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United States Department of Agriculture

Agricultural Research Service

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2004 Annual Performance Report
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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 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 2004.  Forty-four 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 FY 2004, 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.  Ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  If food safety pathogens are both antibiotic resistant and also hyperinvasive, they can easily make animals sick and pose an exceedingly dangerous public health threat.  ARS scientists at Ames, Iowa, demonstrated that rumen protozoa can engulf and hold viable bacterial pathogens, such as Salmonella, and that after surviving within rumen protozoa, the Salmonella were more invasive than other similar antibiotic sensitive Salmonella. 


IMPACT/OUTCOME:  Since rumen protozoa can be a reservoir for pathogens, they could be released during bouts of illness when acidic conditions kill the protozoa.  This provides another intervention point (protozoa) for eliminating a reservoir of foodborne pathogens, thus improving the safety of meat and dairy products. 


ACCOMPLISHMENTS:  An ARS laboratory in College Station, Texas, has developed very promising candidates to kill the human pathogen, E. coli O157:H7 in cattle, and significantly help prevent contamination of beef.  In studies to satisfy FDA requirements for human safety, ARS scientists at Fargo, North Dakota, used radio-labeled compounds to demonstrate that a large proportion of chlorate residues are converted to a non-toxic metabolite (chloride ion), and are present as natural products in edible tissues of cattle.  In an earlier stage of product development, ARS scientists at College Station, Texas, demonstrated that certain other chemicals called nitrocompounds also effectively kill pathogenic E. coli, and Salmonella. 


IMPACT/OUTCOME:  The work of these two ARS laboratories with two different chemicals will help provide cattle and swine industries with practical intervention strategies that eliminate foodborne pathogens from food producing animals.


ACCOMPLISHMENTS:  ARS scientists in College Station, Texas, in collaboration with English scientists, were able to stimulate certain cells in the chicken, called heterophils, to kill enteropathogenic bacteria in the chicken’s own gut.  This is a potentially new method for increasing resistance of birds to colonization by important food poisoning microorganisms, such as Salmonella and Campylobacter, and provides information essential for highly effective new vaccines.  This same laboratory with a broiler breeder industry partner identified new immunologically efficient lines of chickens resistant to bacterial colonization by enteropathogenic bacteria.


IMPACT/OUTCOME:  These birds possessing their own genetic bacterial resistance phenomena could provide a very efficient and cost-effective means of minimizing bird colonization by food poisoning bacteria that would greatly enhance poultry food safety. 


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.  Ensure that these technologies can be utilized by regulatory agencies and/or producers to help assure safe food products.


ACCOMPLISHMENTS:  To better understand the genetic pathways required for the formation of mycotoxins, such as aflatoxins and fumonisins, ARS scientists in Peoria, Illinois, and New Orleans, Louisiana, have continued to expand the scope of their Expressed Sequence Tag (EST) libraries of fungal genes in collaboration with The Institute for Genomic Research (TIGR). The fumonisin library consists of 86,400 individual sequences that most likely correspond to approximately 11,000 unique genes, while a 7,214 element aflatoxin EST gene microarray (a technique for measuring expression of genes in mass numbers) has been constructed to significantly speed the detection of fungal genes governing aflatoxin formation.  


IMPACT/OUTCOME:  These rapid bioassays are helping identify markers and inhibitors related to reproduction/survival, virulence, and toxin formation for the fungi that produce these mycotoxins.   Already ARS scientists at Albany, California, have conclusive evidence that gallic acid levels in aflatoxin resistant tree nut varieties increases with maturity and is maintained throughout the growing season, rather than declining as in more susceptible varieties.  This research will identify those fungal genes that can be targeted for controlling mycotoxin contamination through genetic engineering or marker assisted breeding of susceptible commercial crops, thus further protecting the public health.


ACCOMPLISHMENTS:  ARS scientists in Tuscon, Arizona, and Dawson, Georgia, have led the world in the successful development of atoxigenic strain technology to prevent aflatoxin from contaminating susceptible crops.  In Georgia, development of this technology for aflatoxin biocontrol in peanuts was licensed to Circle One Global as Afla-guard®, Inc. and received Section 3 registration in May 2004, from the EPA.


IMPACT/OUTCOME:  Approximately 50 tons of Afla-guard® was commercially applied to the 2004 peanut crop in Georgia and Alabama.  In Arizona, further development of atoxigenic strain technology with the previously registered product AF 36, continued in 2004, in collaboration with many industry partners.  Product application was made to nearly 30,000 acres of cotton including 5,000 acres in south Texas, and requests were made to EPA for Experimental Use Registrations providing for expanded application to cotton in southern California and pistachios in the central valley of California. Use of this technology will help keep harmful toxins out of the food supply.


ACCOMPLISHMENTS:  An ARS laboratory in Peoria, Illinois, developed rapid, easy to perform, quickly learned fluorescence polarization immunoassays for measuring the fumonisin and zeaaralonone mycotoxins in maize and deoxynivalenol in wheat.  The reagents and labware for this immunoassay are easy to use and easily obtained. 


