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
Exposure Assessment Facility Core
- 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.
Integrative Health Sciences Facility Core
- 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.
Health and Exposome Research Center; Understanding Lifetime Exposures (HERCULES)
- 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 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. More information on the Jones Lab may be found here.
Targeted Exposure Analysis (Dana Barr, PhD, Co-Lead): A unique suite of multiple types of mass spectrometers allows for measurement of any chemical in multiple biological matrices. With state of the art analytical technologies and complementary scientific experience, assays can be developed to target specific research needs.
Clinical/Population Research Services (Carmen Marsit, PhD; Miriam Vos, MD; and Tom Ziegler, MD; Co-Leads): This component of the IHSFC is designed to provide services to promote translation of basic science concepts into practical clinical and population research designs that can significantly promote incorporation of environmental health sciences (i.e., exposome research) into clinical medicine and population-based health research.
- Environmental Health Sciences Data Core: Lance Waller, PhD, Director, Biostatistics. Eberhard Voit, PhD, Co-Director, Systems Biology. The EHDSC aims to expand and foster a data, analytic, and collaborative ecosystem for exposome-related research. The team has a strong body complementary expertise in mathematical modeling and systems biology, allowing personalized work with each investigator to assist in developing the best approach for their specific work.
- Pilot Projects Core: Edward Morgan, PhD, Director
- Biostatistical Consulting Center: Director; Renee Moore, PhD
- Community Outreach and Engagement Core: Director: Michelle Kegler, DrPH
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.
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: email@example.com 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.
Research Center in Environmental Health Science
- Rutgers University Cell and DNA Repository. As the world's largest university based biorepository, RUCDR has been perfecting the science of biobanking, bioprocessing and analytics since 1999. By utilizing a technologically advanced infrastructure and the highest quality biomaterials, RUCDR scientists work to convert precious biosamples into renewable resources thereby extending research capabilities. RUCDR understands that research goals and objectives vary from project to project so we give each client individual and customized attention to ensure "best fit" service. The RUCDR has a vast array of unique resources, all of which can be accessed through the Center. See - http://rucdr.org/whats-new
- A wide range of shared equipment through Core Facilities available through The NIEHS Center for Environmental Exposures and Disease. These facility cores provide access to state-of the-art equipment and expertise in Next Generation sequencing, mass spectrometry, 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.
- DNA and RNA Sequencing/Analysis Instrumentation
- Analysis of DNA Methylation
- Analysis of Circadian Rhythm
- Controlled Human Exposure Facility
- Bioinformatics and Computational Biology
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 Core Center
- Inhalation facilities for toxicology studies at the Center for Health and the Environment
- Inhalation facilities at the California National Primate Research Center
- Mouse Biology facility with broad capabilities for metabolism, cardio, immune, and CNS outcomes
- Sensor technology from PRISMS award, focus on use for asthmatics, Pl: Cristina Davis.
- ICP-MS for high resolution analytics for an array of metals on small volume materials (environmental media as well as biologic, including hair, dried bloodspots, etc.)
Chicago Center for Health and Environment
Biomarkers Core: Beyond making available state-of-the-art, user-friendly facility and services. Technologies and types of measurements that will be provided including qualitative and quantitative analysis of a wide variety of biomarkers and environmental toxins using ultrahigh-pressure or high performance liquid chromatography-mass spectrometry (UHP)LC-MS and gas chromatography-mass spectrometry (GC-MS) measurements and measurement of metals in biological specimens and environmental samples using inductively-coupled plasma (ICP)-MS.
Trace Elements/Metals analysis by ICP-MS. Equipped for quantitative and qualitative analysis of a full spectrum of heavy metals and metalloids in trace and larger concentrations in biological and environmental samples. Trace metal quality sample preparation is also available. Trace Metals are typically analyzed including mercury, arsenic, lead, cadmium, manganese, zinc, gadolinium, gold and platinum. Materials are frequently analyzed including tissue, soil, water, nails, hair, urine, blood and milk.
Biomarkers/toxins analysis by LC/MS. Seven state-of-the-art LC/MS are available for services, providing identification and quantitative analysis for different sample matrices including tissue, water, blood and urine. The analytes include protein/peptide, nucleic acid, carbohydrate, lipid and other organic compounds. Sample preparation and bioinformatics services are also available.
Targeted/untargeted Metabolomics/proteomics by LC/MS. Taking advantage of technologies such as nanoLC, UHPLC and SFC (super-critical fluid chromatography), both targeted and untargeted metabolomics/proteomics services are available for complex samples in the Biomarkers Core, aiming to improve diagnosis, prevention and monitoring of many diseases through metabolic and proteomic profiling.
