Program Highlights Archive

2014 Program Highlights

In Project 1, we have found strong statistical evidence for two pathways of benzene metabolism with one operating maximally at environmental levels of exposure.  We have also applied our novel adductomics methodology, developed with previous NIEHS funding, to explore the possibility that unanticipated protein adducts might serve as promising biomarkers of benzene exposure.  This will facilitate identification of benzene exposure and aid in studying its immediate and later-life health impacts.

In Project 2, we demonstrated that dichlorovinyl cysteine (DCVC) causes DNA damage that results in substrates for translesion synthesis and recombination.  Our results from in vitro studies support a mutagenic mode of action for TCE toxicity, mediated by the metabolite DCVC. These findings are the first to provide mechanistic and genetic evidence supporting DCVC genotoxicity as a likely contributor to TCE-induced renal cancer.  Additioanlly, our newly developed semi-solid medium based screening method in human haploid cells allows efficiently and simultaneously screening and generating mutant colonies from cells resistant to exposures of chemicals of interest.

In Project 3, we found biologically plausible major reductions in breast cancer mortality during high exposure to inorganic arsenic in drinking water which could not be attributed to bias or confounding.  Inorganic arsenic shows promise in the treatment of advanced breast cancer, and a clinical trial assessment would be the next step.  Also, based in part on research conducted for the UC Berkeley Superfund Research Program, our nonprofit partner Project Well, together with sister NGO Aqua Welfare Society (based near Kolkata, West Bengal), continue to provide clean, arsenic-safe drinking water to villages in West Bengal, India.

The research associated with Project 4 lead to the discovery of a new biosynthesis carbon fixation pathway that plays a major role in syntrophy within microbial communities.  The role of carbon monoxide as both a toxic product of biosynthesis by dechlorinating bacterium Dehalococcoides mccartyi and a beneficial substrate to fermenting syntrophic bacterium Syntrophomonas wolfei indicates a new type of syntrophy and material exchange within microbial communities that may have widespread implications for microbial ecology.

Research in Project 6 resulted in the development of a compact and inexpensive treatment system that has the potential to be employed for wellhead treatment or point-of-use treatment in situations where water is contaminated with organic chemicals.  The system has numerous advantages over existing approaches because it can be operated without the need to replenish reagents or replace materials (e.g., as is the case with activated carbon).  A provisional patent was filed for the device on January 2, 2015.   Additional research is being conducted to test the long-term performance of the system, incorporate sensors and reduce the cost of the electrodes.

Researchers in Core C successfully developed and applied a series of chemoproteomic technologies to comprehensively map proteome-wide interactions of environmental chemicals in complex biological systems to better understand how chemicals drive complex human diseases. For example, we used a functional chemoproteomic approach called activity-based protein profiling (ABPP) coupled with metabolomic platforms to discover that widely used organophosphorus (OP) pesticides directly inhibit 20 serine hydrolases involved in various important biological functions.  In our most recent and innovative efforts, we have developed and applied a next-generation chemoproteomic approach termed reactivity-based proteomic profiling (RBPP), which uses reactivity-based chemical probes to map functional sites in the proteome, to comprehensively map proteome-wide interactions of environmental chemicals in complex biological systems to understand their toxicological action.  Using this RBPP platform, we have screened various environmental and Superfund chemicals for their reactivity with proteins directly in native proteomes, and have already uncovered multiple heretofore unrecognized mechanisms of toxicological action.  For example, we have found that the fungicide chlorothalonil and herbicide acetochlor both directly inhibit multiple enzymes involved in fatty acid oxidation, leading to biochemical changes that result in an accumulation of fat in vivo.  We have also discovered that a bioactivated metabolite of the Superfund chemical benzene directly inhibits a tumor-suppressor PP2A.



All undergraduate, graduate and postdoctoral trainees are first familiarized with both overall and specific project goals and then provided with all necessary safety training.  They are then assigned a mentor and supervisor who will begin training on research methodologies and procedures.  Each trainee works with their mentor to establish an Individual Development Plan (IDP), which takes into account the Trainee’s knowledge, experience, and personal goals.  A training plan is developed with short- and long-term goals and it is reviewed at least annually.  The mentor and supervisor monitor progress and work with the Trainee to ensure incremental success and suggest possible areas of classroom learning or research to help further the Trainee’s goals.  Trainees also actively participate in internal and external scientific meetings and forums.  Trainees are encouraged to develop presentations and talks for scientific meetings.  Internal practice opportunities are provided at recurring meetings.

2014 Annual Meeting
UC Berkeley trainees were instrumental in developing a complete experience for other SRP trainees at the 2014 Annual Meeting.  They developed a moderated, interactive career panel plan with speakers from industry, academia, and public policy.  They secured a nationally recognized speaker on communication skills to discuss leadership, career development, and a guide to selling your skills and yourself.  They also developed a series of successful interactive games and exercises to allow trainees from different universities and backgrounds to mix, explore, and network.

Project 1: Trainee Advancement
Hasmik Grigoryan was a post-doctoral trainee working on our novel adductomics methodology to look for promising biomarkers of benzene exposure.  After an exhaustive and competitive recruitment, we hired her as an Assistant Researcher in Prof. Rappaport’s laboratory.

Project 2: Vanessa De La Rosa
After delays caused by scheduling and family illness, Vanessa De La Rosa was able to present her work resulting from her KC Donnelly Externship award at the 2014 SRP Annual Meeting.  She worked at the UNC SRP Swenberg Lab on trichloroethylene (TCE) genotoxicity and possible approaches to better understand exposure pathways.  Her project utilized the DT40 avian cell system to examine DNA damage and repair by investigating the role of DNA repair pathways in mediating TCE toxicity, thereby elucidating toxicity mechanisms of this top Superfund contaminant,

Vanessa De La Rosa was consistently very active in diversity recruiting, mentoring and outreach including serving as chair from 2009-2014 of the Berkeley chapter of SACNAS, a group whose mission is to engender an inclusive community that fosters interaction among Chicano/Latino, Native American, and other underrepresented minorities in order to improve leadership opportunities and promote excellence in science by increasing support for trajectories in the S.T.E.M field.  In addition to her work on the UCB campus, she also helped organize events at the national meetings.  She was a member of the Biology Scholar Program from 2009-12 where she provided mentoring to IMSD and MARC Program undergraduate scholars through workshops, group meetings throughout the year. She was also a MARC/IMSD Peer Mentor 2011-2014, where she mentored undergraduate MARC and IMSD fellows through monthly workshops and in a lab setting.  She was a member of the Berkeley EDGE Program from 2008-2014 and assisted in recruiting minority students to pursue graduate studies in the STEM fields at UC Berkeley and mentored enrollees during their first year.  Finally, she serves as a Society of Toxicology Undergraduate Diversity Initiative Program Peer Mentor 2007-present and mentor underrepresented undergraduates interested in graduate school in toxicology at the annual national meeting.

Project 3
Dr. Md Al Fazal Khan, based at our collaborating institution, icddr,b, in Bagladesh made significant strides in pursuit of his Ph.D. with his work related to our project.

