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Should Humans Eat Meat? [Excerpt]

Food Crisis | Scientific American - Fri, 07/19/2013 - 12:01pm
Editor's Note: The following is an adapted excerpt of Should We Eat Meat?: Evolution and Consequences of Modern Carnivory , by Vaclav Smil. Wiley-Blackwell, May 2013. [More]

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U.S. Farmers View Climate Change as Just Another Weather Challenge

Food Crisis | Scientific American - Tue, 07/16/2013 - 3:01pm
If it isn't torrential downpours , then it's too dry . If there's one thing U.S. farmers can count on, it's bad weather and, perhaps as a result, many of them don't think...

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

Agricultural Research Service | USDA - Thu, 05/16/2013 - 12:38pm


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'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.

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

Agricultural Research Service | USDA - Mon, 05/13/2013 - 8:46am
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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.


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.

Olive Oil Assays May Help Assure Authenticity

Agricultural Research Service | USDA - Thu, 05/09/2013 - 9:40am
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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.


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.

New Yeast Strain Could Lower Costs for Cellulosic Ethanol Production

Agricultural Research Service | USDA - Thu, 05/02/2013 - 9:39am
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ARS researchers have developed a new strain of yeast that could improve ethanol production and costs. Micrograph courtesy of Zonglin Lewis Liu, ARS.


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.

Pig Stress Syndrome Linked to Gene Defect

Agricultural Research Service | USDA - Mon, 04/29/2013 - 9:45am
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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.


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.

Two Approaches for Optimizing Water Productivity

Agricultural Research Service | USDA - Fri, 04/26/2013 - 9:46am
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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.


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

Agricultural Research Service | USDA - Thu, 04/25/2013 - 10:29am

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.

Improved Vitamin B12 Test May Help Young and Old Alike

Agricultural Research Service | USDA - Mon, 04/22/2013 - 9:30am
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A new vitamin B12 assay developed by ARS scientists requires only a tiny drop of blood. Click the image for more information about it.

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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.

Temperament Plays Key Role in Cattle Health

Agricultural Research Service | USDA - Mon, 02/25/2013 - 11:20am
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Even tempered cattle can be more productive and respond better to vaccines, according to research by ARS animal scientist Jeff Carroll (left) and animal physiologist Ron Randel from Texas AgriLife Research and Extension Center. Click the image for more information about it.


Temperament Plays Key Role in Cattle Health By Sandra Avant
February 25, 2013

U.S. Department of Agriculture (USDA) and university scientists have found that cattle temperament influences how animals should be handled, how they perform and how they respond to disease.

The team of researchers looked at stressful events—such as weaning, transportation and vaccination—that beef cattle experience during routine management practices. The researchers examined interrelationships of stress and cattle temperament with transportation, immune challenges and production traits.

Studies were conducted by animal scientist and research leader Jeff Carroll at the Agricultural Research Service (ARS) Livestock Issues Research Unit (LIRU) in Lubbock, Texas; associate research professor Rhonda Vann at Mississippi State University's Brown Loam Branch Experiment Station; animal physiologist Ron Randel at Texas AgriLife Research, The Texas A&M University (TAMU) System, in Overton; and endocrinologist Tom Welsh, Texas A&M AgriLife Research and TAMU Department of Animal Science, in College Station.

Between 24 and 36 calves were used for each study, depending on the trial. An exit velocity system, which measures the rate at which an animal exits a squeeze chute and crosses a certain distance, was used to select for temperament. A pen scoring system was used in conjunction with exit velocity to calculate an overall temperament score for cattle selected as the calmest, the most temperamental or as intermediate.

When challenged with a bacterial toxin, cattle showed dramatic differences in sickness behavior, depending on their temperament. The more temperamental animals failed to show behaviors that allow detection of sick animals, whereas calm animals immediately displayed visual signs and became ill. Studies also revealed that temperamental cattle did not have the same vigorous immunological response to a vaccine as less temperamental cattle in the same herd.

In related research, the team found that the main cause of stress for cattle was not transportation itself, but being handled and loaded into a trailer.

