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United States Department of Agriculture

Agricultural Research Service

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ARS Annual Performance Report for FY 2005
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1 - Introduction
2 - Table of Contents
3 - Goals 1 and 2
4 - Goal 3
5 - Goal 4
6 - Goal 5
7 - Goal 6
Goal 3



Analysis of Results:  This goal is related to food safety and the security of the U.S. agricultural production system (crop and livestock protection).  Under Goal 3, 17 Indicators (in Italics) are aligned under 8 Performance Measures.  As the National Programs evolve, the Agency will report more accomplishments achieved by collaborative research at multiple locations involving more than one scientific discipline.  Thus, we anticipate reporting fewer accomplishments, but accomplishments that are broader in scope that make greater contributions to American agriculture.  While it is not possible to report research accomplishments numerically, the progress projected in these Indicators was completed or substantially completed during FY 2005.  Forty-one significant accomplishments are reported below.


OBJECTIVE 3.1:  Provide Science-Based Knowledge on the Safe Production, Storage, Processing, and Handling of Plant and Animal Products and on the Detection and Control of Toxin-Producing and/or Pathogenic Bacteria and Fungi Parasites, Mycotoxins, Chemical Residues, and Plant Toxins So As To Assist Regulatory Agencies and the Food Industry in Reducing the Incidence of Foodborne Illnesses.


Performance Measure 3.1.1:      Develop new on-farm preharvest systems, practices, and products to reduce pathogen and toxin contamination of animal- and plant-derived foods.




During 2005, ARS will


using new detection and quantitation methodologies, including genomic technologies, and through the study of epidemiology, ecology and host pathogen relationships, intervention strategies, and antibiotic resistance in food producing animals, develop practices, products, and information that will reduce preharvest pathogen and toxic residue contamination of animal-derived food products.  ARS will also ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  Shiga toxin producing E. coli O157:H7 were isolated from various fair environments following human outbreaks of E. coli O157:H7.  Scientists at Clay Center, Nebraska, collaborated with two State Departments of Agriculture and the Center for Disease Control (CDC) in the investigation of these human outbreaks of E. coli O157:H7 at fairs and petting zoos in Raleigh, North Carolina, and Tampa, Orlando, and Plant City, Florida.  These scientists developed methodology to isolate E. coli O157:H7 from the various fair environments and thus helped determine the likely outbreak vehicle and sources.  In collaboration with State officials working at a contaminated fair site, these scientists determined that E. coli O157:H7 can survive for many months in agricultural soils and that environmental decontamination techniques against E. coli O157:H7 will probably not be 100 percent effective or may even worsen contamination.


IMPACT/OUTCOME:  This information developed by ARS was used for CDC recommendations to help keep petting zoo and fair sites safe for visitors, and particularly for very young children.


ACCOMPLISHMENTS:  Engulfment of bacterial pathogens, such as Salmonella typhinurium DT104, by rumen protozoa in cattle, increases their virulence.  Easily available and effective substances are needed to kill the protozoa in order to increase both animal productivity and food safety.  Scientists in Ames, Iowa, developed an antiprotozoal screening assay to screen test compounds, particularly non-drug substances, for their ability to kill rumen protozoa.  These scientists found some natural plant extracts, i.e., yucca and rosemary, which effectively control protozoa in the rumen without harming the general fermentation. 


IMPACT/OUTCOME:  Use of these plant extracts which kill protozoa could greatly reduce the incidence and shedding of Salmonella and other pathogens at critical time points in the production of both beef and dairy cattle.


ACCOMPLISHMENTS:  Campylobacter contamination is a serious food safety issue and optimum production practices are needed to reduce the incidence in live poultry.  Scientists at Athens, Georgia, placed day-of-hatch chicks on wood shavings in high (approximately 80 percent) and low (approximately 30 percent) humidity controlled pens and challenged the chicks with C. jejuni (the most commonly found species of Campylobacter).  Significantly higher Campylobacter colonization rates were observed in chickens raised under the high humidity conditions.  Thus, the influence of relative humidity on transmission rates is an important factor influencing transmission of this poultry food safety pathogen.


IMPACT/OUTCOME:  This information demonstrating that high humidity enhances the transmission of Campylobacter jejuni could lead to practical applications in production practices to help reduce Campylobacter colonization in broilers.


using new detection and quantitation methodologies, including genomic technologies, and through the study of crop/fungal/toxin relationships, production practices and expert systems, breeding targets for resistant crops, biocontrol technologies, and chemical toxicity, develop practices, products, and information that will reduce preharvest fungal/toxin contamination of plant-derived food products.  ARS will also ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  New sources of genes that bring about aflatoxin resistance in corn are needed.  Insect damage and their associated ear mold toxins cause hundreds of millions of dollars in losses each year.  Thus, incorporation of new insect resistance genes into corn could reduce mycotoxins.  Scientists in Peoria, Illinois, found that plant derived genes that either killed insects or enhanced resistance to insects is in direct correlation to expression of the genes.  The corn plants that expressed both genes had significantly less damage by caterpillar and beetle pests.  


IMPACT/OUTCOME:  Incorporation of these genes into corn through multigenic transgenic means could result in reduced levels of mycotoxins, thus increasing both the safety and the exportability of U.S. corn.


ACCOMPLISHMENTS:  Genes encoding many different aspects of corn physiology must be identified and introduced for use in selective breeding of aflatoxin resistant corn.  Scientists in New Orleans, Louisiana, and their cooperators used proteomics, the study of proteins, to identify fungal resistance related and stress responsive proteins/genes in corn.  Genes encoding many of these resistance associated proteins (RAPs) have been cloned, and two have been further characterized.  Corn lines selected for superior agronomic traits, ear rot resistance, and aflatoxin resistance (in either temperate or tropical backgrounds) for 7 to 8 generations are now undergoing final testing for aflatoxin resistance.


