NIEHS Environmental Health Sciences Core Center Resources
Welcome to the CEG-hosted Web portal for NIEHS Environmental Health Sciences Core Center Resources. We are pleased to share with you this convenient tool for “one stop shopping” for state-of-the-art laboratory services, data analysis and other research services available from the CEG and other NIEHS-funded centers of excellence. If you have any comments or questions, please let us know. Thank you for visiting our site!
Please fill this form to send us an update or addition to an EHS core center you manage.
EHS Core Center Resources
Center for Environmental Health in Northern Manhattan
Grant number: P30 ES009089
- Access to a large suite of inductively coupled plasma mass specs (ICP-MS) including high-resolution magnetic sector instrument with different introduction systems as well as ICP-MS that are somewhat more unique for public health, such as a laser ablation ICP-MS and multi-collector ICP-MS for high precision isotope ratios.
- Ultra-clean, high precision, automated weighing system for particulate filters with the following diameters 14 mm, 15 mm, 25 mm, 37 mm, 47 mm, where the long term reproducibility of filter blanks over months to years is ±1.2 µg (short term reproducibility during pre-weighing or post weighing is ±0.08 µg).
- Elemental composition of environmental samples by energy dispersive x-ray fluorescence (XRF) or high-resolution, magnetic-sector ICP-MS (see above).
- Optical analysis of black carbon concentrations on Teflon filters using an integrative sphere and continuous light source.
- C-14 analysis of black carbon or compound-specific PAH to distinguish fossil fuel sources from more modern sources (biomass, etc).
- PAH analyses on environmental samples, including alkylated-PAHs by GC-MS/MS and PAH metabolites in biological samples by LC-MS/MS.
- Exposure assessment expertise and equipment for collecting ambient, residential and personal samples for airborne pollutants (VOCs, particles, allergens, microbes), as well as for collecting water, soil and dust samples.
- Collection of settled dust and airborne samples for analyses of allergens, fungi and bacteria. Analyses for allergens to many indoor inhalant allergens by ELISA. Phadia CAP system for measuring IgE and IgG antibodies to commercially available allergens along with the capabilities of developing assays to novel allergens.
- The Biomarker Lab of the Integrative Health Sciences Facility Core processes and stores biological samples, and isolates DNA and RNA. It also offers the following analytical services:
- Candidate SNP genotyping
- Measures of DNA methylation using pyrosequencing; coordination of services for epigenome-wide DNA methylation analysis with partner lab
- Commercial ELISAs
- PAH-DNA adducts in biological samples by chemiluminescence ELISA
- Immunoassays for aflatoxin B1 and PAH-albumin adducts
- Nanoparticle Tracking Analysis to count and characterize size and distribution of biological (exosomes, extracellular vesicles) and non-biological nature
- Telomere length analysis
- Mitochondrial DNA markers of damage and abundance
- Coordination of services with partner labs for GWAS, EWAS, transcriptomics, deep sequencing.
- The Trace Metal Laboratory of the Integrative Health Sciences Facility Core has the ability to obtain analyses of biological samples for a broad array of metals including: lead, mercury, arsenic, iron, manganese, cadmium, copper, zinc, chromium, sodium, cobalt, platinum, potassium and others.
- Consultations on the design of observational, clinical, and experimental studies with an experienced epidemiologist.
- Biostatistical consultations with one of three senior biostatisticians.
- Data management.
- Statistical methods with genomics and epigenetics.
- Multi-omics integration.
- Training and guidance on handling and analyzing Geographical Information Systems (GIS) data.
- Bayesian models
- Latent class methods.
- Mixed effects models.
- Clustering analyses.
- Identifying, accessing, and analyzing the growing number of large data repositories in the public domain (“big” data).
- Offers educational and training programs on the use of these methods.
- Assists with analysis and interpretation of data, and manuscript preparation.
- Fosters attention to the development of new methods/tools.
HERCULES Exposome Research Center
Health and Exposome Research Center; Understanding Lifetime Exposures
- Integrated Health Sciences Facility Core
Untargeted Exposure Analysis (Dean Jones, PhD, Director): Untargeted Metabolomics is a standardized high-resolution protocol used to obtain a global view of metabolism and environmental exposures. The platform is suitable for use as a central reference for exposome research because of the expansive coverage (>20,000 chemical signals), including hundreds of know intermediary metabolites and a broad spectrum of environmental chemicals, food, pharmaceuticals, and microbiome-derived metabolites. High resolution metabolomics provides a central anchor for exposome research enabling generalized integration of multiple exposure metrics, measures of biologic response of an individual to exposures and metabolic changes consistent with disease pathophysiology to characterize environmental contributions to disease. Core request form: https://emoryhercules.com/facility-cores/metabolomics/.
Targeted Exposure Analysis (Dana Barr, PhD): The laboratory has 8 mass spectrometers (GC-MS/MS and GC-MS; 3 HPLC-MS/MS and HPLC-MS, FTMS and ICP-MS) that enable the analysis of the entire gamut of environmental toxicants, hormones, and other organic and inorganic compounds ranging from metals to proteins. With state-of-the-art analytical technologies and complementary scientific experience, assays can be developed to target specific research needs. Core request form: https://emoryhercules.com/facility-cores/targeted-analysis/ .
A partnership between Baylor College of Medicine, the University of Texas Health Science Center at Houston School of Public Health, and the University of Texas Medical Branch
Grant number: P30 ES030285-03
GC-CPEH Facility Cores (PIPELINE FC and IHSFC) provide GC-CPEH investigators priority access to world-class expertise and cutting-edge technologies supporting precision environmental health research. The resources include in-house services, consultation with our navigators, or placing "3rd party fee-for-service" orders that could not be processed in-house. It relies on core facilities labs and resources at Baylor College of Medicine (BCM), Houston, TX; University of Texas Health Science Center (UTHSC), Houston, TX; and University of Texas Medical Branch (UTMB), Galveston, TX. For each of the PIPELINE /IHSFC Resources listed below, a Navigator with subject matter expertise and a record of both publications and funded grants is available to assist Center investigators with optimizing Resource utilization. If you have any questions about the GC-CPEH Facility Cores, contact us by email at email@example.com.
- PIPELINE Facility Core (Promoting Impact of Precision EHS Research by Leveraging Instrumentation, Next-gen and Emerging Technologies): The PIPELINE Core, led by Chris Amos, PhD, and Cristian Coarfa, PhD, provides a wide range of analytical assays, precise environmental exposures, and extensive phenotyping services. PIPELINE FC Resources available to GC-CPEH investigators are:
- Integrated Microscopy, BCM (Navigator: Michael Mancini, PhD). Services offered include light microscopy, Super-resolution microscopy (SIM and STORM), live imaging (ultrafast and long-term), multi-dimensional spatial analysis, high throughput microscopy, image analytics.
- Genomics, Epigenomics, and Transcriptomics:Genomic and RNA Profiling (GARP), BCM (Navigator: Daniel Kraushaar, PhD). Services offered include sample quality control, RNA-Seq, ChIP-Seq epigenomics, Whole Genome Sequencing, Whole Exome Sequencing, Whole Genome Bisulfite Sequencing, Targeted Sequencing, Spatial Transcriptomics, NanoString Gene Expression Assays.
- Genomics, Epigenomics, and Transcriptomics: UTHealth Human Genetics Center, UTHealth (Navigator: Alanna Morrison, PhD). Services offered include Illumina Whole Genome and Consortium Arrays, Custom Mid to High-Plex Genotyping, Custom Low to Mid-Plex Genotyping, Epigenetics: Methylation Analysis, Illumina laboratory best practices and quality control, genomic data analysis and quality control, sample handling and storage.
- Genomics, Epigenomics, and Transcriptomics: Next Generation Sequencing, UTMB (Navigator: Steve Widen, PhD).Services offered include ChIP-Seq, de novo assembly, variant identification, SNPs, transcriptome (reference-guided or de novo), miRNA and small ncRNA Sequencing, Quantitative - RNA-Seq expression analysis, Exome Sequencing (cancer or custom panels).
- Mass Spectrometry Proteomics, BCM (Navigator: Anna Malovannaya, PhD). Services offered include consultation and project design, 365 proteome profiling, protein complex identification by IP/MS, post-translational modification (PTM) analysis, “Per-Band” Sequencing, data analysis.
- Mass Spectrometry Proteomics, UTMB (Navigator: Bill Russell, PhD). Services offered include intact molecular weight measurement, protein identification from gel bands, protein identification from complex mixtures, identification of post-translational modifications, SILAC, iTRAQ, and label-free quantification of peptides and proteins, small molecule quantification, metabolomics.
- Metabolomics, BCM (Navigator: Nagireddy Putluri, PhD). Services offered include sample preparation and quality control, targeted steady-state analysis, unbiased steady-state metabolomics, lipidomics, metabolomic flux analysis.
- Microbiome and Metagenomics, BCM (Navigator: Kristi Hoffman, PhD). Services offered include DNA and RNA Extraction, targeted amplicon sequencing, untargeted virome amplicon sequencing,metagenome and complete genome sequencing, qualitative PCR, data analysis.
