Environmental Health Research at Penn
Affinity Groups
Affinity Group I
Oxidative Stress and Oxidative Stress Injury
Affinity Group Leader: Dr.Ian Blair
Group Description
The aim of the Affinity Group in Oxidative Stress and Oxidative Stress
Injury is to assess the biological effects of environmentally-induced oxidative stress and ensuing cell, tissue, and organ injury. Environmental factors studied by members of this affinity group include asbestos, environmental estrogens, diesel exhaust emissions, heavy metals, insecticides, nanoparticles, polycyclic aromatic hydrocarbons (PAH), PM2.5, and tobacco smoke. Exposure to these factors results in oxidative stress by the generation of reactive species (superoxide anion, hydrogen peroxide, hydroxyl radical, peroxynitrite, and nitrogen dioxide) at rates and quantities that overwhelm protective mechanisms of the cell. All of these factors are important from the standpoint of urban environmental toxicology and public health. A unique aspect of this Affinity Group is the identification of new biomarkers of oxidative stress and the development of stable isotope dilution LC/MRM/MS methodologies for their detection and quantitative measurement in biological samples. Investigators in this affinity group have overlapping research interests that relate to oxidative stress in: lung disease; lung cancer; cardiovascular disease, neurodegenerative disease; and reproduction.
Oxidative Stress and Oxidative Stress Injury Group Members:
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Affinity Group II
Reproduction, Endocrinology, and Development (READ)
Affinity Group Leader: Dr. George Gerton
Group Description
The aims of the Affinity Group in Reproduction, Endocrinology, and Development are to evaluate the effects of environmental stressors and endocrine disrupting chemicals, and the express risk offered by them for impaired fertility, reduced fecundity, adverse pregnancy outcomes, and dysregulation of steroid hormone metabolism and signaling. Adverse pregnancy outcomes are of relevance to Southeastern Pennsylvania, which has a disproportionate level of low weight births, pre-term births, and infants with birth and developmental defects. Investigators in this Affinity Group have interests in the following:
- Environmental exposures that affect gametogenesis; reproductive aging
- Genomic imprinting in the pre-implantation embryo
- Adverse pregnancy outcomes and pre-term birth
- Male reproductive tract development
- Steroid hormone metabolism and signaling
Reproduction, Endocrinology, and Development Affinity Group Members:
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Affinity Group III
Lung and Airway Disease
Affinity Group Leader: Dr. Michael Beers
Group Description:
The aim of the Affinity Group in Lung and Airway Disease is to determine the interactions between environmental exposures and the lung within the context of a genetic predisposition for the induction and progression of airway diseases (asthma or COPD) and lung cancer and mesothelioma. Three major areas of investigation are in airway hyper-responsiveness (AHR) with a focus on ozone-exacerbated asthma and innate immunity, environmental tobacco smoke and chronic lung disease, and tobacco and environmental carcinogenesis (TEC) with a focus on lung cancer and mesothelioma.
Lung and Airway Disease Affinity Group Members
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Affinity Group IV
Gene-Environment Interactions
Affinity Group Leader: Dr. Alexander Whitehead
Group Description:
The aim of the Affinity Group in Gene-Environment Interactions is to identify individual susceptibility to diseases of environmental etiology based on predisposing genetic factors and their association with altered metabolomic, transcriptomic and proteomic phenotypes that are evoked by environmental toxicants and nutritional stress. Diseases of interest are complex traits, in which the interaction of multiple genes with exposures will determine susceptibility, onset and progression of disease, and response to treatment. The concepts that environment exposures alter gene expression patterns via DNA methylation, chlorination and oxidation, and via histone methylation and acetylation, are exciting developments in EHS. In particular, the epigenetic changes in DNA that can lead to heritable changes in gene expression potentially underpin the developmental origins of some of the adult diseases that are addressed in several projects proposed by the ERD and GEI affinity groups. Investigators in the GEI affinity group include molecular epidemiologists/geneticists, experts in exposure biology, and computational biology.
