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Research Cores

Facility Cores

Community Outreach and Education Core (COEC)

Membership Guidelines

Funding Base Initiatives

Environmental Health Research at Penn

Research Cores

Research Core I
Oxidative Stress and Oxidative Stress Injury

Co-Director: Dr. Ian Blair
Co-Director: Dr. Harry Ischiropoulos

Core Description
The CEET Research Core in Oxidative Stress and Oxidative Stress Injury has a focused theme on environmental exposures that result in oxidative stress and resultant cell, tissue and organ injury. Oxidative stress occurs when an insult generates reactive oxygen species (superoxide anion, hydrogen peroxide, hydroxyl radical, etc.) that overwhelm protective mechanisms of the cell. The members have overlapping research interests that relate to four general areas of interest - cardiovascular disease and diabetes, lung disease, cancer, and neurodegenerative disease that may result from oxidative stress The twelve members are experts in their chosen area and in many instances have made significant contributions to understanding the chemistry, biology and health consequences of oxidative stress. Therefore, the Core will serve as a focus to bring together all of the major investigators at PENN working in the area of oxidative stress, with particular relevance to environmental health.
The research interests of the Core investigators are under a common theme, which is to understand the consequences of oxidative stress in disease, including cardiovascular disease and diabetes, lung disease, cancer, and neurodegenerative disease. Environmental agents that will be studied include polycyclic aromatic hydrocarbons, air-pollutants (ozone and fine particulate matter, etc), heavy metals, and organophosphate pesticides. Current research within the Oxidative Stress Core is focused on the development of high sensitivity LC/MS methodology based on the use of capillary chromatography and nanospray ionization. Over the next several years, we believe that this may play a role in the routine analysis of oxidative DNA modifications. When coupled with stable isotope dilution methodology and immunoaffinity purification, this will afford unparalleled sensitivity and specificity for the analysis of specific biomarkers of oxidative stress.

All Oxidative Stress and Oxidative Stress Injury Core Members:

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Research Core II
Endocrine and Reproduction Disruption

Co-Director:  Dr. George Gerton
Co-Director: Dr. Sam Parry

Core Description
The CEET Research Core in Endocrine and Reproduction Disruption will focus on the roles of environmental factors, mainly environmental estrogens and anti-androgens, and their risks for impaired fertility, fecundity, adverse pregnancy outcomes. These outcomes of immediate relevance to S.E. Pennsylvania which has a disproportionate level of low weight births, births that fail to go to term, and infants with birth and developmental defects. Environmental agents to be studied include PAHs, PCBs, pesticides, phthalate esters and phytoestrogens. The mechanisms whereby these environmental exposures disrupt cell signaling, nuclear receptor signaling and modulate enzymes that regulate nuclear receptor ligand availability will be examined. The effects of endocrine disruption on male and female germ cells, gametogenesis, fertility, pregnancy outcome, and male reproductive tract development will be focal points. This Core is comprised of 16 investigators with broad expertise in basic, translational, and clinical research in endocrinology, reproductive biology, molecular epidemiology and environmental health. The tradition of collaboration among these investigators ensures a multi-dimensional approach to scientific endeavors. This Core will form a natural alliance with the Center for Research on Reproduction & Women's Health (CRRWH).

All Endocrine/Reproduction Disruption Core Members:

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Research Core III
Lung and Airway Disease