- Single Cell Genomics, BCM (Navigator: Rui Chen, PhD). Services offered include Single Cell RNA Profiling, Single Cell ATAC-seq, Smartseq RNA profiling.
- Multi-Omics Data Analysis, BCM (Navigator: Cristian Coarfa, PhD). Services offered include consultation primary analysis of profiling data by different high-throughput platforms, integrative multi-omics analysis, and data deposition.
- Inhalation Toxicology Core (ITC), UTMB (Navigator: Bill Ameredes, PhD). Services offered includeInhalation/Exposure Laboratories including gaseous and aerosol toxicants; allergens; topical dermal and ocular exposures; intravitreal and systemic exposures, tobacco and e-cigarette smoking/vaping inhalation, hazardous chemical-approved exposure facility, airway/lung physiology function assessment, ocular and skin response assessment, cell culture exposure facilities, integration with UTMB Imaging Network for lung and eye toxic responses; fixed and live-cell imaging; microCT-PET-SPEC, molecular optical imaging (IVIS) and Optical Coherence Tomography (OCT).
- Mouse Metabolism and Phenotyping, BCM (Navigator: Christopher Ward, PhD). Services offered include imaging, blood serum/plasma analysis, cardiopulmonary, metabolism, cellular metabolism, glucose metabolism, lipid metabolism, whole-body metabolism, other tests & challenges, surgical and anesthesia.
- Protein and Monoclonal Antibody Production, BCM (Navigator: Kurt Christensen). Services offered include consultation, recombinant protein expression, protein and MAb purification, hybridoma / monoclonal antibody production, peptide synthesis (3rd-party fee-for-service), biochemical assays (3rd-party fee-for-service).
Integrated Health Sciences Facility Core (IHSFC): The IHSFC, led by Elaine Symanski, PhD and Philip Lupo, PhD, provides access to expertise and capabilities to foster translational studies (basic sciences into clinical and population studies) that can ultimately be disseminated to the community. IHSFC resources available to GC-CPEH investigators are:
Population and Clinical Science (Navigators: Michael Scheurer, PhD, George Delclos, PhD, Winnie Hamilton, PhD, Lance Hallberg, PhD, and Philip Lupo, PhD).Services offered include consultation, designing and conducting population and clinic-based investigations of the impact of environmental exposures on human health:
- Access to BCM biorepositories/Prospective biospecimen collection, processing, and sample storage (Population Sciences Biorepository (PSB); Human Tissue Acquisition and Pathology Biobanking (HTAP-Biobanking); Research Tissue Support Service (RTSS); Peribank
- Study design assistance for epidemiological and clinical studies (IRB protocol assistance; REDCap (digital questionnaires) (ICTR); Database development)
- Forthcoming: Mobile-Clinical for Outreach and Community Health (Mobi-COACH)
- Exposure Assessment (Navigators: Elaine Symanski, PhD, Abiodun Oluyomi, PhD, Lawrence Sowers, PhD). Services offered include consultation on modeling strategies for environmental health assessment, geospatial analyses and mapping, peptides and small molecules analysis, and exposure biomarkers development.
- Community Engagement (Navigators: Elaine Symanski, PhD, and Winnie Hamilton, PhD). Services offered include consultation on community-engaged approaches involving critical partnerships with stakeholders to heighten the relevance and impact of research activities and translate and disseminate scientific findings for lay audiences.
Harvard NIEHS Center for Environmental Health
- Trace Metals Laboratory for quantitative analysis of a full spectrum of heavy metals and metalloids in trace concentrations in biological and environmental samples. Trace metals typically analyzed include Mercury, Arsenic, Lead, Cadmium, Manganese, Zinc, Gadolinium, Gold, Platinum. Materials frequently analyze include soil, filters, water, nails, hair, urine, blood, and breast milk.
- Fine Particle Concentrators supply inhalation exposure chambers with test environments where ambient particle concentrations have been increased by up to 50 times without altering the composition of gases. The four inhalation Chambers used for exposures of animals (<=20kg) to air pollutants while continuously monitoring several physiologic responses.
- Nanotechnology and Nanotoxicology Health Laboratory examines the unique environmental health and safety concerns raised by engineered nanomaterials and nanotechnology applications. The VENGES system allows for creation of engineered nanomaterials and analysis of toxicological effects both in vivo in rodents and in cell culture systems.
- Exposure Core provides spatio-temporal predictions of multiple ambient air pollutants [PM2.s, PM2.s components (Elemental Carbon, Organic Carbon, Sulfates, Nitrates), N02, and 03] that ambient monitoring, leverage remote-sensing satellite data, land-use regression, and the Geos-Chem chemistry transport model.
- Bioinformatics and Biostatistics Core provides advanced methods and software, including modeling the health effects of multi-pollutant mixtures; distributed lag modeling of critical windows associated with prenatal exposures in prospective pre-birth cohorts, and heterogeneity of these effects across subpopulations (e.g. by gender); models and macros for longitudinal mediation analysis; models (iSKAT) and software for G x E interactions.
Transdisciplinary Center on Health Effects of Early Environmental Exposures
- Integrated Health Sciences Facility Core (IHSFC): Exposure Biomarker Laboratory and a Molecular Biomarker Laboratory. The IHSFC also contains a Biospecimens sub core that is home to Mount Sinai’s Placenta Biobank and a Clinical Population Access Sub core designed to increase access to Mount Sinai’s clinical practices for EHS research. The IHSFC provides expert consultation to center members interested in measuring environmental exposure biomarkers, including untargeted chemical assays and targeted assays as well as information on appropriate sample matrices; on collection protocols that avoid contamination; on proper storage of samples; and on analytical methodologies. We also work with the CEC to assist in Citizen Science initiatives around measures of air quality and the report back of lab results on exposures to research participants. Director: Manish Arora, BDS, PhD, MPH.
- PhenotypeCore |Phenotyping and Stress Assessment Facility Core (PSAFC): Consultation on a range of topics including respiratory studies, cognitive and behavioral studies, and endocrine assessments. Center-member access to the Physiological Assessment of Children’s Environmental Risk (PACER) Laboratory. PACER lab has established and validated protocols that can be implemented to assess functioning of key regulatory systems susceptible to environmental influences from early development through childhood to adolescence.Consultation on environmental and physiological stress measures, as a major objective of our Center is to promote a better understanding of social context as a modifier of chemical toxicants. The laboratory also has the capacity to assess a range of pulmonary function tests, and offers ambulatory equipment, which allows for onsite and offsite deployment. We have established protocols for neurobehavioral and neurocognitive tests that can be administered in the field as well as in this laboratory. Through the PSAFC, Center investigators have access to the Human Immune Monitoring Center (HIMC), which is focused on establishing methods for deep profiling of patient samples using polychromatic flow cytometry and immunogenomics. Leader: Dr. Rosalind J. Wright
- Biostatistics and Bionformatics Facility Core: This core includes faculty members from the Division of Biostatistics, the Department of Environmental Medicine and Public Health and the Department of Genetics and Genomics. We provide expert consultation in environmental health related data, including a focus on complex mixtures, untargeted chemical analysis and geospatial modeling such as air pollution and built environment measures. We provide expert consultation on informatics, machine learning, big data analysis, data storage and management, as well as study design and epidemiology principles. Our goal is to ensure that analysis of complex interactions from data generated in basic science, genetic, clinical, and epidemiological studies fits an appropriate biological framework. We provide state-of-the-art services in high-dimensional database management and in the computing and analysis of environmental “big” data. Leader: Dr. Chris Gennings.
Center for Environmental Health Science
Grant number: P30 ES00210
Animal Models Facilities Core
Contact: Prof. James Fox
The Animal Models Facilities Core, directed by Professor James Fox of the Division of Comparative Medicine and the Department of Biological Engineering, provides Center members with the latest technology for the application of animal models to environmental health research. Center members are provided with an extensive array of services including state-of-the-art pathology and imaging support, transgenic resources and a centrally-managed AAALAC-approved animal holding and surgical facility. The Core is staffed with experienced personnel and equipped with essential equipment to generate genetically engineered mice, cryopreserve sperm and embryos, rederive imported mice from embryos, provide colony management, prepare and analyze tissue samples by histological and image analysis.
Bioimaging and Chemical Analysis Facilities Core
Contact: Dr. Bogdan Fedeles and Dr. Michael DeMott
This Facilities Core is overseen by Drs. Bogdan Fedeles and Michael DeMott. The Bioimaging and Chemical Analysis Facilities Core is a central resource in analytical chemistry, separation science, metabolomics, and proteomics for Center members. It is a world-class chromatography and mass spectrometry facility, and provides CEHS members with state-of-the-art chemical separation, identification, and quantification capabilities, along with consultation for training, experimental design, and data interpretation.
Genomics and Informatics Facilities Core
Contact: Dr. Stuart Levine
The Genomics and Informatics Facilities Core, led by Dr. Stuart Levine, provides CEHS researchers with access to state of the art instrumentation, services and expertise in the areas of genomics, systems biology, bioinformatics, and BioIT. These tools provide researchers a broad spectrum of technologies to understand cell state and how environmental stresses result in perturbations of the cellular systems and human health. The core services are available either through walkup or assisted services and training is available in all areas.
