland (did i spell that right??) anyway, stay tuned as we have more of this coming up...


Friday, January 26, 2007

The Biggest DNA Ever Made

Again I stress that this is old news...but here's the thing.. I was looking around the other day for the longest DNA ever made (synthetic ofcourse) and look what i found on

there are some links here which will take u to
We've already mentioned about Codon Devices here to read it..

Matthew Herper, 07.13.06, 6:00 AM ET

A tiny startup says it has created a stretch of DNA more than 35,000 letters long.

The company, Codon Devices of Cambridge, Mass., believes it is the longest piece of DNA ever ever commercially shipped--but that's only the latest step in a race to create bigger and bigger pieces of genetic material.

Codon is aiming to become the leading player in a new field called "synthetic biology," creating tools by which cells and their genetic material can be more precisely engineered in order to create new medicines and industry. In this case, the DNA was constructed for Microbia, another Cambridge biotech that is developing drugs and creating microbes that can be used in manufacturing chemicals.

The creation of ever-longer stretches of man-made DNA is allowing researchers to make new strides in understanding how multiple genes work together.

"This is basically the next step in synthetic biology," says Brian Baynes, Codon's chief scientific officer. "People have been doing a lot of work with synthetic genes for a number of years, but they've been stuck with one gene."

On a piece of DNA as long as the one made for Microbia, ten or more genes may be present. By studying more than one gene at once, researchers hope to get a better picture of how they work in concert to produce an organism. Another advantage: These stretches can also be made to contain all the DNA letters that occur between genes. Scientists once thought of that stuff as junk, but many now believe it may regulate how the genes work or provide some other function.

Scientists playing in the synthetic-biology toolbox have also managed to make living cells do things nature never designed. One setup created blinking lights; another made photographic film composed of living bacteria in a Petri dish.

Codon was founded a year ago on the idea that scientists would need a company that could sell tools used in creating such custom-designed biological systems (see: " Photoshop For DNA").

Other companies are also in the business of making DNA for drug companies and other research organizations, which save time by using newer DNA synthesis methods instead of laboriously copying cells and inserting or deleting bits of genetic material.

Blue Heron Biotechnology, a company that is in the sole business of synthesizing DNA, says it made a piece of DNA that was 27,000 letters long while working with academic researchers. But the company says it sees itself as more of a supplier to synthetic biologists than as a player in the field. "I am optimistic that in a few years things like synthetic biology will be half or more of our market," says Chief Executive John Mulligan. "We're a pure DNA foundry."

Codon says that within a year or two it hopes to create DNA fragments that are as much as 100,000 letters long, and that eventually they might make 1-million-letter fragments.

"Codon's charge from the beginning has been to industrialize this space and create something well beyond synthetic biology that we call constructive biology," says Chief Executive John Danner. He says that by December of this year he hopes to have more DNA production capacity than all his competitors currently have combined.

Awesome stuff considering its just a start up...while we look out even more, stay tuned because, this blog is soon gonna be the definative Gene Synthesis Blog

Invitrogen and Blue Heron Biotechnology Enter into Strategic Development and Distribution Relationship

CARLSBAD, Calif.--(BUSINESS WIRE)--Dec. 12, 2006--Invitrogen Corporation (Nasdaq:IVGN), a global leader in life sciences, today announced they have entered into a strategic development and distribution relationship with Blue Heron Biotechnology. Invitrogen will invest in Blue Heron in exchange for worldwide rights to distribute Blue Heron's custom gene synthesis services. Under the terms of the agreement, Invitrogen will become the exclusive worldwide distributor of Blue Heron's synthetic genes. The financial terms of the agreement were not disclosed.

Blue Heron Biotechnology's proprietary GeneMaker(R) platform can synthesize any gene sequence, with perfect accuracy regardless of length or complexity, which makes it ideal for the synthetic biology market. Researchers worldwide are increasingly turning to synthetic genes as a convenient, cost-effective alternative for traditional cloning. Accurate and rapid synthesis of synthetic genes has allowed pharmaceutical and biotechnology companies to speed the drug discovery process through an ability to rapidly and accurately synthesize known genes, and produce from them novel proteins, new vaccines and diagnostics.