IMPACT/OUTCOME:  The assays offer faster, environmentally friendly alternatives to traditional instrumental methods, and ELISAs (enzyme linked immunosorbent serologic assays).  They will be useful screening tools to determine mycotoxin contamination.  Since mycotoxins are unevenly distributed in any contaminated plant commodity, there is a great need for methodology to determine the contamination of a large volume of potentially contaminated grains.  These tests help fulfill that need.


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 2004, 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  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:  ARS scientists at the Richard Russell Research Center, Athens, Georgia, designed and constructed a second generation prototype in-line, real-time, portable multispectral imaging system that can capture images of every poultry carcass on the processing line and detect fecal contamination at a rate greater than 140 birds per minute.  This process goes well beyond the rate at which an inspector can evaluate.  A decision tree has been incorporated in the in-line system software and has virtually eliminated false positives while retaining high fecal detection accuracy (99 percent).  The next step is to integrate a new carcass washing system developed by the research team so that any contaminated carcass can be reprocessed and passed safely into the food supply.


IMPACT/OUTCOME:  Implementation of the entire system in processing plants will have enormous effects.  It will free inspectors to evaluate only contaminated carcasses, enabling FSIS to redeploy thousands of inspectors to other safety tasks.  It will also assure the increased safety and quality of the product for the consumer, thus financially increasing profits for the poultry industry.


ACCOMPLISHMENTS:  ARS scientists at various locations took the lead to develop methods and 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 including: Campylobacter, Salmonella, E. coli O157:H7, and related E. coli, Listeria, Yersinia, C. perfringens, B. cereus, Cryptosporidium, hepatitis A, Noroviruses, Fusarium species, and products of their growth, such as toxins.  New sampling methods were also developed which included a method to capture cells from any sample size and type, and enumerate without, or with minimal enrichment, currently the most time limiting step.  In collaboration with Purdue University, ARS scientists developed an inexpensive, micro-fluidic and electronic bio-chip that detects cell growth, metabolites, such as toxins, and differentiates living and dead cells in very small samples/volumes.


IMPACT/OUTCOME:  The focus of development was utility and cost-effectiveness for the end user.  Technologies were transferred to the end users, mainly FSIS and FDA, who will work with ARS to refine them for (automated) day-to-day use.  Development of the microchips will allow industry to incorporate this technology into food packages before shipping.  Spoilage could be monitored (by GPS) during transportation, and/or by retailers and consumers through an enzyme-based color change.


ACCOMPLISHMENTS:  ARS scientists at Wyndmoor, Pennsylvania, developed a variety of fast, rugged, inexpensive, non-solvent portable new methods to screen foods for drugs, chemical residues including pesticides, and bacterial toxins.


IMPACT/OUTCOME:  Development of these tests will have a significant and immediate impact for FSIS and FDA, generating savings in materials, equipment, and labor costs.  For example, in the screening of milk tankers for tetracycline, 6.4 million man hours will be saved.  In addition, $1.6 million will be saved from elimination of the solvent.  Current commercial toxin tests costing $12 – $20 per sample were reduced to less than $1 per test.


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. Ensure that these technologies can be implemented into HACCP and GMP protocols and have efficacy for approval by FSIS and FDA.


ACCOMPLISHMENTS:  ARS scientists at the Richard Russell Research Center, Athens, Georgia, examined eggs collected from commercial plants from various stages of processing and analyzed them microbiologically and for quality.  Various methods are currently used to assess microbial quality of shell eggs, but no single method has been shown to be superior to others under all circumstances.  The study showed that microorganisms on the surface of eggs were significantly reduced through washing.  The microbiological safety, interior quality of the egg, along with the functional characteristics, remained at a high level through ten weeks of refrigerated storage.


IMPACT/OUTCOME:  This research will assist egg processors and regulators providing validation of current commercial practices; providing evidence that a more effective sanitizer could potentially improve egg microbiology; and indicating that sell-by dates could potentially be adjusted allowing for marketers to reach a broader customer base.  This latter impact would be particularly beneficial to producers of specialty eggs (i.e., reduced cholesterol, high omega fatty acid, cage-free, pasteurized, etc.) who are now limited to regional marketing due to concern over additional transportation time cutting into sell-by time windows. 


ACCOMPLISHMENTS:  The 2002 Farm Bill and the Richard B. Russell National School Lunch Act allow irradiated ground beef, on a voluntary basis, to be distributed in the National School Lunch Program (NSLP) in order to prevent foodborne illness caused by bacteria such as E. coli O157:H7.  However, there were consumer concerns, based on questions from school district administrators and parents, that irradiation might change the sensory quality of the product.  ARS scientists at the Eastern Regional Research Center, Wyndmoor, Pennsylvania, examined frozen ground beef patties distributed as a part of the NSLP that had been irradiated under commercial conditions.  The study showed that irradiated ground beef could not be distinguished from non-irradiated ground beef when tested for overall liking, flavor, taste, texture, or aftertaste.  Further, irradiation did not affect palatability of frozen ground beef patties used in the NSLP.