Pesticide analysis by LC/MS. Followed the standardized EPA protocol, LC/MS analysis on common pesticides has been established in the core, including DTT, glyphosate, atrazine and simazine from food, water and biological fluids.
Trace organic pollutant analysis by GC/MS. For the analysis of volatile molecules including many pesticides and halogenated persistent pollutants, GC-MS measurement is available. The samples can be prepared from soils, sediment, dust, sludge, air sampling cartridges, and human blood and tissues.
Integrated Health Sciences Facility Core (IHSFC) provides investigators with necessary tools and methodologies to address environmental impacts on human health by pproviding infrastructure and services to support the design and implementation of EHS research projects that integrate components of basic science, public health research, clinical intervention studies, and patient-oriented EHS research. In this context, the IHSFC provides access to trained research personnel with experience recruiting a diverse study sample in Chicago and beyond as well as the infrastructure and expertise for the planning, collection, storage and processing of specimens, and expert advice in environmental exposure assessment approaches.
Environmental health science study design and performances and analysis services. The primary activity areas include study design optimization, protocol design, development of a sample selection and statistical analysis plan, informed consent, questionnaire development services, data collection and data management, quality assurance, study management and tracking, provide assistance in using advanced methods for data analysis, e.g. multiple exposure modeling, air pollution modeling, and design of laboratory Investigations.
Participant recruitment and access to existing population studies. Both hospital-based recruitment and community-based recruitment of study subjects is availabilities. The IHSFC facilitates access to existing UofC and UIC hospital and population studies including The ChicagO Multiethnic Prevention And Surveillance Study (COMPASS.uchicago.edu) , UIC Cohort of Patients, Family and Friends (UIC Cohort), and The Health Effects of Arsenic Longitudinal Study (HEALS).
Environmental exposure assessment. Extensive air pollution monitoring (ambient, indoor, and personal) resources and resource development are the CACHET focus. Water and soil assessment are also available.
Sample collection and storage. Provide guidance for and access to sample processing and banking as well as short term storage of biosamples from pilot studies and appropriate storage of environmental samples.
Microbiome Core supports scientists who are investigating fundamental questions;and developing new applications and tools;to understand and harness the capabilities of microbial systems in different ecosystems including humans, water, soil, plants, and the built environment. The Microbiome Core has extensive technology capability and access to both laboratory and computational tools that are necessary for identifying the bacterial, fungal, and viral organisms and communities that may change in response to external pressures.
Microbial Community Analysis by Amplicon Sequencing. Genomic DNA extraction is available using multiple systems, including the PowerSoil-htp 96-well Soil DNA Isolation Kit (MoBio). For amplicon sequencing, PCR is carried out on the 16S rRNA V4-V5 or 18S rRNA V9 region or ITS1 and 2, which can be performed and sequenced using the Illumina MiSeq or HiSeq platform to generate ~100,000 + 250 bp paired end reads per sample.
Initial Data Processing for Amplicon Sequencing. All amplicon sequencing data will be analyzed using the QIIME platform using standard protocols (Earth Microbiome Project: e.g., \
Shotgun Metagenomic Analysis. To explore the functional genes, pathways and genomes found in a sample, shotgun metagenomic analysis is available. Libraries will be sequenced on the HiSeq2000 platform with 2x151bp runs generating a depth of 15 million reads per run, multiplexed at 8 metagenome libraries per lane of HiSeq.
Shotgun Metatranscriptomic Analysis. To explore transcriptionally active genes and pathways, especially associated with re-assembled genomes, shotgun metatranscriptomic analysis can be performed.
Statistical Analyses for Microbiome Data. Examples of the statistical analytics that can be performed to identify particular biomarkers include evaluation of characteristics across groups to identify biomarkers will be performed using Pearson χ2 test for categorical data and one-way ANOVA for continuous variables; microbial diversity summarized using Chao1 estimator and Shannon index; UniFrac distances, which characterize the between-sample microbial community structure and compositional variance; DESeq2, coupled with multiple testing correction, will be used to perform differential abundance analysis to identify clinically relevant taxa; and logit models will be generated using both clinical and microbiome data as independent variables to contrast differences across clinical groups.
Culturing and Genomic Analysis. In order to grow bacteria isolated from different human body sites, various techniques can be applied under both aerobic and anaerobic growth conditions. The facility 900-plate capacity Bactron chamber can be used to grow bacterial and fungal isolates of organisms identified as a biomarker of a particular state by amplicon and shotgun metagenomic approaches.
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
- Tier I core facilities: Currently include the Geonomics, Epigenomics, and Sequencing Core (GESC), Genotyping Core, and Flow Cytometry 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.