Co-Director: Dr. Reynold Panettieri
Co-Director: Dr. Steven Albelda

Core Description:
The Research Core in Lung and Airway Disease of the CEET focuses thematically on the interaction between environmental exposures and the lung within the context of a genetic predisposition for the induction and progression of airway diseases [asthma or chronic obstructive lung disease (COPD)], parenchymal lung diseases (sarcoid or berylliosis) or lung cancer.  This core reasons that genetically determined aberrant injury-repair responses to environmental exposures induce lung disease and promote disease progression as described in Figure 1. The genetic determinants for the onset of lung disease may differ from those that promote disease progression. Furthermore, the unique site of lung injury and repair determines whether individuals develop predominantly airway disease, parenchymal lung disease or lung cancer. The Core will elucidate the molecular and cellular mechanisms and signaling pathways that govern normal repair processes at different lung sites and how environmental exposures and genetic pre-disposition pre-determine aberrant repair in individuals. 
The Core will use state-of-the-art cell, molecular, genetic and clinical epidemiological approaches to identify and to determine the contribution of altered injury-repair responses in promoting lung disease. To empower the investigators to accomplish these goals, the Core has three research groups. The Animal Models Research Group assists investigators in developing animal models of environmental lung disease using intranasal, intratracheal or systemic administration of challenge and test exposures and evaluating tissues for lung injury parameters. The Human Studies Research Group assists investigators in obtaining tissue, blood and DNA from well-characterized subject populations with lung disease. The Epithelial/Mesenchymal Cell Function Group assists investigators in culturing lung-derived epithelial, smooth muscle and fibroblasts from healthy or well-characterized lung disease subjects or in culturing the same cell types from animal models.

Figure 1: A hypothetical model describing lung disease as a consequence of aberrant injury-repair responses induced by environmental exposures.

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Research Core IV
Genes and the Environment

Co-Director: Dr. Tim Rebbeck
Co-Director: Dr. Alexander Whitehead

Core Description:
The Research Core in Genes and the Environment of the CEET will have a thematic focus on genetics and response to environmental exposures. In the broadest sense it will focus on differential interactions between different “genotypes” and environmental exposures (carcinogens, tobacco smoke, air-pollutants, xenobiotics, exogenous hormones and sunlight) that mandate or modify the risk of adverse health effects. Genetic profiles will ultimately determine who is at risk from environmental exposures, what is the level of risk, who is susceptible to disease, and who will respond to treatment. Emphasis will be on the identification of genes, genetic traits and gene interactions that are determinants of environmental exposure (GE), determinants of susceptibility to diseases with environmental etiology (GD), determinants of chemoprevention (GP), determinants of disease outcome (Go), and determinants of therapeutic response (GT), Figure 2.

Research emphasis will be placed on (1) elucidating the interactions between environmental exposures (e.g. chemical carcinogens such as polycyclic aromatic hydrocarbons (PAH)) and the genetic determinants that govern lung cancer (e.g. smoking, the metabolic activation of PAH, the ensuing oxidative stress, and DNA-damage and repair); (2) elucidating the interactions between environmental exposures, e.g. UV sunlight and daylight and the genetic determinants of melanoma and sleep-apnea, respectively; (3) elucidating the interactions between environmental exposures and the genetic determinants of hormone dependent malignancies e.g. prostate and breast cancer; and (4) elucidating the interactions between environmental exposures and the genetic determinants of birth-defects.

All Genes and the Environment Core Members:

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Facility Cores

Facility Core I  
Toxicogenomics

Spring 2008 Genomics Workshop

Description of Services
The resources that comprise the Toxicogenomics Facility Core include the following:

• PENN Microarray Facility;
• The Molecular Diagnosis and Genotyping Core Facility; and
• The Bioinformatics Facility

Services include:

• Wide range of commercial and customized microarrays for transcript profiling
• Nucleic Acid Extractions
• DNA extraction from blood, tissues (fresh, frozen, paraffin-embedded tissue blocks), buccal cell specimens, mouthwash collections and cells
• RNA extraction from blood and tissues (fresh or frozen)
• PCR Assays
• PCR
• RT-PCR
• Multiplex PCR, PCR-RFLP
• Real-time quantitative PCR
• SNP Genotyping
• DNA Fragment Sizing and Quantitation, including Microsatellite Analysis
• Gene Expression Analysis by Real Time PCR
• Mutation Screening by Denaturing High Performance Liquid Chromatography (dHPLC)
• Sequencing
• Extensive Bioinformatics and Biomedical Informatics Support/Consultation
• Training in all techniques

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Facility Core II   
Toxicoproteomics

