University of Texas at Austin, Ph.D.
EREF Scholar 2006
Development of a Targeted Method for Sequencing Biodegradation Genes
Where Are They Now? Susan is currently an assistant professor at Colorado State University in Fort Collins, Colorado.
Project Description (while EREF Scholar):
Susan’s research focused on development of molecular biology tools for investigating waste biodegradation. Molecular biology tools, such as quantitative polymerase chain reaction (qPCR), allow researchers to study biodegradation at a fundamental level, offering new insights into what factors promote successful degradation. Tools that track genes involved in biodegradation can tell us if the bacteria present can degrade the waste materials. Furthermore, tools that track the activity of these genes can be used to determine if the bacteria are actively degrading the waste materials. However, to apply these tools to genes involved in biodegradation the gene sequences must be known. Although an increasing number of genomes are being sequenced, it is not economically feasible to sequence the genomes of all bacteria relevant to waste treatment. Therefore, tools that can rapidly sequence biodegradation genes are needed.
Susan developed a gene sequencing tool that allows researchers to isolate and sequence biodegradation genes without sequencing the entire genome of a bacterium. This tool, Prokaryotic SSH PCR cDNA Subtraction, was developed and validated using a bacterium Pseudomonas putida mt-2 that degrades toluene. The gene subtraction tool was able to isolate and sequence genes involved in toluene degradation, even though most of the P. putida mt-2 genome’s approximately 5500 genes are not related to toluene degradation.
Once gene sequences are obtained, qPCR assays targeting those genes can be developed. Susan developed qPCR assays and reverse transcriptase qPCR (RT-qPCR) assays to quantify genes and gene expression (indicator of activity) for biological treatment of the widespread groundwater contaminant perchlorate. Results showed that bioreactors containing higher levels of genes and gene expression involved in perchlorate degradation were more effective at treating perchlorate-contaminated water. These assays can help develop improved bioreactors for perchlorate treatment. Susan’s current research involves development and use of similar tools to optimize breakdown of biodegradable municipal and agricultural waste materials for energy generation.
Susan was born and raised in Los Angeles, California. There the smoggy Los Angeles air first inspired her interest in environmental protection. She obtained bachelor’s degrees in Environmental Science and Molecular and Cellular Biology from the University of California at Berkeley in 1999. Subsequently, she obtained an M.S.E. in environmental and water resources engineering and a Ph.D. in civil engineering from the University of Texas at Austin in 2005 and 2009, respectively.
Susan is currently an assistant professor at Colorado State University in Fort Collins, Colorado. Her research focuses on the development of molecular biology tools for investigating, monitoring, and optimizing biological treatment processes for municipal and agricultural waste. She hopes that these tools will help scientists and engineers develop an understanding of what occurs on a molecular scale when bacteria degrade waste materials, and that this knowledge will allow more widespread use of biological treatment processes. She enjoys living near the mountains in Fort Collins with her husband, son and three cats.
I. PEER-REVIEWED PUBLICATIONS
1. De Long, S.K., Kinney, K.A., Kirisits, M.J. qPCR assays targeting genes and gene expression for microbial perchlorate reduction. Manuscript in preparation.
2. De Long, S.K., Kinney, K.A., Kirisits, M.J. (2008) A Targeted Method to Sequence Prokaryotic Biodegradation Genes: Prokaryotic SSH PCR cDNA Subtraction. Appl. Environ. Microbiol. Jan;74(1):225-232.
3. Teitzel, G.M., Geddie, A., De Long, S.K., Kirisits, M.J., Whiteley, M., Parsek, M.R. (2006) Survival and Growth in the Presence of Elevated Copper: Transcriptional Profiling of Copper-Stressed Pseudomonas aeruginosa. J. Bacteriol. Oct;188(20):7242-7256.
4. Fanton, C.P., Rowe, M.W., Moler, E.J, Ison-Dugenny, M., De Long, S.K., Rendahl, K., Shao, Y., Slabiak, T., Gesner, T.G., MacKichan, M.L. (2006) Development of a Screening Assay for Surrogate Markers of Chk1 Inhibitor-Induced Cell Cycle Release. J. Biomol. Screen. Oct;11(7):792-806.
5. Holmes, L.E., Campbell, S.G., De Long, S.K., Sachs, A.B., Ashe, M.P. (2004) Loss of Translational Control in Yeast Compromised for the Major mRNA Decay Pathway. Mol Cell Biol. Apr;24(7):2998-3010.
6. Ashe, M.P., Slaven, J.W., De Long, S.K., Ibrahimo, S., Sachs, A.B. (2001) A Novel eIF2B-dependent Mechanism of Translational Control in Yeast as a Response to Fusel Alcohols. EMBO J. Nov 15;20(22):6464-6474.
7. Ashe, M.P., De Long, S.K., Sachs, A.B. (2000) Glucose Depletion Rapidly Inhibits Translation Initiation in Yeast. Mol Biol Cell. Mar;11(3):833-848.
II. CONFERENCE PRESENTATIONS AND OTHER PUBLICATIONS
A. Conference Presentations
De Long, S.K., M.J. Kirisits, K.A. Kinney. “Perchlorate-Reducing Gene Targets for Bioremediation Applications” Platform Presentation, Battelle Remediation of Chlorinated and Recalcitrant Compounds Conference, Monterey, California, May 2008.
Kirisits, M.J., S.K. De Long, K.A. Kinney, S.A. Desai, J.C. Brown. “Characterizing the Microbial Community in a Bioreactor Treating Perchlorate-Contaminated Groundwater” Platform Presentation, AWWA Inorganic Contaminants Workshop, Albuquerque, New Mexico, January 2008.
De Long, S.K., M.J. Kirisits, K.A. Kinney. “Development of a Targeted Method to Identify Prokaryotic Biodegradation Genes” Platform Presentation, Battelle Remediation of Chlorinated and Recalcitrant Compounds Conference, Monterey, California, May 2006.
De Long, S.K., M.J. Kirisits, K.A. Kinney. “Applying Molecular Tools to Water Treatment Processes: An Efficient Method to Obtain Key Gene Sequences” Platform Presentation, Water Environment Association of Texas Conference, Austin, Texas, April 2006.
B. Conference Proceedings and Posters
De Long, S.K., B.A. Afshar, A.E. O’Neil, K.A. Kinney, and M.J. Kirisits. “Gene Targets for Bioreactors Treating Perchlorate-Contaminated Water” Poster Presentation, International Water Association Young Water Professionals Conference, Berkeley, California, July 2008.
Kirisits, M. J., S. K. De Long, K. A. Kinney, S.A. Desai, and J. C. Brown. (2008) “Characterizing the Microbial Community for a Bioreactor Treating Perchlorate-Contaminated Groundwater” Proceedings of the Inorganic Contaminants Workshop. Albuquerque, New Mexico.
De Long, S.K., K.A. Kinney, M.J. Kirisits. “Optimization of Suppression PCR for Suppressive Subtractive Hybridization (SSH) PCR cDNA Subtraction” Poster, American Society of Microbiology General Meeting, Toronto, Ontario, Canada, May 2007.
De Long, S.K., M.J. Kirisits, K.A. Kinney. “Development of a Method to Efficiently Determine Gene Sequences Relevant to Pollutant Biodegradation” Poster, American Society of Microbiology General Meeting, New Orleans, Louisiana, May 2004.
C. Links to Abstracts for Peer-reviewed Papers: