Tools, Cores & Labs

The Agricultural Systems and Microbial Genomics Laboratory (ASMG Laboratory) was established to support Dr. Dou and Dr. Pitta in their research endeavors.

Dr. Pitta is the ruminant nutrition and microbiologist at the Center for Animal Health and Productivity (CAHP), New Bolton Center, University of Pennsylvania.

Research at the ASMG lab focuses primarily on the gut microbial composition of ruminants utilizing advanced molecular methodologies. The alimentary tract of a ruminant is colonized by millions of microbes living in a symbiotic relationship with the host. Therefore, knowledge of the microbial composition of the entire gut can provide insights into improving the overall health and productivity of the animal. Our research  also has broad environmental implications into such diverse applications as methane mitigation, reduction of the spread of antibiotic resistance, and human health.

The recent advent of next generation sequencers has greatly enhanced our ability to explore community microbial populations. The ASMG lab has the capabilities to perform genomic, metagenomic, and metatranscriptomic studies including sample preparation, genomic DNA and RNA extraction, and generation of 16S amplicon libraries for sequencing on next-generation platforms. The sequenced data is analyzed at the ASMG laboratory utilizing the appropriate bioinformatics tools for data interpretation.

The ASMG group collaborates with other researchers and clinicians both within the University of Pennsylvania as well as at other institutions. Our research is routinely published and presented at conferences. We also work with students from multiple backgrounds, ranging from high school through postdoctoral, who have used their time in our lab to further develop their knowledge of microbial genomics and its applications. 

Read More About The ASMG Laboratory - Microbial Genomics

We study the biological basis of diseases caused by microbes -- whether it be a parasitic worm, a pathogenic bacterium, or a complex microbial community in the gut. Our group makes up the Center for Host-Microbial Interactions, at Penn Vet, and our research leverages a diverse skill set that cuts across the disciplines of genomics, microbiology and immunology. We engage in collaborative projects that benefit from close interactions with veterinarians and human clinicians alike. Our research embodies the idea of 'One-Health' - that humans, animals and the environment are interconnected, and that we all live in a microbial world. We are located at the The University of Pennsylvania, in The Department of Pathobiology at the School of Veterinary Medicine.

Read More About The Beiting Laboratory

Nitrogen, Phosphorus, and Integrated Management

Nitrogen and phosphorus are essential nutrients for growing plants and animals. Insufficient nutrients diminish yields; excessive applications translate to wasted resources and environmental pollution. The work of Dr. Dou’s group features an integrated system nutrient management approach, coupling nutrient optimization in animal feeding with manure management and targeted nutrient application to crops for enhanced production efficiency and reduced environmental footprint.

• Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

Integrated whole farm management based on nutrients (pathogen) flow pathway

 

 

Pathogens, Antimicrobial Resistance (AMR), and Livestock Farming 

Livestock animals are important reservoirs of zoonotic pathogens as well as antimicrobial resistant determinants (antibiotic residues, AMR microbes, and AMR genes).  What happens to these “microbial pollutants” in the post-shed environment? How long do they survive under different management conditions? What is their distribution pattern in the intrinsically linked farming sectors and the dissemination pathways to the broader terrestrial and aquatic ecosystems? What intervention may help mitigate relevant risks associated with animal farming concerning food safety and public health? The research of Dr. Dou’s group addresses some of these critical issues.

• Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

Food Waste, Food Security, and Sustainability

Sustainable food security is an issue that intersects many of the contemporary challenges the world is struggling to deal with today, e.g. water scarcity, water pollution, resource limitation, land degradation, habitat and biodiversity loss, climate change, and hunger and poverty.  Dr. Dou collaborates with national and international experts to examine sustainable food security issues from multiple dimensions, such as food waste reduction and reuse, engaging, and empowering smallholder farmers, etc. 

• Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

Developing Novel Feeds from Food Waste and Crop Residue Biomass from Cows

Livestock farming is at a crossroads, its sustainable future challenged by competing interests for limited resources and urgent need to mitigate environmental and climate footprints, amid a rapidly growing global demand for animal protein. One viable solution overlooked, is to leverage the innate ability of animals as nature’s most effective recyclers, able to utilize a wide variety of plant biomass materials as feed resources in producing meats, milk, and eggs. This project will deploy an innovative sequential fermentation approach to create novel feeds for dairy cows using food waste of fruit and vegetable discards and post-harvest crop residues such as wheat straw and spent mushroom substrates, abundantly available but currently wasted or landfilled. 

• Please see relevant projects and publications in 'Research Projects' and 'Publications' tab below.

Read More About The Dou Laboratory

At the Harty Laboratory, we focus our research on three main areas:

1. The molecular dynamics and biological significance of virus-host interactions during late stages of RNA virus assembly and egress.
2. The identification and development of host-oriented therapeutics as a new class of antiviral inhibitors.
3. The interplay between the host innate immune response and RNA virus infection.

