The CSFC provides TiCER scientists with access to and training in advanced analytical and characterization tools for quantifying agents of exposure, as well as for identifying biological markers established by the effects of exposure in experimental model systems. This ability to quantitatively measure exposure and the biological effects of exposure will allow investigators to develop cause-and-effect relationships and predictive models. The CSFC is comprised of three foundational components: analysis and quantification of potential environmental toxicants; various 'omics and compositional analyses of biological samples; and metabolomic capabilities for identifying and quantifying metabolite signatures. In addition, the CSFC works in conjunction with the DSFC on an integrative component connecting microbiota composition, microbiota and tissue metabolite profiles, and transcriptomic data. Thus the CSFC provides TiCER scientists with unparalleled analytical capabilities to comprehensively characterize toxicants and their responses, spanning from host genomics to microbial metabolites.
The CFSC Components
The Chem Science facility core (CSFC) comprises three foundational components that provide Center investigators analytical abilities to characterize exposure and response to environmental and associated toxicants. Specifically, the CSFC integrates technical expertise, analytical capabilities, and instrumentation across the Texas A&M campus under a single umbrella. The three components that serve as the foundation for the CSFC are:
The resources available at GERG facilitate environmental exposure studies by enabling detection and quantitative analysis of potential environmental toxicants in complex mixtures using gas and liquid chromatography-based mass spectrometry systems (GC/MS/MS) and LC/MS/MS.
QUANTIFICATION OF POTENTIAL ENVIRONMENTAL TOXICANTS THROUGH GERG
The exposure assessment component of the CSFC provides a suite of analytical services to Center investigators for quantitative targeted and untargeted analyses of samples using a range of LC/MS/MS and GC/MS/MS instruments, expertise, and standardized methods. The instumentation available through the CSFC includes:
- Agilent Ion mobility GTOF LC/MS/MS GC/MS with autosamplers (6)
- Agilent GC/MS/MS (1)
- Shimadzu LC/MS (1)
- Agilent 6470 LC/MS/MS (1)
- Agilent Ion Mobility GTOF LC/MS (1)
- Agilent Rapidfire 365 high through MS system (1)
- GC FID (4)
- GC ECD (2)
- HPLC (2)
- Leca GC/GC/TOFMS
- Hg analyzer (1)
- Nutrient analyzer (1)
- ASE systems (2)
- Thermal Desorber, Head space GC/MS (1)
The list of toxicants that can be analyzed include, but not limited to:
- polycyclic aromatic hydrocarbons (PAHs)
- perchloroethylene (PCE)
- polychlorinated biphenyls (PCBs)
- polybrominated di-ethyl ethers
- volatile organic compounds (VOCs)
The CSFC will not only use existing methodologies but also advance the development of new high-throughput methods for the detection of pollutants in environmental and biological samples. Partnering with the Community Engagement Core, these activities will also support dissemination of exposure-related findings to stakeholders and engaged communities.
The CSFC leverages the resources and expertise at the GERG (directed by the co-investigator Dr. Knap) for providing these resources to the Center members. GERG has been performing these analyses for more than 30 years and has documented expertise in all the relevant methodologies.
GENOMIC AND COMPOSITIONAL ANALYSIS OF BIOLOGICAL SAMPLES THROUGH TIGSS
Genomic information is becoming increasingly important in a variety of research fields. Many methods have been developed to assess genetic makeup, gene expression, and genomic architecture. The rise of next-generation sequencing has seen the cost per giga-base decrease while the amount of data produced increases.
Although ability to acquire data has increased, there is now a significant need for expertise in genomic methodologies to assist in experimental design and implementation. The advances in genomic technologies presents unparalleled opportunity to understand how genes and genomes are affected by environmental stimuli. The ability to assay whole genome, transcriptome, and microbiomes have allowed investigators unprecedented insight into the complex nature of these interactions.