"Invitrogen recognizes the tremendous new possibilities that gene synthesis offers life science researchers," said Nathan Wood, Vice President of Cloning and Protein Expression. "We have developed a broad array of products that complement Blue Heron's GeneMaker(R) platform and this agreement continues to enhance our portfolio offerings to our customers."

Invitrogen is a leading provider of recombinant cloning and protein expression products, as well as the premier provider of the largest fully sequenced human open reading frame clone collections. Gene synthesis builds upon this strength and will be especially useful in emerging fields such as synthetic biology.

"Partnering with a life sciences leader such as Invitrogen is an important milestone in Blue Heron Bio's continued growth and signals an important milestone for the overall gene synthesis market as well. We are very pleased to be able to make our gene synthesis services available through Invitrogen's unmatched distribution and marketing channels," said John Fess, CEO of Blue Heron Biotechnology.

As part of the agreement, the companies will co-develop new products and services for the research and bio-pharmaceutical markets.

Reactivated gene shrinks tumors, MIT study finds

Many cancers arise due to defects in genes that normally suppress tumor growth. Now, for the first time, MIT researchers have shown that re-activating one of those genes in mice can cause tumors to shrink or disappear.

The study offers evidence that the tumor suppressor gene p53 is a promising target for human cancer drugs.

"If we can find drugs that restore p53 function in human tumors in which this pathway is blocked, they may be effective cancer treatments," said David Kirsch of MIT's Center for Cancer Research and Harvard Medical School, one of the lead co-authors of the paper.

The study is published in the Jan. 24 online edition of Nature. It was conducted in the laboratory of Tyler Jacks, director of the Center for Cancer Research, the David H. Koch Professor of Biology and a Howard Hughes Medical Institute investigator.

P53 has long been known to play a critical role in the development of many tumors--it is mutated in more than 50 percent of human cancers. Researchers have identified a few compounds that restore p53 function, but until now, it has not been known whether such activity would actually reverse tumor growth in primary tumors.

The new MIT study shows that re-activating p53 in mouse tumors dramatically reduces the size of the tumors, in some cases by 100 percent.

"This study provides critical genetic evidence that continuous repression of a tumor suppressor gene is required for a tumor to survive," said Andrea Ventura, an Italian postdoctoral associate in the Center for Cancer Research and first author of the paper.

In normal cells, p53 controls the cell cycle. In other words, when functioning properly, it activates DNA repair mechanisms and prevents cells with damaged DNA from dividing. If DNA damage is irreparable, p53 induces the cell to destroy itself by undergoing apoptosis, or programmed cell death.

When p53 is turned off by mutation or deletion, cells are much more likely to become cancerous, because they will divide uncontrollably even when DNA is damaged.

In this study, the researchers used engineered mice that had the gene for p53 turned off. But, they also included a genetic "switch" that allowed the researchers to turn p53 back on after tumors developed.

Once the switch was activated, p53 appeared in the tumor cells and the majority of the tumors shrank between 40 and 100 percent.

The researchers looked at two different types of cancer--lymphomas and sarcomas. In lymphomas, or cancers of the white blood cells, the cancer cells underwent apoptosis within 1 or 2 days of the p53 reactivation.

In contrast, sarcomas (which affect connective tissues) did not undergo apoptosis but went into a state of senescence, or no growth. Those tumors took longer to shrink but the senescent tumor cells were eventually cleared away.

The researchers are not sure why these two cancers are affected in different ways, but they have started trying to figure it out by identifying the other genes that are activated in each type of tumor when p53 turns back on.

The study also revealed that turning on p53 has no damaging effects in normal cells. The researchers had worried that p53 would kill normal cells because it had never been expressed in those cells.

"This means you can design drugs that restore p53 and you don't have to worry too much about toxic side effects," said Ventura.

Possible therapeutic approaches to turn on p53 in human cancer cells include small molecules that restore mutated p53 proteins to a functional state, as well as gene therapy techniques that introduce a new copy of the p53 gene into tumor cells. One class of potential drugs now under investigation, known as nutlins, acts by interfering with MDM2, an enzyme that keeps p53 levels low.

