ARS scientists have developed the basis for a faster, more accurate test for all strains of the foot-and-mouth disease virus, which causes a highly contagious and economically devastating disease in cattle and other cloven-hoofed animals. Click the image for more information about it.

USDA scientists discover how foot-and-mouth disease virus begins infection in cattle   Technologies improve FMD detection and control

USDA'S Novel Cell Line Identifies All Foot-and-Mouth Virus Serotypes

By Sandra Avant
May 16, 2013

WASHINGTON—U.S. Department of Agriculture (USDA) scientists have developed a new cell line that rapidly and accurately detects foot-and-mouth disease virus (FMDV), which causes a highly contagious and economically devastating disease in cattle and other cloven-hoofed animals.

The cell line was created by Agricultural Research Service (ARS) scientists at the Plum Island Animal Disease Center, Orient Point, N.Y. ARS is USDA's chief intramural scientific research agency. The research, published online in the Journal of Clinical Microbiology, supports the USDA priority of promoting international food security.

"This important breakthrough is an example of how ARS scientists are working to improve agricultural productivity in the face of increasing demand for food," said ARS Administrator Edward B. Knipling. "This new cell line will help in the global effort to control a disease that can cause significant economic losses."

"The new cells detect the FMD virus in field samples that come directly from naturally infected animals faster than existing cell lines currently used for diagnostics," said Luis Rodriguez, research leader at Plum Island's Foreign Animal Disease Research Unit (FADRU). "The new cells are the first permanent cell line capable of identifying all seven serotypes of FMD virus."

The United States has not had an FMD outbreak in more than 80 years. However, the disease is still a serious threat and is considered to be the most economically devastating livestock disease worldwide. Outbreaks in other countries have resulted in the slaughter of millions of animals to prevent the disease from spreading.

Being able to rapidly detect the virus during outbreaks would allow researchers to quickly develop the appropriate vaccine among the seven serotypes and dozens of subtypes, thereby saving valuable time and millions of dollars.

The novel cell line stems from earlier research where FADRU scientist Hernando Duque isolated a primary cell receptor, called alpha v beta 6, which allows FMD virus to attach to and enter the animal's cells and replicate, Rodriguez said. Molecular biologist Michael LaRocco was a member of the team, led by former ARS scientist Barry Baxt, which created the new cell line.

The approach used to make the new cell line consisted of cloning the FMD receptor genes from bovine (cattle) tissue and incorporating them into a cell line previously established at Plum Island, and then comparing them to other cells currently used in diagnosing and studying FMD.

FADRU molecular biologist Peter Krug designed tests to validate the cell line by comparing it to other cell types using virus samples from animal tissues. The new cell line proved to be faster and more reliable than all current diagnostic cell lines in detecting virus in FMD-infected cattle and pig tissue samples from numerous countries.

"Other cell types currently used to diagnose FMD don't survive long and have to be obtained directly from animals as primary cell cultures, causing variation from one batch to the other," Rodriguez said. "This new cell line can be continually grown in culture, maintains susceptibility to FMDV much longer, and doesn't require getting new cells from animals repeatedly."

Scientists have applied for a patent on the new cell line and are making plans to distribute it to diagnostic laboratories in the United States and other countries.

Read the magazine story to find out more.

Baking farm-raised Atlantic salmon maintains its healthy levels of omega-3 fatty acids as long as the fish is not over cooked, according to ARS research. Click the image for more information about it.

Keeping in-demand smoked salmon safe to eat   Got fish? Nutrition studies explore health benefits   Franklin fish lab opens with a splash

Farm-raised Salmon Retains Healthy Omega-3s When Baked

By Rosalie Marion Bliss
May 13, 2013

U.S. producers of farm-raised salmon are working hard to help fill today's growing demand for seafood. Now U.S. Department of Agriculture (USDA) nutritionist Susan Raatz, physiologist Matthew Picklo, and cooperators have found that farm-raised Atlantic salmon maintains its healthy levels of omega-3 fatty acids when baked.