Integrative Health Sciences Facilities Core
Contact: Prof. Michael Yaffe and Prof. James Fox
The CEHS research portfolio extends from basic studies of the chemistry of our environment, to clinical studies of how exposure impacts human health and, ultimately to policy recommendations that protect and improve public health and welfare. The Integrative Health Sciences Facilities Core (IHSFC) enhances the impact of laboratory research by lowering the barriers to clinical translation of basic studies into new clinical practice. In doing so, the IHSFC amplifies the impact of CEHS by facilating delivery of our science and engineering advances to improve human health. The strength of the IHSFC lays in its leadership, which is comprised of basic researchers, leaders in technology development, animal researchers, clinicians, and an epidemiologist.
Research in Environmental Health Sciences
- Integrative Health Sciences Facility Core (IHSFC)
Environmental epidemiology services; ethical issues and QC/QA support; exposure sampling and assessment; 4) clinical facility for research of environmental hazards; and Lanzhou University School of Public Health.
- Specialized Inhalation Exposure Facility
27 dynamic, stainless steel, glass, and Plexiglas Laskin-type inhalation exposure chambers; 7 small Plexiglass exposure chambers; specialized glove-box isolator housing for carcinogens or infectious agent exposures. Completely equipped combustion furnaces (e.g., wood dust and coal exposures); a particle concentrator facility for chronic exposures to concentrated ambient PM; a diesel exhaust exposure system. Supplementary calibration facilities and sampling equipment with analytical chemistry equipment specialized equipment for the generation of highly standardized gaseous, vapor, and particulate inhalation atmospheres of different composition, including cigarette-smoke and e-cigarette aerosol generators (for both main-stream and side-stream smoke
- Molecular Cell and Analytical Services Facility Core
ChIP-Seq and RNA-Seq. Yeast Screen. ABI 7900 HT RT-PCR. ABI 7300 RT-PCR. Beckman Coulter Biomek 2000 Laboratory Automation Workstation, PSQ HS 96 DNA PyrosequencerTM, Beckman Coulter CEQ8000 Automated DNA Sequencer. Affymetrix GeneChip. Nanodrop ND-1000. Molecular Dynamics Storm 860 Phosphorimager. Nanodrop NN-3300. MACSQuant Flow Cytometer. Beckman Coulter Epics XL-MCL Flow Cytometer. Beckman Coulter Counter Model Z2. FRET Imaging System. Ciphergen ProteinChip® System Series 4000 SELDI-TOF-MS. Solaar Atomic Absorption system (Model M6). XRF (Jordan Valley)
- Environmental Health Statistics and Bioinformatics Facility
Expert statistical and bioinformatics collaboration and consulting
Center for Human Health and the Environment
- Genomics Sciences Laboratory: The Genomic Sciences Laboratory (GSL) is the primary genomics core of NC State University, and we are the Systems Technology Genomics Core for the Center for Human Health and the Environment (CHHE). The GSL’s primary mission is to extend expertise in Next Generation Sequencing (NGS) study design and sample preparation, as well as provide Sanger (3730xl) and NGS capabilities for CHHE members. The GSL currently operates multiple NGS platforms, including Illumina MiSeq, NextSeq 500, and HiSeq 2500, as well as the new PacBio Sequel long-read sequencing platform. Our facility enables CHHE researchers to conduct advanced genomics research utilizing transcriptomic analysis (RNAseq), DNA protein interactions (ChIPseq), epigenetics (Bisulfite Sequencing), as well as other molecular genetic studies including, but not limited to, SNP analysis, eQTL analysis, Genotyping by Sequencing (GBS) and Genome Wide Association Studies (GWAS).
- Integrative Health Sciences Facility Core: Comparative Toxicogenomics Database (CTD) aims to inform hypothesis development about the effects of environmental exposures on human health. You can contact us for help with using CTD, providing educational materials for courses, and/or for custom curation requests: http://ctdbase.org/
- Comparative Pathology Core (CPC): The CPC mission is to provide pathology expertise to assess the effects of environmental factors in diverse animal models. Three board-certified CPC veterinary pathologists and a network of pathologists with specialized organ system expertise provide advanced pathology evaluation for environmental health science (EHS) projects. Pathologists provide consultation on all aspects of experimental pathology, including experimental design, sample collection, tissue processing, pathology tissue assessments and training. Collaboration on EHS grants and publications with environmental health scientists is one of the goals of the CPC. The CPC is located at the internationally recognized College of Veterinary Medicine at North Carolina State University, Department of Population Health and Pathobiology, and interfaces with a full-service medical histology laboratory. Website: https://chhe.research.ncsu.edu/facility-cores/comparative-pathology-core/
- System Technologies Core: Bioinformatics: CCHE Bioinformatician Dereje Jima has more than 12 years’ experience in biomedical research; software development, bioinformatics, high throughput sequence analysis (Exome, Whole Genome Sequencing, RNA-Seq, ChIP-eq, FAIRE-Seq, microRNA discovery); expression and genotyping microarray data analysis (Illumina, Agilent and Affymetrix plat forms ); statistics skill in R, Bioconductor and S-Plus; programming skill in Perl, PHP, Python, shell, standard Java and C++; strong database management skills using MYSQL, Filemaker Pro, and Access; and advanced skill in parallel Linux node computing. Dr. Jima conducts bioinformatics analysis and research in support of projects across and in collaboration with CHHE members and the Bioinformatics Research Center (BRC). He provides consultations at the design stage of research studies to ensure that the experimental designs are valid, efficient, and correctly powered. His expertise includes cancer genomics, immunology, infectious diseases, epidemiology and application development; his domain expertise includes proteomics, metabolomics, genomics, personalized medicine, and biosignature discovery. He has worked with collaborators on discoveries relating to cancer, infectious disease, immunology, environmental exposure and application development and have analytical capabilities of whole genome/exome sequencing, RNA-Seq, ChIP-Seq, FAIRE-Seq, small/long ncRNA transcriptome, microbiome, and expression/genotype microarrays. Contact: firstname.lastname@example.org Phone: 919-515-5932
- BRC Website: Bioinformatics Consulting and Service Core
- CHHE Bioinformatics: https://www.chhebio.org
- Metallomics, Metabolomics, and Small Molecules Section: The goal of this section is to provide guidance and expertise in small molecule and elemental study design, method development, sample preparation, and sample analysis. With the equipment and capabilities available, CHHE members have the opportunity to study a wide range of environmental applications and analytes, ranging from pesticides to perfluorinated chemicals to trace metal analysis. This section is supported by additional resources available through NC State’s Molecular Education, Technology, and Research Innovation Center (METRIC), a world-class, state-of-the-art measurement science facility that includes modern mass spectrometry, nuclear magnetic resonance spectroscopy, electron paramagnetic spectroscopy, and x-ray crystallography instrumentation supporting small molecule and macromolecule research. Mass spectrometry instrumentation available through METRIC includes: 6560 Agilent ion mobility spectrometry-QTOF mass spectrometer with a Rapidfire 365 SPE platform and Agilent 1290 UPLC System, QE HF with Easy nanoLC 1200 UPLC System with Autosampler, QE HF X with Vanquish Horizon UPLC System and ZipChip TM CZE System with Autosamplers, QE HF X with Nano Proflow 2D UPLC System with Autosampler, TSQ Altis Triple Quadruple Mass Spectrometr with Horizon Vanquish and Eksigent nanoflow UPLC, QE Plus with Custom IR-MALDESI Source for Direct Analysis and Mass Spectrometry Imaging, ICAP RQ ICP-MS with Ultimate LC System and Autosampler, 5800 MALDI TOF/TOF, 5975 GC/MS with NIST and Wiley Libraries, Exactive Plus with LC System for Accurate Mass / Elemental Composition Determinations. Please contact Dr. Jeffrey Enders for more information on this section.
- Proteomics Section: The goal of the Proteomics Section is to provide CHHE members with expertise in experimental design, sample collection, preparation, and analysis for successful implementation of proteomics research. Current instrumentation includes the Q-Exactive HF mass spectrometer equipped with an ultra-high pressure Easy-nLC 1200 nanoflow liquid chromatography system which offers high resolving power and high mass measurement accuracy. For targeted peptide quantitation, the lab is equipped with the TSQ Quantiva triple quadrupole mass spectrometer coupled to the Easy-nLC 1000. The CHHE Proteomics Section will enhance the ability of scientists working in the field of EHS to identify and capitalize on emerging opportunities in systems biology and uses both global and targeted protein methodologies to identify and characterize critical proteins/complexes/pathways/receptors that are affected by, or respond to, chemical and environmental exposures. The Proteomics section is also supported by additional METRIC resources (see above). Please contact Dr. Jeffrey Enders for more information on this section.
