Using Genetics, Genomics and Systems Biology to Find the Answers
At the Engineer Research and Development Center’s (ERDC) Environmental Genomics and Conservation Genetics Lab (EGECL), located in the ERDC Environmental Laboratory (EL), researchers on the Environmental Genomics and Systems Biology (EGSB) team find ways to protect ecological health from chemical, physical and biological stressors — including existing and emerging contaminants, climate change and invasive species — to ensure range sustainability and limit liability. This team accomplishes its mission by utilizing omics (information derived from the genome and the pattern genes are expressed) and systems biology applications (mechanistic linkage of biological processes across organizational scales).
Another team of EGECL researchers, the Conservation and Ecological Genetics Team (CEGT), explores ways in which genetics can be used to manage natural resources on Department of Defense (DOD) and USACE civil works lands. This group manages the Center for eDNA Application and Research (CeDAR) within the EGECL. CeDAR is a cutting-edge facility focused on basic and applied research, consultation and application of environmental DNA (eDNA) to a broad array of challenges.
A Well-equipped Facility that Promotes Cutting-edge Advances in Genetics (including eDNA), Genomics and System Biology Research
The EGECL is a multifaceted laboratory designed for state-of-the-art genetics (including eDNA), genomics and systems biology research, providing a number of resources that enhance advanced approaches in these specialized areas. The facility is equipped with the following assets:
- A total of 4,000 square feet of general laboratory space
- High-throughput, real-time qPCR
- Low/medium throughput, next-generation DNA sequencer
- Low throughput, capillary-based DNA sequencer
- Medium/high throughput, microarray hybridization infrastructure
- High throughput, 2uM microarray scanner
- Computational software for systems biology modeling and bioinformatics analyses
- Access to the Information Technology Laboratory (ITL) High Performance Computing facilities
- CeDAR, which occupies 2,200 square feet of space, and which has access to high-throughput and advanced technologies in use (and in-house), including:
- Life Technologies ViiATM 7 real-time PCR instrument
- Life Technologies 3500XL genetic analyzer
- BioRad PharosFXTM DNA imager
- 8 PCR thermal-cyclers
- Invitrogen E-gel systems
- 390 square feet of clean room space
The following EGECL/EGSB capabilities and services provide forward-looking approaches for assessing environmental risks and the pro-active management of Army facilities:
- Omics - experiments, analysis, data mining, functional development
- Full-service Gene Expression technology development, assays, analysis, interpretation
- Genome-wide Association Studies - linking phenotypes to genomic structural variants
- Adverse Outcome Pathway (AOP) development and archiving
- Mechanism of action and molecular target discovery
- Low/medium throughput nucleic acid sequencing
- Predictive mathematical modeling of molecular systems and other biological processes (e.g., toxicokinetics/dynamics)
- Bioinformatics - sequence assembly, genome annotations, biomarker identification, inference of biological networks and other software developed at customer’s demand
With advanced capabilities, including next generation massive parallel sequencing, conventional capillary sequencing, real-time PCR, and cutting edge methodologies, the EGECL/CEGT — in its CeDAR facility — provides state-of-the-art capabilities for working with aquatic eDNA and other demanding DNA resources. In addition to studying and applying eDNA to resolve challenges, the EGECL/CEGT in its CeDAR:
- Has or is developing approaches and tools for using eDNA to monitor invasive black car, Dreissenid mussels and endangered sturgeon
- Conducts pioneering research into the use of:
- Aquatic eDNA sampling for characterizing the faunal communities that utilize limited water resources in desert landscapes
- Scat-based eDNA approaches for characterizing food resources utilized by endangered or sensitive species, such as bats
- Nectar-based eDNA approaches for understanding pollination community dynamics
In 2013, the EGECL/EGSB collaborated with the U.S. Environmental Protection Agency to develop a highly robust mathematical model for predicting the effects of endocrine disruption on the hypothalamus-pituitary-gonad-liver axis. This model was developed to predict adverse effects of environmental chemical exposure on reproduction in fish. The collaboration was a test case for using this technology to proactively manage ranges by determining risks associated with chemical hazards. In December of 2013, the value of this model to risk and hazard assessment was recognized by the whole of the U.S. Army.
In 2010, the EGECL/CEGT assisted the USACE Lakes and Rivers Division and their partners with processing large numbers of invasive silver and bighead carp eDNA samples from the Chicago Area Waterways System. The EGECL/CEGT successfully implemented a high-throughput eDNA processing capability with stringent quality assurance measures to meet that demand.
In 2011, EGECL/CEGT was a leader in a major multiagency research effort, funded by the Great Lakes Restoration Initiative, to study a wide variety of factors surrounding the nature and use of eDNA data for Asian carp. The results of these studies have been improved eDNA sample processing methods and detection tools, as well as new insights into vectors for eDNA transport and fate in the environment. The establishment of CeDAR was a direct outgrowth of this important work.
ERDC Points of Contact
Questions about EGECL/EGSB?
Contact: Dr. Kurt Gust
Or questions about the EGECL/CEGT?
Contact: Dr. Richard Lance
Phone: (601) 634-3971