A postdoc in the Smith Lab, Dr. Fenna Sillé, has recently resubmitted a K99/R00 NIH Pathway to Independence grant application on the effects of early-life arsenic exposure on macrophage function and tuberculosis (TB) risk.

Project 4
Alexandra Polasko is female undergraduate student who participated in project 4 was so inspired by the research that she performed that she applied to present her results at the national American Geophysical Union meeting as was accepted.  Her presentation there was such a positive experience, that she has decided to apply to graduate programs in Environmental Engineering in order to pursue a PhD in this important STEM field.  Inspiring more women to pursue degrees in engineering is extremely beneficial for the field and for the Superfund program.

Project 6
Graduate Trainee Tom Bruton won an award for the best student poster at the Groundwater Resources Association’s Conference on Emerging Contaminants in February 2014 (  Tom’s poster, “Fate of Perfluoroalkyl Acid Precursors in Chemical Treatment of AFFF” was of considerable interest to attendees from industry, engineering consultants and regulators because existing methods for remediating sites ocntamianted with these materials are expensive and impractical.

Core C
Daniel Medina-Cleghorn, a Superfund trainee, has published two papers this year in ACS Chemical Biology describing the development and use of our activity-based proteomic technologies and discovering novel mechanisms of toxicities for organophosphorus pesticides and flame retardant chemicals. He also presented this work at the Enzymes, Coenzymes, and Metabolic Pathways Gordon Conference and the Superfund Annual Meeting. We are now in the process of preparing a manuscript describing our new reactivity-based protein profiling (RBPP) technology for screening and mapping proteome-wide interactions of environmental chemicals. Daniel is actively searching for a Postdoc.

Core D Trainee Advancement
Reuben Thomas came to the UCB SRP as a post-doctoral trainee.  He was subsequently awarded the academic position of Assistant Researcher in our program.  His statistical and bioinformatics expertise was instrumental in specific aims progress in Projects 1, 2, and 3 and Cores C and D.  This year Reuben has recently accepted a Staff Research Scientist position at the Gladstone Institute at UCSF.



Project 3
In a study published EBioMedicine, the Project 3 team, in collaboration with researchers at Stanford University and Pontifical Catholic University of Chile, presented results of breast cancer mortality data from a region in Chile where residents were inadvertently exposed to high levels of arsenic, a naturally occurring element found in many minerals. Instead of an increase in mortality, as with many other cancer sites, the study found that breast cancer deaths were cut in half during the period that coincided with high arsenic exposure. The effect was more pronounced among women under age 60, with mortality in these women reduced by 70 percent.

“What we found was astonishing,” said study lead author Dr. Allan Smith, “We’ve been studying the long-term effects of arsenic in this population for many years, focusing on increased disease and mortality attributed to the historical exposure to arsenic in this population.”  A geothermal water source originating in the Andes Mountains was found to have 80 times higher arsenic concentration than the levels recommended by WHO.

The medicinal use of arsenic is not entirely new. Arsenic trioxide was approved in 2000 by the Food and Drug Administration as an effective treatment for a rare type of leukemia.  So should arsenic now be used to treat breast cancer?  “Not yet,” said Smith. “We do not know if the treatment will work, but carefully designed clinical trials should take place as soon as possible based on this new evidence.”

Project 6
UC Berkeley urban-water expert and Project 6 Leader, David Sedlak, was selected as the 2014 recipient of the National Water Research Institute Clarke Prize for his pioneering research on advancing the way water resources and urban water infrastructure are managed, including implementing water reuse and reducing the discharge of emerging contaminants.  His work has served as the foundation for major policy and technical initiatives to reduce the effects of these contaminants and protect public health.

As California grapples with what state water officials have called a drought of “epic proportions,” Sedlak has been watching for signs that people are ready for a water revolution.  In his recently published book Water 4.0: The Past, Present and Future of the World’s Most Vital Resource, Sedlak outlines what he calls the first 3 revolutions in water management and posits predictions for the fourth.  Water 1.0 applied to the first revolution, the aqueducts of the Roman Empire.  Water 2.0 involved treating drinking water, first by filtration and later with the addition of chlorine. Water 3.0 gave us sewage treatment plants.  How we deal with our current water management problems will be Water 4.0, the next revolution in our water system.  Instead of finding new ways to pipe in water from other areas, Sedlak projects, among other ideas, significant growth in water recycling, rainwater harvesting and seawater desalination.

Research in Project 6 resulted in the development of a compact and inexpensive treatment system that has the potential to be employed for wellhead treatment or point-of-use treatment in situations where water is contaminated with organic chemicals.  The system has numerous advantages over existing approaches because it can be operated without the need to replenish reagents or replace materials.

Core C
This year, the Core C team developed and applied a series of chemoproteomic technologies that enable the mapping of proteome-wide interactions of environmental chemicals.  They are now expanding upon their newly developed reactivity-based protein profiling (RBPP) approach to be able to rapidly screen and identify large numbers of environmental chemicals for their direct protein targets, and coupling RBPP technologies to metabolomic platforms to gain a comprehensive understanding of toxicological mechanisms.  Even when used against just a handful of chemicals, they have already uncovered previously unrecognized mechanisms of toxicity for widely used environmental chemicals.  They anticipate that over the next year, they will radically expand their efforts towards understanding how environmental chemicals directly interact with molecular targets in complex living systems, and how these interactions alter physiological biochemistry to cause toxicological action.  They are also working towards integrating these platforms into a pipeline for assessing chemical safety within both pharmaceutical and chemical companies.  Core C Leader Dan Nomura and his team recently started working with BASF, through the new California Research Alliance by BASF (CARA), to implement these strategies into their toxicological pipeline for emerging chemicals.

2013 Program Highlights

Developing and marketing a cheap, reliable, and easily portable system for mercury detection

Related Video: Plasmonic Mercury Sensing with Gold Nanoparticles

A development first reported last year has now been brought to fruition and the resulting technology has been patented and commercialized.  We demonstrated the utility of gold nanoparticles as the basis of a stand-alone, inexpensive, and sensitive mercury sensor for both source and ambient environmental monitoring. In the first phase of this supplemental project we developed and built a prototype mercury sensor. The sensor design combines a nanoparticle chip (similar to that described above) mounted on a mirror, flow cell, electric heater, thermocouple, optics, light-source, and detector.  We machined the cell (composed of three metal parts and one air tight gasket fitting) from a 2.5” diameter bar of aluminum. With a CNC mill and lathe we were able to build it to tight tolerances and successfully kept the fluid/optical alignments. Sample gas enters the cell through a 1 mm diameter nozzle 3 mm above the chip. The flow from the nozzle impinges on the surface of the chip, which enhances the sensitivity. During the exposure the visible light absorbance is monitored in changes in the reflected light.  The sensor can also be regenerated by heat for reuse.

Heavy metals such as mercury and arsenic continue to pose significant human and environmental health risks. They are found in many Superfund sites, as well as throughout the world.  Development of sensors that can be used in remote locations and developing countries will help policy makers fill gaps in emission monitoring of mercury identified by the European Commission’s Global Mercury Observation System.  Cheap, sensitive sensors for measuring toxicants will allow more environmental measurement, and could reduce the exposure of humans and animals.