Pacific Northwest Center for Translational Environmental Health Research
Grant number: P30 ES030287
Zebrafish Biomedical Research Core: The Zebrafish Biomedical Models Facility Core is unique worldwide as a facility equipped to conduct biomedical research using zebrafish as aquatic research models. It primarily consists of a self-contained fish hatchery and high throughput screening facility for toxicity and behavioral studies
- Large scale embryo production systems
- Robots for embryo handling
- Automated dechorionation
- Static or daily chemical renewal
- High throughput bioactivity screening
- Cognitive and social behavioral assessments
- Cardiovascular fitness
- CRISPR/Cas9 technology application to develop zebrafish lines
- Morpholino knockdown
- Transcriptomics (RNA, and small RNA)
- Develop special and defined diets
- Xenograft model
- Mechanisms and chemoprevention
- Gene x environment interaction
- Epigenetic and transgenerational effects
- Microbiome interrogation
- Adult exposures (reproductive and transgeneration endpoints)
Chemical Exposure Core: The CXC is an state of the art facility specializing in Environmental Sampling. The core offers passive sampling devices (PSDs) including low density polyethylene (LDPE) for stationary monitors as well as silicone wristbands/dog-tags for personal exposure monitoring. The core also offers analytical services for sample PSD extracts, enabling EHS CC members to measure concentrations of environmental toxins in personal exposures, air, water, sediments, and soils.
- Organic quantitative screen for passive samplers, 1530 chemicals
- Flame Retardants, new and legacy, for passive samplers
- Polycyclic aromatic hydrocarbons (65 parent and alkylated) for passive samplers
- Polycyclic aromatic hydrocarbons for plasma samples
- Forensic polycyclic aromatic hydrocarbon alkylated series for passive sampler
- Pesticides quantitative analysis for passive samplers
- Polychlorinated biphenyls quantitative analysis for passive samplers
- Volatile organic chemicals quantitative analysis for passive samplers
- Silicone wristband passive samplers
- Military style ‘dog-tags’ passive samplers
- Silicone, companion animal, passive sampler tags
- Environmental stationary monitors low density polyethylene
- Air environmental stationary monitoring passive samplers
- Water environmental stationary monitoring passive samplers
- Pore air, sediment and soil, stationary passive samplers
Training Videos and FAQs
- Passive sampling videos, preparation
- studying the environment with passive sampling
- Exposure to environmental chemicals and passive sampling, chemical analysis
Community Engagement Core: The Community Engagement Core facilitates collaborations between stakeholders and researchers in the Pacific Northwest. The CEC collaborates with the Oregon Clinical & Translational Research Institute (OCTRI) Research Liaisons and the Oregon State University Extension Service to identify environmental health concerns throughout the Pacific Northwest. The Core emphasizes stakeholder-engaged research to ensure research is relevant, with an emphasis on translating research results to improve environmental public health. The core helps stakeholders and researchers initiate engaged research, translate research results and return data to study participants.
- Stakeholder Engagement. To facilitate stakeholder engagement, the core offers consultations, stakeholder engagement studios, and the Discovery Index to identify common interests between researchers and stakeholders.
- Research Translation. To facilitate broad dissemination of research results, the CEC provides support in the development of research translation materials, such as infographics, videos, online interactive elements like virtual lab tours, and development of study specific websites.
- Research Dissemination. The CEC specializes in the development of report-back materials. This can include the return of environmental or personal sampling data to study participants and stakeholders.
- Evaluation. Through a partnership with the OCTRI Evaluation Core, evaluation support is provided.
Integrated Health Sciences Facility Core: The IHSFC provides connections and resources to establish team science-based collaboration to transform the way we perform environmental health research across an enhanced definition of NIH-defined T0-T4 translation.
- Catalyze team-based science and stakeholder-engaged research projects
- Facilitate the connections and leverage existing resources
- Assist environmental health research team building and help identify and match expertise and resources
- Consultative services available for:
- Human subject research support:
- Assist with regulatory compliance (e.g. IRB, FDA) and development of grant proposals and protocols.
- Human trial planning and the coordination of study participants including recruitment and retention, basic clinical testing procedures, administration of study test materials, and the collection and processing of blood, urine and other biological samples.
- Clinical Research Nurse Coordinator time (hourly basis) for subject screening and sample collection
- Biostatistics support: Biostatistics assistance on study design, grant proposal preparation, data analysis and results interpretation to Center Investigators as they plan, implement and prepare publications on their projects. Dr. Jiang is also interested in collaborating to develop customized statistical methods when existing tools are not available.
- Bioinformatics support
Center for Environmental Exposures and Disease (CEED)
Grant number: P30 ES005022
Recently, Professor Philip Demokritou, formerly a faculty member at the T.H. Chan School of Public Health at Harvard University and Director of the NIEHS-funded Harvard Center for Nanotechnology and Nanotoxicology (HCNN), joined our team at Rutgers University as the Henry Rutgers Chair and Professor of Nanoscience and Environmental Bioengineering. Dr. Demoknitous is establishing at Rutgers a Nano-biosciences and Advanced Materials Research Center (NAMC). The NAMC will integrate material & exposure science and nanotoxicology risk assessment to pave the way towards safer development of nano and other advanced materials. The Center will bring together ALL stakeholders -- industry, academia, policy makers and the general public -- to work together towards addressing EHS challenges from emerging materials.
Research priorities of the NAMC center include interactions of advanced materials with biological and environmental systems and their potential EHS implications; development of novel methods for the physico-chemical and biological characterization of materials across their life cycle using in-vitro and in-vivo systems; development of safer by design advanced materials to minimize EHS Risks; development of advanced material approaches for emerging 21st Century public health challenges such as food safety and quality, air disinfection, agri-chemical delivery and biomedical applications. The NAMC Center will be part of the NIH/NIEHS National Health Implications Research (NHIR) Consortium, which was formed by NIEHS to assess potential adverse health effects of emerging engineered nanomaterials (ENMs).
A wide range of shared equipment through Core Facilities is available through the NIEHS Center for Environmental Exposures and Disease. These facility cores provide access to state-of the-art equipment mass spectrometry, including ICMPS with ion speciation, multi-laser cell sorting, flow cytometry, image analysis, confocal microscopy, bioinformatics, biostatistics, computational biology, as well as molecular pathology and histology. All of these cores are available to the project at reduced cost as a service and/or a in a collaborative mode, both of which include consultation and training as required.
Nano/Advanced Materials capabilities through the Rutgers NAMC Center (PI and Director, P. Demokritou):
A wide range of state of the art equipment and instrumentation for the characterization of engineered and environmental nanoparticles in biological and environmental media are available to investigators and students. In addition, NAMC Center has in place state of the art platforms to synthesize a wide range oh engineered and environmental nanoparticles including systems to synthesize metal and metal oxides, cutting edge 2D/3D ENMs such as CNTs, graphene, h2BN, nanocellulose, advanced nanocomposites, etc. NAMC also has in place exposure generation platforms for environmental nanoparticles such as thermal incineration platforms to generate combustion related nanoparticles from wild fires and secondary nanoplastics, electronic cigarette exposure systems, etc. NAMC also houses the NIEHS/NHIR Reference ENM repository, the most extensive material library currently available at the national and international level for nanotoxicology research which includes more than 50 materials which are currently used in nanotoxicology and nanobiology research across the NIEHS/NHIR consortium.
Multi-laser Cell Sorting and Animal imaging
DNA and RNA Sequencing
High resolution Mass Spectrometry/ ICPMS with ion Speciation/ Metabolomics
Analysis of DNA Methylation
Analysis of Circadian Rhythm
Controlled Human Exposure Facility
Bioinformatics and Computational Biology/ Modeling
Chicago Center for Health and Environment
Grant number: P30 ES0277792
Integrated Health Sciences Facility Core (IHSFC) ensures that CACHET members at both institutions have stewardship, support, and access to key infrastructure for their translational research projects in Chicago and global locations. In addition to providing tailored, specialized statistical methods and analytical support for complex environmental scenarios, IHSFC interfaces with other facility cores to arrange specific services for users’ translational studies.
Study Design, Population Cohorts, and Biobank provides CACHET members with: 1) infrastructure and services to design and implement translational EHS research; 2) access to trained research personnel with experience in recruiting diverse study participants; 3) infrastructure and expertise for planning, collection, processing, and storage of specimens; 4) access to existing cohorts; and 5) support to enhance translational research partnerships.
Human Population Exposures provides expert advice on environmental exposure assessment approaches. Services include: 1) consultation on methods and existing data sources; 2) device deployment and data collection; 3) data management; and 4) advanced data sciences and computational services.
Biostatistics and Modeling provides statistical and quantitative modeling support to CACHET investigators. These leaders develop statistical methodologies to promote new EHS research directions, including complex exposure modeling with highly correlated or mixed exposures, geo-spatial analyses, and gene-environment analyses, enabling the IHSFC to provide tailored statistical methods and analytical support for complex EHS research.
Community Engagement Core (CEC) engages Chicago communities and stakeholders in an iterative multi-directional process to identify and address environmental hazards of concern. The CEC’s long-term goal is to build transdisciplinary research teams that directly address emerging community concerns, translate findings into action, and disseminate research results to the community, healthcare providers, regulators, and policymakers. With support from IHSFC, CACHET members design, implement, and analyze studies that include external collaborations with other EHS Centers or institutions when outside expertise is required. The CEC disseminates findings using a community-first communication model.