Gene-Environment Interactions Affinity Group Members:
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Facility Cores
Molecular Profiling Facility Core
The Molecular Profiling Core (MPC) was formed in April 2008 to provide CEET investigators with the resources to conduct integrated “omics” and biomarker research related to toxicant exposure and response. This was accomplished by combining the resources of the existing Toxicogenomics, Toxicoproteomics, and Biomarker Facility Cores into a single Facility Core. Each of these individual areas has a dedicated Technical Director who has considerable expertise in the application of the relevant technology to toxicology research. The MPC provides an integrated systems biology approach to identify molecular fingerprints of exposure and response.
Facility Service I
Toxicogenomics
Request Toxicogenomics Consultation (You must indicate whether you are a CEET member in your request to gain priority access.)
The mission of the Toxicogenomics component of the Molecular Profiling Core is to foster both basic and translational research into environmental health science within the CEET. Existing institutionally supported genomics resources have been expanded to provide coordinated, focused support for environmental toxicology projects in the CEET. This is accomplished by providing scientific consultation, instrumentation, and technical expertise for high throughput RNA transcript profiling, high-throughput genotyping, massively parallel sequencing, and toxicogenomic data analysis.
Services Available
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Target Preparation and Sequencing
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Massively Parallel Sequencing
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Quantitative PCR
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Custom Multiplex Genotyping
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Whole Genome Profiling
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Transcript Profiling
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DNA Profiling
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Molecular Diagnosis and Genotyping
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Bioinformatics and Data Analysis
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Quality Control for User Projects
Request for Services
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Facility Service II
Toxicoproteomics
Technical Director : Chao-Xing Yuan |
Request Toxicoproteomics Consultation (You must indicate whether you are a CEET member in your request to gain priority access.)
The mission of the Toxicoproteomics Core is to provide and disseminate state-of-the-art scientific and technical knowledge in toxicoproteomics that will contribute to the research programs of investigators within CEET. This will be accomplished by exploiting and evaluating the impacts of discoveries in toxicoproteomics, through focused efforts in: instrumentation, protein separation and detection, and bioinformatics.
Services Available
- Gel-based proteomics .
- Applied Biosystems Qstar-Pulsar
- Thermo Scientific LTQ Mass Spectrometer
- Thermo Scientific LTQ-XL Mass Spectrometer
- Thermo Scientific LTQ-FT mass spectrometer
- Protein Sequencing by 2D-LC-MS/MS
- Peptide and Protein Identification
- Post-translational Modifications
- Quality Control
Request for Services
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Facility Service III
Biomarker
Request Biomarker Consultation or Services (You must indicate whether you are a CEET member in your request to gain priority access.)
The mission of the Biomarker Facility is to foster the use of sophisticated analytical methodologies to detect biomarkers. Biomarkers can be analyzed in model systems, in vivo and ultimately patient populations. The Core provides diverse analytical services primarily based on LC/MS methodology. Immunologically based assays are developed when they are required.
Technical Director: Clementina A. Mesaros, PhD
Biomarker Core Facility
Center of Excellence in Environmental Toxicology
841 BRB II/III
Philadelphia, PA 19104-6160
Tel. 215.573.9878
Fax 215.573.9889
Services provided by the Biomarkers Core Facility include:
1. LC-MS assays for urinary endogenous DNA-adducts
2. LC-MS assays for polycyclic aromatic hydrocarbon-derived adducts
3. Chiral LC/electron capture/MS assays for plasma and urinary lipids, eicosanoids, and isoprostanes
4. LC-MS assays for 8-oxo-dGuo
5. LC-MS assays for saturated and unsaturated fatty acids
6. LC-MS assays for RNA-adducts
7. LC-MS assays for lipid hydroperoxide-derived GSH adducts
8. LC-MS assays for plasma estrogens
9. LC-MS assay for androgens
10. LC-MS assay for other steroids
11. LC-MS assay for red blood cell folates
12. LC-MS assay for nicotine, cotinine, 3-hydroxy-cotinine, and glucuronides
13. LC-MS assay for urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and glucuronide.
14. Stable isotope dilution LC/MS assays for novel biomarkers
Project Forms and Submission Guidelines
To begin a project:
1. Schedule a consultation with Clementina Mesaros, PhD, email: mesaros@upenn.edu
2, Complete the Biomarkers Sample Submission Form (at the bottom of this page) and submit it on-line (link also below). If you are not affiliated with the University of Pennsylvania, substitute Penn-specific items with sufficient information for billing from the Center for Excellence in Environmental Toxicology. You will receive a confirmation email containing your Facility Project ID. Use this on all correspondence and sample description forms.