IMPACT/OUTCOME:  This progress could lead to an official release in the next 2 to 5 years of these resistant lines which also will have superior agronomic performance.


Performance Measure 3.1.2:  Develop and transfer to Federal agencies and the private sector systems that rapidly and accurately detect, identify, and differentiate the most critical and economically important foodborne microbial pathogens.




During FY 2005, ARS will


develop innovative methods and advanced technology systems that: rapidly and accurately detect, identify, and differentiate the most critical and economically important foodborne contaminants, such as bacterial, viral, and protozoan pathogens; drug and chemical residues; and pathophysiological and processing surface contamination.  ARS will also ensure that the technologies are transferred to the Food Safety Inspection Service (FSIS) and the Food and Drug Administration (FDA); the Department of Homeland Security; and industry for implementation into Hazard Analysis Critical Control Point (HACCP) programs, and Good Manufacturing Practice (GMP) protocols for both large and small producers and processors.


ACCOMPLISHMENTS:  At the request of the FSIS, ARS scientists at Beltsville, Maryland, evaluated the accuracy and reliability of temperature indicator devices used by consumers.  The thermometers selected were: digital probe, bimetal probe, forks/tongs, remote wireless, as well as disposable indicators that change color at specified temperatures.  None of the thermometers tested consistently reached the end point temperature within the manufacturer's recommended time and several models did not reach the end point temperature even after an extended time period.  At the manufacturer's recommended time, the remote wireless thermometers were the least accurate.  The accuracy of the other thermometers was dependent on the meat product and the cooking method.  Because the thermometers indicated that the temperature was lower than the actual temperature, consumers using these thermometers when cooking meat products would actually cook the product to higher temperatures ensuring food safety but reducing the quality of the product.


IMPACT/OUTCOME:  FSIS is concerned that consumers cook meat products to safe end point temperatures before consumption.  As a result of this research, FSIS will revise their food safety information on consumer use of instant-read-thermometers to further reduce the potential for foodborne illnesses.


ACCOMPLISHMENTS:  Efficient methods are needed by regulatory agencies to detect pesticide residues in foods to ensure their safety for the consumer.  However, a serious issue is the cost of maintaining the testing equipment to ensure it is in optimal condition for use.  Such costs are often prohibitive for routine testing laboratories.  Scientists at Wyndmoor, Pennsylvania, developed a different approach called automated direct sample introduction.  It reduces the need for frequent instrument maintenance by eliminating many contaminants before final analysis.  This step also improves the detection of the pesticides.


IMPACT/OUTCOME:  Regulatory agencies, such as FSIS, that implement this approach will benefit considerably through significant cost savings and ease of use, and by improved detection efficiency.


ACCOMPLISHMENTS:  ARS scientists at various locations took the lead in developing new and better technologies that have regulatory, industry, and research use.  A variety of new, improved and innovative methods were developed to detect, differentiate, type, and quantify numerous foodborne pathogens.  For example: scientists at Wyndmoor, Pennsylvania, developed a portable fiber optic biosensor that can detect very low levels of E. coli O157:H7 bacteria in ground beef within five hours.  Higher levels of contamination can be detected in even less time.  The biosensor and battery pack can be carried in a briefcase, allowing assays to be performed at the farm, processing plant, distribution center, and retail store.  ARS scientists at Dover, Delaware, developed a real-time molecular method to quickly and easily detect a broad spectrum of Noroviruses (NV), and hepatitis A and E viruses in the stools of infected individuals.  This method involves the detection of viral genes through the polymerase chain reaction.  The assay allows over 90 percent of the strains of NVs circulating in the world today to be detected within three hours.  ARS scientists at Albany, California, characterized over 300 Campylobacter strains through the identification of very specific proteins which are particular to certain species and sub-species.  The technology which can be used for any pathogen of concern, including E. coli O157:H7 and Salmonella, provides a fast, high throughput method for identifying and differentiating specific species and strains.


IMPACT/OUTCOME:  Technologies were transferred to the end users, mainly FSIS, FDA, CDC, and DHS who work with ARS to refine them for (automated) day-to-day use.  Methods for virus detection will find extended use since they are a problem in water and foods such as shellfish, and are commonly associated with outbreaks on cruise ships and Navy vessels, and among troops particularly in Operation Desert Storm.


determine the microbial ecology and transmission of human pathogens during animal, plant, and seafood (shellfish) processing, and identify the critical control points to reduce contamination. Develop innovative postharvest intervention strategies for improving the microbial and chemical safety of foods while reducing the impact on quality and consumer acceptance. ARS will also ensure that these technologies can be implemented into HACCP and GMP protocols and have efficacy for approval by FSIS and FDA.


ACCOMPLISHMENTS:  Shell eggs are required to be cleaned/washed before packaging and marketing.  The current Federal guideline in the U.S. requires that the wash water be at least 90º F or 20º F warmer than the warmest egg entering the processing facility.  In the hot summer months using wash water at high temperatures can cause the egg to become too hot leading to conditions that allow bacteria in and on the eggs to grow.  ARS scientists at Athens, Georgia, in collaboration with scientists at Auburn University, examined the effects of using cool water washing of shell eggs on the microbial and physical quality of the final product. The research indicated to the regulatory agencies and industry that shell eggs can be commercially processed using cooler water without any reduction in their safety.


