Tag Archives: sequencing

How sequencing foods’ DNA could help us prevent diseases

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Davey Alba asks in Wired, what’s almost as important to life as food? Food safety.

Last year, in the US, according to the CDC, one in six people were affected by food-borne diseases, resulting in 128,000 hospitalizations, 3,000 deaths, and an economic burden totaling $80 billion.

Scientist from IBM Research and Mars Incorporated have announced the Sequencing the Food Supply Chain Consortium, a collaborative food safety organization that aims to leverage advances in genomics and analytics to further our understanding of what makes food safe.

The researchers will conduct the largest-ever metagenomics study of our foods, sequencing the DNA and RNA of popular foods in an effort to identify what traits keep food safe and these can be effected by outside microorganisms and other factors. Eventually, the researchers will extend the project “from farm to fork,” examining materials across the length and breadth of the supply chain.

In this way, IBM Research and Mars are joining many others, including the San Francisco-based startup Hampton Creek, who hope to supercharge food R&D using data analysis. After reinventing Google and Facebook and so many other online operations, the big data movement is now moving into other industries, ranging from medicine and healthcare to the development of new industrial materials.

“We want to get a baseline for safe food ingredients, all the way up and down the food supply chain, including what makes healthy biochemistry,” says James Kaufman, public health manager for IBM Research. “If you can understand what a normal, healthy microbiome looks like, you can figure some things out about how that microbiome will respond to the unknown.”

Essentially, the scientists are hoping to uncover what combination of microbes that makes food ingredients safe, and what factors affect the structure of these microbial communities, including exposure to new pathogenic organisms and other impurities that may not have ever come up yet. It is these unknowns, Kaufman explains, that can eventually make food unsafe—whether that’s the evolution of new organisms, a misguided attempt at innovating food, or even because of an intentional act of terrorism.

And for no particular reason, here are the Beatles, who today in 1969, made their last public performance on the roof of Apple Records in London.

U2 sucks.

 

Gene sequencing refines threatening Cryptosporidium list

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Twenty-six species of Cryptosporidium have been recognised and 18 species declared non-valid in a recent shake-up of the parasite’s taxonomy using DNA sequencing techniques.

crypto.farm.walesCryptosporidium is the second biggest cause of infant diarrhoea and death in developing countries, and is found across 95 nations, including Australia.

The parasite spreads by reproducing in the small intestine of its hosts, generating spore-like oocysts that are shed in the faeces and then consumed in contaminated food or water.

Current testing for Cryptosporidium relies on immunoassays and microscopy, techniques that can identify the presence of oocysts, but not their species.

Since 20 of the 26 species are known to infect humans, this can have important implications for public health.

“Most of [the oocysts] look the same under the microscope, so the only way you can tell them apart is by looking at their DNA,” says Murdoch University Professor Una Ryan, who worked with the US Centre for Disease Control and the US Department of Agriculture on the taxonomy project.

The team used a variety of DNA sequencing and typing techniques to identify gene fragments that are used to characterise each species.

Listeria being sequenced to better understand food poisoning

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Chances are you’ve heard of mapping genes to diagnose rare diseases, predict your risk of cancer and tell your ancestry. But to uncover food poisonings?

The nation’s disease detectives are beginning a program to try to outsmart outbreaks by routinely decoding the DNA of potentially deadly bacteria and viruses.

listeriaThe initial target is Listeria, the third-leading cause of death from food poisoning and bacteria that are especially dangerous to pregnant women. Already, the government credits the technology with helping to solve a listeria outbreak that killed one person in California and sickened seven others in Maryland.

“This really is a new way to find and fight infections,” said Dr. Tom Frieden, director of the Centers for Disease Control and Prevention.

With genome sequencing becoming faster and cheaper, the CDC is armed with $30 million from Congress to broaden its use with a program called advanced molecular detection. The hope is to solve outbreaks faster, foodborne and other types, and maybe prevent infections, too, by better understanding how they spread.

“Frankly, in public health, we have some catching up to do,” said the CDC’s Dr. Christopher Braden, who is helping to lead the work.

As a first step, federal and state officials are rapidly decoding the DNA of all the Listeria infections diagnosed in the U.S. this year, along with samples found in tainted foods or factories.

It’s the first time the technology has been used for routine disease surveillance, looking for people with matching strains who may have gotten sick from the same source.

The Listeria project began as officials were investigating some sick Maryland newborns and their mothers. Genome sequencing showed publix.deli.warningthose cases were linked to a California death, helping investigators determine which foods to focus on, said Dr. Robert Tauxe, CDC’s leading foodborne disease sleuth.

Standard tests prompted recall of the FDA’s suspect, a brand of Hispanic-style cheese. Last month, the government announced that sequencing also confirmed listeria from the recalled cheese matched germs from the patients.

“We expect to be able to match more and more of what we find in people to what we find in food,” as the project grows, Tauxe said.