Instrumentation
1 Applied Biosystems API 4000 This LC-MS/MS System is an enhanced high performance triple quadrupole mass spectrometer system that is widely used in the pharmaceutical industry for drug metabolism and pharmacokinetic studies. It has the Turbo V Source and is equipped with both TurboIonSpray and APCI probes. Analyst software is used for data acquisition and processing. The proprietary Curtain Gas interface technology combined with improved gas dynamics reduces maintenance and permits enhanced high flow rate performance. The Turbo V source permits rapid exchange between APCI and TurboIonSpray probes for enhanced flexibility
2. Thermo Scientific TSQ Quantum-AM mass spectrometer The Thermo Finnigan TSQ Quantum Ultra AM LC/MS/MS System represents the current state-of-the-art in commercial instruments with electron capture APCI capabilities. The Ion Max source in this instrument has interchangeable ESI and APCI probes, a titanium skimmer with hard-edged skimming, and a larger aperture for increase of robustness and sensitivity. It has a redesigned ion transfer tube lens with wider aperture for enhanced ion focusing and ion transmission. The new “Ion Max” source also allows full probe adjustment in the x, y, and z directions with two view ports and a quick release probe lever. The probe position can be optimized for maximum robustness and sensitivity with any given combination of flow rate, solvent, and ionization mode. Its new, ultra high temperature, self-cleaning APCI probe, with ceramic heater, virtually eliminates carryover. The Finnigan TSQ Quantum Ultra's innovative technology provides the widest linear dynamic range and lowest sensitivity limits of any triple quadrupole mass spectrometer on the market (5-6 orders of magnitude). The instrument has the powerful capability of routine accurate mass measurements on the chromatographic timescale. Its redesigned analyzer control circuitry allows full advantage to be taken of the high-resolution HyperQuad mass analyzers. This makes it possible to conduct high-resolution analyses with minimal loss of sensitivity. The TSQ Quantum Ultra AM does not suffer from centroid mass shifts as is observed with hybrid instruments such as quadrupole-time of flight systems which use an array detector with a time-to-digital converter. This type of detector has an inherent “dead time” after an ion at a given m/z strikes the detector. The instrument analyzer includes stabilized analyzer control board, integrated vacuum manifold with two RF only square quadrupole ion optics, two 250 mm hyperbolic quadrupole mass analyzers, ninety degree square quadrupole collision cell, 15 kV dynode. Also an off axis electron multiplier detection system can be used for positive and negative ion detection. The TSQ Quantum is controlled by Xcalibur, a robust data system for data acquisition and processing.
3. Thermo Scientific LTQ-XL Mass Spectrometer The LTQ-XL instrument dedicated to biomarker detection extends the excellent MSn performance of the LTQ, incorporating more techniques to generate structural information through Thermo Scientific’s innovations in ion trap technology. Thermo LTQ XL is the only mass spectrometer that offers Pulsed Q Detection (PQD) and collision induced dissociation (CID). PQD is a technique that eliminates the low mass cut-off concern inherent with all ion traps. This results in extensive coverage for predicted and unpredicted tryptic peptides. Fast polarity switching for high-sensitivity analysis of unknowns, high resolution isolation (HRI), intelligent Data Dependent™ acquisition, and optional high resolution accurate mass functionality are all tools to help provide confident routine structural identification of biomarkers.
4. Waters Xevo represents a significant improvement over current triple quadrupole LC-MS systems. The instrument is equipped with a Waters ultra high performance liquid chromatography (UPLC), which makes it possible to conduct high pressure chromatography, which significantly improves separations of complex mixtures.