IMPACT/OUTCOME:  The research indicated that washing with cooler water enhanced the product quality. It also was more cost effective for the typical shell egg washing company to maintain the cooler wash water temperature during processing.  A commercial transfer study was conducted in two separate shell egg processing facilities showing the efficacy of the processing change.


ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, developed new washing procedures and sanitizer treatments for whole and fresh cut cantaloupe.  Hot water surface pasteurization with water at 170º F for three minutes using commercial scale equipment resulted in reductions of E. coli and Salmonella populations in excess of 99.999 percent. Experimental and simulation data on thermal penetration profiles indicated that the internal temperature of melons treated with hot water did not increase rapidly compared to the rind temperature.  Edible flesh 10 millimeters from the surface of the rind remained cool regardless of the process temperature.  The data clearly demonstrate the efficacy and utility of this treatment for reducing the risk of foodborne illness from consumption, while maintaining sensory qualities and extending the shelf life of fresh-cut cantaloupes.  Cut melon pieces could also be directly treated with nisin plus sodium lactate or sodium lactate plus potassium sorbate to effectively reduce pathogen populations without adverse effects on quality attributes.


IMPACT/OUTCOME:  Outbreaks of foodborne illness due to consumption of fresh and fresh-cut produce, especially cantaloupe, contaminated with bacterial pathogens continues to be a concern to regulatory agencies and industry.  This research will directly assist the FDA in developing good agricultural practices and good manufacturing practices, and developing a Guide to Minimize Microbial Safety Hazards for Fruit and Vegetables for industry. 


undertake genomic and proteomic analyses of pathogens affecting food safety.  ARS will also develop bioinformatic databases and tools, and predictive user-friendly models to understand pathogen behavior and acquisition of virulence characteristics under various stress conditions.  In addition, the Agency will determine the key risk factors of human pathogens in foods, and evaluate systems interventions for their impact, which will allow regulatory/action agencies to make critical food safety decisions that impact public health and food security.


ACCOMPLISHMENTS:  Genetic sequencing and annotation of microbial genomes yields fundamental information about the organism and is critical for definitive knowledge about pathogens.  ARS scientists from Albany, California, in collaboration with The Institute for Genomics Research (TIGR), sequenced the genomes of four different species of foodborne Campylobacter.  The sequence data revealed new information regarding the population structure, virulence factors, lateral transfer of DNA, gene regulation, and metabolism of Campylobacter species.  The Albany scientists subsequently developed a new genotyping system used to genotype about 500 strains of Campylobacter isolated from a variety of sources including humans, animals, and food.  A strong association between animal host and sequence type was identified that indicated potential biological fitness differences among Campylobacter strains.


IMPACT/OUTCOME:  The availability of new genetic information increases our understanding of why a bacterium can make you sick (pathogenicity and virulence), and how it can survive and grow in foods even under stressed conditions.  The information facilitates the development of better and more rapid detection technologies so that the human illnesses can be attributed to a particular food source.  Such research also increases our understanding of the epidemiology of outbreaks of foodborne illness, and furthers the development of data for risk assessment, which is used by FSIS, FDA, and other regulatory agencies worldwide to reduce foodborne diseases.


ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, produced robust models that now enable risk assessors and food safety managers to predict the activity of Listeria monocytogenes in ready-to-eat delicatessen salads at different storage temperatures and product formulations, and in commercially prepared cheeses.


IMPACT/OUTCOME:  Predicting L. monocytogenes in ready-to-eat foods is a high priority for FDA/FSIS. The models developed by ARS directly assist Federal regulatory agencies in developing risk assessment information for consumers, and food companies in designing salad formulations that present lower health risks.  In addition, ARS’ research also helps U.S. food companies meet new Federal regulations.


OBJECTIVE 3.2:  Develop and Deliver Science-Based Information and Technologies To Reduce the Number and Severity of Agricultural Pest, Insect, Weed, and Disease Outbreaks.


Performance Measure 3.2.1:  Provide scientific information to protect animals from pests, infectious diseases, and other disease-causing entities that affect animal and human health.




During FY 2005, ARS will


further determine partial and full genomic sequences of important animal pathogens (target four priority diseases) to better understand the evolution of new variants, determinants of virulence, host range specificity, and factors that enable evasion from host defense mechanisms.


ACCOMPLISHMENTS:  ARS scientists at the National Animal Disease Center in Ames, Iowa, have successfully sequenced the full genome of the RB51 vaccine strain of Brucella abortus.  This sequence is currently being compared to its parent strain and other B. abortus strains to identify genetic differences which may influence protection, immunologic responses, and virulence.  Preliminary work has identified genetic differences when RB51 is compared to its parent strain or a sequenced field strain.  It is anticipated that this sequence will be valuable for identifying genes that mediate protection and assisting in development of new vaccines for wildlife or domestic livestock that induce greater protection.

IMPACT/OUTCOME:  Comparative microbial genomics, studies to identify genetic variations associated with differences in phenotypic or biological traits, is a powerful way to identify genes and gene products that may be important in protection and may be useful in developing improved vaccines and diagnostic tests.


ACCOMPLISHMENTS:  Bovine babesiosis is a tick borne, hemoparasitic protozoal disease.  The United States is currently free of the disease, but there is a significant threat of re-introduction into the United States from Mexico.  An effective vaccine would provide an important tool to alleviate this threat.  Babesial parasites have a complex life cycle, including sexual stages in tick vectors and asexual reproduction during the erythrocytic stage in the mammalian host.  Ideally, an effective anti-babesial vaccine will include parasite antigens of known function that will induce immune responses that prevent disease in the mammalian host and block transmission from tick vectors.  ARS scientists in Pullman, Washington, have successfully constructed 45,000 expressed sequence tags (ESTs) covering 35 to 60 percent of the genes (and 13,000 coding regions) of Babesia bigemina and Babesia bovis.


