FDA SCIENTIST WORKING TO CREATE DNA BAR-CODES TO IDENTIFY FISH SPECIES

FROM:  U.S. FOOD AND DRUG ADMINISTRATION 

Have you sometimes wondered if that "wild caught" salmon actually came from an aqua farm? Or if the "U.S. catfish" in the display case might have been born and raised in Vietnam?

Is that "red snapper" actually red snapper and worth the premium price?

Scientists at the Food and Drug Administration (FDA) are able to answer those questions through a project that creates DNA barcodes to identify individual fish species. The massive project is part of an effort aimed at solving the problem of species substitution.

Species substitution can result in cheap fish being labeled as pricy ones, but mislabeling can also threaten public health. For example, in 2007, a prohibited and highly toxic variety of puffer fish, also known as fugu or blowfish, was smuggled into the U.S. in boxes labeled as "headless monkfish." This deception resulted in illnesses in multiple states.

A series of cutting-edge tests must be conducted to create the barcodes, which look much like the lines of different thicknesses on Universal Product Code (UPC) labels used to identify and scan manufactured products. However, unlike the barcodes you see on packages in the supermarket, the barcodes that identify different fish species will not be attached to the fish.

Instead, once a fish species is identified through DNA testing and other high-tech techniques in FDA labs, the newly created barcode unique to that species is entered into a database, which could be thought of as a library or catalogue of commercial fish species.

When encountering a fish or fish product (fillets, fish sticks, sushi, etc.) whose species is unknown, inspectors with the equipment and know-how can create a barcode for that fish and compare it against FDA's database to seek a known match.

The agency has trained more than 20 FDA analysts around the country to use that procedure in many of its regional field laboratories and are now performing the analysis on a regular basis.

"GEL MICRODROPLETS" HELP SCIENTISTS EXAMINE MULTI-ORGANISM GENOME

Los Alamos National Laboratory.  Credit:  U.S. Department Of Energy.

FROM: LOS ALAMOS NATIONAL LABORATORY
New Culturing Tool Reveals a Full Genome From Single Cells
Gel microdroplet culturing reveals intraspecies genomic diversity within the human microbiome

LOS ALAMOS, N.M., March 15, 2013—A new technique for genetic analysis, "gel microdroplets," helps scientists generate complete genomes from a single cell, thus opening the door to understanding the complex interrelationships of bacteria, viruses and eukaryotes that form "microbiome" communities in soil, in humans, and elsewhere in the natural world.

Microbes live in complex communities that function together as a whole in order to survive and thrive in their natural environments. Microbes survive almost everywhere, and they make up the majority of the living organisms on Earth and contribute to all aspects of human life, such as health, energy and even climate change.

Most types of bacteria cannot grow in the laboratory as a pure, isolated culture, however, due to complicated interactions that support their growth. This makes research challenging, as identifying a single organism’s genetic profile fails to take into account the interrelationships that are extremely important to understanding the microbe’s roles and capabilities in its specific location.

Scientists from Los Alamos National Laboratory and the J. Craig Venter Institute in San Diego have made a breakthrough that gives researchers the bigger picture of the multi-organism genome, using the complete genome from a single cell.

The technique used over the past few years, metagenomics, avoids the need for culturing to produce mixed genetic info for the whole community. However, many of the biological questions, such as how the mixed bacterial or viral community members interact with each other, cannot be answered without genomic information about the various individual species in the community. The Los Alamos group, led by Cliff Han, Michael Fitzsimons (formerly of LANL), and Armand Dichosa, has been developing technologies to fulfill the need.

The technology has the potential to generate complete genomes from single cells of traditionally uncultured species. Using gel microdroplets (GMD), the science team created dozens to hundreds of identical cells from single cells, while keeping such cells separated from the rest of community and maintaining the cells’ ability to communicate with other community members.

From mixed bacterial communities inhabiting the human mouth and digestive gut, researchers captured single cells within microscopic GMD and incubated them in a defined growth medium.

The characteristic pores and channels of the agarose-based GMD allow for the movement of nutrients, chemical signals and metabolic wastes to and from the living cell as if it were in its natural environment. The captured single cells multiply to microcolonies of hundreds, thereby producing sufficient quantities of identical genomic templates. Ultimately, this allows for the completion of several genomes from the same bacterial species.

By completing and comparing the genomic profiles of these species, researchers found significant variations within the genomes of the same orally-located species, with few differences found from within gut-resident species. Such findings show how significantly active (or inactive) bacteria are in recombining specific segments of DNA with each other and raise questions as to how we identify a "species" if something as important as its neighborhood interactions can change its genetic profile.