In follow-up studies, the MIT researchers are looking at other types of cancer, such as epithelial (skin) cancer, in their mouse model, and they plan to see if the same approach will also work for tumor suppressors other than p53.

This research was funded by the Howard Hughes Medical Institute, the National Cancer Institute, the American Italian Cancer Research Foundation and the Leaf Fund.

Other authors on the paper are Margaret McLaughlin, a former postdoc in Jacks' lab, now at Novartis; David Tuveson, also a former postdoc, now group leader at the Cambridge Research Institute (United Kingdom); Laura Lintault, a research affiliate in the Center for Cancer Research; Jamie Newman, graduate student in MIT's Department of Biology; Elizabeth Reczek, a former graduate student in Jacks' lab, now a postdoctoral fellow at Brigham and Women's Hospital; Ralph Weissleder, a professor of radiology at Harvard Medical School and director of the Center for Molecular Imaging Research; and Jan Grimm, a former postdoc in Weissleder's lab, now at Memorial Sloan Kettering Cancer Center.

Genes and Chromosomes: The Building Blocks of Life

Every human being has 20,000 to 25,000 genes that determine the growth, development and functions of our physical and biochemical systems. Genes are normally packaged into 46 chromosomes (23 pairs) inside our cells.

The pairs numbered 1 to 22 are the same in males and females and are called autosomes. The 23rd pair are sex-determining chromosomes. Females have two Xs and males have one X and one Y.

Sperm and egg cells are different from other body cells. These reproductive cells each have only 23 unpaired chromosomes. When a single sperm and egg come together when pregnancy begins they form their own new cell with 46 chromosomes. The human being that results is genetically unique, with a blueprint half from each parent.

Gene Synthesis Gets Cheaper - 2

Well in our previous article we just saw how Gene Synthesis got cheaper...

just to round up on that a bit, i was eagerly looking at some ads that would show companies lookin at this technology.. for one we know that, world wide, Codon Devices gives 1bp at $0.79 !! that is like really low and based on what I've read about Codon Devices, they're pretty good.. also now we have a new contender for their title.. GenScript now is in with $0.75 per base pair!! Hey i'm not tryin to promote any brand here and I don't certainly make the news.. i just see em..

Looks like we have a price war starting..stay tuned for more!

Illumina, Solexa to merge

I know this is old stuff, but as usual the definative Gene Synthesis Blog brings u news that could impact the industry... read on...

SAN DIEGO—Illumina Inc. and Solexa Inc. announced in mid-November a definitive agree­ment under which Illumina will acquire Solexa in a stock-for-stock merger. Under the merger agreement, Solexa stockholders would receive Illumina common stock valued at $14 per share, for a total equity value of approxi­mately $600 million. Illumina also agreed to invest $50 million in Solexa in exchange for newly issued Solexa shares.
The merger announcement comes just months after Solexa began moving its next-generation sequencing platform, the 1G Genome Analyzer, to a handful of select customers and prepares to aggressively launch the product to the broader market in 2007. Furthermore, it joins together compa­nies that have plied the waters of both gene expression and gene sequencing, mar­kets that Illumina officials say are highly complementary and that it estimates in excess of $2.25 billion.
“For around the last 18 months, we and our CEO [Jay Flatley] have been looking at next-generation sequencing technolo­gies,” says John Stuelpnagel, COO of Illumina. “We knew that what we are doing in genotyping and gene expression had great overlap and synergies and that the tech­nologies could play off each other.”
Specifically, Illumina sees cross selling and integration opportuni­ties for researchers using Solexa’s 1G Genome Analyzer for whole-genome resequencing to use those results to conduct additional work on Illumina’s BeadStation for whole-genome genotyping. Likewise, results from the BeadStation for targeted genotyping studies could suggest additional work for target­ed resequencing appropriate for the 1G Genome Analyzer.
“This merger will create the only company today that can offer both analog and digital gene expression,” notes Stuelpnagel. “From Illumina’s standpoint, it was also an opportunity to bring in a sequencing technology that is much farther along than com­peting technologies and to rapidly commercialize it.”
For Solexa, the time to join with Illumina was suitable as it pre­pares to ramp up the production and marketing of its 1G product—a system it maintains has the poten­tial to generate “upwards to 1 bil­lion bases of data in a single run.” The company also says it can cur­rently sequence an entire genome for around $100,000, a figure that is orders of magnitude separated from its nearest competitor.
“We started talking with Illumina about a collaboration to help us with our sequencing tool,” says Omead Ostadan, VP of mar­keting for Solexa. “But as we con­tinued to talk, what we found was there was much more we could do as a company by merging with them both from a technology and a technical standpoint.”
While Solexa will benefit from Illumina’s large sales and support footprint in the global market, there are also opportunities for Illumina’s manufacturing infra­structure to help with the com­mercial ramp up of the 1G.
Still, Stuelpnagel notes, there is no intention of significantly chang­ing the operations at Solexa’s two operating centers in Hayward, Calif. and Cambridge, England.
When the merger is completed, expected in the first quarter of 2007, current Solexa CEO John West will stay on with the compa­ny as senior VP and general man­ger of the sequencing business.