Environmental Biomarkers Core: CACHET has reorganized its former Biomarkers Core into an Environmental Biomarkers Core (EBC) consisting of two Sub-Cores: 1) a mass-spec-based Environmental Exposures Assessments Sub-Core that is P30-specific in its services and resources available to members, and 2) a Biomarkers of Exposure Effects Sub-Core that streamlines member services by leveraging existing institutional resources at UIC and UofC. Both components provide methodologic training, priority access, and considerably subsidized services to CACHET members. Together, the EBC will: 1) provide CACHET members with access to analytical support that enables determination of exposures to environmental toxins in biological and environmental samples as well as biomarkers indicating the physiological effects of and susceptibility to such exposures; 2) develop new assays and acquire new instrumentation to support evolving research within CACHET; and 3) offer expertise in design and interpretation of assay measurements conducted for CACHET members.
A primary role of the EBC is to provide access to advanced analytical measurement. Additionally, the EBC works to develop new assays and analytical procedures to support new research efforts within CACHET. These efforts may include developing and validating new methods for detection and quantitative analysis of specific EDCs, pesticides, and emerging chemicals in environmental or human/animal samples, or measurement of emerging biomarkers of exposure (e.g., targeted/untargeted metabolites) and effects (e.g., short-chain fatty acids, bile acids) in biosamples. EBC also facilitates access to genomics, transcriptomics, microbiome/metabolomics, and other -omics services from existing institutional FCs. Different EBC services are available to all CACHET members on the two campuses; MS at UIC and microbiome, metabolome, and genomics/epigenomics at UofC.
Southwest Environmental Health Sciences Center
Genomics Facilities Core
- Provides four microarray platforms and the associated technologies necessary to use them: 5,760-gene human and mouse cDNA microarrays, 20,000-gene human oligonucleotide microarrays, the Affymetrix GeneChip system, and the GE HealthCare Codelink Bioarrays.
- The oligonucleotide microarrays manufactured on-site by the Genomics Facility Core are made using Sigma/Compugen 60-mers on Corning's ultraGAPS II slides with a GeneMachine OmniGrid and Stealth printing tips from Telechem International. The cDNA arrays are made the same way using cDNA clones produced by the IMAGE consortium.
- Provides quality control analysis of RNA samples using the Agilent Bioanalyzer and real time PCR confirmation of microarray results using an Applied Biosystems Prism 7000 and 7300 Sequence Detection Systems.
- Manufactures CpG island microarrays that are made available for purchase to researchers.
- Can provide next-generation RNAseq solutions through the Ion Torrent Proton platform.
- Can provide microbiome analysis through 16S rRNA gene sequencing or whole genome sequencing.
Cellular Imaging Core
- Superresolution optical microscope - Zeiss Elyra S.1 structured illumination microscope (SIM) capable of 4 color SIM at twice the optical resolution of confocal microscopy. This purchase includes a separate image processing workstation. This instrument was installed in January 2016.
- Upright multiphoton microscope - Zeiss LSM 880 multiphoton with 34 channel spectral detector, GAsP detectors for MP, 6 laser lines plus tunable multiphoton laser, 12 objective lenses, and Zeiss Airyscan module to provide improved multiphoton and confocal resolution. Installed in February 2016.
- Inverted confocal microscope - Zeiss LSM 880 with 34 channel spectra ldetector, 7 laser lines, was installed in January 2016.
NOTE: Unique resources include each of our arsenic (As) species and three recently installed light microscopes. Texas A&M’s Center for Translational Environmental Health Research is the only other center that might have these state-of-the-art scopes. These are fee-for-service microscopes, so while external use is welcome, users would be required to pay for time on the scopes. Technical expertise is on site for all of the scopes at no additional charge.
Integrative Health Sciences Facilities Core
UC-Davis Environmental Health Sciences Center
Community Engagement Core (CEC)
The CEC acts as a bridge between communities and academia by brokering partnerships that solve environmental health problems at the local level. It does this through its pilot projects or other initiatives and Community Stakeholder Advisory Committee (CSTAC), which is made up of government and local leaders in environmental health and justice organizations.
Environmental Exposure Core (EEC): The EEC provides researchers with expertise in study design, exposure assessment and interpretation of data. EEC member laboratories include:
- Exposure Science Laboratory
- Analysis for Organics/Toxicants Laboratory
- Environmental Analysis Laboratory
- Particle Measurement and Modeling Laboratory
- UCD-Interdisciplinary Center for Inductively-Coupled Plasma Mass Spectometry
- Air Quality Research Center
- Primate Inhalation Toxicology Laboratory
- Sensor Development Laboratory
- Aerosol Mass Spectrometry for Toxicant Analysis
Integrative Health Sciences Facility Core (IHSFC): The IHSFC provides researchers with access to experts and resources across a variety of colleges, schools and centers.
- Animal Models. UC Davis’s renowned California National Primate Research Center, Mouse Biology Program and Behavioral Assessment Laboratory support science focused on mechanisms of disease, epidemiological studies and connections between molecular and cellular research to human health.
- Biostatistics. We offer two biostatisticians dedicated to environmental health and omics research, providing essential services to interdisciplinary teams.
- Biomarkers. A partnership with the Genome Center and West Coast Metabolomics Center for exposure and genome, epigenome, transcriptome and metabolome signatures.
- Translational Research. A collaboration with the Clinical and Translational Science Center’s Clinical Trials Resource that helps with experimental design, IRB submissions and regulatory compliance to promote human subjects research on environmental chemical exposures and accelerate development of public health interventions.
UCSF Environmental Research and Translation for Health Center (EaRTH Center)
Grant number: P30 ES030284
Integrated Health Sciences Facility Core: The EaRTH Center IHSFC provides investigators access to environmental health, epidemiology, biostatistics/informatics, and research translation resources to substantially advance their capacity to study adverse health effects of environmental exposures and broadly communicate their research findings. Services include:
- Study Design
- Study population and sample size
- Adding chemical exposures and social stressors to data collection (e.g. survey design)
- Environmental health and chemical data management (e.g. database creation, maintenance, QA)
- Biostatistical analysis (e.g. evaluating multiple chemical exposures/mixtures)
- High-dimensional data analysis
- Omics integration
- GIS –geocoding, geographic attribute data
- Chemical Selection, Measurement, & Model Systems
- Chemical selection for human and lab science studies
- Model systems and interpretation of results
- Scientific Translation
- Communication strategies (e.g. press release, blog, infographics)
- Materials translation (e.g. Spanish language translation, literacy level evaluation and translation)
- Chemical results reporting to research participants
- Mass Spectrometry-Based Global Proteomic Services provides investigators with global mass spectrometry (MS)-based, protein-level data from in vitro, animal, and human studies. These data enable important insights into biological pathways by which environmental factors exert effects in various experimental models and clinical studies. The available experimental workflows support identification and relative quantification of protein biomarkers and other early indicators of biological perturbations associated with environmental exposures or specific genotypes.
- High-Throughput Chemical Screening (HTCS) provides three important services to allow researchers to rapidly test chemical toxicity:
- Collection and maintenance of an environmental chemical library consisting of at least 250 chemicals to ease testing of compounds by providing a standardized set of environmental chemicals.
- Provision of an in vivo budding yeast model system to evaluate the effects of chemical compounds on cell proliferation, meiotic progression, and cell/subcellular morphology.
- Provision of equipment and expertise to perform HTCS in various tissue culture cells for morphological changes using Cell Painting.
- Environmental Chemistry Laboratory (ECL) Biomonitoring Services provides measurements of chemical levels in biological samples (i.e., biomonitoring) and environmental media, including water and dust.
- Targeted biomonitoring of biological samples for chemicals whose presence is well established in human tissue (e.g., PBDEs and PFAS) or for which limited biomonitoring data indicate potential for widespread exposure (e.g., organophosphate flame retardants, new replacement short-chain PFAS).
- Non-targeted/suspect screening analysis using high-resolution MS biomonitoring approaches–a new analytic service not widely available to researchers.
Center for Environmental Genetics
Core Resources:Integrated Health Sciences Facility (IHSF) Core
- Fernald Community Cohort: Data and Biospecimens are available from this cohort of almost 10,000 persons, followed for 18 years. Although about 40% were exposed to uranium from a refinery, the remaining 60% had no exposure beyond the usual variation in normal background exposure.
- Instructional videos on Human Biomonitoring: Principles and Practices: One video on Study Design Principles for studies using biomonitoring and a second video on practical information for Archiving Biospecimens and shipping them. Very appropriate for trainees or new study staff. See: Human Biomonitoring Principals & Best Practices
- MEB-Labs Database contains information about laboratories capable of measuring exposure biomarkers, offered as a resource to the community of environmental scientists. Data elements include the laboratory name, location, contact information, link to website, chemical biomarkers measured, analytic technique, limits of detection, and laboratory publications.
Integrative Technologies Services (ITS) Core
- Genomics, Epigenomics and Sequencing Core: Managed by Xiang Zhang, PhD, the GESC is a one-stop core facility that provides provides genomics- and epigenomics-related services. In addition to having the highest usage among all cores, the GESC offers a wide range of next-generation sequencing services such as RNAseq, ChIPseq, methyl-seq, and ATACseq, which allows CEG members to identify the molecular perturbations under specific environmental exposure. The core routinely provides services such as RNA-seq, miRNA-seq, exome-seq, methyl-seq, ChIP-seq and Illumina Infinium assay including methylationEPIC. It also provides other supportive expertise and welcomes collaboration. The Core is highly rated by researchers for its professional and dedicated service. Please visit the GES Core web site for details and updates.