Charges:
Item code |
Description |
Typical Cost |
110 |
LC/MS analysis, 1-10, per sample |
$100 |
120 |
LC/MS analysis, 11-20, per sample |
$95 |
130 |
LC/MS analysis, 21-30, per sample |
$90 |
140 |
LC/MS analysis, 31-40, per sample |
$85 |
150 |
LC/MS analysis, 41-50, per sample |
$80 |
300 |
Data analysis, per hour |
$60 |
210 |
Sample preparation and LC/MS analysis, 1-10, per sample |
$300 |
220 |
Sample preparation and LC/MS analysis, 11-20, per sample |
$280 |
230 |
Sample preparation and LC/MS analysis, 21-130, per sample |
$260 |
240 |
Sample preparation and LC/MS analysis, 31-40, per sample |
$240 |
250 |
Sample preparation and LC/MS analysis, 41-50, per sample |
$220 |
15% discount for CEET |
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Integrative Health Sciences Facility Core
Director: Reynold A. Panettieri, Jr.
The dual mission of the Integrative Health Sciences Facility Core (IHSFC) is to: (i) provide infrastructural support for the translation of basic science observations into human studies and trials with the ultimate aim of detecting, preventing and/or managing diseases induced or exacerbated by environmental exposures, and (ii) “back translate” environmental health questions derived from the community into testable hypotheses for human studies (Figure 1).

Current and prospective investigators interested in extending their research into human studies may access the IHSFC via this web site. Community-based questions relating to healthy individuals or patients will be channeled through the Community Outreach and Engagement Core (COEC) and framed as scientifically relevant queries to be addressed by CEET investigators using the resources of the IHSFC.
A focus is on predicting who is at risk of exposure, who is at risk for disease, and who will respond to treatment with an emphasis on PERsonalized Environmental/health Medicine (PEREM).
Using integrated and leveraged resources for human research, the IHSFC provides assistance with a broad range of transdisciplinary services including study design, enrollment of research subjects, human and population exposures, data management, access to biological samples, biostatistical analyses, interpretation of results, and manuscript preparation. IHSFC personnel have particular expertise in case-control studies, specimen processing and quality assurance, and analytic methods for characterizing the relationships among molecular data and clinical outcomes using integrative data management systems.
The IHSFC organizes its services across five interactive groups:
Human Studies Design and Performance Services (Group 1)
Population Exposure Services (Group 2)
CEET Virtual Biorepository (Group 3)
Biomedical Informatics and Data Management (Group 4)
Biostatistics Group (Group 5)
Click here to request IHSFC services. (You must indicate whether you are a CEET member in your request to gain priority access.)
Changes in Key Personnel for the Integrative Health Sciences Facility Core (IHSFC) of the Center of Excellence in Environmental Toxicology
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Community Outreach and Engagement Core
The mission of the Community Outreach and Engagement Core of the Center is to translate research information from the Center’s research and its team of interdisciplinary scientists, into tools and resources for community, professional, and Public Health decision-making constituencies, in order to improve clinical and public health. The Center and the COEC are especially focused on the urban environment and particularly on communities with an aging industrial infrastructure such as Philadelphia and many surrounding communities. We are particularly concerned with the effects on vulnerable populations including children, the elderly, and underserved populations.
COEC Members
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Membership Guidelines
There are four categories of CEET Center Investigator membership.
The following information is needed from each applicant:
- A letter indicating why he/she wants to join the Center and how they feel they can contribute to the CEET Mission;
- An Updated CV;
- A brief research description; and
- Grant Support information.
All membership requests will be forwarded to the Affinity Group Leaders and all will be reviewed by the CEET Executive Committee. Applicants will be notified of their status by letter.
I. CEET Investigator. Any member of the standing faculty at the University of Pennsylvania is eligible to become a CEET Investigator. To be appointed to this category the faculty member must have the following: (a) a major research theme in environmental health sciences or research program that fits into the mission of the Center; (b) peer-reviewed external funding and publication record in their area of interest; and (c) must either collaborate with other Center members or participate in Center activities. Junior faculty who have indicated that environmental health is a major research direction but have yet to receive independent federal funding are eligible for affiliate membership.