IMPACT/OUTCOME:  Information from the study was provided to the USDA Food and Nutrition Service, which was subsequently transmitted to schools as part of the USDA NSLP educational program on food irradiation.  Orders for frozen irradiated ground beef patties have now been placed by school districts.


ACCOMPLISHMENTS:  ARS scientists at various locations including Albany, California; Athens, Georgia; Beltsville, Maryland; and Wyndmoor, Pennsylvania, in association with various university collaborators, utilized many of the new, improved, and innovative methods to obtain data on the ecology of specific pathogens on foods, within the production and processing environment.


IMPACT/OUTCOME:  The data transmitted to the regulatory agencies and commodity organizations facilitated the identification of critical control points during food production and processing; allowed development of alternative Hazard Analysis Critical Control Plans (HACCP) systems; and led to the design and validation of alternate pathogen intervention strategies.  One critical outcome was the need to balance the cost of the intervention strategy, practicality of use by the food processing industry, and the effects on food quality.


undertake genomic and proteomic analyses of pathogens affecting food safety.  Develop bioinformatic databases and tools, and predictive user-friendly models to understand pathogen behavior and acquisition of virulence characteristics under various stress conditions. 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:  Bacteria in Campylobacter are the major cause of human bacterial associated gastroenteritis worldwide, responsible for 500 million cases of diarrhea each year.  These bacteria can also cause special types of arthritis and the neurological disease Guillain-Barre which can result in paralysis and death.  ARS scientists, in association with The Institute for Genomic Research (TIGR), sequenced, annotated, and compared the genome of four different Campylobacter species. This information has been used to develop and produce comprehensive Campylobacter. This is important in determining the differences among human and animal isolates of Campylobacter, and for studies of gene expression of Campylobacter exposed to relevant nutrients. Microarrays provide perhaps the most complete view of strain differences and responses to environments.


IMPACT/OUTCOME:  The availability of this new genetic information will make it possible to better address food safety-related problems through the application of powerful genomic and proteomic technologies.  For example, the development of better and more rapid detection techniques, the identification of those proteins essential for bacterial pathogen survival and growth in foods, and the development of data for risk assessment, will ultimately be used by FSIS, FDA and other regulatory agencies worldwide to develop strategies to decrease the public health risk and impact.


ACCOMPLISHMENTS:  Listeria monocytogenes remains a significant national and international regulatory, industry, and public health risk, and economic burden.  However, not all serotypes and/or strains of the bacteria have the same virulence, and capacity or ability to cause disease.  In order to determine which types were critically important, ARS scientists at the National Center for Agriculture and Utilization, Peoria, Illinois, developed a robust phylogenic description for Listeria monocytogenes from a comparative DNA sequence database developed by ARS.  Analyses demonstrated that L. monocytogenes lineages most frequently and least frequently associated with human listeriosis are sister groups, and revealed for the first time that the human epidemic associated serotype 4b is prevalent among strains from both of these lineages.  In addition, a Polymerase Chain Reaction (PCR)-based test for lineage identification was developed and used in a survey of food products demonstrating that lineage prevalence among human listeriosis cases reflects rarity of exposure and not reduced virulence as has been previously suggested.  These data also indicate that lineage 3 isolates are better adapted to the animal production environment than the food processing environment.


IMPACT/OUTCOME:  This research has provided regulatory agencies and food producers genetic information, prevalence and ecological data, and molecular tools required for the development and implementation of the Hazard Analysis Critical Control Plans (HACCP) and regulations that provide maximum protection to consumers while limiting the number and size of product recalls.


ACCOMPLISHMENTS:  ARS scientists in the Center of Excellence for Microbial Modeling and Informatics, Wyndmoor, Pennsylvania, developed the next generation of the Pathogen Modeling Program (PMP) software.  The PMP will be translated into several other languages including Spanish, Chinese, possibly French, and Finnish.  Combase, developed in association with the Institute of Food Research in Norwich, United Kingdom, and the United Kingdom Food Standards Agency which is the relational database behind the models and other predictive microbiology records, was expanded to include Australasia through CSIRO-Food Science Australia.


IMPACT/OUTCOME:  The PMP is utilized by numerous national and international regulatory agencies and various food industries to assist in identifying specific food processing steps that can serve as Critical Control Points in HACCP systems.  The predictive models are an integral part of microbial risk assessment used to support food safety measures adopted by member countries of the World Trade Organization.  Combase is now a global resource for the development of new microbial models, providing the food industry with:  an efficient location of specific food microbiology data; access to improved models that consider the complex nature of pathogen-food interactions; and greater transparency to microbial risk assessment. 


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 2004, 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:  Avian influenza (AI) is one of the most feared infectious diseases.  There are already several occurrences of this virus crossing the species barrier and infecting people, resulting in mortality and high economic losses to the regions experiencing new outbreaks.  ARS scientists in collaboration with the National Veterinary Services Laboratories (Ames, Iowa), Central Veterinary Laboratory (Weybridge, England), and the Chilean Department of Agriculture (Santiago, Chile) described the first field case of recombination for an AI virus that resulted in a low pathogenic avian influenza (LPAI) virus mutating to a high pathogenic (HPAI) form of the virus.  Sequence analysis of all eight genes of a H7N3 LPAI virus and a H7N3 HPAI virus isolated one month apart in Chile showed minor differences between the viruses except at the hemagglutinin (HA) cleavage site where the HPAI had a 30-nucleotide insert.  This insertion likely occurred through a recombination event resulting in a virulence shift, demonstrating a new mechanism of how an influenza virus may evolve to a more virulent form.


IMPACT/OUTCOME:  The understanding of mechanisms for increased virulence of AI will improve our understanding of the pathogenesis of the virus and eventually may improve our ability to predict which low pathogenic viruses may become highly pathogenic.


ACCOMPLISHMENTS:  Avian pneumovirus (APV), now classified as an avian metapneumovirus (AMPV), was first isolated from commercial turkeys in Colorado in 1996.  The disease was reported in the United Kingdom in 1985 and prior to 1996 the disease was exotic to North America.  The virus causes a mild, but rapidly spreading, upper respiratory disease, with adverse effects on weight gain and feed conversion.  Secondary bacterial infections increase the severity of the disease.  APV infections continue to cause productivity losses in turkeys in the Upper Midwest particularly in Minnesota and more recently in Iowa, Wisconsin, and North and South Dakota.  The initial diagnosis of the disease in the United States was delayed because the U.S. isolates were of a different subtype than had been isolated elsewhere and serological assays to detect the new subtype had to be developed.  ARS scientists, in collaboration with scientists at the University of Minnesota, deciphered the entire genomic sequence and compared the AMPV subtype C genes SH, G, and L nucleotides and predicted amino acid sequences with those of human metapneumoviruses (hMPV).  The comparison supported earlier findings that AMPV subtype C was closer evolutionary to hMPV than the other AMPV subtypes A, B, and D.


IMPACT/OUTCOME:  This scientific information suggests that the source of the new APV serotype seen in the United States was derived from humans and not from other avian sources.  This information will be critical as control measures are evaluated to control this emerging infectious disease of poultry.


ACCOMPLISHMENTS:  Vesicular stomatitis virus (VSV) is a viral disease clinically indistinguishable from foot-and-mouth disease, one of the most devastating exotic diseases in livestock.  Outbreaks of VSV, such as the 2004 outbreak in the southwestern United States, sporadically occurs causing serious economic losses due to quarantine and the cost of associated control measures.  The natural cycle of VSV in endemic areas and the factors mediating the emergence of this disease are not understood.  VSV outbreaks occur at 8-10 year intervals.  VSV Indiana subtypes cocal (VSIV-2) and alagoas (VSIV-3) cause outbreaks in Brazil and Argentina.  Little is known about the genomes of these viruses, hindering the development of molecular diagnostic tools for rapid detection.  ARS scientists have determined the full length genomic sequences of the prototype strains of VSIV-2 and VSIV-3, and found genetically conserved areas that could serve as potential targets for rapid detection tests.  In collaboration with the PAHO's PANAFTOSA laboratory in Brazil, ARS scientists have genetically characterized representative viruses from outbreaks occurring in these countries in the last 20 years, including the latest outbreaks in southern Brazil in 1997-1998.


IMPACT/OUTCOME:  ARS has determined the extent of genetic variation among VSV isolates from Brazil and Argentina.  This information will be used to design rapid molecular diagnostic tests that will enable molecular epidemiological studies to better understand the life cycle of this important livestock pathogen.


ACCOMPLISHMENTS:  Brucella abortus, the primary Brucella species infecting cattle, also infects other animals, including humans.  Brucellosis causes abortions, significant economic losses, and is a public health threat.  This disease has been nearly eradicated from cattle in the United States after sixty years of regulatory efforts by the Animal and Plant Health Inspection Service (APHIS) in collaboration with State regulatory personnel and cattle producers.  However, a high percentage of feral swine, and elk and bison in Yellowstone National Park and surrounding areas, are infected with Brucellosis and have the potential to transmit the disease to cattle.  The completion and annotation of the genomic sequence of a field strain of Brucella abortus provided valuable data that led to the development of a molecular test to do epidemiologic tracebacks.  By comparison to the sequences of B. melitensis and B. suis, unique genetic elements were identified.


IMPACT/OUTCOME:  The discovery of unique sequences in the Brucella abortus genome provides new opportunities for developing rapid molecular diagnostic tests to identify and eradicate the different Brucellosis species that can infect our domestic and wildlife animal species.


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


ACCOMPLISHMENTS:  Porcine reproductive and respiratory syndrome (PRRS) virus infections account for up to 15 to 20 percent of the economic losses yearly (nearly $600 million) in the U.S. swine industry.  Methods of PRRS virus intervention (vaccines, therapeutics, genetics, etc.) are limited and new novel strategies are desperately needed.  One reason new intervention strategies have not been forthcoming is the lack of information known about the host cell response to infection by PRRS virus.  ARS scientists demonstrated that PRRS virus infection does not result in the induction of type l interferons as would be expected with most RNA viruses.  Specifically, PRRS actively suppresses the induction of Interferon-beta (IFNB) expression, which also prevents the induction of Interferon-alpha (IFNA).  These results are significant because both IFNA and IFNB are members of the innate immune system, which is typically viewed as the first response of the immune system.  Activation of this response signals other branches of the immune system to become activated and mount a protective immune response.