- CTL ImmunoSpot S6 micro analyzer: designed for scanning and evaluating single cell-based spots that reflect the protein expression, function, and growth of cells. The CEG's CTL ImmunoSpot S6 micro analyzer is highly advantageous in functional characterization of rare cells from limited human samples and in the survey of rare subsets from exposure-related epidemiology studies using high-throughput microplate analyses. In-kind subsidies/matching funds allow members to leverage NIH/NIEHS- or foundation-funded research. CEG Pilot awardees can use their awards as matching funds for qualified, subsidized services.
- Inhalation Core (https://researchdirectory.uc.edu/facilities/41), directed by Dr. Michael Borchers at UC, with the mission to provide a controlled exposure system for rodents to mimic secondhand smoke exposure using a whole body exposure system.
- Fernald Community Cohortwww. (https://med.uc.edu/eh/research/projects/fcc), directed by Dr. Susan Pinney at UC. See above.
- Metallomics Core, directed by Dr. Julio Alberto Landero at UC. The core supports research in all fields related to the analysis of metals and metal species and their interactions within biological and ecological systems using state-of-the-art equipment.
- Proteomics Core, directed by Dr. Ken Greis at UC. This core is committed to providing collaborative expertise & services in proteomics & biological mass spectrometry and is fully equipped with protein separation and mass spectrometry equipment as well as personnel trained to perform comparative analyses of complex protein mixtures and to identify the differentially expressed proteins.
- Transgenic Animal and Genome Editing Core at CCHMC provides streamlined service from DNA to founder animals and uses the latest genome editing technologies, such as CRISPR-Cas9 and TALEN, to generate animals carrying multiple knockout or knock-in alleles in a highly efficient and time-saving fashion.
- Translational Core, directed by Dr. Lilith Reeves at CCHMC. Includes the Viral Vector Core, the Vector Production Facility, the Stem Cell Processing Lab, the Cell Manipulations Lab, and the Translational Trial Development and Support Lab. Specializes in the translation and scale up of gene therapy and cell therapy, including induced pluripotent stem cells (iPSC), in addition to the patient testing associated with these trials.
- Animal Behavioral Core directed by Drs. Charles Vorhees and Michael Williams at CCHMC. This core provides behavioral and nonbehavioral assays to help investigators characterize the nervous system function in mice and rats. The measurement protocols include video tracking and photocell technology.
- NMR-based Metabolomics Core (https://www.cincinnatichildrens.org/research/cores/metabolomics), directed by Dr. Lindsey Romick-Rosendale at CCHMC. This core provides technology that will help clinical and basic scientists develop rapid detection methods as well as elucidate the complex metabolic pathways involved in a number of diseases and infections. The core provides all NMR-related metabolomics services on human and animal cells, biopsies, and biological fluids.
- Pluripotent Stem Cell Facility (https://research.cchmc.org/stemcell/), directed by Dr. James Wells at CCHMC. This core provides high-quality, well-characterized, and reliably archived human embryonic stem cells for distribution to researchers. This core provides investigators with reagents and expertise for the generation of iPSCs as well as expert training in the protocols and techniques for proper handling and manipulation of human pluripotent stem cells.
- Readouts of cellular states produced by "omics" experimental platforms have become indispensable in contemporary environmental health sciences research. The CEG Bioinformatics Core employs advanced computational and data resources, and application of sophisticated bioinformatics methods to help investigators translate omics data into mechanistic understanding of biological processes underlying complex diseases. Directed by Mario Medvedovic, PhD, who also leads the UC component of the multi-institutional BD2K-LINCS Data Coordination and Integration Center (DCIC).
Environmental Health Sciences Research Center
- Our Pulmonary Toxicology Facility (PTF) has two important resources to share. We have extensive capabilities for both in vivo nose-only and whole body exposure systems for nano- to micron-scaled particulate xenobiotics and semi-volatile organics such as PCBs and PAHs. The PTF also has systems for the study of nanomaterials with exposure to human primary epithelial cells or cell lines at a an-liquid interface.
- Our Environmental Modeling and Exposure Assessment Facility performs a variety of exposure assessments in agricultural and rural settings and can collect, characterize and provide particulate matter for others to study.
Center for Appalachian Research in Environmental Sciences (UK CARES)
Analytical Core: Primarily provides services using GC and LC coupled mass spectrometry with multistage and high resolution instruments for quantitation of small molecules of broad relevance to environmental disease researchers. The laboratory contains two Agilent GC MS systems with quadrupole and triple quadrupole mass analyzers as well as electron capture and flame ionization detectors. It contains three ABSciex triple quadrupole linear ion tram mass spectrometer systems with Shimadzu HPLC and UPLC systems as well as an ABSciex quadrupole time of flight mass spectrometer system with HPLC and microflow chromatography systems and a Thermo Q-Exactive quadripole orbitrap mass spectrometer with a dionex UPLC system. The laboratory also contains extensive equipment for sample preparation including automated systems for solid phase and accelerated solvent extraction as well as solvent evaporation including several Caliper Turbovap evaporators and a large volume genevac solvent evaporator. The laboratory can conduct measurements of many different classes of pollutants in biological or environmental matrices including serum and blood plasma, tissues, water and soil. Areas of emphasis include polychlorinated biphenyls, dioxins, polychlorinated benzodifurans, per- and polyfluoroalkyl substances, and bisphenols. Published methods for other established and emerging persistent organic pollutants and biomarkers of exposure to these pollutants can be set up and validated for use in preclinical or clinical studies as needed.
- Director: Andrew J. Morris Ph.D.
- Staff: M. Abdul Mottaleb, Ph.D, Sony Soman, Ph.D. Courtney Hammill, MS.
- Location: B074 BBSRB 741 South Limestone, Lexington KY 40536.
- Contact: 859 323 3749 a.j.morris @uky.edu
UK CARES is led by Director Xianglin Shi, PhD; Professor and William A. Marquard Chair in Cancer Research, Department of Toxicology and Cancer Biology
Center for Integrative Environmental Health Sciences
Grant number: P30 ES030283
Integrated Health Science Facility Core (IHSFC): The multi-disciplinary Integrated Health Sciences Facility Core (IHSFC) provides infrastructure facilitating translational human subjects EHS research for the CIEHS, UofL, and the community. The ultimate goal is to improve public health and clinical practice in affected communities. The IHSFC supports patient-oriented clinical research (e.g., the early detection, prevention, and therapy of environmentally-related disorders); group and population-based research; as well as community engaged/led research. The IHSFC is comprised of two interacting subunits: The Research Administration and Planning Subunit (RAPS) lead by Drs. Luz Huntington-Moskos and Shesh Rai and the Research Implementation Subunit (RIS) lead by Drs. Craig McClain and Janice Sullivan. Matt Cave, M.D., a physician-scientist and recent NIEHS RIVER awardee, directs the IHSFC. The IHSFC interacts with other CIEHS Cores to provide access to state-of-the-art instrumentation and technologies; increase multidisciplinary collaboration; and enhance partnerships with community-based organizations. https://louisville.edu/ciehs/cores/ihsfc
Integrated Toxicomics & Environment Measurement Facility Core (ITEMFC): The Integrated Toxicomics & Environment Measurement Facility Core (ITEMFC) organizational design is to create a central resource for CIEHS members, allowing them to understand, access and effectively use environmental ‘omics and measurement resources currently available at the UofL. The ITEMFC enables and supports integrated services for Genomics and Transcriptomics, Proteomics, Metabolomics, Metallomics, Environmental Exposures and Assessments, and Microbiome studies. The ITEMFC will work closely with other CIEHS facility cores to plan research project support, support of CIEHS investigator and pilot project grant applications as well as pursue support of broad dissemination of ITEMFC capabilities and research successes to the affected or interested populations with greater Louisville community and beyond to national and international stages. Michael L. Merchant, PhD ITEMFC director and Proteomics shared resource director.https://louisville.edu/ciehs/cores/itemfc
Biostatistics and Informatics Facility Core (BIFC): The goal of the BIFC is to provide state-of-the-art statistical support in design, analysis and dissemination of findings of a range of basic science, translational, clinical, population health and environmental epidemiology studies. Provide support for the integration of multi-omics data from both animal and human studies, facilitate integration of exposure data with lifestyle factors to identify effect modifiers and mediators of the health effects of environmental exposures, and educate center investigators, staff and trainees in new methods related to statistics/omics approaches applicable to their research activities. Shesh Rai, Ph.D. is the BIFC Director.