Our model virus systems to interrogate these topics include:

• Filoviruses (Ebola and Marburg viruses)
• Arenaviruses (Lassa fever and Junín viruses)
• Rhabdoviruses (VSV)
• Retroviruses (HIV-1 and HTLV-1)

Read More About The Harty Laboratory

Dr. Christopher Hunter's research team has been working on various aspects of basic parasitology since 1984.

For nearly 25 years, Dr. Hunter's team has focused on understanding how the immune response to Toxoplasma gondii is regulated to allow the development of protective immunity as well as to limit T cell mediated pathology in multiple sites including the gut and brain.

Read More About The Hunter Laboratory

Welcome to the Lennon Mucosal Immunology Laboratory where we study Inflammatory Bowel Disease (IBD).

We believe that by studying naturally occurring IBD in dogs and cats we can improve treatment for people and pets with this debilitating condition. 

• Visit our new lab website...

Read More About The Lennon Mucosal Immunology Laboratory

Research Interests

Our main research interest is innate immune recognition and elimination of pathogens. Our work focuses on the interaction between mosquitoes and the animal and human pathogens they transmit. As the most species-rich group of animals on the planet occupying a vast array of ecological niches, insects are a fantastic example of the potency of innate defenses.

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PoveLab on TV and in the news:
★ The changing landscape of mosquito- and tick-borne diseases
★ News piece by Tom Avril in Philly.com
★ TV spot by John McDevitt for CBS 3 Philly
★ See us on Xploration Awesome Planet "Insects" (Season 3 Episode 10)
★ View UPenn Spotlight on Our Work

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Rather than passive or willing carriers of pathogenic organism, mosquitoes are actually amazing pathogen killers. Taking mosquito interactions with malaria parasites as an example, the vast majority of the parasites ingested when a mosquito bites a malarious person are attacked and eliminated before they can mount an infection in the mosquito. It is the few parasites that survive (even one is sufficient), that are ultimately responsible for disease transmission. Similar interactions occur between mosquitoes and the other pathogens they transmit, like canine heartworm (Dirofilaria) and arboviruses (Zika, Dengue, Yellow Fever, West Nile, and Chikungunya).

Arthropod vectors such as mosquitoes, sand flies and ticks are responsible for transmission of a large number of animal and human diseases worldwide. Studying these organisms may reveal general insights about innate immune defense mechanisms as well as provide novel avenues for controlling the terrible diseases they spread.

Some of the questions we are addressing:

• What is the basis of pathogen recognition by the mosquito innate immune system and how do some pathogens manage to escape?
• What is the biochemical mechanism leading from innate recognition to pathogen killing?
• How is mosquito complement regulated?
• How does steroid hormone signaling regulate mosquito immunity?

Read More About The Povelones Laboratory

The Reference Andrology Laboratory provides complete testing of neat, cooled and frozen-thawed semen from mammalian and avian species. The primary purpose of these services is to aid practitioners in their differential diagnosis of individual/herd/flock reproductive problems.

These services are also frequently used by practitioners and studs as a third-party quality control component in an ongoing stud auditing process.

The laboratory strives to perform objective, validated techniques for assessing samples for the basic spermiogram parameters of sample volume, motility, morphology, and concentration. With advanced notification, we will also try to accommodate requests for supplemental assessment techniques on sperm subcellular structures. We also offer semen extender analysis and microbiological testing of the extended semen product and purified water used in extenders. 

Read More About The Reference Andrology Laboratory

Dr. Scott's current research is focused on understanding the development, regulation and maintenance of CD4+ and CD8+ T cells in order to design new vaccines and immunotherapies for infectious diseases.

The laboratory primarily focuses on experimental murine infections with the protozoan parasite, Leishmania, which provides a well-characterized model of T helper cell differentiation.

Read More About The Scott Laboratory

Welcome to the Striepen lab

We study the cell and molecular biology of parasites, and use our findings to develop new treatments. Most of our research is focused on Cryptosporidium and Toxoplasma, two protozoan parasites that threaten small children and those with weakened immune systems.

For the latest updates on our research, please visit https://www.striepenlab.org/.

Read More About The Striepen Laboratory

Check out the new Vaughan Laboratory Website

Dr. Vaughan’s research is focused on defining and understanding the relevant cell types and molecular mechanisms by which the mammalian lung is able to regenerate after severe injury. He is especially interested in elucidating the means by which epithelial progenitors contribute to repaired airway and alveolar units after various lung insults (influenza, ARDS, fibrosis). His studies suggest that physiological lung function is in fact dictated by progenitor cell fate choices after injury.

Dr. Vaughan and his group have developed a novel orthotopic cell transplantation assay which allows for the direct assessment of engraftment, proliferation, and differentiation potential of these stem cells. Further, he is actively investigating the roles of the Notch, Wnt, and BMP pathways in regulating the differentiation potential and fate of expanded progenitor cells post-injury.

Dr. Vaughan is part of the CAMB (DSRB) graduate group, and is a member of the Penn Institute for Regenerative Medicine (IRM).

• Read a recent interview with Dr. Vaughan by the Institute of Regenerative Medicine at the University of Pennsylvania...