IMPACT/OUTCOME:  The lack of a vaccine for control of babesiosis leaves U.S. cattle vulnerable to this disease if it was re-introduced from Mexico.  Various estimates of the cost associated with a re-introduction have been made; a conservative estimate would be $500 million per year.  Babesia vaccine development requires the characterization of the protective immune mechanisms, the identification of protective antigens from the parasites, and the development of effective delivery systems.


ACCOMPLISHMENTS:  Bordetella bronchiseptica is an important respiratory pathogen of pigs associated with the porcine respiratory disease complex.  When pathogenic bacteria encounter their host, they react by turning on specific genes which enable them to establish an infection and cause disease.  ARS scientists at the National Animal Disease Center in Ames, Iowa, successfully created a microarray of B. bronchiseptica genes.  Using the B. bronchiseptica genome sequence, a DNA microarray was designed on which each gene of the bacteria was represented.  As an initial experiment, this microarray was used to monitor which genes of B. bronchiseptica were expressed when the bacteria were grown at 37 degrees C and 23 degrees C, representing body temperature and room temperature, respectively.


IMPACT/OUTCOME:  Until recently, monitoring what genes are turned on or off in response to infection has been difficult.  With the advent of microarray technology and whole genome sequencing, ARS has been able to identify proteins that are produced during infection that are potential vaccine candidates.


further investigate the pathogenesis of important animal pathogens (target two priority diseases) to better understand tissue tropism, disease transmission, virulence and the identification of phenotypic markers.


ACCOMPLISHMENTS:  Intensive genetic selection for fast growing high yield birds has led to tremendous improvements in production efficiency.  However, selection pressure for rapid growth has negatively affected the normal development of the musculoskeletal system.  ARS scientists have been investigating the molecular mechanisms of tibial dyschondroplasia (TD), a common poultry skeletal problem, using a disease model that employs thiram (a fungicide) to disrupt chondrocyte growth and differentiation with the goal of finding whether this important skeletal problem can be prevented using nutritional means.  ARS scientists examined the changes in gene expression and the cellular and metabolic alterations in the growth plate during early periods of the onset of TD.  These studies revealed that TD was not induced by an aberrant pattern of gene expression in the growth plate, but was due to the death of endothelial cells that cause capillary vessel degeneration that leads to subsequent chondrocyte death. 


IMPACT/OUTCOME:  These studies provide insight into the pathogenesis of TD.  They will be useful in identifying the nutritional factors that may help prevent blood vessel death and TD. 


ACCOMPLISHMENTS:  ARS scientists have determined critical innate immune markers required for effective immune responses against porcine reproductive and respiratory syndrome (PRRS).  Ongoing genetic studies with University Nebraska-Lincoln scientists indicate that there may be correlations between levels of certain innate cytokines and resistance to PRRS associated pathologies.  ARS scientists have demonstrated that PRRS virus infection does not result in the induction of type I interferons in MARC 145 cells as would be expected with most ribonucleic acid viruses. 


IMPACT/OUTCOME:  These results are significant because both IFNA and IFNB (type I interferons) are members of the innate immune system, which is typically viewed as the first responder of the immune system.  Activation of this response signals other branches of the immune system to become activated and mount a protective immune response.  The fact that PRRS virus is capable of suppressing the activation of this response may explain the general delayed immune response to PRRS virus infection.  Elucidation of the mechanism of PRRS virus suppression of the type I interferon response may provide targets for novel vaccination approaches to control this important disease.


ACCOMPLISHMENTS:  Vesicular Stomatitis Virus (VSV) causes a disease in horses, cattle, swine, and occasionally sheep and goats that resembles foot-and-mouth disease.  Although generally self-limiting, it can have severe economic consequences by reducing production through recrudescence and secondary bacterial infection. Transmitted by a number of biting flies, the common biting midge of the Northern Plains is one of the important vectors in the United States.  ARS explored the physiology of the transmission of VSV by this biting midge vector, Culicoides sonorensis, by creating cDNA libraries of the insect’s midgut cells and salivary glands during the process of infection.


IMPACT/OUTCOME:  The creation of cDNA libraries provides a tool for determining which biting midge genes are involved in the infection process of the fly.  Beyond biological interest, an understanding of the physiological mechanisms of vector infection will provide additional targets for suppression of VSV transmission.  Potential mechanisms to disrupt transmission include genetic alteration of the biting midges to make them non-susceptible to VSV, creation of transmission blocking vaccines (administered to livestock) that disrupt the vector infection process, or the use of antiviral preparation administered to flies.


further investigate the epidemiology of important animal diseases (target two priority diseases) to better understand their ecology and life cycle and provide effective disease surveillance to facilitate the development of control strategies and prevent disease transmission.


ACCOMPLISHMENTS:  ARS scientists have discovered an avian rotavirus in specimens from turkeys with poult enteritis and broiler chickens with runting-stunting syndrome.  Rotaviruses are well known enteric pathogens that have been minimally characterized in poultry.  Initial pathogenesis studies were performed with clinical specimens containing rotavirus.  Identification of the viral agents associated with poult enteritis and the new similar condition in chickens, broiler runting-stunting syndrome, is critical to controlling the disease. 