Services and technologies: Services provided includes (a) Generate hypotheses based on background data and sample size calculation related to miRNA, RNA-Seq, Proteomics, Metabolomics and Microbiota data for animal studies involving balanced ANOVA Model; (b) Analysis of animal studies with simple approach (two-group comparison) and efficient ANOVA models, and design and analyses of clinical studies involving retrospective and prospective clinical studies- cross sectional, cross-over and longitudinal; (c) Analyses with FDR correction of miRNA, RNA-Seq, Proteomics, Metabolomics and Microbiota data; (d) Statistical consideration section for protocols and grants, and provide data, safety and monitoring in clinical trials; (e) Develop and validate R and SAS programs and perform statistical analysis and prepare statistical reports, and develop efficient and robust biostatistics and bioinformatics methods. Analysis includes methods such as survival analysis, longitudinal analysis, missing data analysis, high-dimensional data analysis including GWAS, Microbiome data, RNA-Seq (NGS) data, Proteomics data, Microarray data, Pathway and network analyses. Areas of special interest include repeated measures models, measurement error, spatio-temporal methods, computational biology, statistical genetics, clinical informatics and Bayesian methods. https://louisville.edu/ciehs/cores/bifc
Michigan Center on Lifestage Environmental Exposures and Disease (M-LEEaD)
Grant number: P30 ES017885
Exposure Assessment Core: The Exposure Assessment Core supports the design, implementation and analysis of exposure assessments, and provides assistance to ensure that exposure assessments and analytical data generated are sound, quality assured and reflect state-of-the-art knowledge and expertise.
The Core provides assistance with sample collection, storage, preservation, processing, and analysis for environmental and biological samples, and referral services to supporting laboratories for analytes not measured by the Core itself. The Core also provides consultations regarding exposure data, including study design, data cleaning, data interpretation, error calculations, and the use of environmental models and databases, such as those pertaining to air quality (including ambient and indoor), water quality (including surface, ground and drinking water), and soil quality (including waste sites, vapor intrusion).
Integrated Health Sciences Core:
Consultation on community-based environmental health problems: The IHSC provides translational consultation to assist Center investigators in identifying ways that our associated biorepositories and Cores can be used in preparing pilot projects or full grant proposals. Biostatistical consultation and collaboration are provided to help ensure that Center studies are well designed, and that appropriate statistical methodology is used in their analysis. This service includes guidance with general study design, feasibility, specimen collection fundamentals, case report form development and human subjects regulations, as well as re-directing investigators to appropriate collaborators for more in-depth and specialized collaboration or consultation (e.g., detailed study design or assay methods).
Biorepository services: A service of the Integrated Health Sciences Core; identifies physical facilities and best practices for specimen collection, storage, labeling, and retrieval, and referrals to potential collaborators with existing biorepositories.
Omics and Bioinformatics Core: Provide genomic analysis resources for all Center-related projects. Researchers will have access to full services for epigenomics experiments; individual labs may submit cells for DNA/RNA extraction or ChIP-DNA for ChIP-Seq. The core will perform sample library preparation for the main DNA methylation platforms and sequencing applications, RNA-seq, or ChIP-seq. Prepared samples will be sent directly to the UM DNA Sequencing core, and generated data will be sent directly for bioinformatics service. In addition to the Epigenomics-related services described above, Center researchers can directly request access to technologies such as whole-genome sequencing, small RNA sequencing, microarrays, etc. ChIP-seq, microarrays, microRNA expression, HumanMethylation450 BeadChip, reduced representation (RRBS) or whole-genome (WGBS) bisulfite sequencing, MeDIP-seq, MethylCap-seq, hmeDIP-seq, and Enrichment testing (pathway analysis).
UNC Center for Environmental Health and SusceptibilityWebsite: https://sph.unc.edu/cehs/center-for-environmental-health-and-susceptibility/
INTEGRATED HEALTH SCIENCES FACILITY CORE (IHSFC): The Integrated Health Sciences Facility Core (IHSFC) facilitates translation of research from laboratory models to human studies.
- The IHSFC reduces timelines for project implementation by connecting CEHS members with professional scientific support for human studies, patient recruitment, population-based studies, survey research, and biospecimen processing.
- The IHSFC serves a broad base of users.
- The IHSFC supports a high-caliber biospecimen processing (BSP) subcore. IHSFC provides concierge services to connect CEHS members with this core, which also responds to CEHS members’ requests for new methods and offers special pricing and prioritization for CEHS members. The IHSFC/BSP subcore provides storage capabilities for CEHS member samples.
- The IHSFC includes a Population Engagement Research Collaboration (PERC) subcore that provides access to a professional staff of trained interviewers and medical record abstractors; and facilitates access to rapid case ascertainment (RCA) through the NC Central Cancer Registry and hospital-based recruitment through the office of clinical and translational research (OCTR).
- The IHSFC seeks opportunities for collaboration with the Community Engagement Core (CEC).
- The IHSFC supports the Pilot Projects Program, meeting with all applicants who have human studies components, assisting with Institutional Review Board approval and protocol development, and connecting members with study resources, technical support, and Facility Cores including the CEC as needed to address community-level project needs.
- The IHSFC supports rigor and reproducibility throughout human studies research by implementing best practices for human studies, through reliance on state-of-the-art biospecimen processing protocols, and through expert, professional staff for patient and participant research contact and communication. These supports are further bolstered by excellence in downstream core facilities, from genomics to bioinformatics and biostatistics. Rigor and reproducibility are supported at all stages of human studies.
MOLECULAR ANALYSIS AND STATISTICAL SUPPORT (MASS) CORE: The Molecular Analysis and Statistical Support (MASS) Facility Core is a concierge and advanced scientific support core that connects campus-wide networks to offer expertise, technical support, methods development, oversight, and tracking. MASS integrates university services and fills expertise and methods gaps for CEHS members. MASS functions as a research accelerator by providing highly qualified expertise and staffing, together with connections to relevant on-campus services. The MASS reduces time to data collection and interpretation by at least six months.
The two thematic foci of this support unit are Molecular Analysis and Statistical Support.
Molecular Analysis. The molecular analysis needs of CEHS investigators evolve over time and the MASS provides scientific support, networks, negotiated pricing, and priority access for members to utilize a range of University-wide subcores and to support novel methods development to meet members’ needs. The MASS develops new technologies and capabilities within existing cores and negotiates relationships with partner subcores. Three major domains and core-relationships have been sustained over time and are strategically integrated in Center: Biomarker Mass Spectrometry (BMS), Pathology Services Core (PSC), and Office of Genomics Research (OGR).
Statistical Support. With support from the UNC Department of Biostatistics, one of the top four departments of biostatistics nationwide, the MASS delivers state-of-the-art support in areas ranging from personalized medicine to clinical trials to epigenetics and covering topics such as study design, power calculations, dose-response analysis, longitudinal data analysis, survival analysis, causal inference, semi-parametric methods, statistical genetics, gene-environment interaction, and bioinformatics. Key features include: Integration between data design and acquisition, Highly-qualified personnel, rapidly mobilized for standardized work flows, Cost-effectiveness, and Novel methods development.
Center of Excellence in Environmental Toxicology
- Exposure Biology Informatics Core: Visual analytics laboratory and machine learning.
- Translational Biomarker Core: Q-Exactive HF hybrid Orbitrap Mass Spectrometer for targeted and untargeted metabolomics.
- In Vitrocell smoking machine for in vitro exposures to cigarette and E cigarette smoke.
- Human exposure chamber for inhalation studies on ambient exposure to ozone and diesel exhaust.
- Biobank of human biospecimens in the lung and airway disease and reproduction arenas.
- Q-Exactive HF hybrid Orbitrap Mass spectrometer for metabolomics.
Note: While these unique resources are sharable, sharable does not mean without cost when "fee" structures exist at our institution.
Environmental Agents as Modulators of Disease Processes
Grant number: P30 ES00127
- Inhalation Facility Core for animal, human, and in vitro exposures to ambient air pollution and laboratory-generated atmospheres that contain particulates, gases, or mixtures thereof. Examples include concentrated ambient ultrafine particles, diesel exhaust particles, ozone, metal/metal oxide nanoparticles, diacetyl, and electronic cigarette (vaping) aerosols. Exposure characterization data are provided and samples can also be provided for additional offline measurements.
- Behavioral Sciences Facility Core that includes both human and animal behavioral testing built on backward-forward translation and the use of the same behavioral testing paradigms in humans and animals for facilitating translation. It incorporates assessments for domains including motor, sensory, complex function and social behaviors. Human testing relies on the use of computerized/ipad tests from Cambridge cognition, while animal testing includes a suite of mazes, elevated plus maze, gait scan, auditory startle and operant testing chambers for rats and for mice.
- Elemental Analysis Facility Core has a suite of instruments for analyses of metals and trace elements in various biological, chemical or environmental samples spanning the range of ppt to ppm levels. Instrumentation includes ICP-MS, ICP-OES and AAS. Additional capabilities include solvent and chromatographic separation methods for analyses of complex mixtures and organo-metal speciation using GC and LC separation systems.
- Epigenetic Facility Core provides DNA methylation analyses using the Qiagen PyroMark Q24 Advanced technology. The core provides full service for investigators who wish to conduct targeted methylation studies, as well as hands-on training sessions for users who want to be actively involved in the studies, from designing assays to running the equipment and obtaining data. In addition, the Core provides assistance in data analyses and interpretation.
- Biostatistics Core works closely with EHSC researchers to assist in the planning of environmental health studies and analysis of environmental health data. The Core provides EHSC investigators with biostatistical support needed for their research, works with EHSC investigators to develop new biostatistical methodology, provides training in biostatistical methods to EHSC members and their trainees, and offers guidance to early stage faculty in conjunction with the Career Development Program.