U.S. Application Nos. 61/585,542 and 61/587,546. January 10, 2013 (filed).  The International Patent Application has been accorded serial number PCT/US2013/021066.

James JZ*, Lucas D, Koshland CP (2012) Gold nanoparticle films as sensitive and reusable elemental mercury sensors. Environ Sci Technol. 46(17):9557-62. PMCID: PMC3446241.

James JZ, Lucas D, Koshland CP (2013). Elemental mercury vapor interaction with individual gold nanorods. Analyst. 138(8):2323-8.  PMID: 23446550. [PMCID Journal – In Process].

Superfund research supports initiative to bring safe drinking water wells to developing countries

Based in part on research conducted for the UC Berkeley Superfund Research Program, Project Well (based in California), together with sister NGO Aqua Welfare Society (based near Kolkata, West Bengal), commenced work to develop a sustainable, community-based water program to provide arsenic-safe drinking water to the villagers of North 24 Parganas, Nadia and Murshidabad districts, in West Bengal, India.

Crystal-clear drinking water extracted by shallow and deep borewells (locally known as tubewells) is plentiful in the villages of West Bengal, but it is often contaminated with arsenic.  Between 2001 and 2013, Project Well designed and constructed 277 modern dugwells.  These dugwells tap into arsenic-free shallow aquifers and so provide safe drinking water.  The Project Well dugwells are sheltered and the water is extracted by a hand pump, preventing any external contamination such as with E.coli bacteria.  Since 2009, after extensive research and field testing, Project Well modified the design to that of bore-dugwell which we have named “bi-tech wells” which cost approximately US$700 to construct.  This is cheaper than other options.

Project Well is a pioneering water program that has three major components: 1) construction, 2) monitoring & maintenance and 3) training & education until sustainability is developed amongst general public.  Training and support lasts for several years.

To complete the sustainability mission, last year 53 water communities were handed the ownership of their water supply.  This year 51 more communities will take charge of their own wells so that the program can expand further.  “Taking charge” means the communities maintain the wells, including applying chlorine based disinfectant.  The field workers in charge of these wells inspect these wells quarterly and continue monthly visits of the other wells.  This method of nano-management has now become web-based through partnering with Peer Water Exchange, PWX, where individual reports are uploaded including direct from the field via mobile texting.  This enables both the funders and implementers access the reports from anywhere in the world with internet access which is open to public.

Providing affordable and sustainable safe drinking water is a human necessity.

Smith AH, Yunus M, Khan AF, Ercumen A, Yuan Y, Hira-Smith M, Liaw J, Balmes J, von Ehrenstein O, Raqib R, Kalman D, Alam DS, Streatfield PK, Steinmaus C. Chronic respiratory symptoms in children following in utero and early life exposure to arsenic in drinking water in Bangladesh. Int J Epidemiol 42:1077-1086, 2013.

Ferreccio C, Smith AH, Durán V, Barlaro T, Benítez H, Valdés R, Aguirre JJ, Moore LE, Acevedo J, Vásquez MI, Pérez L, Yuan Y, Liaw J, Cantor KP, Steinmaus C. Case-control study of arsenic in drinking water and kidney cancer in uniquely exposed northern Chile. Am J Epidemiol 178(5):813-818, 2013.

Further study confirms that benzene is metabolized more extensively at environmentally-relevant concentrations

Project 1 had previously shown that benzene metabolism was 9-fold greater at air concentrations below 1 ppm and that benzene is apparently metabolized by two pathways, one of which accounts for about 70% of the metabolism below 0.1 ppm.  These findings had important implications for the risk assessment of benzene, as they indicated that extrapolating linearly from high exposed worker population data would underestimate the risk posed at lower environmental exposure levels. Because of this, industry scientists reanalysed of our data and argued that our conclusions regarding enhanced benzene metabolism below 1 ppm were not justified (Price et al.,Carcinogenesis, 33, 2094-9, 2012). In response, Rappaort and colleagues in Project 1 conducted additional analyses and showed that the methods and arguments presented by Price et al. were scientifically unsound and that their results were unreliable (Rappaport, S.M., et al. Carcinogenesis, 34, 2-9, 2013).  Price et al. (Carcinogenesis, 34(7), 1692-6, 2013) then provided additional calculations – based on Rappaport et als response – to suggest that only trivial fractions of benzene were metabolized below 1 ppm and also argued that the original results were biased due to incorrect selection of low-exposed subjects for estimation of background levels of metabolites arising from catabolism.  In our rebuttal (Rappaport, S.M., et al. Carcinogenesis, 34(7), 1689-91, 2013) we showed that Price et al.’s new calculations were also erroneous and that the ‘correct’  calculations provided further support for our conclusions regarding low-dose benzene metabolism.

Rappaport SM, Kim S, Thomas R, Johnson BA, Bois FY, Kupper LL (2013) Low-dose metabolism of benzene in humans: science and obfuscation. Carcinogenesis. 34(1): 2-9. PMID:23222815. (PMC Journal – In Process).

S.M. Rappaport, B.A. Johnson, F.Y. Bois, L.L. Kupper, S. Kim and R. Thomas, Ignoring and Adding Errors do not Improve the Science, letter to the editor, Carcinogenesis, 34(7): 1689-1691 (2013) PMID: 23528242.

Toxicity of Arsenic to the Immune System

Although extensive research has focused on investigating As carcinogenicity, growing evidence indicates that As also has deleterious effects on the immune system. This may potentially play a role in As carcinogenesis of various tissues through reduced immune surveillance. However, the specific effects of As on immune function remain poorly understood. Therefore, we considered that further investigation of As immunotoxicity is warranted and conducted a PubMed search of As exposure and non-cancer immune-related effects through October 2012. We summarized the known toxicological effects of As on immune function in humans, laboratory animals and in vitromodels, and identify possible future research directions to help close the gaps in knowledge. Studies show that As significantly impacts both innate and adaptive immune defenses. Likely mechanisms involve altered expression of key immune regulators, induced apoptosis, oxidative stress and inflammation in circulating lymphocytes and monocytes, impaired lymphocyte activation and macrophage function, and altered cellular and humoral immunity.

Dangleben NL, Skibola CF, Smith MT (2013) Arsenic immunotoxicity: a review. Environ Health. Sep 2;12(1):73. PMID 24004508. (PMCID Journal in Process).