However, transportation duration and conditions were found to have negative effects on intramuscular fat or marbling, which is used for fast sources of energy by cattle being transported. Marbling determines the quality grade of beef. Lower levels of marbling reduce quality grade. Temperamental cattle have less fat stores, indicating that temperament makes a difference in the final quality grade.

ARS is USDA's principal intramural scientific research agency.

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

The Lifetime Journeys of Manure-based Microbes

Agricultural Research Service | USDA - Fri, 02/22/2013 - 9:45am
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ARS scientists are studying the fate of cow manure in feedlots and in fields with an eye to increased food and environmental safety. Click the image for more information about it.

The Lifetime Journeys of Manure-based Microbes By Ann Perry
February 22, 2013

Studies at the U.S. Department of Agriculture (USDA) are shedding some light on the microbes that dwell in cattle manure—what they are, where they thrive, where they struggle, and where they can end up.

This research, which is being conducted by Agricultural Research Service (ARS) scientists at the agency's Agroecosystems Management Research Unit in Lincoln, Neb., supports the USDA priority of ensuring food safety. ARS is USDA's chief intramural scientific research agency.

In one project, ARS microbiologist Lisa Durso used fecal samples from six beef cattle to identify a core set of bovine gastrointestinal bacterial groups common to both beef and dairy cattle. She also observed a number of bacteria in the beef cattle that had not been reported in dairy cows, and identified a diverse assortment of bacteria from the six individual animals, even though all six consumed the same diet and were the same breed, gender and age.

In another study, Durso collaborated with ARS agricultural engineer John Gilley and others to study how livestock diet affected the transport of pathogens in field runoff from manure-amended soils. The scientists added two types of manure to experimental conventional-till and no-till fields at 1-, 2-, or 4-year application rates. The manure had been collected from livestock that had consumed either corn or feed with wet distillers grains.

After a series of simulated rain events, the team collected and analyzed samples of field runoff and determined that neither diet nor tillage management significantly affected the transport of fecal indicator bacteria. But they did note that diet affected the transport of bacteriophages—viruses that invade bacteria—in field runoff.

Gilley also conducted an investigation into how standing wheat residues affected water quality in runoff from fields amended with 1-, 2-, or 4-year application rates of manure. The scientists found that runoff loads of dissolved phosphorus, total phosphorus, nitrates, nitrogen, and total nitrogen were much higher from plots with residue cover. The team also observed that runoff from fields amended with 4-year application rates of manure had significantly higher levels of total phosphorus and dissolved phosphorus than fields amended with 1-year or 2-year manure rates.

Results from these studies have been published in Foodborne Pathogens and Disease, Applied and Environmental Microbiology, and Transactions of the ASABE.

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

New Tool Gets to the Root of the Matter

Agricultural Research Service | USDA - Tue, 02/19/2013 - 12:50pm
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A new tool developed by ARS and Cornell University researchers is giving scientists faster and more detailed looks at three-dimensional root architecture as it develops; here with Azucena rice. Click the image for more information about it.

New Tool Gets to the Root of the Matter By Dennis O'Brien
February 19, 2013

A U.S. Department of Agriculture (USDA) scientist and his colleague at Cornell University have developed a new tool for studying how roots take shape in the soil.

The three-dimensional imaging system and software package, developed by Agricultural Research Service (ARS) scientist Leon V. Kochian in Ithaca, N.Y., and Randy T. Clark of Cornell, allows scientists to collect data on root systems faster than ever before, and to study root architecture in unprecedented detail. Root systems play a critical role in crop health, and like any structure, they have their own architecture.

Called "RootReader3D," the system gives scientists the ability to analyze root structures and growth patterns, to compare one root system with another, and to genetically map and explore traits that give plant roots the capacity to reach into the soil and collect water, phosphorous, and other nutrients.

Kochian is director of the ARS Robert W. Holley Center for Agriculture and Health at Ithaca, and Clark is a doctoral student in his laboratory. ARS is USDA's principal intramural scientific research agency, and this research supports the USDA priority of promoting international food security.

Previous systems allowed scientists to take three-dimensional images of root systems growing in gels, but those systems required up to an hour to collect enough data for a single three-dimensional image. With the RootReader3D system, scientists can produce images of more than 100 root systems a day, providing the information needed to conduct genetic mapping experiments.