IMPACT/OUTCOME:  Poult enteritis mortality syndrome (PEMS) is a highly infectious disease of young turkeys. PEMS was first reported in North Carolina in 1991.  Since then, PEMS and similar disease conditions have been reported in most regions where turkeys are commercially produced and are costing the poultry industry millions of dollars annually.  The major impact of PEMS is due to mortality and decreased production as turkeys are stunted and grow poorly when affected by the disease.  Currently the agent or agents that cause PEMS are unknown. 


ACCOMPLISHMENTS:  New methods were developed and validated by ARS scientists for geographically extensive and site intensive surveys and inventories of parasites in ungulate hosts based on the application of molecular sequence data.  Protostrongyle nematodes include pathogenic parasites that reside in the pulmonary system, skeletal musculature, or the central nervous system of their ruminant hosts.  Identification based on either adults in tissue and tissue spaces, or larval parasites in feces has remained problematic, and has hampered a detailed understanding of host distribution and geographic range.  Such information is critical in defining the potential for disease, and the degree to which parasites may be shared among a number of different ungulates.  A combination of comparative morphology and molecular analyses were applied to define the host and geographic range for Parelaphostrongylus odocoilei in North America.  Molecular identification of larvae indicates that the protostrongylid parasite occupies a broader geographic range in western North America than previously reported.  A total of 2,124 fecal samples from 29 locations from thinhorn sheep, bighorn sheep, mountain goats, woodland caribou, mule deer, and black-tailed deer were tested. 


IMPACT/OUTCOME:  This research provided significant molecular epidemiological data and represents the first study to combine extensive fecal surveys, comparative morphology, and molecular diagnostic techniques to comprehensively describe the host associations and geographic distribution of a parasitic helminth.  The development of such “epidemiological probes” will have significant applications in veterinary and conservation medicine.


ACCOMPLISHMENTS:  Vesicular Stomatitis Virus (VSV) infects animals worldwide, with constant transmission in the tropics and seasonal, sometimes epizootic, transmission in temperate regions.  A variety of biting flies (black flies, sand flies, biting midges) are known to transmit the virus.  ARS has shown that in addition to the biting midge, Culicoides sonorensis, the sand fly, Lutzomyia apache, and grasshoppers (through ingestion by livestock) are important in the transmission of VSV.


IMPACT/OUTCOME:  The addition of Lutzomyia apache to the list of vectors is of interest because this sand fly is not generally targeted for vector control and also because it could become a vector of invasive pathogens like Rift Valley Fever virus.  The discovery that it is a vector of VSV should lead to additional studies of its basic bionomics so that entomologists can develop the means for its management. Infection with VSV from the ingestion of grasshoppers is a surprising finding.  It remains to be discovered whether or not this occurs over a broad enough area that it justifies control.


ACCOMPLISHMENTS:  West Nile virus (WNV) was suddenly introduced into the New York City area in 1999 and has since spread throughout the United States and most of the Western Hemisphere.  The virus is harbored in the wild bird population and is transmitted to horses and people by a number of different mosquitoes.  Most infected horses have to be euthanized and about 20 percent of infected people have the disease with mild to fatal complications.  Older and immunocompromised people are particularly at risk of neuroinvasive disease that can cause long term disability or death.  In 2005, there were 2,819 cases and 105 deaths, making a total of 19,525 cases and 771 deaths since 1999.  In 2002 alone, there were 14,571 equine cases.  ARS discovered that WNV transmission in Wyoming is associated with the production of methane from coal fields, a process that creates abundant larval habitats for the major vector species, Culex tarsalis.


IMPACT/OUTCOME:  WNV transmission in Wyoming has been surprising intense, considering its high elevation and northern location.  Poorly drained prairie and flood plains of seasonal rivers create abundant sites for mosquitoes in the summer, so that identification of the vector of WNV in the State was not obvious.  ARS research definitely implicates Culex tarsalis as the major vector.  A major source for this species was found to be the water accumulated in an industrial process to extract methane from coal fields.  This knowledge will enable entomologists the means to design integrated control programs to suppress the populations of Culex tarsalis thereby reducing the risk of WNV transmission.


Performance Measure 3.2.2:    Identify, develop, and release to the U.S. agricultural community genetic markers, genetic lines, breeds, or germplasm that result in food animals with improved (either through traditional breeding or biotechnology) pest- and disease-resistance traits.




During FY 2005, ARS will continue to identify genetic markers and genes (target one marker, gene, or gene cluster) from food animals that can be used to identify animals with disease resistant traits.


ACCOMPLISHMENTS:  ARS scientists in Pullman, Washington, in collaboration with Colorado State University and the Canadian Food Inspection Agency, have described the distribution of the chronic wasting disease (CWD) prion protein in elk and the genotypes in elk susceptible to disease.  Their research also demonstrated the first confirmed case of CWD in an elk of the relatively rare genotype 132LL, thereby ruling out this genotype as conferring resistance to disease under field conditions.


IMPACT/OUTCOME:  Current control measures for transmissible spongiform encephalopathies in livestock depend on identification of the most appropriate tissue for diagnostic testing and identification of candidate resistant genotypes.  The genetic analysis performed by ARS scientists provides the scientific basis for selecting the brain as the most reliable indicator of disease in elk, in contrast to the tests for deer, which rely on lymphoid tissue. 


Performance Measure 3.2.3:    Develop and transfer tools to the agricultural community, commercial partners, and Federal agencies to control or eradicate domestic and exotic diseases that affect animal and human health.




During FY 2005, ARS will continue to discover and develop novel technologies (target two high priority diseases) to detect and control diseases of food animal pests that impact animal and human health, animal production, and trade.