With promising results of this human microbiome study, the team has begun to use GMD to culture bacteria and archaea in their native environments, such as wetland and water environments. Researchers want to capture known, rare and elusive species that cannot grow in laboratory settings, and also to provide completed genomes of these novel species that may, again, offer insight into the vital contributions of bacteria and archaea in local ecology and global climate change.

"We have demonstrated a novel approach for fully sequencing genomes of microorganisms found in complex communities," said Dichosa.

Previously, complete community genomes had been an unattainable goal because neither of the two competing technologies, shotgun metagenomics or single-cell sequencing, can recover a nearly complete genome from a single organism in a diverse sample. "We believe using GMDs to sequence complete genomes from environmental samples shows great promise and will allow for the first time a high throughput technology for exploring community pan-genomics," said Han.

Los Alamos National Laboratory, a multidisciplinary research institution engaged in strategic science on behalf of national security, is operated by Los Alamos National Security, LLC, a team composed of Bechtel National, the University of California, The Babcock & Wilcox Company, and URS for the Department of Energy’s National Nuclear Security Administration.

Los Alamos enhances national security by ensuring the safety and reliability of the U.S. nuclear stockpile, developing technologies to reduce threats from weapons of mass destruction, and solving problems related to energy, environment, infrastructure, health, and global security concerns.

THE THINGS THAT LIVE WHERE NO THINGS SHOULD

Hot spring in Yellowstone.  Credit:  Wikimeidia Commons.

FROM: NATIONAL SCIENCE FOUNDATION
How to Thrive in Battery Acid and Among Toxic Metals
In the movie Alien, the title character is an extraterrestrial creature that can survive brutal heat and resist the effects of toxins.

In real life, organisms with similar traits exist, such as the "extremophile" red alga Galdieria sulphuraria.

In hot springs in Yellowstone National Park, Galdieria uses energy from the sun to produce sugars through photosynthesis.

In the darkness of old mineshafts in drainage as caustic as battery acid, it feeds on bacteria and survives high concentrations of arsenic and heavy metals.

How has a one-celled alga acquired such flexibility and resilience?

To answer this question, an international research team led by Gerald Schoenknecht of Oklahoma State University and Andreas Weber and Martin Lercher of Heinrich-Heine-Universitat (Heinrich-Heine University) in Dusseldorf, Germany, decoded genetic information in Galdieria.

They are three of 18 co-authors of a paper on the findings published in this week's issue of the journal Science.

The scientists made an unexpected discovery: Galdieria's genome shows clear signs of borrowing genes from its neighbors.

Many genes that contribute to Galdieria's adaptations were not inherited from its ancestor red algae, but were acquired from bacteria or archaebacteria.

This "horizontal gene transfer" is typical for the evolution of bacteria, researchers say.

However, Galdieria is the first known organism with a nucleus (called a eukaryote) that has adapted to extreme environments based on horizontal gene transfer.

"The age of comparative genome sequencing began only slightly more than a decade ago, and revealed a new mechanism of evolution--horizontal gene transfer--that would not have been discovered any other way," says Matt Kane, program director in the National Science Foundation's (NSF) Division of Environmental Biology, which funded the research.

"This finding extends our understanding of the role that this mechanism plays in evolution to eukaryotic microorganisms."

Galdieria's heat tolerance seems to come from genes that exist in hundreds of copies in its genome, all descending from a single gene the alga copied millions of years ago from an archaebacterium.

"The results give us new insights into evolution," Schoenknecht says. "Before this, there was not much indication that eukaryotes acquire genes from bacteria."

The alga owes its ability to survive the toxic effects of such elements as mercury and arsenic to transport proteins and enzymes that originated in genes it swiped from bacteria.

It also copied genes offering tolerance to high salt concentrations, and an ability to make use of a wide variety of food sources. The genes were copied from bacteria that live in the same extreme environment as Galdieria.

"Why reinvent the wheel if you can copy it from your neighbor?" asks Lercher.

"It's usually assumed that organisms with a nucleus cannot copy genes from different species--that's why eukaryotes depend on sex to recombine their genomes.

"How has Galdieria managed to overcome this limitation? It's an exciting question."

What Galdieria did is "a dream come true for biotechnology," says Weber.

"Galdieria has acquired genes with interesting properties from different organisms, integrated them into a functional network and developed unique properties and adaptations."

In the future, genetic engineering may allow other algae to make use of the proteins that offer stress tolerance to Galdieria.

Such a development would be relevant to biofuel production, says Schoenknecht, as oil-producing algae don't yet have the ability to withstand the same extreme conditions as Galdieria.

-NSF-