To test their system, the researchers grew two very different varieties of rice, Azucena and IR64, in transparent gels and tracked root growth by imaging the plants and their roots for 10 days. The researchers found that they were able to delineate greater detail in the two root systems than ever before. Azucena had deeper roots than its irrigated cousin IR64, and the two root systems were significantly different in their "bushiness," how their root volume was distributed, and the vertical position of the center mass of the root system.

These results were published and featured on the June 2011 cover of Plant Physiology.

The researchers hope the data they collect using RootReader3D will help scientists identify genes controlling important root developmental traits. The goal is to help plant breeders develop varieties of rice and other crops with roots that make them better equipped to handle drought, heat, poor soil quality, and other stress factors in a changing world.

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

New Club Wheat is Tough on Fungi

Agricultural Research Service | USDA - Thu, 02/14/2013 - 10:38am
Read the magazine story to find out more.


A new tool developed by ARS and Cornell University researchers is giving scientists faster and more detailed looks at three-dimensional root architecture as it develops; here with Azucena rice. Click the image for more information about it.

New Tool Gets to the Root of the Matter By Dennis O'Brien
February 19, 2013

A U.S. Department of Agriculture (USDA) scientist and his colleague at Cornell University have developed a new tool for studying how roots take shape in the soil.

The three-dimensional imaging system and software package, developed by Agricultural Research Service (ARS) scientist Leon V. Kochian in Ithaca, N.Y., and Randy T. Clark of Cornell, allows scientists to collect data on root systems faster than ever before, and to study root architecture in unprecedented detail. Root systems play a critical role in crop health, and like any structure, they have their own architecture.

Called "RootReader3D," the system gives scientists the ability to analyze root structures and growth patterns, to compare one root system with another, and to genetically map and explore traits that give plant roots the capacity to reach into the soil and collect water, phosphorous, and other nutrients.

Kochian is director of the ARS Robert W. Holley Center for Agriculture and Health at Ithaca, and Clark is a doctoral student in his laboratory. ARS is USDA's principal intramural scientific research agency, and this research supports the USDA priority of promoting international food security.

Previous systems allowed scientists to take three-dimensional images of root systems growing in gels, but those systems required up to an hour to collect enough data for a single three-dimensional image. With the RootReader3D system, scientists can produce images of more than 100 root systems a day, providing the information needed to conduct genetic mapping experiments.

To test their system, the researchers grew two very different varieties of rice, Azucena and IR64, in transparent gels and tracked root growth by imaging the plants and their roots for 10 days. The researchers found that they were able to delineate greater detail in the two root systems than ever before. Azucena had deeper roots than its irrigated cousin IR64, and the two root systems were significantly different in their "bushiness," how their root volume was distributed, and the vertical position of the center mass of the root system.

These results were published and featured on the June 2011 cover of Plant Physiology.

The researchers hope the data they collect using RootReader3D will help scientists identify genes controlling important root developmental traits. The goal is to help plant breeders develop varieties of rice and other crops with roots that make them better equipped to handle drought, heat, poor soil quality, and other stress factors in a changing world.

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

New Club Wheat is Tough on Fungi

Agricultural Research Service | USDA - Thu, 02/14/2013 - 10:38am
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Cara, a new white winter club wheat developed by ARS researchers, boasts high levels of disease resistance, especially to rusts, plus outstanding flour quality. Click the image for more information about it.


New Club Wheat is Tough on Fungi, But Tasty in Baked Goods By Jan Suszkiw
February 14, 2013

Pacific Northwest wheat growers now have added insurance against outbreaks of yield-robbing fungi, thanks to "Cara," a new, white winter club wheat cultivar developed by U.S. Department of Agriculture (USDA) scientists.

According to Kim Garland-Campbell, a geneticist with USDA's Agricultural Research Service (ARS) in Pullman, Wash., "Cara" is the product of a cooperative wheat breeding effort to combine high grain yields and flour quality with resistance to multiple fungal diseases. Of particular concern is stripe rust, a disease caused by the fungus Puccinia striiformis, which has inflicted yield losses of up to 40 percent in Washington and other Pacific Northwest states.