Two omega-3 fatty acids, EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid), are abundant in oily fish such as salmon, tuna, mackerel, and herring. Some data have shown that consuming 250 milligrams daily of EPA and DHA—the amount found in a 3-ounce salmon fillet—is associated with reduced risk of heart-disease.

Raatz and Picklo are with the Agricultural Research Service (ARS) Grand Forks Human Nutrition Research Center in Grand Forks, N.D. ARS is USDA's chief intramural scientific research agency.

While eating seafood rich in omega-3 fatty acids is known to reduce risk of heart disease, it has not been known whether baking causes loss of omega-3s in farm-raised Atlantic salmon. The team also examined the extent to which baking Atlantic salmon alters healthful fatty acids through oxidation that leaves unhealthy compounds, such as toxic omega-3 oxidation byproducts.

The researchers demonstrated that baking salmon to the proper temperature does not decrease its content of beneficial omega-3 fatty acids. They found that baking actually decreases the presence of fatty acid oxidation byproducts. Preparing the fish based on restaurant and safety guidelines—to a tender-but-safe 145 degrees Fahrenheit rather than overcooking—was a key factor, according to authors.

The research was published in the Journal of Agricultural and Food Chemistry.

Read more about this research in the May/June 2013 issue of Agricultural Research magazine.

Read the magazine story to find out more.

Research from ARS, including tests to assure authenticity of olive oil, may help strengthen America's olive oil industry. Click the image for more information about it.

Molecular biology provides clues to health benefits of olive oil   Olive fruit fly damage pinpointed by x-ray vision   Olives may be rescued by helpful wasp

Olive Oil Assays May Help Assure Authenticity

By Marcia Wood
May 9, 2013

When the label on a bottle of olive oil misrepresents what's inside, shoppers may not be getting what they thought they paid for. Mislabeling is also of concern to chefs, retailers, and America's olive growers and olive oil processors—especially those newly entering the domestic olive oil market. They face tough international competition: An estimated 98 percent of all olive oil consumed in the United States is imported.

Help may be on the way in the form of laboratory assays developed by U.S. Department of Agriculture (USDA) researchers and their colleagues. These tests add to the array of options for quality-control analyses of olive oil.

Agricultural Research Service (ARS) chemist Talwinder Kahlon's assay relies on PCR (polymerase chain reaction) technology to compare olive DNA to that of canola and sunflower plants. Oil from these plants is sometimes mixed with olive oil, but not disclosed on the label. ARS is the principal intramural scientific research agency of USDA.

Kahlon's test focuses on key regions of two genes, matK and psbA-trnH, which occur widely throughout nature, including in olive, canola, and sunflower. The DNA sequence of specific regions of these two genes, Kahlon notes, provides a reliable basis of comparison, and can be used to detect the presence of the non-olive oils at concentrations of 5 percent or higher.

Though using PCR technology to detect specific plant DNA in olive oil isn't new, the team's approach offers several improvements. For instance, the olive, canola, and sunflower "DNA barcodes" that the scientists developed—to serve as the basis for comparing these plants' DNA—are based on not just a single olive tree or sunflower or canola plant. Instead, each barcode is a broadly representative composite, known as "consensus DNA."

Olive oil is made up of triglycerides, which are molecules composed of fatty acids. These fatty acids are the focus of the approach that ARS chemist Jiann-Tsyh (Ken) Lin developed. The assay is based on ESI-MS (electrospray ionization-mass spectrometry) and enables scientists to glean details about variations in specific triglycerides of interest, referred to as regioisomers. From that, users can develop ratios of regioisomers that can be used to determine whether the sample contains undisclosed oils.

The value of ESI-MS for analyzing plant fatty acids has been recognized since at least 1994. But Lin's ESI-MS protocol helps make this application simpler.

Lin developed the protocol for his research with castor, a plant that produces an inedible, top-quality industrial oil. About six years ago, he chose olive oil as a model for testing his assay.

Both scientists work at ARS' Western Regional Research Center in Albany, Calif.

Read more about this research in the May/June 2013 issue of Agricultural Research magazine.

Read the magazine story to find out more.

ARS researchers have developed a new strain of yeast that could improve ethanol production and costs. Micrograph courtesy of Zonglin Lewis Liu, ARS.

USDA scientists use commercial enzyme to improve grain ethanol production   Making tomorrow's bioenergy yeasts strong   A quick way to grade grasses for ethanol yields

New Yeast Strain Could Lower Costs for Cellulosic Ethanol Production

By Ann Perry
May 2, 2013

A new strain of yeast that could help streamline cellulosic ethanol costs and production has been developed by U.S. Department of Agriculture (USDA) researchers. This work, which supports the USDA priority of developing new sources of bioenergy, was conducted by Agricultural Research Service (ARS) scientists at the agency's National Center for Agricultural Utilization Research in Peoria, Ill. ARS is USDA's chief intramural scientific research agency.

ARS molecular biologist Zonglin Lewis Liu and his colleagues determined that this yeast strain can break down and ferment the sugars in corn cobs left behind after the compound xylose—which is sometimes used for industrial activities—has been extracted. The new strain of yeast, Clavispora NRRL Y-50464 (Y-50464), can tolerate cob-derived compounds that interfere with yeast growth and fermentation rates.

It is able to grow rapidly at 98.6 °F, so it thrives at the higher temperatures needed to optimize simultaneous saccharification and fermentation (SSF) rates. SSF is a one-step process in cellulosic ethanol production that combines releasing and fermenting feedstock sugars.

The researchers compared how quickly Y-50464 and another yeast strain could release and ferment the sugar in corn cob residues after the xylose had been extracted. The new yeast strain was able to start consuming the residue at a steady rate 24 hours after the test began. The comparison yeast didn't grow at all under the same conditions.

The scientists added the enzymes cellulase and beta-glucosidase, which are often used to break down residues and extract sugars, and observed that Y-50464 reached its peak ethanol production rate of 25.7 grams per liter 5 days after the experiment began. But the yeast actually produced more ethanol, 26.6 grams per liter in 5 days, without the addition of beta-glucosidase.

Testing by Liu's group confirmed that Y-50464 contains beta-glucosidase, which means that using this yeast for cellulosic ethanol production would eliminate the need to include the cost of an additional enzyme to the process. Liu will continue exploring options for combining the desirable characteristics of Y-50464 with additional enzymes to further improve bioprocessing for advanced biofuels production.

Results from this work have been published in Bioresource Technology and Bioenergy Research.

Read more about this work in the May/June 2013 issue of Agricultural Research magazine.

Read the magazine story to find out more.

ARS researchers have found that a newly identified pig stress syndrome is caused by a genetic mutation. Click the image for more information about it.

Scientists use new method to help reduce pig mortality   Test identifies Red Angus carriers of bone disease   Tryptophan-enriched diet reduces pig aggression

Pig Stress Syndrome Linked to Gene Defect

By Sandra Avant
April 29, 2013

A defect in a gene called dystrophin is the cause of a newly discovered stress syndrome in pigs, U.S. Department of Agriculture (USDA) scientists have found.

Stress-related issues like transportation cost the U.S. swine industry an estimated $50 million a year. Producers as well as researchers have long suspected that undetected stress-related syndromes are affecting the health and well-being of pigs.

This notion was confirmed when scientists at the Agricultural Research Service (ARS) Roman L. Hruska U.S. Meat Animal Research Center (USMARC) in Clay Center, Neb., discovered a stress syndrome in two 3-month-old male siblings that died after being transported from one facility to another. The novel syndrome is different than the classical porcine stress syndrome, which was eliminated from U.S. swine herds years ago.