One of the goals of the CSFC is to provide Center members the infrastructure and technical expertise in genomic methods and analysis.
Specifically, the core provides standardized workflows for profiling, identifying, and quantifying genomic and epigenetic data from different tissue and sample types (tissue, cell populations, single-cells, fecal material, and water samples) through the TIGSS Molecular Genomics Workspace. In addition, the CSFC also offers Center members state-of-the-art services for microbiome research (microbial metagenomic, whole genome sequencing, or bacterial 16s rRNA profiling), thus enabling Center investigators to address a number of questions on host, microbe, and environment interactions.
The CSFC also provides study design consultation, standardized genomic analyses workflows, and advanced bioinformatics support in conjunction with the DSFC.
Instruments available through the CSFC for genomic analysis include:
- Illumina MiSeq Sequencer (1)
- Illumina NextSeq 500 Sequencer (1)
- Illumina NovaSeq 6000 Sequencer (2 as part of Texas Genomics Core Alliance)
- Oxford Nanopore GridION Mk1 Sequencer (1)
- Oxford Nanopore MInION Sequencer (1)
- Illumina iScan Array Reader (1)
- Fluidigm C1 Single Cell Autoprep System (1)
- Fluidigm BioMark HD (1)
- 10X Genomics Chromium System (1)
- Eppendorf EpMotion 5075 (2)
- Bio-Rad QX200 Droplet Digital System (1)
- Agilent Tape Station (1)
- BioTek Cytation 5 (1)
METABOLOMIC CAPABILITIES FOR IDENTIFYING AND QUANTIFYING METABOLITE SIGNATURES THROUGH IMAC
Increasing experimental evidence suggests that small molecules or secondary metabolites produced by different cells, tissues, and organs in the body are important for understanding the host response to different environmental exposures. While gene expression and proteomics methodologies provide information on the expression of different genes and their products (proteins), they do not provide information on the actual molecules that are produced as end products of different cellular pathways.
Thus, identifying and quantifying the complete panel of produced metabolites (i.e., the metabolome) provides a measure of the functional output of the different biochemical pathways in cells, tissues, or hosts. Moreover, this data also complements the information provided by genomics and proteomics.Since environmental exposure causes pronounced changes in metabolism, the identification and quantification of metabolites that represent these changes is crucial to understanding the adverse effects of environmental toxicants and identifying biomarkers for exposures.
Challenges that limit the application of metabolomic technologies for the identification of biomarkers include:
- detection of low-abundance metabolites
- the need for multiple metabolomic techniques for the same sample due to the diversity in metabolite properties
- lack of predictive tools for metabolomic analysis
Therefore, establishing state-of-the-art metabolomics capabilities is integral to achieving the Center’s goals. The CSFC provides Center members study design consultation, standardized LC/MS/MS and GC/MS/MS metabolomic analyses workflows, and advanced bioinformatics support through leveraging the resources and expertise at the Integrated Metabolomic Analysis Core (IMAC).
IMAC is a state-of-the-art metabolomics facility that is equipped with several high-end mass spectrometers for metabolomic studies. The instruments available to Center members through IMAC and its partner cores in the Texas A&M Chemical & Biological Mass Spectrometry Facility include:
- Thermo Exactive Orbitrap MS with HPLC
- Thermo QExactive Plus Orbitrap MS with UHPLC (2)
- Thermo Quantiva triple quadrupole LC/MS (1)
- Thermo Altis triple quadrupole (1)
- Thermo EVO 8000 triple quadrupole GC/MS system
- Thermo Fusion Orbitrap LC/MS
- Bruker FT-ICR MS
- Sciex 4000 QTrap LC/MS
- Applied Biosystems MALDI-TOF MS (2)
GERG833 Graham Road College Station, Texas 77845
TIGSSVeterinary Research Bldg College Station, TX 77845 +1-979-845-5941
IMAC300 Olsen Bl,
College Station, TX 77843