In fact, the release and subsequent sale of "Cara" in 2009 coincided with a stripe-rust epidemic that had overcome the resistance present in cultivars of club wheat that had been planted at the time, notes Garland-Campbell, who works at the ARS Wheat Genetics, Quality, Physiology and Disease Research Unit in Pullman. ARS is USDA's principal intramural scientific research agency.

Based on 60 yield trials conducted in plots where stripe rust was present in Oregon and Washington, "Cara" outperformed most other commercial cultivars, with two-year averages ranging from three to 18 percent better than the other wheats used in the evaluations.

"Cara," which was derived from crossing three diverse wheat germplasm sources, is primarily adapted to the Palouse and other rust-prone areas of the Pacific Northwest that receive 15 to 24 inches of precipitation annually. In addition to stripe rust, "Cara" carries genes for fungal disease resistance to straw breaker foot rot and powdery mildew.

"Cara" also scored high on standard industry evaluations for milling, baking and other end-use properties. For example, like other club wheats, flour milled from "Cara" has low viscosity and protein content, coupled with high "break flour" and "weak gluten," characteristics ideal for making air-leavened cakes, sugar snap cookies, biscuits, pastries and other soft, fluffy-textured baked goods.

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

Studying Bed Bug Actions for New Management Tactics

Agricultural Research Service | USDA - Mon, 02/11/2013 - 11:08am
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ARS scientists are identifying new compounds to control bed bugs. Click the image for more information about it.

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Studying Bed Bug Actions for New Management Tactics By Sandra Avant
February 11, 2013

Learning more about the behavior of bed bugs is one approach being used by U.S. Department of Agriculture (USDA) scientists to identify compounds to help control these pests.

The resurgence of bed bugs over the last decade has caused problems in major U.S. cities where they infest homes, apartments, hotels, shelters and even places of work. The small, blood-feeding insects are not known to transmit diseases, but they can cause severe reactions in people who are allergic to them. Bed bugs usually go unnoticed until their numbers increase significantly, and getting rid of them can be costly.

Entomologist Mark Feldlaufer and chemist Kamlesh Chauhan at the Agricultural Research Service (ARS) Henry A. Wallace Beltsville Agricultural Research Center (BARC) in Beltsville, Md., have identified two new alarm pheromones—4-oxo-hexenal and 4-oxo-octenal—in immature bed bugs. The releasing of alarm pheromones, which are defensive compounds, causes aggregated bed bugs to scatter.

Scientists collected cast skins that retain chemicals from the bed bug's scent glands and then used gas chromatography and mass spectrometry technology to analyze and identify compounds. Swedish researchers subsequently identified the same compounds from a related species, the tropical bed bug, demonstrating that the compounds are biologically active.

This indicates that alarm pheromones may have implications in bed bug management, according to Feldlaufer, who works at BARC's Invasive Insect Biocontrol and Behavior Laboratory. By causing insects to disperse, the likelihood of bed bugs coming into contact with a control agent increases.

ARS and University of Nevada-Reno scientists also identified 17 compounds in the bed bug's outer protective layer of skin, a discovery they believe may play an important role in bed bug aggregation behavior.

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

ARS is USDA's principal intramural scientific research agency.

Virus Helps Scientists Identify "Who's Who" Among Two Veggie Enemies

Agricultural Research Service | USDA - Fri, 02/08/2013 - 9:30am
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ARS plant pathologist Carolee Bull is sorting out "who's who" between two easily confused bacteria that attack and ruin some of the same crops, such as broccoli, cabbage, and cauliflower. Click the image for more information about it.


Virus Helps Scientists Identify "Who's Who" Among Two Veggie Enemies By Marcia Wood
February 8, 2013

Natural warfare between a virus and a Pseudomonas bacterium is helping U.S. Department of Agriculture (USDA) scientists continue to learn about the bacterium's ability to kill arugula, broccoli, and several other cruciferous vegetables.

USDA plant pathologist Carolee T. Bull and her colleagues use the virus, known as PBSPCA1, as the basis for a lab test that helps quickly identify Pseudomonas cannabina pv. (pathovar) alisalensis. Bull works in the Agricultural Research Service (ARS) Crop Improvement and Protection Research Unit in Salinas, Calif. ARS is USDA's chief intramural scientific research agency.