Molecular biologist Dan Nonneman and his colleagues in the USMARC Reproduction Research Unit mapped the stress disorder to a genetic mutation in dystrophin. Mutations in dystrophin, which cause DMD—Duchenne muscular dystrophy—are associated with muscle weakness that can lead to death.

To map the disease, scientists re-mated the original parents of the affected siblings to produce additional litters. The 250 offspring, which included 49 affected piglets, were genotyped, and one chromosomal region containing the dystrophin gene was associated with the syndrome.

Piglets affected by the syndrome had an abnormal heart rate when treated with an anesthesia and monitored. The heart rate of unaffected pigs undergoing the same treatments remained steady. Animals with the stress condition had half as much dystrophin protein as their unaffected siblings. Pigs suspected of having the syndrome also had three times as much creatine phosphokinase, an enzyme used to monitor heart and muscle diseases.

The gene is located on the X chromosome, and the syndrome is found primarily in males that inherit the affected X chromosome from their mother. Animals seem more susceptible at two months of age, a time when piglets are transported from nursery to grower facilities.

Read more about this research in the April 2013 issue of Agricultural Research magazine.

ARS is USDA's chief intramural scientific research agency, and this research supports USDA's priority of promoting international food security.

Read the magazine story to find out more.

ARS researchers are helping farmers make the most of scarce irrigation water by connecting a variety of sensors (held here by ARS personnel) to variable rate irrigation systems so that crops only receive as much water as they actually need. Click the image for more information about it.

USDA irrigation research: Good to the last drop   A new tool for mapping water use and drought   Developing strategies in a desert watershed that sustain regional water supplies

Two Approaches for Optimizing Water Productivity

By Dennis O'Brien
April 26, 2013

U.S. Department of Agriculture (USDA) researchers in Bushland, Texas, are helping farmers make the most of their water supplies in a region where they depend on the Ogallala Aquifer, a massive underground reservoir under constant threat of overuse.

Steve Evett, Susan O'Shaughnessy and their colleagues in the Agricultural Research Service (ARS) are developing soil, water and plant stress sensors and automated irrigation systems designed to irrigate fields only when absolutely necessary. ARS is USDA's principal intramural scientific research agency.

The researchers are working on two complementary approaches. One system applies water based on crop water stress levels detected by wireless sensors mounted on the pipelines of above-ground commercial irrigation systems. The sensors determine variable water needs as the irrigation system moves across a field.

In the other approach, sensors in the soil trigger irrigation based on soil water content. That technology is designed for urban sites and is being adapted so that it will work in agriculture.

The effectiveness of the aboveground system has been verified in numerous studies. In one, the researchers cultivated early- and late-maturing sorghum for two years and used 16 prototype wireless sensors on a center-pivot irrigation system to monitor crop canopy temperatures as the system moved across the fields. Instruments recorded weather data as the system moved. The researchers compared its effectiveness with a system in which irrigation was applied based on readings taken with a neutron probe, an accurate research tool that growers avoid because of cost and regulatory issues.

The results, published in Agricultural Water Management, showed the automated system was as effective as the manual method, producing similar grain yields and water-use efficiency levels. For the study, the sensor network was mounted on a six-span center pivot, but the technology could be adapted to other types of irrigation systems.

To develop the subsurface soil sensors, Evett and his colleagues established a cooperative research and development agreement with Acclima, Inc., of Meridian, Idaho, which makes sensor-based systems for irrigating lawns, shrubs and ornamentals. For those uses, Acclima's systems only need to monitor water content to depths of about 4 to 6 inches, but sensors used in agriculture would need to take deeper readings.

To that end, Evett and his Acclima partners are developing new technology that uses hollow, plastic tubes that can be drilled deeper into the soil. The tubes are divided into segments that attach to each other for drilling to any desired depth. Prototype designs tested in water and test fluids, and in clay and loam soils, have shown that the approach is feasible. ARS and Acclima have filed for a patent on the technology.