IMPACT/OUTCOME:  That PRRS virus is capable of suppressing the innate immune response may explain an important mechanism this virus uses to evade the immune host response, a critical step in the design of effective biotherapeutics and vaccines to control this important swine disease. 


ACCOMPLISHMENTS:  One of the major concerns with Transmissible Spongiform Encephalopathies (TSEs) is that Bovine Spongiform Encephalopathy (BSE) has been shown to cross the species barrier to cause a unique TSE in human beings.  Although there has not been a similar demonstration that Chronic Wasting Disease (CWD) could present any risk to human health, the BSE experience has raised many questions about the potential hazard CWD and other TSEs present for transmission to other animal species, especially domesticated livestock and wildlife.  ARS scientists have focused on direct experimental challenge studies to assess the relevance of the species barrier as predictive models for future risk assessments.  CWD transmission studies with cattle showed that although abnormal prion (PrPres) amplification occurred following direct CWD inoculation into the brain of cattle, none of the affected animals had classic histopathologic lesions of spongiform encephalopathy.  Furthermore, only 38 percent of the inoculated cattle demonstrated amplification of PrPres. Although intracerebral inoculation is an unnatural experimental route of exposure, it is the most severe challenge possible.  The results of these interspecies transmission studies suggests that cattle are either resistant to CWD or that CWD transmission  may require long incubation periods of up to five years. 


IMPACT/OUTCOME:  These studies provide information about the clinical and pathological disease characteristics that can be expected if a TSE crosses the species barrier; thus enabling animal health specialists to recognize such situations should they occur.  Additional transmission studies in the natural host will focus on determining the modes of transmission and disease development so that appropriate intervention strategies can be devised that will control the spread of these diseases.


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 was one of the first laboratories to conduct poultry-related research for both the Severe Acute Respiratory Syndrome (SARS) virus and West Nile Virus in the United States.  The SARS virus emerged in Southeast Asia and infected over 8,400 humans causing over 800 deaths.  Early epidemiologic evidence suggested a zoonotic potential for the virus with animals in the live animal markets in China.  The source of the virus causing SARS is still unknown but animals may be the source or may be contributing to the spread of the virus.  ARS scientists conducted a study to determine if chickens, turkeys, ducks, geese, and Japanese quail were susceptible to the SARS virus and could spread the virus to humans.  The study failed to demonstrate that the SARS virus could grow in these birds.  These data indicate that the common five domestic poultry species were not the reservoir and will not spread the SARS virus to humans.  Similar research with West Nile Virus was conducted that showed the common poultry species could be infected with these viruses, but clinical disease seldom occurred and that with low levels of viremia, these species were unlikely to spread the virus.


IMPACT/OUTCOME:  This research contributed to our understanding of the host range (identification of susceptible animal species) of two new and emerging diseases, which is vital to our understanding of disease transmission and the epidemiology of these zoonotic diseases (diseases humans acquire from animals).


ACCOMPLISHMENTS:  Listeria monocytogenes is a bacterium capable of causing serious disease in humans and animals.  L. monocytogenes infection of cattle and sheep can lead to disease of the central nervous system and death.  Human listeriosis is a potentially fatal foodborne disease often associated with the consumption of contaminated dairy products.  ARS scientists, in collaboration with Washington State University, developed the first biologically relevant model that can be used to assess L. monocytogenes strain virulence.  Six human epidemic strains and six environmental strains were assayed for invasiveness using an oral inoculation mouse model.  Variation in strain invasiveness was observed and epidemic strains were significantly more invasive than environmental strains.


IMPACT/OUTCOME:  In order to understand the epidemiology and epidemic potential of L. monocytogenes isolates, it is important to effectively access their virulence.  The development of a validated model to assess virulence is a critical step towards understanding why some strains cause epidemics whereas others do not.  The oral inoculation mouse model will be used to evaluate the virulence potential of genes present in epidemic strains and provide valuable insight into understanding the epidemiology of this animal and human health threat, resulting in the application of early control measures at the farm level.


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 2004, ARS will continue to identify genetic markers and genes (target one marker or one gene) from food animals that can be used to identify animals with disease resistant traits.


ACCOMPLISHMENTS:  Mastitis is one of the most costly diseases in animal agriculture, with economic losses estimated to be $1 to 2 billion annually in the United States.  More than one-third of the Nation's herd of 9.5 million dairy cows experience at least one episode of mastitis during each lactation.  Increasing the mammary gland’s level of resistance to a wide range of pathogens, including coliforms and environmental pathogens, could have a significant impact in curtailing this costly disease.  A primary target is the white blood cells called neutrophils, which are considered the first line of defense against the bacterial pathogens responsible for Mastitis.  ARS scientists successfully applied a proteomics approach using mass spectrometry to determine the proteome (the entire protein profile) of the neutrophil of the cow.  Over 250 major proteins were identified.  Most are involved in glycolysis and energy transformations.  However, many proteins were also involved in the function of the phagosome and the enzymes involved in phagocytosis and killing of bacteria. 