Southern California Environmental Health Sciences Center
- Integrative Health Sciences Facility Core (IHSFC) facilitates study logistics (project planning, clinical assessment facilities, access to populations and study subjects, IRB interactions, study design issues), as well as the multi-tiered responsibilities associated with preparation, handling, analyses, and storage of environmental and biological samples generated in the course of Center-related research. The IHSFC core also performs a range of molecular biological analyses using a variety of platforms and coordinates outsourcing of specialized assays to collaborating laboratories and companies.
- The Exposure Factors Facility Core (EFC) addresses a full range of exposure assessment and spatial analysis needs. Exposures in this context are broad in scope and include chemical, physical, social, built environment, other stressors such as ambient light at night and noise, and behaviors and activities that affect individual interactions with their surrounding environment. Services include advice on environmental sampling design; instrument selection and deployment; field operations and logistics; sampling protocols; social and built environment data resources; spatiotemporal modeling; remote satellite imagery; machine learning approaches to data analysis; ecologic momentary assessment (EMA) of real-time exposures and geographic and psychosocial context; assessment of ultraviolet (UV) radiation exposure; and a robust assortment of geospatial analysis platforms. The EFC works closely with the other SCEHSC Facility Cores to provide guidance on exposure assessment strategies and approaches for SCEHSC pilot projects, NIEHS and other funded research.
- Biostatistics Facility Core (BFC) provides statistical and computational support for planned and ongoing research projects. This support includes study design consultations, study sample size or power recommendations for appropriate project-related analytical methodologies, spatial statistics, and bioinformatics approaches. The BFC also gives Center members access to statistical and bioinformatics resources by matching appropriately trained statisticians and informatics specialists to the analytical needs of investigators. Software has been developed by the BFC with an eye toward implementation by any investigators studying genomic and environmental factors related to complex human traits. The BFC continues to maintain and support the power/sample size program Quanto, which computes sample size and power for several study designs (e.g. case-control, matched case-control, case-parent trio) and for several types of hypotheses (e.g. environmental effects alone, gene-environment (GxE) interactions). GxEscan, developed by members of the BFC, performs a genomewide scan for GxE interaction in a case-control sample. The program implements recently developed efficient two-step methods as well as more traditional (but often less powerful) case-control and case-only analyses. Software downloads available here: http://biostats.usc.edu/software.html
Interdisciplinary Center for Exposures, Diseases, Genomics and Environment (EDGE)
Grant number: P30 ES007033
Core Resources:Genomics, Bioinformatics & Biostatistics, and Microphysiological Systems Facility Core (GBBM-FC)
The Core is comprised of three complementary components: 1) The Genomics Component provides genomics, epigenomics, transcriptomics, proteomics, and metabolomics resources. 2) The Bioinformatics & Biostatistics Component provides data analysis expertise for all types of OMICs data and beyond. 3) The Microphysiological Systems Component (MPSC) offers access to sophisticated 3D in vitro model systems that mimic the complex cellular architecture of organs. The MPSC offers a unique experimental system for validating discoveries revealed by OMICs analyses. A more detailed description of the services the three components offer is provided below.
Genomics ComponentGene expression
- RNA isolation and QC
- Global transcriptome profiling using Next Generation Sequencing (RNA-Seq)
- Targeted mRNA, microRNA, and lincRNA gene expression profiling (low and medium throughput)
- Single cell RNA-Seq analysis
- DNA isolation and QC
- Genome wide genotyping using high density single nucleotide polymorphism arrays
- Targeted genotyping of single nucleotide and other polymorphisms
- Targeted genotyping of SNPs in Drug Metabolism Enzymes and Transporter genes
- Targeted genotyping of SNPs for ancestry characterization
- Facilitating genome wide exome sequencing
- Facilitating whole genome sequencing
- DNA isolation and QC
- Genome wide methylation profiling using Illumina bead chip arrays or massively parallel sequencing
- Targeted DNA methylation profiling
- Increased sensitivity of detection of gene expression
- Pathogen detection, etc.
- Performing ELISA assays
- Performing Luminex and Meso Scale Discovery multiplex immunoassays (e.g. cytokine profiling)
- Study design consultation
- Technical consultation (e.g. sample preparation)
- Facilitating targeted and discovery proteomics and metabolomics experiments
- Investigating post-translational modifications
- Mass spec based peptide quantifications (e.g. SIM and MRM methods)
- Data analysis consultation
- Nucleic acid isolation and QC
- Facilitating 16S rRNA and metagenomics sequencing
Supporting preparation of manuscripts and grant proposals
Bioinformatics & Biostatistics Component
Experimental design consultation for OMICs and non-OMICs experiments
Comprehensive statistical and bioinformatics analysis of:
- Genomics data (e.g. targeted and whole genome wide genotyping data)
- Epigenomics data (e.g. targeted and whole genome wide methylation data)
- Transcriptomics data (e.g. RNA-Seq data)
- Proteomics data (e.g. targeted and global proteomics data)
- Metabolomics data (e.g. targeted and global metabolomics data)
- Microbiome data (e.g. 16S rRNA and metagenomics data)
Mining of publicly available OMICs data
Multi-omics data integration
Consultation for statistical analysis of non-OMICs data
Supporting preparation of manuscripts, grant proposals
Integrated Health Sciences Facility Core (IHSFC): Clinical & Translational Services
- Two-way facilitation of interaction between basic scientists and clinical/ translational/population-based scientists, to enable innovative approaches that span disciplines. D
- Two-way facilitation of interaction between basic scientists and clinical/ translational/population-based scientists, to enable innovative approaches that span disciplines. D
- A dedicated core facility space for clinical testing, physiological testing, and collection and storage of human samples.
- Controlled-exposure facility for specialized inhalation exposures.
- Assistance with IRB issues, identification of staffing solutions for human subjects research, subject recruitment/screening and retention, laboratory assay coordination and organization and application of toxicokinetic approaches.
- Help developing repositories of samples from well-characterized populations with specific environmental exposures.
- Expert consultation on study design, human subjects review, funding, and community coordination regarding disaster research response (DR2)
- Development of pre-positioned protocols for DR2
- Training on DR2
The Exposure assessment, Biomarkers and Environmental Sensing Facility Core (EABES) of the EDGE Center provides the following capabilities and services to support research and training in the Environmental Health Sciences at the University of Washington:
- Provides expert consultation for Center investigators regarding sampling plans and measurements of exposure to chemical agents and complex mixtures.
- Provides full-service exposure assessment capability including collection of exposure data, chemical analysis of environmental and biological samples for chemical agents, data management and interpretation of exposure data.
- Facilitates access to state-of-the-art instrumentation, ranging from networks of GPS-enabled personal exposure monitors to high end mass spectrometry systems, for measuring exposure and exposure signatures in biological samples.
- Develops and implement sensitive and specific quantitative mass spectrometry-based assays for application to biomarkers of exposure.
- Educates Center investigators about the potential of new and emerging tools and technologies for exposure assessment in EHS research.
- In partnership with the other cores within the EDGE Center, provides leadership in facilitating the innovative integration of exposure science with genomics, epigenetics, proteomics, and metabolomics approaches in EHS research.
Community Engagement Core (CEC)
- Partner with community and stakeholder groups with an interest in or need related to environmental health research and disaster research response (DR2)
- Assist communities to develop action-oriented research and education projects
- Build researcher capacity for community-engaged research and effective public communication
- Leverage collaborations locally and nationally to develop, refine, and promote models and best practices related to public engagement in environmental health sciences and DR2
Center for Urban Responses to Environmental Stressors (CURES)
Grant number: P30 ES020957
Exposure Signatures Facility Core The ESFC measures environmental toxicants and the biological consequences of toxicant exposure in biological samples and in complex environmental matrices. The goal is to integrate measurements of the amount of toxicant exposure with measurements of gene expression, protein abundance or signaling molecule status that indicate the impact of exposure in the individual. The ESFC provides analytical services for Genomics, Proteomics, Toxicants, Metabolites, Lipids, Cytokines, Metals and Flow Cytometry. Co-leaders: Douglas Ruden, PhD, Institute of Environmental Health Sciences, Director of Epigenomics, C.S. Mott Center for Human Growth and Development; Paul Stemmer, PhD, Institute of Environmental Health Sciences, Director of Proteomics Core Facility
Integrative Health Sciences Facility Core The IHSFC facilitates translational research and its impacts by bridging connections between our researchers and our community partners and public health arenas. Through multi-directional communication and team-building, the IHSFC translates community environmental health concerns to and from the CURES research infrastructure. We provide enhanced partnerships and access to resources, including biostatistical and study design support, geospatial analysis and data visualization services, team science-based team building, regulatory and ethical support, and the latest tissues and techniques to enhance our researchers’ ability to characterize environmental stressors impacting Detroit residents. Co-leaders: Graham Parker, PhD, Department of Pediatrics; Samiran Ghosh, PhD, Dept. of Family Medicine and Public Health Sciences and Dept. of Molecular Medicine and Genetics; J. Richard Pilsner, MPH, PhD, Dept. of Obstetrics and Gynecology, Director of Molecular Genetics and Infertility, Institute of Environmental Health Sciences; IHSFC Coordinator: Jessica Worley, MPH, Institute of Environmental Health Sciences