Tuesday, January 23, 2007

Discovery may herald new RNA therapeutics

Very recently in the Journal Nature...

British scientists have taken an
important step toward preventing tumor growth by finding a way of
switching off a gene involved in cell division.

The Oxford University researchers say the mechanism involves a form
of ribonucleic acid, or RNA, a chemical found in cell nuclei. RNA plays
a direct role in the synthesis of proteins, but scientists have known
for some time that not all types of RNA are directly involved in
protein synthesis.

Now, in research funded by the Wellcome Trust and Britain's Medical
Research Council, the Oxford scientists have shown one particular type
of RNA plays a key role in regulating the gene implicated in control of
tumor growth.

"There's been a quiet revolution taking place in biology during the
past few years over the role of RNA," said Alexandre Akoulitchev, a
senior research fellow at the university. "Scientists have begun to see
'junk' DNA as having a very important function. The variety of RNA
types produced from this "junk" is staggering and the functional
implications are huge."

This info is copyright of United Press International....

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Tags: therapeutics | tumor | Synthesis | SCIENTISTS | Role | research | protein | plays | involved | herald | growth | gene | university | Technology | RNA | Oxford | Discovery | Britain

Independent Clinical Data Confirms Accuracy of Gene Expression Test for Heart Transplant Patients

BRISBANE, Calif., Jan. 22 /PRNewswire/ -- For many Americans living
with a heart transplant, invasive heart-muscle biopsies that check for
organ rejection are a fact of life. However, a simple blood test that
analyzes a patient's genes, introduced in 2005, has been evaluated by
leading transplant centers and their experience verifies it can
accurately detect the absence of heart transplant rejection, according
to data reported in a new study authored by a consensus team of
international heart transplant experts and published in the December
2006 edition of the Journal of Heart and Lung Transplantation (JHLT).

In 2006, results from the CARGO (Cardiac Allograft Rejection Gene
Expression Observational) study were published and reported on the
utility of a gene expression profiling (GEP) test, called AlloMap(R)
molecular expression testing, which had been commercially available for
nearly a year. Developed by XDx, a molecular diagnostics company in
Brisbane, Calif., the test is currently offered at 40 transplant
centers in the United States.

"AlloMap testing is not only less
invasive and less risky than biopsy, it also monitors the absence of
organ rejection and raises the suspicion of damage before any damage to
the heart happens. Biopsy records damage that has already occurred,"
says Dr. Mario Deng, the article's corresponding author. Dr. Deng is
director of cardiac transplantation research and associate professor of
clinical medicine at Columbia University College of Physicians and
Surgeons, and a practicing cardiologist at New
York-Presbyterian/Columbia University Medical Center.

Approximately 30 percent of all heart transplant patients reject their
new heart at least once in the first year after transplantation. When
testing reveals organ rejection, a patient's immunosuppressive regimen
is adjusted.