RNA sequencing is a powerful new tool to analyze chemical effects in humans

The transcriptome reflects all forms of gene expression within cells and can be perturbed by chemical exposure (McHale et al, Env Mol Mutagen 2013). Recent developments have shown that transcriptome sequencing (RNA-Seq) has a greater dynamic range than microarrays and the potential to reveal additional transcriptional information. Thus, in the first study of its type, we used RNA-Seq to analyze the transcriptome of mononuclear cells from benzene-exposed and unexposed study subjects. We sequenced RNA from 10 workers occupationally exposed to high levels of benzene (≥5 ppm) in air and 10 matched unexposed control workers, from a large study in which gene expression was previously measured by microarray (Thomas R et al., Env Mol Mutagen 2013). The Pearson correlation between RNA-seq and microarray signals for the 20 subjects was around 0.6. 60% of the transcripts with detected reads from the RNA-seq experiments did not have corresponding probes on the microarrays. Fifty-three percent of the transcripts detected by RNA-seq and 99% of those with probes on the microarray were protein-coding. There was a significant overlap (P < 0.05) in transcripts declared differentially expressed due to benzene exposure using the two technologies. About 20% of the transcripts declared differentially expressed using the RNA-seq data were non-coding transcripts. Six transcripts were determined (false-discovery rate < 0.05) to be alternatively spliced as a result of benzene exposure. Overall, this study shows that RNA-seq can be used to analyze changes in gene expression from chemical exposures and has the potential to reveal a much more comprehensive transcriptome signature of a specific chemical exposure.

R. Thomas, C.M. McHale, Q. Lan, A.E. Hubbard, L. Zhang, R. Vermeulen, G. Li, S.M. Rappaport, S. Yin, N. Rothman and M.T. Smith, Global Gene Expression Response of a Population Exposed to Benzene: a Pilot Study Exploring the Use of RNA-sequencing Technology, Environ Mol Mutagen, 2013 Aug;54(7):566-73. doi: 10.1002/em.21801. Epub 2013 Aug 1,PMID: 23907980.

McHale CM, Zhang L, Thomas R, Smith MT (2013) Analysis of the transcriptome in molecular epidemiology studies. Environ Mol Mutagen. Aug;(54(7):500-17. PMID: 23907930. (PMCID Journal in Process).

Trainee Highlights

Both supported and unsupported Graduate Student Trainees (GSRs) and Postdoctoral Scholar Trainees (Postdocs) are essential to our work.  They are mentored by senior staff and they provide mentoring, guidance, and learning opportunities to peers and less-experienced staff.  Trainees are also offered opportunities to cross-train in related areas of study.  This ongoing information exchange enhances the robustness and viability of our program.  Trainees in each Project and Core are encouraged to develop presentations describing their work for regular lab meetings, providing both an opportunity for speaking experience and project feedback.  Also, we have begun regular Project-wide Trainee meetings to encourage an open exchange between Trainees in each of the Projects and Cores.  As part of this initiative, we are also developing some more formal elements for out Trainee mentoring plans.  We encourage our trainees to attend, submit abstracts, and present at relevant scientific forums, including school science events, NIEHS meetings, and at Northern California and National meetings of the Society of Toxicology.

Project 1:  GSR Sylvia Sanchez recently traveled to Honduras for Global Brigades, the nation’s largest student-run global health and sustainable development organization. Along with UC Berkeley SRP undergraduate Student Assistant Joanna Malbaek, who serves on the Executive Board of the UC Berkeley chapter of the organization, Sylvia organized a successful fundraiser to sponsor the trip designed to help support public health and medical and dental health initiatives in Honduras.

GSR Sarah Daniels received a student travel award to attend the 2013 Environmental Mutagenesis and Genomics Society annual meeting in Monterey, CA, September 21-25, where she further received an award for “Best Student Oral Presentation” award for her presentation to the group.

Project 2:  GSR Vanessa de la Rosa received a “Best Student Presentation” award for her work at the 2013 Northern California Chapter of the Society of Environmental Toxicology and Chemistry meeting in Sacramento, CA, May 8-9.

Former GSR Brandon Gaytán completed his PhD and was offered a position as a California Science and Technology Policy Fellow with the California Council on Science and Technology for the California State Legislature.

Postdoctoral Fellow Hua Shen received an “Emerging Scientist Award” for his work at the 2013 Environmental Mutagenesis and Genomics Society annual meeting in Monterey, CA, September 21-25.

Project 6:  Jean Van Buren received the “Best Poster” award at the 2013 Annual Meeting of the UC Berkeley Superfund Research Program, Berkeley, CA, September 20.

Administrative Supplement: nanotechnology-Based Environmental Testing

Trainees Jay James and Jeffrey Crosby received an award for their work at the Haas School of Business, UC Berkeley: National Science Foundation Innovation-Corps, Bay Area Node, for Best Team Overall, Fall, 2013.  Their collaboration lead to development and production of an inexpensive and reliable mercury detection sensor.  They filed U.S. Application Nos. 61/585,542 and 61/587,546 and their International Patent Application has been accorded serial number PCT/US2013/021066.

2012 Program Highlights

Currently under review.

2011 Program Highlights

Currently under review.

2010 Program Highlights

Project 2: Functional profiling of susceptibility genes

Leaders: Christopher Vulpe and Luoping Zhang

The most important thing Project 2 investigators have discovered in the past year is that a protein called N6AMT1 (short for ‘N-6 adenine-specific DNA methyltransferase 1’) can metabolize arsenic compounds and lower their toxicity.  This is a novel finding and a paper on this is in press in Environmental Health Perspectives. The investigators first used yeast to discover that mutated yeast lacking the gene MTQ2 were altered in their response to arsenic exposure. The human equivalent of yeast MTQ2 is N-6 adenine-specific DNA methyltransferase 1 (N6AMT1). Enhanced expression of N6AMT1 in human bladder cells significantly increased their resistance to the toxicity of arsenic and its metabolites and N6AMT1 was shown to methylate arsenic to a non-toxic metabolite. The investigators showed that N6AMT1 was able to convert monomethylarsonous acid (MMAIII), the most toxic arsenic species, to the less toxic dimethylarsonic acid (DMA) when over-expressed in human bladder cells. The enhanced expression of N6AMT1 in these cells decreased cytotoxicity of both iAsIII and MMAIII. Moreover, N6AMT1 is expressed in many human tissues at variable levels, although lower than those of AS3MT, supporting a potential participation in arsenic metabolism in vivo. Since MMAIII is the most toxic arsenical, our data suggest that N6AMT1 has a significant role in determining susceptibility to arsenic toxicity and carcinogenicity due to its specific activity in methylating MMAIII to DMA, and other unknown mechanisms.

Project 3: Arsenic biomarker epidemiology

Leaders: Patricia Buffler and Martyn Smith

Arsenic in drinking water causes increased mortality from several cancers, ischemic heart disease, bronchiectasis, and other diseases. Project 3 investigators discovered this year that death from tuberculosis is also more likely to occur following arsenic exposure.  Their paper, to be published in the American Journal of Epidemiology, presents the first evidence relating arsenic exposure to pulmonary tuberculosis, by estimating mortality rate ratios for Region II of Chile compared to Region V for the years 1958-2000. The authors compared mortality rate ratios with time patterns of arsenic exposure, which increased abruptly in 1958 in Region II and then declined starting in 1971. Tuberculosis mortality rate ratios in men started increasing in 1968, ten years after high arsenic exposure commenced. The peak male five-year mortality rate ratio occurred during 1982-86 (RR=2.1, 95% CI 1.7-2.6, P<0.001), and subsequently declined. Mortality rates in women were also elevated, but with fewer excess pulmonary tuberculosis deaths (359 among men and 95 among women). The clear rise and fall of tuberculosis mortality rate ratios in men following high arsenic exposure is consistent with a causal relationship. The findings are biologically plausible in view of evidence that arsenic is an immunosuppressant and also a cause of chronic lung disease. Finding weaker associations in women is unsurprising, since this is true of most arsenic-caused health effects. Confirmatory evidence is needed from other arsenic-exposed populations and studies are on-going in other populations.