Description of Services

• 2D Large Format Gel (26 x 20 cm). For separating proteins present in cells, tissues and biological fluids. Good resolution for posttranslational modifications of cellular proteins.
• 2D Small Format Gel (8 x 10 cm). For rapidly screening the major proteins present in cells, tissues and biological fluids.
• SYPRO Ruby Staining and Scanning. Since this staining has a relatively large dynamic range, it is possible to identify low abundance proteins in the presence of more highly abundant proteins. The Typhoon fluorescent detector can scan gels with multiple fluorescent channels. 
• Pro-Q Diamond Phosphoprotein Gel Staining. This fluorescent dye staining provides a sensitive way to profile phosphorylation changes in proteomes.
• Cy2,3,5 Dye Labeling and Scanning. In a typical 2-D in-gel electrophoresis (DIGE) experiment, three protein samples are analyzed in a single 2D gel. Cy2 is used to visualize the standard protein mixture (internal control), Cy3 is used to visualize the proteins from the control sample and Cy5 is used to visualize proteins from the experimental sample. The dyes are fluorescent and can be detected using the Typhoon fluorescence scanner. This provides a highly reproducible tool to determine the differential expression of a proteome in any given experiment. It is a powerful technology for toxicoproteomics analysis.
• Full service Image Analysis (per hour)  Gel images are analyzed by DeCyder software. This is used to provide accurate quantification of proteins that have been regulated by environmental exposures.
• Spot Picking (robotic), Per 96-Well Plate  In combination with the DeCyder software, the automated spot picker can excise specific gel spots prior to protease digestion.
• Trypsin Digestion. Normally, the gel spots containing proteins are subjected to in-gel trypsin digestion prior to identification by mass spectrometry. Alternative protease digests are also available upon request.
• MALDI-TOF Peptide Mapping  This provides peptide fingerprinting. With 4 trypsin-digested fragments it is often possible to use this “fingerprint” to identify proteins that are present in databases.
• TOF-TOF (4700 Proteomics Analyzer)  This provides fingerprinting and sequencing with throughput of 1,000 samples per day. In conjunction with iTRAQ labeling reagent and GPS software version 3.0, this can provide quantification of proteome as an alternative for 2D-DIGE.
• Microflow RP-HPLC/MS/MS For higher certainty in the identification of proteins it is often useful to conduct LC/MS/MS to provide sequence information on peptides that were identified in the MALDI experiment.  It is also useful for peptides that do not ionize well under MALDI conditions. Therefore, the two techniques are highly complementary.
• NanoLC/Nanospray/Qstar-XL NanoLC and Nanospray have a 10-fold better sensitivity than microspray for protein identification. Eksigent’s splitless nanoLC and LCpacking’s 2D-nanoLC provide 1D and 2D online separation for Qstar nanospray respectively.
• NanoLC/Nanospray/LTQ LTQ has much faster scanning than Qstar-XL, providing better sensitivity than Qstar for samples with very little proteins.
• Phosphorylation Site Mapping IMAC affinity purification is used to enrich phosphorylated peptides and multiple enzyme digestions to increase sequence coverage.
• Shotgun Approach of Complex Proteome Analysis Based on the nature of samples, different tools of pre-fractionation of proteins or digested peptides are used to simplify the complexity of samples for identifying low abundant proteins.
• Mass Spectrometry Analysis/Database Search  The data from MALDI and LC/MS analyses can be used to perform automated database searches. If the protein has been previously identified it is possible to use the mass spectrometry information to characterize the protein.
• Peptide de novo sequencing  We created an automated De Novo sequencing software to identify unknown proteins that do not have any DNA or protein sequence information in any database.
• Consultation and Training Services  The Director will be actively engaged in meeting with Center Investigators interested in using the Toxicoproteomics Core. These discussions include selection of proteomics technologies, experimental design, troubleshooting and data interpretation. These consultations are critically important to ensuring that the expensive resources of the Core are used optimally and that Center Investigators who use the Core obtain the best possible results from our services. This service will be free of charge to the new Center members. Where interest exists, investigators will be trained to conduct their own analysis.