"The Cleveland Clinic was the first transplant
center in the United States to use the AlloMap test to follow patients
after cardiac transplant," said Dr. Randall C. Starling, the
editorial's first author and vice chairman of cardiovascular medicine
and section head of heart failure and cardiac transplant medicine at
Cleveland Clinic. "There is clearly a need for new methods to determine
the best way to manage heart transplant patients. Gene expression
profiling appears to be the future, and holds the potential to improve
accuracy of diagnosis, reduce the need for invasive procedures and
reduce cost. Additional research is necessary, but we are encouraged
that gene expression profiling will improve the care of our patients."

Based on the new data published as an invited editorial, in more
than 99 percent of cases, the AlloMap test successfully predicted the
absence of moderate or severe acute cellular organ-transplant
rejection. These results confirm the findings of the CARGO study.

The AlloMap test was developed to rule out rejection, meaning that a
low test score very reliably identifies transplant patients who are not
rejecting their transplanted heart. The primary advantage of the test
is to identify low-risk patients who can be monitored and managed using
noninvasive methods and who may benefit from being more aggressively
weaned off intensive immunosuppressive regimens that are associated
with serious side effects.

"Many of the premier transplant
centers in the United States have incorporated AlloMap testing into
their treatment protocol and physicians are relying on the test to
accurately manage the care of heart transplant recipients," said Pierre
Cassigneul, president and chief executive officer of XDx. "The invited
editorial in JHLT further validates the usefulness and accuracy of
AlloMap testing. We are pleased to see continued confirmation of the
test's abilities from real-world use."

The AlloMap test was
developed by XDx in partnership with eight major U.S. research
universities and presents current immune activity of the transplanted
heart recipient. The test uses real-time polymerase chain reaction
(PCR) and an algorithm to analyze the patient's gene expression. The
AlloMap test is currently being developed for use in lung

Before the availability of AlloMap testing,
heart-muscle biopsy was the only method available for detecting
rejection of the transplanted heart. Invasive heart biopsies are
performed frequently in the first year post-transplant and periodically
thereafter, often for the patient's lifetime.

Currently, the AlloMap test is available to heart transplant patients, ages 15 and older, two months post-transplantation.

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Tags: Transplant | reported | Rejection | published | PATIENT | data | Technology | independent | gene | expression | confirms | CLINICAL | brisbane | Accuracy

Thursday, January 18, 2007

Genetic Engineering of Foods: Is Fish Protein In Your Ice Cream?

The fat and calories in ice cream have many of us doing without the double
dips, but scientists are looking to a little-known fish to pull your
diet out of the deep freeze.

You may have seen it on store shelves: new low-fat ice cream with all the flavor of the real stuff.

But a University of Cincinnati researcher says to stay away from the sweet
treat- that flavor may bring with it some unintended consequences.

As manufacturers strive for that rich and creamy but low fat combination,
it's another combination: a DNA combination that is causing some strong

Ice cream scientists are adding a cloned protein from the arctic pout fish that keeps it from freezing in icy water.

"Their basic approach is to continue to freeze the ice cream and whip it under
agitation down to a much lower temperature," explains Bruce Tharp, a
food scientist with Tharp's Food Tech.

It keeps the ice crystals small and makes a lower-fat flavor taste creamier.

"This is delicious," said one taster. "It doesn't taste any different than the fattening kind."

But it becomes genetically modified, and thats hard for one University of Cincinnati professor to stomach

"I think we're opening the door into a dark room, and we don't know what
the hazards are in the dark room and I would urge caution," said David
Fankhauser, a UC Genetic Specialist.

Some corn, soybeans and sweet potatoes are also genetically modified, but
you wouldn't know because the FDA doesn't require genetically altered
foods to be labeled as such.

Dr. Fankhauser says that's the problem because we still don't know the long-term effects.

"We need to be able to continue monitoring in the population that's
consuming it. Without labeling, how will we know?" Fankhauser said.

It's not all about making foods taste better, either. Genetic modification
can make crops resist bugs and viruses and can increase milk and egg

But until he knows exactly what he's scooping into that cone, Dr. Fankhauser says he'll pass.