2008 Program Highlights

Project 2: Functional profiling of susceptibility genes

Leaders: Christopher Vulpe and Luoping Zhang

Many people are exposed to a variety of toxic chemicals present in the environment on a daily basis. However, only some people develop disease (get sick) as a result. An individual’s chances depend in part on subtle differences in the genes which comprise the genetic blueprint for each person. Unfortunately, for most toxic chemicals, we don’t know where to look for these important variations because we don’t which of the tens of thousands of genes are important for dealing with each toxic chemical. In this project, we are figuring out which genes are the important ones to focus on by using baker’s yeast. By using yeast, we have been able to check thousands of genes for their importance in an individual’s vulnerability to Superfund chemicals. In the past year, the research group led by Dr. Chris Vulpe found several genes associated with the packaging of DNA in a cell (the chromatin) as key to sensitivity to arsenic. Dr. Luoping Zhang’s group further demonstrated the importance of one of these genes in human cells. Arsenic is an established cause of bladder cancer in humans and these findings suggest that alterations in the way that DNA is packaged into chromatin may affect arsenic’s toxicity and carcinogenicity. In the next year, we plan to look to see if these variations in these genes play a role in the likelihood that a person will develop bladder cancer or other diseases after being exposed to arsenic. Understanding the genetic determinants of chemical susceptibility in humans can help identify groups of people that could be at increased risk of developing disease following exposure to toxic agents, and to design prevention and intervention strategies with the aim of preserving public health.

Core B: Research translation

Leaders: Amy Kyle and James Hunt

The Research Translation Core focused this past year on informing policy and stakeholder audiences about key scientific information and principles related to chemical assessment and characterization and about children’s environmental health, both key areas of research for the group as a whole. The Core conducted several formal and informal workshops for stakeholder groups in San Francisco, Oakland, and in Sacramento. The program advised legislative staff about key scientific concepts in the development of several pieces of legislation. This resulted in the inclusion of the concept of ‘hazard traits’ in California’s newly passed green chemistry legislation (AB 1879 and SB 509). This is important because including a concept of ‘hazard traits’ means that the chemical traits of health concern can be further defined and elucidated after legislation is passed and adapted as scientific knowledge and methods improve.

The engineering component of the Core analyzed data from two groundwater plumes containing chromate in the southeastern corner of California to assess groundwater remediation approaches. The monitoring data were reported in over a hundred wells during site investigation and remediation efforts over a 20 year period. These data reveal that chromium as a soluble contaminant has been retained in the groundwater aquifer up to 50 years after release. The analysis showed that pumping out groundwater has not been an effective remediation tool because the source of concentrated chromate present in trapped brines continues to slowly release chromate into flowing groundwater. Discussion with the Stakeholders involved is on-going.

2007 Program Highlights

Project 3: Arsenic biomarker epidemiology

Leaders: Patricia Buffler and Martyn Smith

Project 3 explores the effects of childhood arsenic exposure and the mechanisms that may confer susceptibility to these effects.  The Arsenic Health Effects Research Program led by Dr. Allan Smith has shown that in utero and early childhood exposure to arsenic results in major increases in lung cancer and bronchiectasis mortality in young adults aged 30-49. The program also reported findings of more than a 3-fold increase in mortality from acute myocardial infarction in young adults who had early life exposure to arsenic in drinking water. These findings show that early life environmental exposure to arsenic in drinking water is strongly linked to disease incidence and mortality in adulthood.

Project 5: Nanotechnology-based environmental sensing

Leaders: Catherine Koshland and Donald Lucas

Project 5 made significant progress towards developing a functional arsenic detector in ground water using nanotechnology through the doctoral thesis work of student Martin Mulvihill. Using close-pack arrays of octahedral shaped silver nanocrystals, the chemical sensing of arsenic ions with detection limits as low as 1 part per billion in solution was possible. The sensor is based on surface-enhanced Raman spectroscopy (SERS), where analyte molecules near nanostructured metallic surfaces experience huge enhancements in Raman scattering cross-sections, typically orders of magnitude higher than expected. The nature of vibrational spectroscopy allows for the simultaneous measurement of arsenic in both of its commonly found oxidation states and can discriminate between the two. This is important since the different oxidation states have different toxicities.

The detection is performed directly on the substrate by placing a droplet of the analyte solution onto the nanocrystal monolayer, with no additional sample preparation required. These substrates have been verified to work in the presence of known competing anions, and have been used to accurately characterize the arsenic levels in polluted well water obtained by collaborators in Nevada.

2006 Program Highlights

Project 3: Arsenic biomarker epidemiology

Leaders: Allan Smith and Martyn Smith

Very little evidence exists concerning the possible impairment of children’s intellectual function in relation to arsenic exposure in utero and childhood. Children worldwide are exposed to arsenic in drinking water at concentrations that exceed the standard recommended by the World Health Organization and the U.S. Environmental Protection Agency maximum contaminant level of 10 μg/L. Children are particularly at risk for high exposure in arsenic-affected areas of South Asia such as West Bengal, India.

Acute neurotoxic effects of arsenic in high doses have been well documented. Arsenic poisoning related to occupational exposure causes central nervous system alterations, including impairments of recent memory, learning, and concentration. Children may be particularly susceptible to neurotoxic substances as suggested by findings from studies on the effects of lead, methylmercury, solvents, and PCBs. Experimental animal and petri dish studies, and some limited evidence from the few earlier reports considering children’s intellectual function and arsenic, suggested possible associations between arsenic exposure and neurodevelopment. One recent study of 201 children conducted in Bangladesh, which is neighboring our study region, suggested that current arsenic concentrations in water as low as 10 μg/L were linked to reductions in intellectual functioning in 10-year-old children.

We conducted a cross-sectional study among 351 children aged 5 to 15 years selected from a source population of 7,683 people in West Bengal, India, 2001-2003. Intellectual function was assessed with six subtests from the Wechsler Intelligence Scale for Children, as well as with the Total Sentence Recall test, the Colored Progressive Matrices test and a pegboard test. Arsenic in urine and lifetime water sources including the pregnancy period were assessed using measurements of samples from 409 wells. The test scores were analyzed with linear regressions based on the method of generalized estimating equations incorporating relevant covariates.

This study systematically addresses arsenic exposure from all water sources used over a lifetime (including the pregnancy period), as well as urinary arsenic concentrations, in relation to intellectual function in children. Effects were found for the vocabulary, picture completion, and object assembly tests with reductions between 12% and 20%, but the confidence intervals were broad. Our findings suggest that increased urinary arsenic concentrations reflecting current exposure from all sources, including food, are associated with small decrements in intellectual function testing, whereas little evidence for an effect of long-term arsenic concentrations in drinking water was found.