IMPACT/OUTCOME:  ARS scientists have previously established a clear link between diseases affecting dairy cows around parturition and a poorly functioning immune system.  Efforts to boost the proficiency of neutrophils could have a major impact in controlling periparturient diseases, resulting in a major benefit to dairy producers by reducing economic losses due to culling of infected cows, discarding of affected milk, and cost of veterinary care.  In addition, consumers will benefit from reduction of antibiotic use in the food chain and increased safety of milk through reduced pathogen contamination.  The discovery of the neutrophil proteome will enable scientists to conduct experiments to identify genes associated with highly functioning neutrophils and develop genetic tests to accurately and reliably predict which cows are most susceptible to disease.


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 2004, 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:  ARS played a significant role in providing the Animal and Plant Inspection Services (APHIS) with critical scientific information that enabled the USDA to take swift action when the first Bovine Spongiform Encephalopathy (BSE) case was discovered in Washington State, December 2003.  ARS very quickly applied sophisticated tests developed to inform our regulatory and action agencies that the test samples from the alleged BSE downer cow were of bovine origin (confirming the integrity of the samples), BSE-positive, and that the suspect cow in Washington State came from Canada.


IMPACT/OUTCOME:  Discovering the first BSE-infected cow in the United States had the potential to significantly impact our economy, undermine the confidence of our trade partners in our cattle industry, and curtail our export market of live cattle and meat products.  The tests developed and used by ARS to investigate the Washington State BSE Index Case enabled APHIS and other Federal agencies to move forward rapidly with a decisive action plan to protect consumers and limit the damage to our livestock industries.


ACCOMPLISHMENTS:  An ARS TSE scientist was detailed on special assignment at the request of APHIS and the Agricultural Marketing Service (AMS) to serve in a scientific advisory capacity on the U.S. - Japan BSE Technical Working Group.  This group met three times with a Japanese delegation to establish criteria regarding a return to normal U.S. beef export trade relations with Japan.  As part of this special assignment, the ARS scientist authored a critical chapter entitled "Definition of BSE and the method of Testing," for the U.S. BSE Reference Book.


IMPACT/OUTCOME:  This document is now used by AMS and the International Trade Policy group of the Foreign Agricultural Service in U.S. trade negotiations.


ACCOMPLISHMENTS:  Use of antibiotics and other drugs and chemicals in the dairy industry is one of the greatest threats to food safety.  ARS scientists demonstrated that a biotherapeutic (Poly-X) to prevent mastitis in dairy cows during the dry period was at least as effective as antibiotics.  At dry off, mammary quarters of 40 cows were injected with antibiotics and 40 cows were injected with Poly-X.  At the time of calving, cows treated with Poly-X had less mastitis than cows treated with antibiotics.  A patent application has been filed.  Dairymen and organic farmers will have available a non-antibiotic compound for use during the dry period for dairy cows.


IMPACT/OUTCOME:  The dairy industry needs new tools to overcome the problems associated with the use of antibiotics.  Surveys indicate that at least 5 percent of bulk milk shipments and 30 percent of milk sold to consumers contains detectable amounts of antibiotics and drugs. This presents a potential human health hazard.  Also, the antibiotics approved for treating mastitis are increasingly ineffective, largely due to the appearance of resistant strains.  An effective “non-antibiotic” biotherapeutics to prevent mastitis during the dry period of dairy cows provides a new tool to combat this important disease without relying on traditional drug use and their potential adverse effects on the health of consumers.


ACCOMPLISHMENTS:  Newcastle disease virus (NDV), also known as avian paramyxovirus type 1 (APMV-1), infects all known wild and domestic bird species.  Different NDV strains vary in virulence from those that caused disease and mortality during the 2002-2003 outbreak of exotic Newcastle disease (END) in California to those of low virulence that cause mild or unapparent respiratory infections with reduced flock productivity, the predominant form that occurs in the United States.  END is a reportable disease.  Its presence in commercial poultry has resulted in embargoes of poultry exports from the affected U.S. States.  Currently, there is no method beside animal inoculation to determine the virulence of NDV.  ARS scientists examined the embryonated chicken egg as a model system to evaluate virulence properties of NDV isolates.  Embryos from eggs inoculated with NDV reference and mutated reference strains were collected, formalin fixed, sectioned, and stained with a gene probe and NDV antibodies to detect virus distribution in the tissues and membranes of the embryonated eggs.  Low virulence strains were detected exclusively in the cells of the chorioallantoic membrane, whereas more virulent NDV isolates and mutated strains that were demonstrated to have acquired virulence for chickens were widely disseminated in chicken embryo tissues.


IMPACT/OUTCOME:  The research demonstrates the potential value of using, as an alternative to chicken inoculations, chicken embryos as a model system for evaluating NDV virus virulence.  As a result of ARS’ research, information is provided more quickly on the virulence potential of new NDV isolates, and the response time for implementing control measures is decreased.