Nominations for appointment as a Center Investigator can come from any existing Center Investigator or COEC member and should be made to the appropriate Affinity Group Leader:
II. Community Outreach and Engagement Core (COEC)Member. Any member of the standing faculty at the University of Pennsylvania is eligible to become a COEC member. Applicants must have a sustained interest in working with individuals, communities, health-care professionals, or decision makers to improve the environment and public health. Faculty members with an educational or community outreach program with a focus on some aspect of environmental health may be appointed as a member of the COEC. Members can come from Schools where there are education or outreach programs, which encompass some aspect of environmental health, and not exclusively from Schools where biomedical research is conducted. Nominations for appointment as a member of the COEC can come from any existing Center Investigator or COEC member and should be made to the Director of the COEC.
III. CEET Affiliate Member. Affiliate members are either senior postdoctoral/clinical fellows (seeking a K-award) or junior faculty (Research Associates, Instructors, Research Assistant Professors, Assistant Professors) who are in formative stages of their career and seek mentorship to advance their careers. Individuals in this category are those who have yet to attain independent federal funding in environmental health sciences, have a desire to do so and seek mentorship from the Career Development Core. Individuals in this category may advance to full CEET membership. Individuals in this category are appointed for a three year term only.
IV. CEET Adjunct Members. Adjunct members are extramural environmental health scientists that are actively collaborating with CEET members and by doing so enrich the mission of the Center. The collaboration may be either in research or COEC activities.
Any faculty member within the Schools that comprise the University of Pennsylvania are eligible for membership to the Center as either a Center Investigator and/or a member of the Community Outreach and Engagement Core (COEC).
Center Investigator Reappointment:
All Center Investigators will have their membership reviewed by the Executive Committee every two years.
Reappointment will be based on the following factors:
- A sustained publication record in areas consistent with the mission of the Center;
- Publications with other Center Investigators or COEC members;
- Sustained peer-review grant support in areas consistent with the mission of the Center;
- Participation in Center activities (retreats, seminars);
- Number of trainees participating in the investigators research program;
- Use of Facility Cores; and
- Meaningful participation in or assistance with COEC activities.
COEC Reappointment:
All COEC Members will have their membership reviewed by the Executive Committee every two years.
Reappointment will be based on the following factors:
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A sustained publication record in areas consistent with the mission of the Center;
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Publications with other COEC members or Center Investigators;
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Sustained educational and/or community outreach activities related to environmental health;
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Participation in Center and COEC activities (forums, seminars);
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Number of trainees participating in education programs;
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Meaningful contributions to COEC education or outreach activities.
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Funding Base Initiatives
Developmental Pharmacology (R21) The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), and participating Institutes within the National Institutes of Health (NIH) invite grant applications for research related to developmental pharmacology. The goal of this funding opportunity announcement (FOA) is to encourage multidisciplinary, investigator-initiated, basic and translational research in developmental pharmacology with particular emphasis on the role of ontogeny on drug metabolizing enzymes, transporters, receptors and signaling pathways activity across developmental periods from fetal life to adolescence.
NIH Pathway to Independence Award
The award provides up to five years of support consisting of two phases. The initial award (K99) provides one to two years of mentored, postdoctoral support. The second phase (R00) provides up to three years of independent research support and is activated when the awardee accepts a full time tenure track (or equivalent) faculty position. Applicants must be in postdoctoral positions and may be at nonprofit, for-profit, or governmental agencies, including intramural NIH laboratories. Both U.S. citizens and non-U.S. citizens are eligible.
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Other Centers and Institutes
Center for Clinical Epidemiology and Biostatistics
Center for Research on Reproduction and Women's Health
Institute for Diabetes, Obesity and Metabolism
Institute for Environmental Medicine
Institute for the Translational Medicine and Therapeutics (ITMAT)
Transdisciplinary Tobacco Use Research Center (TTURC)
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