ACCOMPLISHMENTS:  Research into live Mycoplasma gallisepticum (MG) vaccine administration to layer chickens has shown that the pressure (psi) utilized for spray administration is extremely important in impacting subsequent seroconversion (positive blood tests).  A survey of the layer chicken industry showed that pressure settings used for the administration of live MG vaccine varied from 35-70 psi.  Research conducted by ARS scientists using the CPJ Vaccinator to determine the optimum pressure setting to dispense live MG vaccine demonstrated dramatic increases in MG colony counts resulting from using the lower (40 psi) setting as compared to the higher 60 psi setting. 


IMPACT/OUTCOME:  This information is important as it explains one factor (pressure setting of the vaccinator) that can impact the administration of live MG vaccines that may, in turn, result in poor vaccination results.  As a result of poor vaccine test results, re-vaccination must take place, which entails costs of additional vaccine (approximately $1,500 for a 75,000 bird house) and labor. 


ACCOMPLISHMENTS:  ARS scientists, in collaboration with scientists at Mount Sinai School of Medicine and St. Jude's Children's Hospital, successfully used reverse genetics to develop a novel cross-protective vaccine for swine flu.  Preliminary studies indicate this vaccine may have a broader level of cross protection when compared to currently available swine influenza virus (SIV) vaccines that are inactivated or killed.  These studies have also demonstrated a virulence mechanism that will impact the design of future commercially available SIV vaccines. 


IMPACT/OUTCOME:  Swine influenza is a re-emerging disease around the world as a result of several genetic changes in the viral populations being isolated from swine.  This has resulted in a reduced efficacy of current commercially available vaccines.  The availability of a highly effective vaccine for control and eradication may be the first line of defense against emerging swine flu outbreaks.


ACCOMPLISHMENTS:  ARS scientists in Beltsville, Maryland, have discovered a conserved protein named SZ-1 that is highly conserved in Eimeria tenella and two other important protozoans:  Toxoplasma gondii and Neospora caninum. The full length gene from T. gondii was characterized, expressed in a bacterial system, and the cloned protein was used to make antibodies to T. gondii SZ1.  These antibodies are providing important functional genomics research tools that can be used to determine the function of the SZ1 protein, and determine whether this protein might confer cross-protective immunity across Eimeria strains.


IMPACT/OUTCOME:  Coccidiosis is a ubiquitous intestinal protozoan infection of poultry that seriously impairs the growth and feed utilization of infected birds.  This enteric disease is caused by several distinct apicomplexan species of obligate intracellular parasites of the genus Eimeria.  The use of anti-coccidial drugs is the primary control method, but the worldwide emergence of drug-resistant coccidia strains are limiting the effectiveness of existing therapeutics.  This problem is compounded by our lack of understanding of the mechanism(s) that confer(s) drug resistance and the host-parasite and environmental factors that influence coccidiosis susceptibility.  The discovery of highly effective vaccines may provide an important alternative to drug therapy.  Current vaccines, which are comprised of one or more live coccidian species do not provide cross-protection against all seven species of Eimeria.


Performance Measure 3.2.4:    Develop and release to potential users varieties and/or germplasm of agriculturally important plants that are new or provide significantly improved (either through traditional breeding or biotechnology) characteristics enhancing pest or disease resistance.




During FY 2005, ARS will continue to identify and characterize genes of insect resistance in crop plants, closely related non-crop species, and other species, to enhance opportunities for developing host plant resistance, and to incorporate such genes into commercially acceptable varieties.


ACCOMPLISHMENTS:  Researchers at St. Paul, Minnesota; Aberdeen, Idaho; and other ARS locations have assessed the vulnerability of U.S. wheat lines to a new virulent wheat stem rust mutant that has spread across East Africa.


IMPACT/OUTCOME:  The results of greenhouse evaluations conducted under controlled conditions at St. Paul, Minnesota, indicated that many hard red spring wheat and soft red winter wheat lines from the United States are susceptible to the African race.  The results of these evaluations are being distributed to all U.S. wheat breeders so they can promptly begin to incorporate resistance into their breeding lines, thus reducing the vulnerability to this potentially threatening stem rust mutant.


ACCOMPLISHMENTS:  ARS scientists in Frederick, Maryland, and Urbana, Illinois, evaluated nearly 20,000 soybean accessions from the USDA soybean germplasm collection for resistance to soybean rust.  Approximately 300 to 400 soybean lines showed some resistance and will be tested further with individual rust isolates. 


IMPACT/OUTCOME:  Identifying sources of resistance is a key step in the development of rust-resistant commercial soybean cultivars that can be planted by growers thereby reducing potential losses due to rust.


Performance Measure 3.2.5:  Provide fundamental and applied scientific information and technology to protect agriculturally important plants from pests and diseases.




During FY 2005, ARS will


continue to develop fundamental knowledge about insect biology and ecology that provides the foundation for strategies to exclude, detect, and mitigate pest infestations.


ACCOMPLISHMENTS:  Most U.S. pests have been introduced from other parts of the world and cause billions of dollars in damage annually.  Scientists in Beltsville, Maryland, provided 11,145 insect identifications (5,083 of urgent priority) to a broad array of organizations.  In addition, a new species of fruit fly was described from Columbia.  Response to scale pests will now be facilitated by development of an online expert system, which has tools for accommodating a large amount of morphological variation in specimens.  In addition, a comprehensive analysis was completed that describes and illustrates all members of the genus Diuraphis, including the destructive Russian wheat aphid. 


IMPACT/OUTCOME:  The vast majority of identifications are provided to the Animal and Plant Health Inspection Service’s (APHIS) Plant Protection and Quarantine division.  APHIS reports that nine species identified by ARS scientists were new immigrants to the United States.  The new identification of the fruit fly from Columbia will facilitate trade in mangos and other fruit between Columbia and the United States. 