Our findings suggest that arsenic exposure measured in urine is related to decrements in intellectual function scores, which may be in the range of 10% to 20% for some tests. However, the 95% confidence intervals of these estimates were wide. Whether or not these effects have persisting impact needs further investigation. There was little evidence of an association between arsenic drinking water concentrations alone and intellectual function. Current urine concentrations reflecting exposure from all sources appeared to be more relevant than pregnancy, peak, or cumulative exposure based on measurements of water sources. One possible explanation is that the relationship with current exposure relates only to transient effects. However, it is also possible that the lack of findings with past water concentrations is due to incomplete assessment of past exposure, in particular, exposure originating from food. Although the findings need to be confirmed, they add to the body of evidence of adverse health effects in children resulting from exposure to arsenic.

von Ehrenstein OS, Poddar S, Yuan Y, Mazumder DG, Eskenazi B, Basu A, Hira-Smith M, Ghosh N, Lahiri S, Haque R, Ghosh A, Kalman D, Das S, Smith AH (2006) Children’s Intellectual Function in Relation to Arsenic Exposure. Epidemiology. Jan;18(1):44-51. PMID: 17149142. [Abstract] [Full text]

Project 4: Application of comparative genomics, transcriptomics, and proteomics to optimize microbial reductive dehalogenation

Leaders: Lisa Alvarez-Cohen and Gary Andersen

This project seeks to understand and optimize the microbial detoxification of common Superfund pollutants, perchloroethene (PCE) and trichloroethene (TCE) by focusing on the only genus of bacteria, Dehalococcoides, known to completely reduce PCE and TCE to ethene. A better understanding of the genome, transcriptome and proteome of Dehalococcoides will greatly improve our understanding of the physiology of these difficult to grow organisms, so that their abundance and activity at bioremediation sites can be maximized.

We have determined that Dehalococcoides strain BAV1 diverges from that of D. ethenogenes 195 in several major metabolic pathways. Conversely, we determined that ANA enrichment possesses most of the same genes as D. ethenogenes 195 suggesting significant horizontal gene transfer among species. This has furthered a specific aim of the project to identify important genes that are conserved throughout Dehalococcoides spp. as well as those that vary between strains.

We measured the transcriptomic effects of cobalamin (vitamin B12)-limited growth conditions. This stress condition is of particular relevance because cobalamin is a necessary co-factor for reductive dehalogenases but cannot be biosynthesized de novo by this isolate. The findings revealed a cobalamin regulon in this isolate and provided novel genetic targets for monitoring cobalamin stress in Dehalococcoides spp.

Chlorinated solvents are the most common groundwater contaminants at Superfund sites. In situ bioremediation is a promising and cost effective method for remediation of these contaminants. The aim of project 4 is to improve prediction and monitoring which will ultimately optimize system performance at remediation sties.

Work in specific aim 1 involved an enriched anaerobic microbial community (ANAS) that reductively dechlorinates chlorinated ethenes including TCE, cis-dichloroethene (c-DCE) and vinyl chloride (VC). We used whole genome microarrays based upon the chromosome of D. ethenogenes 195 to compare the genomics of strain 195 to those of Dehalococcoides strain BAV1 and the ANAS enrichment. Thus far, we have determined that the genome of strain BAV1 diverges from that of strain 195 in several major metabolic pathway genes including genes typically involved in carbon assimilation, nitrogen fixation, cobalamin usage, hydrogenases, and especially reductive dehalogenases. Conversely, the ANAS enrichment possesses most of the same genes found in strain 195, with the exception of a number of viral inserts containing reductive dehalogenase genes, suggesting significant horizontal gene transfer among species.
As part of specific aim 2, we applied whole-genome microarrays to compare the transcriptome of strain 195 when grown under differing growth conditions. In particular we measured the transcriptomic effects of cobalamin (vitamin B12)-limited growth conditions. This stress condition is of particular relevance because cobalamin is a necessary co-factor for reductive dehalogenases but cannot be biosynthesized de novo by this isolate. The findings revealed a cobalamin regulon in this isolate and provided novel genetic targets for monitoring cobalamin stress in Dehalococcoides spp.

In a related study, we characterized the effects of exposing strain 195 to cell-free supernatants obtained from the ANAS enrichment. To our surprise, the genes that were most strongly down regulated after exposure to the supernatants were involved with cobalamin salvage and recycling, suggesting that members of ANAS biosynthesize additional cobalamin de novo that can be transferred to Dehalococcoides. We intend to further characterize this eco-physiological interaction as it may be crucial for avoiding cobalamin stress and prolonging dechlorination activity in the environment.

Progress on specific aim 3 includes the assembly of defined consortia from combinations of Dehalococcoides and other key species identified in the ANAS enrichment. We were able to grow Desulfovibrio vulgaris Hildenborough (DVH) with strain 195 in syntrophy on a defined medium containing no hydrogen and no sulfate. We will apply qPCR and whole-genome microarrays to compare the transcriptomes of DVH, 195, and the co-culture DVH/195 and to identify genes important in these symbiotic interactions.

With respect to specific aim 5, we have completed the molecular analysis of a microbial community through different phases of enhanced bioremediation at Ft. Lewis East Gate Disposal Yard (Seattle, Washington), a TCE contaminated field site undergoing in situ bioremediation. We applied qPCR to measure the 16S rRNA gene and the three functionally important reductive dehalogenase genes (tceA, bvcA, vcrA) of Dehalococcoides spp. present in the groundwater through different stages of treatment process (biostimulation and bioaugmentation). Quantification of gene concentration and expression suggests that Dehalococcoides spp. were not only present but were physiologically active in the field communities and provided a clear trend of the dynamics of the different strains of Dehalococcoides in response to the manipulations at the site.

Finally, we have expanded our analyses to include application of a whole genome microarray to measure the expression of genes by Rhodococcus sp. RHA1 in response to induction by propane. In these studies we have shown that the propane monooxygenase is inducible and responsible for NDMA degradation by this organism.

2005 Program Highlights

Project 3: Arsenic Biomarker Epidemiology

Leaders: Drs. Allan Smith and Martyn T. Smith

Millions of people are exposed to arsenic-contaminated water in the U.S. and worldwide, and arsenic is ranked first on the most recent priority list of Superfund site hazardous substances. Dr. Allan Smith and the Berkeley Arsenic Health Effects Research Group he leads first identified major potential risks from arsenic in drinking water in a publication in 1992 which has since been cited in the scientific literature more than 300 times (Environmental Health Perspectives, 97:259-267, 1992). Since then, studies by this group and others led the International Agency for Research on Cancer (IARC) in 2002 to classify arsenic in drinking water as an established cause of human bladder cancer, lung cancer, and skin cancer. It is surprising that ingestion of arsenic in drinking water could cause lung cancer, but current evidence suggests that lung cancer is the leading cause of long-term mortality resulting from exposure to arsenic. In Chile, for example, the research group showed that about 1 in 10 persons with high exposure to arsenic in drinking water would eventually die as a result of that exposure (Am J Epidemiol, 147:660-669, 1998). Lung cancer was by far the major contributor to this startling increase in mortality, with smaller contributions from bladder cancer, kidney cancer and skin cancer.