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Facility Core III  
Biomarker

Description of Services

• Liquid chromatography/mass spectrometry (LC/MS) methodology for the analysis of urinary 8-oxo-dGuo.
• LC/MS methodology for the analyses of urinary unsubstituted and substituted etheno-DNA adducts.
• LC/MS methodology for the analyses of urinary DNA-adducts derived from PAH metabolites.
• LC/electron capture-atmospheric pressure chemical ionization (EC-APCI)/MS methodology for the analyses of catechol estrogens in plasma.
• Chiral LC/EC-APCI/MS methodology for the analyses of plasma and urinary bioactive lipids.
• Assist investigators in the design and implementation of their bioassays
• Provide cost-effective service to investigators to expensive state-of-the art methods not routinely available in individual laboratories

Fee Structure: Consultation with Facility Core members is always encouraged and there are no charges for this service.  The services below are listed with the member discount (15 %) included.

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Community Outreach and Education Core

The mission of the Community Outreach and Education 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.

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Membership Guidelines

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 Education Core (COEC).

Center Investigator Membership:
To be appointed as a Center Investigator the faculty member must have the following:

• A major research theme or program that fits into the mission of the Center; and
• Peer-reviewed external funding in eligible areas and a competitive publication record and must have conducted collaborative research in environmentally relevant topics. Exceptions: junior faculty who have indicated that environmental toxicology is a major research direction but have yet to receive independent funding, and senior faculty who wish to change research direction.

Nominations for appointment as a Center Investigator can come from any existing Center Investigator or COEC member and should be made to the appropriate Research Core Director: 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 Core Director and all will be reviewed by the CEET Executive Committee. Applicants will be notified of their status by letter.

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 Membership:
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..

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 COEC Director and all will be reviewed by the CEET Executive Committee. Applicants will be notified of their status by letter.

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:

• A sustained publication record in areas consistent with the mission of the Center;
• Publications with other COEC members or Center Investigators;
• Sustained educational and/or community outreach activities related to environmental health;
• Participation in Center and COEC activities (forums, seminars);
• Number of trainees participating in education programs;
• Meaningful contributions to COEC education or outreach activities.

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Funding Base Initiatives

Title: Disease Investigation through Specialized Clinically-Oriented Ventures in Environmental Research (DISCOVER) [P50]

The National Institute of Environmental Health Sciences (NIEHS) is establishing a new center program entitled "Disease Investigation through Specialized Clinically-Oriented Ventures in Environmental Research (DISCOVER).
 
DISCOVER Center grants will support teams of researchers focused on integrating basic mechanistic environmental health research with patient-oriented and population-based studies to: (1) address critical disease-relevant issues by applying environmental health sciences to understand the etiology, pathogenesis, prognosis, and epidemiology of human disease processes; and (2) facilitate the application of fundamental research findings towards the development of improved clinical or public health practice. Each application should focus on a single disease of environmental etiology.
 
The NIEHS intends to commit a total of $9 million dollars to fund four to six new DISCOVER Center grants that will be awarded over Fiscal Years 2007 and 2008 from this one solicitation. Applicants may request a budget of up to $1.5 million dollars in direct costs annually for a period of five years. Successful applicants must include a minimum of two clinically oriented and two mechanistically oriented research projects. Eligible principal investigators include any individual with the skills, knowledge, experience and resources necessary to carry out the proposed research. It is recommended that the Director or Co-Director of the Center be a physician-scientist. Individuals from underrepresented racial and ethnic groups as well as individuals with disabilities are always encouraged to apply for NIH programs.
 
IPAR-06-179:  Interdisciplinary Partnerships in Environmental Health Sciences (R21)
This initiative is intended to support collaborations between scientists with basic and clinical expertise to advance understanding of the etiology, prevention, and treatment of environmentally-induced human diseases.
Letters of Intent Receipt Date(s):        December 11, 2006 and December 11, 2007
Application Submission Dates(s)        January 11, 2007 and January 11, 2008

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