"Actually, I like to make my own ice cream," said Dr. Fankhauser.

That may be the only way to be absolutely sure the food you're eating isn't genetically modified.

The fish protein is used in Breyer's Double Churned Ice Cream products and in some of their popsicle products.

Breyer's says "consumer reaction to the entire double-churned line has been very positive."

So choose for yourself.

Reported by: Kathrine Nero

Web Produced by: Laura Hornsby

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Tags: SCIENTIST | protein | Technology | Genetic | ENGINEERING | cincinnati

Bio Market Trends

The value of the primary
and secondary U.S. biomanufacturing market in 2006 is estimated to be
approximately $50 billion with a healthy growth rate almost approaching
double digits due to the escalating number of biotech drugs in the
pipeline and skyrocketing sales of approved high-value, life-saving

D/&/amp;MD’s “Biodisposables: Utility and
Technological Advances” market analysis report details and reviews the
implementation, cost-effectiveness, utility, and applications,
including advances in specific apparatus, for disposable biotechnology
equipment, such as filters, mixers, dispensers, connectors, storage
bags, and bioreactors.

The current economic and regulatory
reality, highlighted by the imminent establishment of drug pricing
controls and tightening regulatory and quality standards, indicates the
added pressures that are emerging for pharmaceutical companies to
re-strategize their overall approach. There is a trend toward fewer
blockbuster drugs, as patient populations become smaller and the
associated histories and genetic makeup become stratified as
personalized medicine begins to come into its own.

manufacturers have responded to these trends by developing fully
integrated, turnkey manufacturing–production lines that combine
single-use components with modular software, disposable bioreactors and
equipment, and a disposable stir-tank and mixing system.

research necessary to design and implement a disposable biotech
facility is summarized in this report, including the latest disposable
technologies and applications from leading industry users. In addition,
detailed examples for analyzing cost of goods and savings are provided
to assist professionals attempting to determine the utility of
disposables in their own facility.

The biopharmaceutical
industry in the U.S. grew by an average of 11% annually from 1993 to
2003. Cartridges used for filtering liquids represent a $10.8 billion
dollar market now, but by 2009, sales will reach an annual level of
$14.2 billion. The market for membrane technology used in
biopharmaceutical discovery, development, and commercial production,
estimated at $740 million in 2004, is expected to rise at an average
annual growth rate of 10.7% to more than $900 million in 2008 and to
$1.23 billion in 2009. The average time required to construct a biotech
facility is about five years, putting tremendous pressure on drug
manufacturers to expend capital when the risk of drug failure is still
high. Existing manufacturing plant costs linger between $10–50 million,
depending upon required output and therapeutic bioproduct. At the two
extreme price ranges, a 100-L, $10,000 Mab plant scales up to a
10,000-L plant costing $120 million.

Within the next five
years, it is expected that 25% of all drugs will be biological
products. As discovery and production of these products relies heavily
on membranes, hundreds of membrane products (many single-use) and
processes will continue to be developed to meet the emerging market.

Terryberry has over a dozen peer-reviewed publications in clinical
chemistry research focusing on orthobiologic drug development. Gautam
Thor is the author of scientific and medical publications through
NeuroConsultants. For sample content from D/&/amp;MD’s “Biodisposables:
Utility and Technological Advances” report:

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Tags: drug | Technology | news | Genetic | ENGINEERING

Scientists discover new class of RNA

The last few years have been very good to ribonucleic acid (RNA).
Decades after DNA took biology by storm, RNA was considered little more
than a link in a chain--no doubt a necessary link, but one that, by
itself, had little to offer. But with the discoveries of RNA
interference and microRNAs, this meager molecule has been catapulted to
stardom as a major player in genomic activity.

Now, a team of
scientists led by David Bartel, a professor in MIT's Department of
Biology, has discovered an entirely new class of RNA molecules.

in the journal Cell, the team describes identifying more than 5,000 of
these new molecules, termed 21U-RNAs, in the C. elegans worm. These new
RNAs are named after their distinctive features: Each molecule contains
21 chemical building blocks (or nucleotides), and each begins with the
chemical uridine, represented by the letter U (the only RNA nucleotide
not also found on DNA). In addition, each of the 5,000 different
21U-RNA molecules comes from one of two chromosomal regions.