In ongoing research that dates back to 1998, Bull and her co-investigators have detected and identified this pseudomonad; clarified its taxonomy, or "family tree"; and determined that it is the culprit behind a costly disease called bacterial blight of crucifers. The blight causes water-soaked spots to appear on plant leaves. Eventually, the spots coalesce and turn brown, giving the leaves an unattractive, burnt appearance that makes the vegetable unmarketable.

Early on, the scientists' field, greenhouse, and laboratory studies indicated that the crucifer blight bacterium could be easily confused with a close cousin, P. syringae pv. maculicola, which causes pepper spot disease. The two different pseudomonads kill some of the same vegetable crops, and several standard lab tests can't reliably tell which bacterium is which.

Bull and her colleagues chose the PBSPCA1 virus as the basis for a lab assay that reliably sorts out "who's who" among the two confusing bacteria. Because it can kill the crucifer blight bacterium, but not the pepper spot pseudomonad, the virus can be used to differentiate one from the other.

Bull and her coworkers begin using PBSPCA1 for preliminary diagnoses in 2002, and have continued to improve the assay.

The virus and both of the bacteria are harmless to humans.

The bacterium that the team was to later identify as the cause of crucifer blight began showing up in vegetable fields in California's Salinas Valley in 1995. Bull began investigating the mysterious microbe three years later. Within a few years, her team had resolved much of the confusion surrounding it.

Today, Bull and her co-investigators continue to help growers and plant pathologists in the United States and abroad identify the crucifer blight bacterium. Positive identification matters, especially when growers are deciding what to plant. For example, the Salinas studies have shown that broccoli, cabbage, and cauliflower are vulnerable to both the crucifer blight and the pepper spot bacteria, while some other crops, such as lettuce, are not.

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

Understanding Microbes Blowing in the Wind

Agricultural Research Service | USDA - Wed, 02/06/2013 - 8:31am
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ARS research is shedding new light on hitchhiking by microbes in soils carried off by strong winds, which could lead to better ways to minimize soil damage from wind erosion. Click the image for more information about it.


Understanding Microbes Blowing in the Wind By Dennis O'Brien
February 6, 2013

With help from a wind tunnel and the latest DNA technology, U.S. Department of Agriculture (USDA) scientists are shedding light on the travel patterns of microbes in soils carried off by strong winds. The work has implications for soil health and could lead to management practices that minimize the damage to soils caused by wind erosion.

Wind erosion is an emerging issue in soil conservation efforts. Agricultural Research Service (ARS) scientists have been studying wind-eroded soils since the 1930s, but few studies have focused on the effects of wind on the bacteria, fungi, and protozoa in the soil. ARS is USDA's chief intramural scientific research agency.

Researchers see an increasing need to focus on pathogens and agriculturally important bacteria carried in dust. ARS soil scientist Veronica Acosta-Martinez, with the agency's Wind Erosion and Water Conservation Unit in Lubbock, Texas, focused on bacterial populations that could be classified by DNA sequencing. She worked with Terrence Gardner, a visiting scientist from Alabama A&M University.

Researchers collected airborne dust and samples of a type of organic soil susceptible to wind erosion from fields where potatoes, beets and onions had grown a few years earlier and exposed them to windy conditions using a portable wind tunnel. They characterized the bacteria they found in both the "source soils" and the wind-eroded sediments, focusing on types of bacteria associated with coarse particles and on the types associated with fine dust particles.

They classified the bacteria found in each type of soil and wind-eroded sediment using pyrosequencing, a process that allowed them to identify up to 100 times more DNA in each sample than they would have detected with traditional methods. The study results, published online in the Journal of Environmental Quality, showed that certain types of bacteria, known as Bacteroidetes, were more predominant in the fine dust. Other types, known as Proteobacteria, were more predominant in coarse sediments.

Studies have shown that Bacteroidetes resist desiccation and thus can survive in extreme conditions when carried long distances. The fact that Proteobacteria were associated with coarse eroded sediments, which travel shorter distances, may explain how soils can retain important qualities despite damaging winds. Proteobacteria play an important role in carbon and nitrogen cycling, and their fate in dust storms will be the focus of future research, according to Acosta-Martinez.

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

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