Helene Feil, Ph.D., Associate Specialist
Helene's curriculum vitae

The major goal of my research is to optimize the microbial reduction of pollutants such as trichloroethene (TCE). TCE can be converted to harmless byproducts by a variety of microbial processes. We are looking at the genomic and transcriptomic levels to understand how these microbial communities work together to effectively reduce these toxic chlorinated solvents. I am interested in the interaction of Dehalococcoides strains with anaerobic bacterial and archeal species to identify key metabolic and other important genes used in TCE reduction. My research will also examine the effects of various chemicals on the TCE reduction capabilities of Dehalococcoides spp. A combination of various molecular biology tools such as microarrays, quantitative and RT-PCR , as well as chemical analysis such as gas chromatography will be used to examine the transcriptome of these organisms during the various experiments. The study of stable microcosms for optimal TCE reduction can prove useful for effective bioremediation of polluted sites.

Georgia Green, undergraduate

Georgia Green, an undergraduate in her senior year, is currently working with enriched cultures of Dehalococcoides ethenogenes 195 to determine whether naturally occurring soil constituents, such as humics and quinones, can be used as electron acceptors. A positive result would help explain the wide distribution of Dehalococcoides spp. on the planet, prior to soil and groundwater contamination by chlorinated solvents.

Georgia plans to work with the Lydia Sohn Mechanical Engineering Laboratory to further develop the Electronic Cell Typing technique. Thus far, the technique has been used to quantify DNA in single eukaryotic cells. Georgia hopes to modify the process such that RNA can be quantified in prokaryotic cells. She is working with E. coli as a model species.

David R. Johnson, PhD candidate in Environmental Engineering

My current research focuses on identifying RNA-based phylogenetic and functional biomarkers indicative of microbial communities that completely degrade PCE to ethene. To identify RNA-based biomarkers, I am applying two types of high-density microarrays to analyze the PCE-to-ethene dechlorinating bacterium Dehalococcoides ethenogenes. I am applying a 16S-rRNA phylogenetic array to identify and quantify key organisms that are present and active in Dehalococcoides-containing microbial communities. I am also applying whole-genome arrays to characterize global transcription changes when this organism is subjected to stress conditions, such as cobalamin (vitamin B12) limitations, and as this organism transitions from the exponential to stationary growth phases. Finally, m y previous work focused on applying RT-qPCR to characterize the expression of the tceA reductive dehalogenase gene under differing environmental conditions and to identify correlations between tceA expression levels and reductive dehalogenation activity.

Patrick K. H. Lee, PhD candidate in Environmental Engineering

With the isolation of novel species that possess tremendous metabolic capability and the annotation of their genomes, bioremediation is a promising solution to overcome the problem of TCE contamination in groundwater aquifers. The goals of my research are to optimize the activity of Dehalococcoides spp. in reductive dechlorination and develop molecular biomarkers to monitor the physiology of the organisms in a heterogeneous environment. Available genomic information is used to guide the development of biomarkers that focus on DNA and the more labile RNA. Laboratory experiments as well as field studies are being carried out to test any hypothesis. Tools such as PCR, qPCR, RT-qPCR, microarray, and sequencing are used to achieve the research objectives.

Kristin Robrock, PhD candidate in Environmental Engineering

Kristin is studying the biodegradation of Polybrominated Diphenyl Ethers (PBDEs) which are flame retardants that have been used for thirty years in manufactured products such as computers, TVs, furniture and automobiles. Recently, toxicology studies have shown that penta-brominated PBDEs are endocrine disruptors at low concentrations. They have been banned and removed from the market although more highly brominated PBDEs continue to be used. Anaerobic bacteria, however, are capable of removing bromines from highly brominted PBDEs creating the toxic penta-brominated PBDEs in the process. Kristin is studying which species can degrade PBDEs, the degradation pathway and the timescales involved. She hopes that her data will help regulators ban PBDEs entirely.

Kristin's other interests:

• Kristin has been singing with the University Chorus for four years and loving it. She also enjoys rock climbing, traveling and cooking. Kristin was a founding member of Engineers for a Sustainable World which is a student volunteer group on campus that brings engineering solutions to underserved communities throughout the US and the world. She is currently a member of the Civil and Environmental Engineering Graduate Student Society which organizes research roundtables and other fun social events to create unity within the CEE department.

Christopher M. Sales, PhD candidate in Environmental Engineering

Christopher is studying the aerobic biodegradation of N-nitrosodimethylamine (NDMA), a probably human carcinogen. Found in recycled water from chlorinated secondary wastewater effluent and also as a byproduct of hydrazine-based rocket fuel, NDMA is emerging as an important groundwater contaminant. Recently, the Alvarez-Cohen laboratory has observed a strain of Rhodococcus, while grown on propane, that degrades NDMA faster than all other studied strains. In collaboration with Bill Mohn’s and Lindsay Eltis’ groups at the University of British Columbia, we are currently working on characterizing the enzymes responsible for transformation of NDMA in a similar Rhodococcus strain whose genome has been annotated. Specifically, we are exploring the involvement of propane and alkane monooxygenases in the biodegradation of NDMA using various molecular biology techniques (such as microarrays and qRT-PCR) along with analytical chemical methods (such as GC-MS-MS).

This work will extend beyond NDMA as other cellular assays indicate that propane monooxygenase can degrade a wide variety of xenobiotics as diverse as TCE and MTBE. Therefore, this study may lead to molecular tools and analytical techniques that will help determine the occurrence and expression of these monooxygenase genes as well as conditions that will enhance the activity of the monooxygenase enzymes responsible for the transformation of xenobiotics at in situ bioremediation sites.

Kimberlee West, PhD candidate in Environmental Engineering

Kimberlee is working on ways to make the biodegradation of chlorinated solvents a more effective and efficient remediation strategy. She is studying the gene expression of Dehalococcoides, the only bacteria known to completely detoxify PCE to the innocuous compound ethene. Her interests lie in using molecular techniques like microarrays and quantitative PCR to investigate the genetics of active microbial dechlorination and inactivity to increase the likelihood of successful bioremediation.

Kimberlee’s Other Interests

Zhang Ying, visiting scholar
School of Resources & Environment, Northeast Agricultural University(NEAU), China
Ying's curriculum vitae

It is our goal to identify 16S-rRNA-based phylogenetic and mRNA-based functional biomarkers diagnostic of microbial communities that support the robust growth and activity of chlorinated ethene-degrading organisms. In particular, we will focus on biomarkers indicative of organisms species. Members of this genus can degrade chlorinated ethenes completely to ethene and also degrade a wide range of other chlorinated aromatic and aliphatic pollutants.

The broadest significance of the proposed work is that it will lead to improved strategies for optimizing in situ bioremediation technologies. The biomarkers developed here could shorten the bioremediation process feedback cycle by replacing traditional diagnostics, such as microcosm responses that are monitored over weeks, with appropriate 16S-rRNA- and gene expression-based diagnostics that can be monitored within hours. Furthermore, the insights gained about important ecological interactions within reductive dechlorinating microbial communities will improve our ability to design, construct, and optimize bioaugmentation and biostimulation systems.

Professor Lisa Alvarez-Cohen
Dept of Civil and Environmental Engineering
University of Calfornia, Berkeley