"we can predict where additional 21U-RNA genes might reside," says
Bartel, who is also a member of the Whitehead Institute for Biomedical
Research and a Howard Hughes Medical Institute investigator. "Combining
these predictions with the 5,000 (21U-RNAs) that we experimentally
identified, we suspect that there are more than 12,000 different
21U-RNA genes in the genome." Because each gene typically produces a
unique 21U-RNA, a very large diversity of molecules is made.

are so many 21U-RNA genes spread out over such a wide swath of the
genome, but they all share common requirements for expression and
common structural features," says Bartel lab Ph.D. student J. Graham
Ruby, lead author on the paper.

Although the researchers haven't
yet identified a particular function for these molecules, they believe
that this uniform structure strongly indicates an important role.

Institute Professor and Nobel Laureate Phillip Sharp, a biologist who
was not part of the research team, supports this hypothesis. The fact
that 21U-RNAs share this "common structure and origin suggests an
important function," he says. "It requires function to conserve

Other members of the research team are affiliated
with the Broad Institute of MIT and Harvard and Pennsylvania State
University. This research was supported by the Prix Louis D from the
Institut de France and a grant from the National Institutes of Health.

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Scientists discover new class of RNA

Tags: SCIENTISTS | link | DISCOVER | biology | Technology | RNA

Toward A Genetic Test For Parkinson's Disease

Molecular markers of early Parkinosn’s disease based on gene expression in blood.
Scherzer, C.R., A.C. Eklund, L.J. Morse, Z. Liao, et al. Proc. Nat. Acad. Sci.,104 (3), 955-960 (January 16, 2007).

Parkinson’s disease (PD) is a progressive neurodegenerative disorder
that is difficult to diagnose until significant cell loss has already
occurred in the substantia nigra, as evidenced by abnormally slow
movement and tremor. Even then, other neurological diseases may
confound a clinical diagnosis.

authors of this study provide a first-pass at identifying a set of
genetic markers for diagnosing PD. Their work entailed screening venous
blood of 31 PD patients and 35 controls, 18 of whom had other
neurological diseases such as Alzheimer’s disease and progressive
supranuclear palsy. The microarray analysis used more than 22,000
oligonucleotide probes to find differences in RNA content of the blood.
Eight unrelated genes that are expressed in the brain were identified,
including three implicated in PD: the vitamin D receptor, huntingtin
interacting protein 2, and a protein involved in dopamine transporter
endocytosis. The other five have not been associated with PD

A test of the biomarker’s accuracy found that there
was a significant difference between patients with PD and the normal
and disease controls. Those with a score in the highest third had an
odds ratio of 5.1 for PD, versus 1.9 for the intermediate third of
patients. (The lowest third was used as a reference group with an
assigned score of 1.)

The microarray analysis also identified
22 genes whose expression was altered in PD patients, but lacked
predictive power since they were found at abnormal levels in other
neurodegenerative diseases. Further investigation of these genes seems
warranted, as they may shed light on disease pathology. Indeed, one,
the heat-shock protein 70-interacting protein ST13 gene may afford an
opportunity to follow disease progression.

In all, this study
provides enticing leads to follow for the development of a
biomarker-based diagnostic test for Parkinson’s disease, as well as an
assay for assessing disease progression.
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Tags: progressive | NEUROLOGICAL | Genetic | disease | DIAGNOSE | Technology | Parkinson

Gene Synthesis Gets Cheaper

A new method for synthesizing specific DNA sequences could revolutionize the production of genes in the laboratory (Nature, 23 Dec 04, Vol. 432, No. 7020, pp. 1050-1054). The technique, which uses programmable 'DNA microchips', looks set to slash the current cost of gene synthesis.

The DNA microchips are tagged with thousands of different short DNA sequences called oligonucleotides. These form two groups: 'construction' oligonucleotides, which act as templates for the replication of corresponding genetic sequences, and 'selection' oligonucleotides, which reinforce production of the correct sequences to minimize errors. A single-step reaction then assembles these short DNAs into much longer stretches of sequence.