ACCOMPLISHMENTS:  Poult Enteritis Mortality Syndrome (PEMS) is a highly infectious disease of young turkeys.  PEMS and similar disease conditions have been reported in most regions where turkeys are commercially produced, including the Southeastern United States, Texas, California, Arkansas, Missouri, and Israel.  PEMS has been called one of the most devastating emergent diseases to strike the poultry industry in recent years.  Since its emergence in the early 1990s, outbreaks of PEMS have annually cost the turkey industry millions of dollars in losses.  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.  PEMS appears to be a complex disease, possibly involving multiple pathogens.  Some anecdotal evidence suggests that immunosuppression may be involved.  Real-time reverse transcriptase polymerase chain reaction (RRT-PCR), a new molecular rapid diagnostic technique, which is highly specific and highly sensitive (superior to standard RT-PCR), was developed and applied to the detection of three viruses commonly associated with PEMS, turkey astrovirus, turkey coronavirus, and turkey reovirus.  Laboratory validation for these tests with clinical samples from experimental cases was successfully completed with optimization of sample types and times determined for each of the three viruses.  This assay is superior to previous tests and will accurately identify infected turkeys.


IMPACT/OUTCOME:  Previously, no rapid or specific diagnostic tools were available for the detection of the viral agents associated with PEMS.  The development of a highly specific and sensitive RRT-PCR assay will enable scientists to decipher the role turkey astrovirus, turkey coronavirus, and turkey reovirus play in causing PEMS and may lead to the modification of management practices to minimize the impact of this disease.


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 2004, 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:  Sustainable sugarcane production in Florida is a challenge due to susceptibility of sugarcane to a wide array of disease and insect pests.  After eight years of testing, ARS scientists at Canal Point, Florida, in collaboration with researchers at the University of Florida, Belle Glade, Florida; and the Florida Sugar Cane League, Inc., Clewiston, Florida, released sugarcane cultivars CP 97-1944 and CP 97-1989.  These two new cultivars add genetic variability for disease and insect resistance while producing at sustained levels of profitability in Florida. 


IMPACT/OUTCOME:  These releases are significant since sugarcane in Florida is almost always grown as a monoculture, so new cultivars are continuously needed for resistance to intense disease and insect pressures.


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




During FY 2004, 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:  The pink hibiscus mealybug (PHM) can destroy more than 200 plant species by injecting them with toxic saliva while sucking their sap.  The exotic insect pest recently invaded California and Florida, and has proven difficult to track and monitor.  ARS scientists in Beltsville, Maryland, have discovered two compounds that together make up the female PHM’s sex pheromone.  The compounds provide a timely method with which to monitor and ultimately reduce infestations. 


IMPACT/OUTCOME:  Officials with the Animal and Plant Health Inspection Service (APHIS) are using the new pheromone as a sex lure to survey the degree of mealybug pest infestations in California and Florida and to track the effectiveness of biological control efforts against the pest.  ARS has applied for patent protection for the invention and already has received requests to license the technology.  The new blend of synthetic pheromones also could help crop producers manage the pests safely through either mass trapping or disruption of mating activity.


ACCOMPLISHMENTS:  Fundamental research on fungal pathogens, including how these pathogens survive and successfully infect their insect hosts in field and greenhouse environments, will foster the development of safe, effective alternatives to chemical insecticides.  Scientists in Ithaca, New York, have found that a single application of Bacillus thuringiensis (Bt) together with the fungus, Beauveria bassiana, has resulted in an 81 percent reduction in target populations of large larvae of the Colorado potato beetle. 


IMPACT/OUTCOME:  These results indicate the strong potential for using these agents as the key components of an integrated biocontrol program for Colorado potato beetle management.


ACCOMPLISHMENTS:  Enticing new lures developed by ARS scientists at Wapato, Washington in cooperation with Washington State University could make backyard gardens, fruit orchards, and crop fields places of no return for pesky caterpillars that cause millions of dollars in losses.  The lures, derived from molasses and floral odors, tantalize both male and female moths, and have been developed as an alternative to chemically controlling the pests—loopers, cutworms, fruitworms, armyworms, and corn earworms.  The insects fly into the opening of a lure-dispensing trap, never to escape.


IMPACT/OUTCOME:  The molasses-derived lure is now commercially available for garden use as the product SMARTrap.  The floral-based lures are in their second year of field tests.  So far, use of the floral lures in a “killing station” reduced the number of alfalfa loopers by 75 percent.


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


ACCOMPLISHMENTS:  The winter wheat-fallow production system in the Pacific Northwest is characterized by winter annual grass weeds and wind erosion.  There are no economically viable conservation cropping systems to solve these problems.  ARS scientists at the Land Management and Water Conservation Research Laboratory in Pullman, Washington, along with two university partners, developed a system for planting facultative spring wheat in November (rather than the normal March planting) in lieu of late-planted winter wheat when conditions are dry in the Fall. 


IMPACT/OUTCOME:  During the drought year of 2002-2003, this system was used.  It was more competitive against weeds, improved grain quality, and yielded 20 percent more compared to winter wheat.  Adoption of this alternative conservation cropping system would reduce the impact of weeds and erosion susceptibility, and increase air quality.


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 allowing for 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 development of an unwanted population of herbicide-resistant rice x red rice hybrids, a key management consideration in herbicide esistant 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:  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:  The detection assay was used by regulatory officials to accurately determine and identify a new outbreak of soybean rust in the southern United States in November 2004 which resulted in implementation of response planning.


ACCOMPLISHMENTS:  ARS isolated pathogenic fungi from pears shipped from China.  Pathogenicity testing was completed with other fruit-associated species.  After morphological and genetic characterization of the Chinese strains, the causal agent was determined to be a new species unknown to the United States.   


IMPACT/OUTCOME:  This research protected the U.S. pear industry from the introduction of potentially damaging exotic fruit pathogens.


ACCOMPLISHMENTS:  A unique and highly virulent strain of Fusarium oxysporum was discovered in cottonseed imported from Australia into California as a feed for cattle.  This strain devastated cotton production in areas of Australia where it occurs, resulting in 98 percent yield losses.


IMPACT/OUTCOME:  Identification of the highly virulent isolate from Australia resulted in the initiation of steps to more thoroughly disinfect cottonseed before it is allowed into the 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 2004, 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 tarnished plant bug damages a large number of crops throughout the United States, including fruits, vegetables, forestry nurseries, fiber crops, and seed crops.  ARS scientists in Newark, Delaware, have completed a long-term study documenting that a foreign parasitoid (Persistenus digoneutis) permanently controlled and reduced the tarnished plant bug and also demonstrated that a native parasite was not eliminated by this new introduction. 


IMPACT/OUTCOME:  These findings should increase confidence in the safety of classical biological control methods used against pest insects.


ACCOMPLISHMENTS:  Many insect pests in the United States are of foreign origin, introduced accidentally with few or no natural enemies.  ARS scientists in Montpellier, France, proved that an isolate of an entomopathogenic fungus collected in China proved more virulent than the current commercially available fungus when applied to the Formosan subterranean termite colony, but not when applied to individual termites.


IMPACT/OUTCOME:  This accomplishment is important because this experimental portal (individual and grouped) and analysis suggests an effective way to compare pathogen virulence among social insects. Also, scientists in Peoria, Illinois, have shown that an application of a bioinsecticidal fungus to trees infested with the Formosan subterranean termite significantly reduces the pest numbers and foraging activities.


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:  Invasive saltcedar (Tamarix spp.) shrubs from Eurasia infest many Western U.S. riparian areas and 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; and the Grassland Protection Research Unit, Temple, Texas.  The first biological control agent for saltcedar, the beetle Diorhabda elongata, was released in 1999 at 10 sites in 6 States.  The beetle has spread over 100 miles since release.  Use of aerial imagery and ground assessments shows that the beetle has totally defoliated saltcedar at many sites and is beginning to severely damage saltcedar on a landscape basis.  The impact of natural enemies is being evaluated on saltcedar and on native plant communities (cottonwoods and willows). 


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


ACCOMPLISHMENTS:  The invasive tree, Melaleuca quinquenervia, was introduced to South Florida in the late 19th century as an ornamental plant, but this fast growing, fast spreading tree has displaced native plants and animals, dried up wetlands, and created major fire hazards.  The spread of melaleuca is being thwarted in Florida, thanks to a cooperative program that utilizes the tree’s natural enemies in Australia.  The collaborative effort (TAME) is being carried out by ARS in cooperation with the University of Florida’s Institute of Food and Agricultural Sciences, and the South Florida Water Management District.  The purpose of TAME is to demonstrate the effective integration of biological control with other management strategies, including use of herbicides and mechanical removal of melaleuca.  The first natural enemy released against melaleuca was the melaleuca leaf weevil, oxyops vitiosa.  More than 8,000 of the weevils were released at 13 locations in 1997.   A second agent, the psyllid, Boreioglycapsis melaleucae, was released in 2002, and has spread widely since then.


IMPACT/OUTCOME:  The combination of the weevil and psyllid has been so successful that melaleuca is no longer threatening many of the natural areas in which it was dominant.


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


ACCOMPLISHMENTS:  ARS developed the first genetic map for the Fusarium head blight pathogen, the major fungal pathogen of wheat that produces several mycotoxins harmful to humans.


IMPACT/OUTCOME:  The map has been used in genetic diversity studies, and to validate and align the genomic sequence of the pathogen. 


ACCOMPLISHMENTS:  ARS examined genetic variation in over 300 strains of Phytophthora infestans, causal agent of potato late blight.  ARS was able to demonstrate greater levels of genotypic diversity and that population structures differed from one location to another.


IMPACT/OUTCOME:  The major impact of understanding pathogen diversity will be to ensure that cultivars resistant to late blight have nonspecific resistance not limited to virulence genes in the current local populations of the pathogens.
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Last Modified: 8/17/2005
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