Read more about the research in the April 2013 issue of Agricultural Research magazine.

New Issue of Healthy Animals Now Online

By Sandra Avant
April 25, 2013

The Agricultural Research Service (ARS) today posted a new issue of Healthy Animals. This semi-annual online newsletter compiles ARS news and expert resources on the health and well-being of agricultural livestock, poultry and fish.

Twice a year, one article in Healthy Animals focuses on a particular element of ARS animal research. The current issue focuses on research to combat stable flies, the most damaging arthropod pest of U.S. cattle.

Other research highlighted in this issue includes:

• Sheep Make Impact on Soil: Growers are learning how grazing sheep on uncultivated fields affects soil quality.
• Citrus Not So Sweet for Ticks: Chemicals found in citrus and millipedes repel ticks.
• Tales of Cattle Temperament: Depending on their temperament, cattle respond differently to stressful events as well as disease.

Professionals interested in animal health issues might want to bookmark the site as a resource for locating animal health experts. An index lists ARS research locations covering 70 animal health topics. These range from specific diseases, such as Lyme disease, to broad subjects such as nutrition or parasites.

The site also provides complete contact information for the 25 ARS research groups that conduct studies aimed at protecting and improving farm animal health.

To receive an e-mail alert about each issue's online posting, contact Sandra Avant, ARS Information Staff, or sign up online.

ARS is the principal intramural scientific research agency of the U.S. Department of Agriculture.

Read the magazine story to find out more.

A new vitamin B12 assay developed by ARS scientists requires only a tiny drop of blood. Click the image for more information about it.

Listen to podcast.

Researchers analyze metabolites in blood   Potential Indicators of type 2 diabetes investigated   Luteolin stars in study of healthful plant compounds

Improved Vitamin B12 Test May Help Young and Old Alike

By Marcia Wood
April 22, 2013

In the United States, the very young and the elderly are among the groups at risk of becoming deficient in vitamin B12, an essential nutrient. Now, a team of U.S. Department of Agriculture (USDA) scientists led by research chemist John W. Newman has developed and tested an improved method for measuring an indicator of the body's stores of B12 in blood.

Importantly, the blood sample can be very small in volume. That's an advantage in both medical and research situations. Blood samples that are taken from newborns and infants—for health exams at a hospital, or perhaps for use by medical or nutrition researchers—are typically very small. In addition, a small amount of sample is often the norm in complex, large-scale studies in which blood samples from volunteers have to be allocated among many researchers, each of whom may need it for a different research purpose.

Newman and his colleagues have shown that a specimen of only 25 microliters of blood plasma or serum—the equivalent of about one-half of a drop of water—can be analyzed with speed, accuracy, reliability and precision using an analytical technology called UPLC-ESI-MS/MS (ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry).

If the assay is performed using robotics, the sample could perhaps be as small as 5 microliters, according to Newman.

His team built upon earlier work in which scientists elsewhere used an older technology to measure the same indicator compound that Newman's group selected, namely, MMA (methylmalonic acid). MMA can build up in the bloodstream if there isn't enough vitamin B12 in the body.

The 25-microliter sample size needed for the new MMA assay represents a 4- to 10-fold reduction in the volume of specimen required for other MMA-based B12 tests. Samples take only about four minutes to process, according to Newman, who works at the Agricultural Research Service (ARS) Western Human Nutrition Research Center in Davis, Calif. ARS is the chief intramural scientific research agency of USDA, and the B12 research supports the USDA priority of improving children's health and nutrition.

In developing the assay, Newman collaborated with Lindsay H. Allen, director of the ARS research center, and with three other ARS colleagues: chemist Theresa L. Pedersen, physical scientist William R. Keyes, and nutritionist Setareh Shahab-Ferdows. The team documented the research in a peer-reviewed article published in 2011 in the Journal of Chromatography B.

Read more about this research in the April 2013 issue of Agricultural Research magazine.