ACCOMPLISHMENTS:  The red flour beetle is the first agronomic pest species to be sequenced.  It represents the joint efforts of the ARS Grain Marketing and Production Center, Biological Research Unit, Manhattan, Kansas; Kansas State University; and the Baylor College of Medicine’s Human Genome Sequencing Center.  The genome sequence scaffolds were merged with genetic and physical maps, resulting in map position assignment for 75 percent of the genome.  Planning and coordination of the genome analysis and annotation efforts were initiated at the International Tribolium Genomics Meeting in Gottingen, Germany, in August 2005. 


IMPACT/OUTCOME:  The analysis of this sequence will have far reaching impacts on understanding physiological adaptations of pest and beneficial beetle species, and the identification of novel targets for pest control exploitation.


ACCOMPLISHMENTS:  Radio transmitters have been used to track everything from antelope to zebra, but not insects.  Scientists from the ARS Northern Plains Area, University of North Carolina-Chapel Hill, and University of Toronto-Mississauga, placed miniature radio transmitters on Mormon Crickets to study their behavior and movement.  Mormon Crickets are notorious for their huge and devastating swarms (or bands), and their ability to migrate hundreds of miles in the Western States.  Why and how these swarms are formed and maintained has been a mystery until now.  The researchers demonstrated that Mormon crickets form migratory swarms to avoid being eaten by their predators.  Once the swarms are formed, the movement of individual crickets within these groups is induced simply by contact with other crickets, thereby providing a mechanism to explain the constant long-term movement of these insect groups across the landscape.


IMPACT/OUTCOME:  This research helps explain why insects around the world, such as the infamous desert locust in Africa, form migratory bands and provides important information on the movement of individuals within these groups.  This knowledge will form the basis for predictive movement models that will aid in managing Mormon crickets and desert locusts.


continue to develop fundamental knowledge about weed biology, ecology, and risk analysis that provides the foundation for strategies to exclude, detect, and mitigate weed infestations.


ACCOMPLISHMENTS:  Intercrossing between rice and ecotypes of weedy red rice, a dominant weed in the Southern United States, may reduce yield when herbicide-resistant rice systems are used.  DNA/PCR microsatellite fingerprinting analyses were conducted to quantify rates of outcrossing between rice x red rice crosses (including imidasolinone-resistant rice cultivars), foreign rice cultivars, and red-seeded rice relatives from throughout the world at the ARS’ Dale Bumpers National Rice Research Center, Stuttgart, Arkansas.  A method was developed enabling distinguishing crosses using DNA marker analysis. 


IMPACT/OUTCOME:  These analyses may allow the rice industry to identify (or rule out) the parental lines that are responsible for the development of an unwanted population of herbicide-resistant rice x red rice hybrids, a key management consideration in herbicide-resistant rice systems.


continue to develop fundamental knowledge about plant disease biology and ecology that provides the foundation for strategies to exclude, detect, and mitigate pest infestations.


ACCOMPLISHMENTS:  Scientists at Corvallis, Oregon, developed methods for trapping and identification of aerial borne spores of hop and grape powdery mildew pathogens that are suitable for PCR analysis.


IMPACT/OUTCOME:  These methods allow for highly accurate assessments of when an epidemic begins in a specific field and the timing of fungicide applications.  More accurate determinations of the environmental conditions favorable for spore movement can be determined leading to more accurate assessments of disease outbreaks.


ACCOMPLISHMENTS:  ARS has developed rapid, reliable pathogen detection and identification procedures for accurate and timely disease diagnosis for soybean rust and other high profile pathogens on the USDA Select Agent List.


IMPACT/OUTCOME:  ARS has provided this assay to diagnosticians across the United States and Canada as part of a national surveillance system.  The detection assay was used by regulatory officials to accurately determine and identify a new outbreak of soybean rust in the Southern United States. 


Performance Measure 3.2.6:    Provide needed scientific information and technology to producers of agriculturally important plants in support of exclusion, detection, and early eradication; control and monitoring of invasive insects, weeds and pathogens; and restoration of affected areas.  Conduct biologically-based integrated and areawide management of key invasive species.




During FY 2005, ARS will


continue to develop and demonstrate technologies for excluding, detecting, and mitigating native and invasive insect pests, including integrated pest management (IPM) and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  The Russian wheat aphid is a serious pest of wheat and barley in the Western States.  Resistant wheat varieties served as the cornerstone for managing Russian wheat aphid until 2003, when a biotype (AKA strain) of the aphid appeared that was able to feed on, injure, and kill the resistant wheat.  The aphid-resistance in these wheat varieties was based on the same wheat gene.  In 2005, ARS scientists at the Wheat, Peanut and Other Field Crops Research Unit in Stillwater, Oklahoma, discovered three new Russian wheat aphid biotypes differing in their ability to injure wheat with unique resistance genes.  One of the new biotypes is especially troublesome because it damages all commercially available sources of plant resistance.  While the new biotypes still occur in low numbers in the field, they may become numerous in the near future.  This information was quickly disseminated to wheat breeding programs in the United States. 


IMPACT/OUTCOME:  Due to these population monitoring activities by the ARS, scientists in the United States have a head start in finding and developing new sources of Russian wheat aphid resistance before the new biotypes become abundant.


