Examination advanced DNA technologies to Benefit Reclamation Projects

Project ID: 6600
Principal Investigator: Jacque Keele
Research Topic: Invasive Species
Funded Fiscal Years: 2016
Keywords: None

Research Question

The advance in genetic analysis methods and instruments has started a revolution in the ways that researchers
can design experiments and analyze samples. These technologies can be used to conduct population studies,
microbiome analysis, transcriptome analysis and whole genome sequencing. This is a scoping project to gather
information on the current molecular biology technologies available and explore how these technologies could be
applied to research being performed at Reclamation.
The field of molecular biology is dynamic and rapidly advancing. From the inception of polymerase chain reaction
(PCR), thirty years ago, where one gene was analyzed, to today where next generation sequencing (NGS) is used to
analyze a whole microbiome of an environmental sample with tens of thousands of sequences, the technology has
made huge leaps forward. As the technology used to analyze genetics has advanced, there have been different
instruments and protocols developed to meet the needs of researchers. For example, there is the HiSeq 2000 and
MiSeq NGS sequencing instruments used for NGS with pros and cons associated with each. There are also several
different instruments for performing quantitative PCR and digital PCR that should be investigated. The decision
on which instruments and protocols to use is important because it impacts the outcome of the analysis.

Need and Benefit

As the field of molecular biology advances it will play a larger role in ecological and biological field studies. One
such area role is using NGS for the analysis of an environmental microbiome samples. For this assay, an
environmental sample is taken and the whole microbial community is analyzed. One advantage of this technology
is that it can detect bacteria that cannot be cultured in the laboratory setting thus the only evidence of their
existence is thought DNA analysis. Having access to this data can help give a fuller picture of the ecology of a site.
A second area where NGS could be useful is in the analysis of fish stomach samples. Knowing the organisms that
a fish is feeding on can increase a fishery biologists understanding of the fish that they are studying and
successful adaptive management.
In addition, digital PCR is an up and coming technology that could change how PCR is performed. Unlike
traditional PCR where the one reaction is performed per sample; in digital PCR a single sample partitioned into
many separate reactions on a chip and then amplified. This separation gives a more sensitive measurement of the
nucleic acid amounts. This technology is just starting to be used and it is important to understand if it would suit
Reclamation needs.

Contributing Partners

Contact the Principal Investigator for information about partners.

Research Products

Bureau of Reclamation Review

The following documents were reviewed by experts in fields relating to this project's study and findings. The results were determined to be achieved using valid means.

Examination advanced DNA technologies to Benefit Reclamation Projects (final, PDF, 1.7MB)
By Jacque Keele
Publication completed on September 30, 2016

The last ten years have seen an explosion of different molecular techniques and methods. These technologies can be used for a wide range of applications and research projects. The goal of this scooping project was to summarize some of these technologies and determine which ones could be of use at Reclamation and also if specialized equipment or reagents would have to be purchased. Reclamations Detection Laboratory for Exotic Species (RDLES) currently uses polymerase chain reaction (PCR), but there are additional technologies that can be used by RDLES to further Reclamations mission. Some of these technologies include other PCR techniques and methods, next generation DNA sequencing, and finally protein analysis methods.

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Last Updated: 4/4/17