- Tier II core facilities:
- 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 Cohort (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 (https://www.cincinnatichildrens.org/research/divisions/d/dev-biology/core), directed by Dr. Yueh-Chiang Hu at CCHMC. This core 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 (https://www.cincinnatichildrens.org/research/cores/animal), directed by both 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
Michigan Center on Lifestage Environmental Exposures and Disease (M-LEEaD)
Exposure Assessment Core: provides analytical services and coordination of services to advance the application of exposure measurements, including methods development, sample analysis, and quality assurance work.
Consultation on community-based environmental health problems: A service of the Integrated Health Sciences Core; provides assistance in developing statistically rigorous assessment methods for community outreach and engagement. In addition, the graduate students in the Department of Biostatistics run a community outreach organization called STATCOM which offers free consultation to non-profit organizations to help with community-based projects.
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 & Bioinformatics Core: provides expert assistance in the design and implementation of a broad range of studies that use high throughput technology, including consultation on study design, technology platforms, and sample preparation. Specific support services for genomics and epigenomics studies include RNA-seq, 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 Susceptibility
- Integrative Health Sciences Facilities Core (IHSFC): DATA & SAMPLE RESOURCES -- Data with clinically annotated linked biospecimens for environmental health research include North Carolina and UNC Health Care associated population- and hospital-based case-control and cohort studies with longitudinal data, often with over-sampling of African Americans and focus on health disparities. Large participant sets anchor and integrate the three CEHS translational research themes: (1) Cancer: UNC Health Registry (7,500 oncology patients); NC-LA PCaP (2,200 population-based incident prostate cancer cases); and CBCS (population-based >7,000 incident breast cancer cases, with extensive follow-up). (2) Developmental Disease: NBDPS (National Birth Defects Prevention Study, population-based, case control with over 35,000 mother-infant pairs); PIN (Pregnancy, Infection and Nutrition Study, includes over 3,000 women-infant pairs); Add Health Study (adolescent to adult health among 7-12 graders, nationally representative, over 5,000 subjects). (3) Cardio-Pulmonary Disease: SPIROMICS (Intermediate outcomes of COPD, over 2,500 subjects); HH LENOIR (CVD risk factors in low income and minority population, 550 subjects) RESEARCH INFRASTRUCTURE & SERVICES: Study design, methods and implementation consultation • Human biospecimen collection support services including high-throughput processing, (with emphasis on DNA/RNA extraction), storage and disbursement. • State-of-the art electronic tracking systems for sample, patient and data sharing processes with reporting. • Data linkages to » State vital statistics » Community and environmental data » Public and private insurance claims and » Electronic medical records
- Molecular Analysis Facility Core (MAFC): Provides a wide array of analytical services and platforms including DNA/protein extraction from cells and tissues; DNA damage and response analyses (DT40 or TK6 mutant cell lines); gene mutation assays (PIG-O, HPRT, TK-MLA, Litron’s MicroFlow micronucleus); mammalian genotyping, gene methylation profiling, epigenetic analysis; library preparation and high throughput sequencing; retrieval of archived, annotated, human tissues (FFPE); tissue micro-array design and construction, histopathology and slide staining services such as in situ hybridization for mRNA, fluorescence in situ hybridization (FISH) for DNA, and immunohistochemistry (IHC) for proteins; digital image technology to quantify analytes from intact tissue sections; integration of data from pathology, genomics, proteomics, and other tissue-based analyses; quantitative analysis of small molecule biomarkers such as DNA adducts, metabolites, and environmental toxicants by LC-MS/MS; single and multi-element analysis of trace metals and metalloids in water, soil, plant, and tissue extracts, urine, and blood by ICP-MS; and speciation analysis of arsenic and chromium in water and urine. Furthermore, in partnership with other UNC core facilities, the MAFC also identifies and coordinates additional analytical support services including: proteomics; metabolomics; cytokine analysis; and microbiome analysis.
- Biostatistics and Bioinformatics Facility Core (BBFC): Supports comprehensive statistical and computational support for data acquisition, analysis and interpretation needs of laboratory, clinical, and population-based investigations in environmental health studies. BBFC faculty members have exceptional biostatistical and bioinformatics expertise in an era of ever increasing data complexity. This includes computational methods for the analysis of high-throughput sequencing assays to facilitate biomedical and biological research. BBFC also provides an annual 3-credit hour course, ”Biostatistics for Laboratory Scientists,” to train new environmental researchers in biostatistical methods. BBFC offers training in partnership with ongoing training programs at UNC, including a Big Data to Knowledge (BD2K) and an interdisciplinary NIEHS T32 program.
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
- Inhalation Core Facility for both animal and human exposures to ambient air pollution and to other generated atmospheres.
- Behavioral Sciences Core Facility 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.
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.