To test their method, George Church and his colleagues assembled all 21 genes used by the bacterium Escherichia coli to create one part of its protein-assembly apparatus, called the ribosome. By tweaking the sequences of the construction oligonucleotides, they were able to increase the efficiency with which these genes were translated into protein, bringing closer the goal of creating a complete artificial ribosome in the lab. If successful, the technique could radically cut the cost of assembling gene sequences, which currently yields about nine DNA 'letters' for every dollar spent. The researchers hope that with this new method, a dollar could potentially buy 20,000 letters of highly accurate code.

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Tags: oligonucleotides | Synthesis | sequence | Production | microchips | gene | Technology | gets | cheaper

Columbia University licenses next-generation DNA sequencing technology

Columbia University announces today that it recently executed an
exclusive license agreement for a next generation DNA sequencing
technology to Intelligent Bio-Systems (IBS), Inc. This innovative
DNA-sequencing technology was invented by Dr. Jingyue Ju, professor of
Chemical Engineering and head of DNA Sequencing and Chemical Biology at
the Judith P. Sulzberger, M.D. Columbia Genome Center at Columbia
University. The fundamentals of this new technology are being published
on-line today by in the Proceedings of the National Academy of Sciences
(PNAS). This research paper describes the details of the Sequencing by
Synthesis Chemistry and how the approach overcomes accuracy limitations
of other next generation DNA sequencing systems.

It was also recently announced that Columbia University in
collaboration with the Waltham, Mass. based Intelligent Bio-Systems, is
one of only two recipients of the Near-Term Technology Development for
Genome Sequencing grants from the National Human Genome Research
Institute (NHGRI) of the National Institutes of Health (NIH)
( This grant of $425,000 is for the
development of a "High-Throughput DNA Sequencing by Synthesis Platform."

"The collaboration between Dr. Ju at Columbia and Intelligent
Bio-Systems is an important development to bring this powerful
technology to both researchers and clinicians in the near future," said
Dr. Steven Gordon, Chief Executive Officer at IBS. "Completing the
license was a key step in uniting Dr. Ju's seminal sequencing chemistry
and IBS's molecular biology and engineering expertise. We are poised to
offer a simple, cost effective platform that will enable many
researchers and clinicians to use this next-generation DNA sequencing
technology in their own laboratories."

Dr. Ju is a prolific inventor of new technologies for
applications in genomics using chemistry and molecular engineering
approaches. He is credited with being one of the primary inventors of
the fluorescent energy transfer chemistry for 4-color Sanger sequencing
being used by virtually all of the current generations of DNA
sequencers that were used to complete the Human Genome Project.


About Columbia Genome Center

From its conception in 1995, the Judith P. Sulzberger, M.D.,
Columbia Genome Center (CGC) has served as a bridge between the
biomedical and science/engineering communities of the two Columbia
University campuses, the main campus in Morningside Heights and the
Medical Center campus in Washington Heights. The CGC was born as an
interdisciplinary consortium of scientists and engineers dedicated to
the generation of technology, information science, systems biology, and
population genetic theory required to transform information from the
genome to the study of biology and the practice of medicine. Today,
more than 70 scientists collaborate on initiatives to further
illuminate the genome.

About Columbia University

Founded in 1754 as King's College, Columbia University in the
City of New York is the fifth oldest institution of higher learning in
the United States and is one of the world's leading academic and
research institutions, conducting pathbreaking research in medicine,
science, engineering, the arts, and the humanities. For more
information about Columbia University, visit

About Intelligent Bio-Systems, Inc.

Intelligent Bio-Systems, Inc. is a privately held company
located in Waltham, Mass. Since founding in 2005 it has focused on the
development of next-generation DNA sequencing, gene expression and
diagnostic systems based on proprietary instruments, chemistry, and
consumables. The company has committed to deliver working instruments
to the laboratories of a few early access collaborators during the
coming year.

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Columbia University licenses next-generation DNA sequencing technology

Tags: sequencing | next-generation | License | generation | university | Technology | DNA | Columbia