Some substances that cause lung cancer also cause other types of lung disease. For example, smoking causes emphysema in the lungs, as well as lung cancer. Asbestos causes lung cancer, but also causes asbestosis in the lungs. Since arsenic in water was such a potent cause of lung cancer, the research group thought that perhaps it might also cause other lung effects. Recent findings by the Arsenic Health Effects Research Group provide strong evidence that this is indeed so.

The research team has conducted population-based investigations of the effects of arsenic in drinking water on lung function in West Bengal, India. They recently identified lung function deficits in men consuming high concentrations of arsenic in drinking water (Am J Epidemiol 2005 Sep;162(6):533-41). These impacts were so strong, that in this population they exceeded lung function effects due to smoking. Epidemiologic studies of ingested arsenic to date have been based on respiratory symptoms; this is the first systematic population-based study of arsenic ingestion that objectively measured lung function.

The research team also found that bronchiectasis in the lungs is greatly increased in subjects with arsenic-caused skin lesions (Epidemiology 2005 Nov; 16(6);760-5). This study involved high resolution computed tomography scans (HRCT) with readings by scientists in both India and the Untied States who did not know if the x-rays they were assessing came from persons exposed to arsenic or not. The findings suggested that persons who have high exposure to arsenic in water and develop arsenic-caused skin lesions are about ten times more likely to have evidence of bronchiectasis in the lungs than comparable persons not exposed to arsenic.

The non-cancer effects of arsenic are not just confined to the lungs. The Arsenic Health Effects Research Group has also been studying the effects resulting from exposure to arsenic during pregnancy and childhood. They recently identified a six-fold increase in rates of stillbirth in women with arsenic exposure (Am J Epidemiol, in press).

The results of these studies highlight the importance of investigations into long-term health effects of arsenic. Exposures to arsenic cause multiple effects in different parts of the body, and the research group will be increasingly giving priority to investigating the long-term consequences of exposure to arsenic during childhood.

Project 8: Development of Tools For Monitoring in situ Bioremediation

Leaders: Drs. Lisa Alvarez-Cohen and Mark Conrad

In situ bioremediation uses naturally occurring microorganisms to degrade contaminants in place with the goal of creating harmless chemicals as end products. The technology was developed as a less costly, more effective alternative to the standard pump-and-treat methods used to clean up contaminated groundwater sites. The goal of Project 8 is to develop tools for evaluating the progress of in situ bioremediation in the field.

Lisa Alvarez-Cohen and Mark Conrad, co-leaders of Project 8, made significant progress on both molecular biology and stable isotopic approaches over the past year. They recently developed a rapid test can be used to determine whether key bacteria are producing the appropriate enzymes needed to biodegrade chlorinated solvents, one of the most prevalent groundwater contaminants at Superfund sites. This test is based up the precise quantification of molecules within bacteria that lead to the production of solvent degrading enzymes. Specifically, this technique utilizes an internal standard along with quantitative PCR to enable the precise quantification of gene expression in bacterial communities. This technique has been tested and validated with microbial communities that biodegrade chlorinated solvents. Results demonstrated that losses experienced at each step of the nucleic acid processing prior to qPCR could be quantified and compensated for by the internal standard technique, leading to absolute quantification of molecule copy numbers. Because this technique is more accurate and faster than previous alternatives, it could greatly facilitate site assessment, application design, and bioremediation monitoring, leading to substantial cost savings for application of in situ bioremediation. Further, this technique will facilitate the measurement of a wide variety of gene expression in both environmental and laboratory samples, potentially leading to advances in both fundamental and applied science. This technique has recently been published (1,2).

1) Johnson D R, Lee PKH, Holmes VF, Alvarez-Cohen L (2005) Transcriptional Expression of the tceA Gene in a Dehalococcoides-Containing Microbial Enrichment. Applied and Environmental Microbiology, 71: 7145-7151. PMID: 16269753. [Abstract] [Full text]

2) Johnson DR, Lee PKH, Holmes VF, Alvarez-Cohen L (2005) An Internal Reference Technique for Accurately Quantifying Specific mRNAs by Real-Time PCR with Application to the tceA Reductive Dehalogenase Gene. Applied and Environmental Microbiology, 71:3866-3871. PMID: 16000799. [Abstract] [Full Text]

2004 Program Highlights

Project 1: Biomarkers of chemical exposure and leukemia risk

Leaders: Drs. Martyn T. Smith and Patricia A. Buffler

Benzene is a ubiquitous environmental contaminant.  It has been found at over half of the National Priorities List sites identified by the Environmental Protection Agency, and we are all routinely exposed to benzene via second-hand cigarette smoke, automobile emissions and gasoline vapors.  Benzene is one of the most frequently used chemicals in American industry as it is used as a solvent and to make plastics, resins, adhesives, synthetic fibers, lubricants, dyes, detergents, drugs, and pesticides. Workers in shipping, automobile repair, shoe manufacture, and refining/transportation of oil and gasoline are routinely exposed to benzene fumes.  U.S. occupational guidelines limit benzene exposure to one part per million (ppm), but workers in developing countries are thought to be exposed to much higher levels of benzene.

While it is well documented that long-term exposure to high levels of benzene reduces white blood cell counts and can cause leukemia in people, the impacts of exposure at levels below 1 ppm in the air are uncertain.  Dr. Martyn Smith, Program Director of the University of California-Berkeley SBRP, and Dr. Stephen Rappaport, of the University of North Carolina-Chapel Hill SBRP, are collaborating with researchers from the National Cancer Institute and the Chinese Center for Disease Control to study the impacts of long-term exposure to low levels of benzene.

They conducted a cross-sectional study in a region near Tianjin, China including 250 shoe workers exposed to benzene-containing glues and 140 unexposed age- and sex-matched controls who worked in 3 clothes-manufacturing factories.  They conducted extensive exposure assessments for 16 months, testing air samples in the factories as well as at each worker’s home.  Using blood and urine samples, the researchers linked individual air-monitoring data to end-points including white blood cell and platelet counts, lymphocyte subsets and progenitor cell colony formation.

As expected, workers exposed to benzene at levels of 1 ppm and higher had fewer total white blood cells, granulocytes, lymphocytes, B cells, and platelets than did unexposed workers.  The researchers also found that compared to controls, workers exposed to less than 1 ppm benzene had significantly decreased numbers of all types of white blood cells and platelets.  On average, these workers had 15% to 18% fewer granulocytes and B cells than unexposed workers, even after controlling for smoking and other potential confounding factors.

Because benzene affected nearly all blood cell types, the researchers suspected that benzene is toxic to progenitor cells – the unspecialized “parent” cells from which all other blood cells develop.  They cultured samples from exposed workers and controls using colony-forming assays to measure the proliferative potential of progenitor cells.  The scientists observed highly significant, dose-dependent decreases in colony formation of progenitor cells from exposed workers.  Further, benzene caused a greater proportional decrease in colony formation than in levels of differentiated white blood cells and granulocytes, suggesting that early progenitor cells are more sensitive than mature cells to the toxic effects of benzene.  This is the first study to find that benzene exposure affects the ability of progenitor cells to grow and multiply in humans.