- Spatial and Exposure Analytics Facility Core (SEAC) supports Center members’ developing research requiring real-time capture of high dimensional exposure and time-activity data and rapidly evolving new technologies for mobile device data collection including time-activity information and ecological momentary assessment (EMA). The core also furnishes more traditional exposure measurement equipment, spatial sciences, and geographic information systems (GIS) exposure modeling services. The SEAC provides an effective interface for Center investigators to access spatial analysis and modeling resources by matching appropriately trained spatial scientists with investigators’ analytical needs.
- 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, G´E interactions). GxEscan, developed by members of the BFC, performs a genomewide scan for gene-environment (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
Center for Exposures, Diseases, Genomics, and Environment (EDGE)
Functional Genomics, Proteomics & Metabolomics Facility Core
- Global transcriptome and miRNA profiling using microarrays
- Global transcriptome profiling using massively parallel sequencing (RNA-seq)
- Targeted mRNA, microRNA, and lincRNA gene expression profiling (low and medium throughput)
- Single nucleotide polymorphism (SNP) analysis using microarrays
- Targeted genotyping of single nucleotide polymorphisms (SNPs)
- Targeted genotyping of SNPs in Drug Metabolism Enzymes and Transporter genes (DMET)
- Targeted genotyping of SNPs for ancestry characterization Methylation profiling using targeted enrichment, bisulfite conversion, and massively parallel sequencing
- Targeted DNA methylation profiling Genome-wide copy number variation survey using microarrays
- Targeted copy number variation analysis In situ hybridization using QuantiGene View RNA Assays for mRNA and microRNA
- Support preparation and review of manuscripts and grant proposals
Basic proteomic services
- Consultation on experimental design, including sample preparation
- Assistance with finding collaborators to perform discovery proteomics
- Assistance with getting experiments addressed at UW Proteomics Centers
- Typical mass spec runs
- Investigations on post-translational modifications
- Mass spec based peptide quantifications (e.g. SIM and MRM methods)
- Consultation on data analysis
- Consultation on protein validation by ELISA, Luminex (fluorescent bead- or magnetic bead-based), or TaqMan assays
- Perform protein validation by ELISA, Luminex (fluorescent beador magnetic bead-based), or TaqMan assays
- Perform immunohistochemistry using specific antibodies Integrative
Environmental Health Sciences Facility Core
Bioinformatics & Biostatistics Services:
- Comprehensive support and analysis of mRNA and microRNA expression array data and miRNA target prediction
- Comprehensive support and analysis of biological networks and pathways using numerous packages including: weighted correlation network analysis (WGCNA), gene ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), and gene-set enrichment analysis (GSEA).
- Assistance in the analysis of methylation profiling data derived from targeted enrichment, bisulfite conversion, and massively parallel sequencing
- Advanced analysis of proteomics data
- Advanced analysis of metabolomics data
- Support for integration of different types of OMICs data
- Facilitate analysis of RNA-seq and ChIP-seq data generated by massively parallel sequencing
- Support preparation & review of manuscripts, grant proposals
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.
Exposure Assessment, Biomarkers & Environmental Sensing Facility Core:
- Expert consultation regarding sampling plans and measurements of exposure to chemical agents (e.g., volatile organic compounds, metals, particulates)
- Full-service exposure assessment capability including loaning sampling & analysis equipment such as GPS-enabled personal exposure monitors, collection of exposure data, chemical analysis of environmental and biological samples for chemical agents, and interpretation of exposure data
- Development of tissue and biofluid metabolomic profiling as a tool for discovery of biomarkers of exposure and environmentally induced disease
- Development of sensitive and specific quantitative mass spectrometry-based assays for application to biomarkers of exposure
Center for Urban Responses to Environmental Stressors (CURES)
Exposure Signatures Facility Core measures toxicants and the biological consequences of exposure to toxicants for individuals and in real-world samples from our environment. 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. Co-leaders: Susan Land, PhD, Dept. Obstetrics and Gynecology, Director of Applied Genomics Technology Center, WSU; Douglas Ruden, PhD, IEHS, Director of Epigenomics, C.S. Mott Center for Human Growth and Development, LED, WSU; Paul Stemmer, PhD, IEHS, Director of Proteomics Core Facility, EMI, WSU
Integrative Health Sciences Facility Core provides one-on-one consultations, biostatistical and study design support, and access to the latest environmental science technologies and research models; recruits rapid-response “dream teams” of environmental health specialists from the Center and beyond to address emerging environmental health problems identified by the community. Co-leaders: Graham Parker, PhD, Department of Pediatrics, WSU; Samiran Ghosh, PhD, Dept. of Family Medicine and Public Health Science and Dept. of Molecular Medicine and Genetics, WSU; Malcolm Cutchin, PhD, Dept. of Health Care Sciences, WSU