Dr. Vaughan is currently seeking new graduate students to join his laboratory team. He welcomes inquiries for potential rotations from incoming students. Contact Dr. Vaughan directly at andrewva@vet.upenn.edu

Read More About The Vaughan Laboratory

The Wildlife Futures Program, a science-based, wildlife health program serves to increase disease surveillance, management and research to better protect wildlife across the Commonwealth of Pennsylvania and beyond. Read More About The Wildlife Futures

The Aquaculture Laboratory provides necropsy and diagnostic testing of commercial and ornamental fish. With facilities at both NBC and the Manheim Field Office, the Aquaculture Laboratory is easily accessible for live fish drop-off.  The laboratory provides testing for diagnostics purposes only. Any regulatory testing should be submitted through the Pennsylvania Veterinary Laboratory. More information can be found on the PADLS website.

As part of PADLS, the Aquaculture Laboratory supports PADLS’ program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

Read More About The Aquaculture-PADLS

The Avian Pathology service strives to provide the best possible diagnostic service to Pennsylvania and regional producers, hatcheries, service personnel, feed companies, and breeder companies. Over the past decade, the service has expanded to include pet bird cases submitted by regional veterinarian, pigeons, waterfowl and birds of prey cases submitted by local wildlife organizations, backyard poultry flocks, and exhibition/show birds. Services include avian necropsies, serologic testing, virus isolation, and PCR. The board certified veterinary staff is not only qualified to provide accurate diagnostics but also advise on the treatment, control, and eradication of infectious diseases. Avian field investigation also adds to the array of services available.

As part of PADLS, the Avian Pathology service supports PADLS’ program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

Read More About The Avian Pathology Laboratory-PADLS

Located in the northwest part of Lancaster County, the Field Office is a convenient location for veterinarians, farmers, and wildlife rehabilitators living in the western part of the county. The Field Office provides services in both avian pathology and aquaculture including necropsies of birds and fish and sample drop-off for microbiological testing, serology, and toxicology. Clinical and environmental samples received at the Field Office are taken to New Bolton Center for testing.

As part of PADLS, the Field Office supports PADLS’ program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

Read More About The Field Office Lancaster County-PADLS

The Mammalian Pathology Laboratory Service at New Bolton Center is a constituent of the Pennsylvania Animal Diagnostic Lab System (PADLS) and provides complete autopsy and biopsy services to the patients of New Bolton and referrals from veterinarians throughout the state. Out-of-state cases are accepted for an additional fee (see PADLS fee schedule). Specialties include orthopedic pathology, infectious disease, veterinary forensics and translational animal models. Various histochemical and immunohistochemical techniques are employed to identify a variety of infectious agents and specific cell components in histology sections.

The combined resources and technical expertise of leading pathologists and scientists of New Bolton Center's Mammalian Pathology Laboratory Service, in conjunction with PADLS, provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support animal producers to ensure a safe, secure, and abundant food supply.

Read More About The Mammalian Pathology Laboratory-New Bolton Center-PADLS

The microbiology laboratory is separated into three subgroups: Clinical Microbiology, Molecular Microbiology, and PEQAP.

Located in the Myrin Building on the New Bolton Campus, the Clinical Microbiology laboratory is equipped with the latest technology and a knowledgeable support staff to provide diagnostic microbiology testing. Consultation and field investigation are also available. Testing includes aerobic, anaerobic, and fungal culture, and antibiotic susceptibility testing. 

Molecular Microbiology uses sophisticated techniques to isolate and identify viruses and bacteria including polymerase chain reaction (PCR) and real-time reverse transcriptase-PCR. These methods are commonly used to identify Avian Influenza, Salmonella spp., and Streptococcus equi (Strangles).

In addition to standard microbiological testing, the microbiology laboratory also performs egg testing as part of the Pennsylvania Egg Quality Assurance Program (PEQAP) and the FDA Egg Safety Rule. Farms that participate in these programs demonstrate their concern about food safety and produce a quality egg which helps to assure consumer confidence in eggs.

As part of PADLS, the microbiology laboratory supports PADLS' program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply. 

Read More About The Microbiology Laboratory-PADLS

Located in the Myrin Building on the New Bolton Campus, the toxicology laboratory is equipped with the latest technology and a knowledgeable support staff to provide full veterinary diagnostic toxicology services. Animals can be exposed to toxic chemicals in a number of ways: ingestion of contaminated feed or foreign objects, inhalation, or skin contact. Through identification of such toxic chemicals, the toxicology laboratory helps to diagnose and prevent toxicosis in agricultural animals, pets, and wildlife. In addition to toxins, the laboratory has the ability to identify the levels of nutritionally relevant compounds including metals and vitamin E in animal samples.

As part of PADLS, the toxicology lab supports PADLS' program objectives and mission. The combined resources and technical expertise of leading scientists at PADLS laboratories provide state-of-the-art diagnostic technology supporting veterinarians’ efforts to advance animal and public health initiatives and support producers in assuring a safe, secure, and abundant food supply.

Read More About The Toxicology Laboratory-PADLS