ACCOMPLISHMENTS:  The tarnished plant bug is a serious pest of cotton that is becoming more resistant to insecticides, requiring growers to use higher and higher levels of chemicals to achieve the same level of control.  Within a few years, insecticides may no longer be effective against this pest.  The tarnished plant bug is being thwarted thanks to a program that includes use of alternative host destruction, host-plant resistance, fungal pathogens, and remote sensing technology by ARS scientists based in Stoneville, Mississippi, in cooperation with cotton growers and university scientists in Mississippi, Louisiana, Tennessee, and Arkansas.  Grower adoption of the technology is 86 percent in the Mississippi Delta and 33 percent in Arkansas, a State where the technology was demonstrated for the first time in 2004.  Adoption of the technology is approximately 33 percent in Louisiana and Tennessee.  Across the four states, the technology is applied to approximately 1.47 million acres of cotton. 


IMPACT/OUTCOME:  A cost/benefit analysis of the program on over 21,000 acres demonstrated benefits of $10.28 for every $1 applied to using the technology.  Economists have determined the technology produced a $5.48 savings per acre in reduced insecticide costs.  The savings in reduced insecticide costs for the technology was $8.1 million.


ACCOMPLISHMENTS: Accurate and inexpensive methods are needed for monitoring wheat fields to determine the presence of Russian wheat aphid or greenbug infestations.  Wheat farmers and scientist cannot always easily detect aphid infestations or do not have the time to closely monitor their fields.  ARS scientists from the Wheat, Peanut and Other Field Crops Research Unit, Stillwater, Oklahoma, in collaboration with the cooperators at the Texas Agricultural Experiment Station, developed remote sensing technology for identifying greenbug and Russian wheat aphid-infested fields.  Images obtained from aircraft enable the detection of Russian wheat aphid and greenbug infestations.  Fields with high aphid infestations can be differentiated from fields with low infestations by unique "spatial signatures".  


IMPACT/OUTCOME: Ultimately, this technology could be applied for broad scale monitoring of wheat fields for greenbug and Russian wheat aphid infestations using existing satellites in the earth’s orbit.


continue to develop and demonstrate technologies, including risk analysis, for excluding, detecting, and mitigating native and invasive weed pests, including IPM and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  In-crop herbicidal options, especially herbicides that can be applied to control a broad-spectrum of grass and broadleaf weeds at the start of a growing season when weeds have their greatest impact on sugar yields, are limited.  Scientists at the Sugarcane Research Unit in New Orleans, Louisiana, evaluated herbicides alone and in mixtures for control of Bermuda grass, itchgrass, morning glory, and seedling johnsongrass when applied as single and sequential applications.  They found that morning glory in particular could be controlled under sugarcane crop canopy. 


IMPACT/OUTCOME:  Results of this research were used to support manufacturer petitions to the Environmental Protection Agency for two herbicides, which were received in time for the 2004 growing season.


ACCOMPLISHMENTS:  The Australian melaleuca tree (Melaleuca quinquenervia) is an extremely aggressive invasive plant that alters the drainage of South Florida, and affects natural areas, outcompeting valuable native species.  Restricting the invasiveness of melaleuca requires reducing its ability to produce massive amounts of seeds.  ARS scientists at the Invasive Plant Research Laboratory, Fort Lauderdale, Florida, in collaboration with Florida Department of Environmental Protection, U.S. Army Corps of Engineers, South Florida Water Management District personnel, and other partners, released two biological control agents:  a tip-feeding weevil (Oxyops vitiosa; 1997) and a sap-sucking psyllid bug (Boreioglycaspis melaleucae, 2002). 


IMPACT/OUTCOME:  Both species are contributing to the successful biological control of melaleuca.  In particular, the psyllid has spread throughout the infestation of melaleuca, and is significantly affecting growth and survival of the weed.  In fact, melaleuca is almost gone from public lands.


ACCOMPLISHMENTS:  Invasive saltcedar (Tamarix spp.) shrubs from Eurasia infest many Western U.S. waterways where they cause significant economic and environmental losses.  Detailed studies on foreign exploration and host specificity testing for natural enemies of saltcedar were conducted by ARS scientists at the European Biological Control Laboratory, Montpellier, France; the Western Regional Research Center, Albany, California; the Grassland Protection Research Unit, Temple, Texas; and the Crop Bioprotection Research Unit, Peoria, Illinois.  The first biological control agent for saltcedar, the beetle Diorhabda elongata, was released in 1999 at 10 sites in six States.  The beetle continues to cause widespread defoliation and death of saltcedar.  A pheromone trap was developed this year that enables detection of the leading edge of the spread of the beetle.  Additional populations of the beetle are being sought in their native range that are better adapted to areas where the beetle is not performing as well due to a climatic mismatch.  Impacts of the beetle continued on saltcedar and on native plant communities (cottonwoods and willows). 


IMPACT/OUTCOME:  This research is important as it interfaces with on-going investigations of biologically based saltcedar control, provides revegetation strategies for land managers that are interested in removing and replacing saltcedar, and assists in evaluation of the impact of the program on an endangered bird.


continue to develop and demonstrate technologies for excluding, detecting, and mitigating emerging and re-emerging plant disease pests, including IPM and areawide approaches, and deliver IPM components and systems to ARS customers.


ACCOMPLISHMENTS:  Scientists from the Molecular and Plant Pathology Laboratory at Beltsville, Maryland, identified candidate biomarkers that can distinguish strains and species of plant pathogenic phytoplasmas and spiroplasmas.  The biomarkers are potentially significant for survival of the pathogens in their hosts and in disease development. 


IMPACT/OUTCOME:  This accomplishment provides new knowledge important for understanding the mechanisms involved in pathogenicity and transmission of these pathogens by insect vectors.

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Last Modified: 4/3/2006
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