The researchers then examined the influences of genetic variation in 3 enzymes responsible for activating and detoxifying benzene. They found that exposed subjects with variation in 2 enzymes (MPO and NQO1) were especially susceptible to benzene-induced lowering of white blood cell counts.

The results of this study highlight the importance of investigations into long-term health effects, including increased occurrence of blood diseases such as leukemia, in workers exposed to low levels of benzene.

Lan Q, Zhang L, Li G, Vermeulen R, Weinberg RS, Dosemeci M, Rappaport SM, Shen M, Alter BP, Wu Y, Kopp W, Waidyanatha S, Rabkin C, Guo W, Chanock S, Hayes RB, Linet M, Kim S, Yin S, Rothman N, Smith MT (2004) Hematotoxicity in workers exposed to low levels of benzene. Science 306(5702):1774-6.

2003 Program Highlights

Project 6: Historical Exposure Assessment

Investigator: James R. Hunt

Preliminary results from this project are assisting the US Navy and the US EPA in efforts to reach closure on a site remediation plan for the former Alameda Naval Air Station, a Superfund site with significant contamination of estuarine sediments.  Contaminants in freshwater and marine sediments are a challenge at many U.S. and international sites. Sediments accumulate contaminants from many sources over long time periods.  Radioisotopic tracers arising from natural sources and from atmospheric nuclear weapons testing are being applied at the former Alameda Naval Air Station where additional radioisotopic tracers were added by the use of radium in luminescent paints.  Sediment cores collected in November 2002 are being gamma counted and reveal a very detailed record of sediment contamination during and immediately following World War II.  Sediment analysis at a one-centimeter interval has demonstrated annual variations in sediment levels of contaminants and tracers.  The sediment profile has maintained the chronology of sediment contamination likely due to the anaerobic conditions that precluded sediment mixing by benthic organisms.  These results are being shared with the US EPA and the US Navy in their joint efforts to reach a remedial decision.  This effort is providing greater spatial coverage than was possible during routine site characterization and utilizes one of the contaminants, radium, as a tracer for sediment dispersal and deposition.  This site-specific tracer has the potential to greatly limit the need for trace metal analysis if other contaminants are strongly correlated with the radium levels.  It is likely that the US EPA program manager for the joint project will be working with the University researchers to develop additional site-specific data.

Sediment cores from the former military base are also being analyzed for their detailed spatial distribution of trace metals using x-ray fluorescence in undisturbed cores. The approach uses frozen sediments subjected to an intense x-ray beam at Advance Light Source at the Lawrence Berkeley National Laboratory.  The method is being developed as a quantitative tool using standard reference materials representative of an estuarine sediment matrix and then actual estuarine sediments from contaminated sites in the San Francisco Bay Area.  These data are providing a means for estimating the three dimensional distribution of contaminants as is needed in site characterization and our modeling efforts. Extending from point measurements to a three dimensional representation will be done through tools developed in geostatistics for mineral and groundwater resource evaluation.

2002 Program Highlights

UC Berkeley is proud to have been involved in the NIEHS Superfund Basic Research Program since its inception. In 1987, Dr. Martyn T. Smith, Professor of Toxicology in the School of Public Health, assembled a distinguished research team of biomedical scientists spanning three institutions, UC Berkeley, UC San Francisco, and the California Department of Health Services. For the past 15 years, the UC Berkeley Superfund Basic Research Program has continued to strive for scientific breakthroughs that lead to demonstrable innovations in human health protection and toxic waste remediation.

The highly collaborative atmosphere of the UC Berkeley Superfund research program has led to considerable scientific progress – some notable advances are as follows:

  1. Drs. Kent Udell and James Hunt and showed that liquid solvents trapped in soils are able to move towards ground water supplies via a process called dense vapor migration. They also demonstrated that steam injection effectively removes these trapped solvents from soils at hazardous waste sites. Initial SBRP funding lead to a very successful full-scale demonstration of Steam Enhanced Extraction at Lawrence Livermore National Laboratory and then to a showcase industrial application at the Visalia Pole Yard in Visalia, California one of the first sites placed on the National Proiority List. That project is considered a break-through application of remediation technology, thus earning an EPA Remediation Technology Development Award for “for technical excellence in the development of in situ thermal treatment technologies”. The application of Steam Enhanced Extraction at that site decreased the financial liability of the site by $85 million for a cost of about $15 million, showing a clear financial incentive for publicly owned corporations to take a more aggressive approach to environmental restoration.  This advance is further highlighted below.
  2. Dr. Catherine Koshland’s group identified key conditions for toxic byproduct production in combustion and waste incineration, showing that at sub-optimal temperatures relatively innocuous compounds such as ethyl chloride can be converted into highly hazardous chemicals such as vinyl chloride.  The group went on to develop an in situ real time technique for detecting and monitoring chlorinated hydrocarbons in incinerators that has since been extended to ammonia and several metals.
  3. Dr. Allan Smith led a study of lung and bladder cancer patients who were exposed to naturally occurring arsenic in drinking water. His population-based studies in Nevada and Chile uncovered a high incidence in bladder cancers from arsenic exposure, and he showed that methylation does not protect from arsenic-related carcinogenesis at low levels of exposure. Using a novel micronucleus assay developed in the laboratory of Dr. Martyn Smith, the researchers were the first to demonstrate that concentrations of arsenic in drinking water at the US standard of 50 ppb produced increased levels of genetic damage in bladder epithelial cells of humans who drank the water. They went on to perform an intervention study that showed a decrease in genetic damage in the bladder following a reduction in arsenic exposure.  This work on arsenic has reduced uncertainty in the risk assessment process and had a profound effect on arsenic environmental regulation.  It is further highlighted below as a notable advance.
  4. Drs. Buffler, Smith and Wiencke have produced new insights into the natural history and environmental etiology of childhood leukemia.  Their study, based in Northern California, aims to enroll up to 1,000 cases and incorporates molecular cytogenetic characterization of the cases. They sequenced various specific DNA changes found in childhood leukemia in 56 patients and showed that these rearrangements could be commonly detected in the neonatal blood spots (Guthrie cards) of the cases. These findings show that most childhood leukemias begin in utero and that maternal and peri-natal exposures are likely to be critical.  Indeed, the investigators also found that exposure to indoor pesticides during pregnancy and the first year of life raises leukemia risk, but that later exposures do not.
  5. Our outreach program, the Children’s Environmental Health Network has played a key role in the emergence of pediatric environmental health as a credible and recognized field of research. They have created a national “network” of health professionals, researchers, policy makers and advocates addressing children’s environmental health.  In addition, they have defined a national research agenda on children’s environmental health by convening national conferences at which researchers can share their findings, raise new research questions, and together craft a child focused national research agenda.
Technology Transfer of Steam Injection for Soil and Groundwater Cleanup

Project Investigator: Kent S. Udell

A decade of NIEHS support of scientific research, process development and technology transfer has paid large dividends for the national and international remediation community. The support of the fundamental science of thermal remediation at the University of California at Berkeley has generated new national and international industry, and a solid technical basis for EPA policy on source removal for soil and groundwater cleanup. It is now clear that many sites previously considered as untreatable can be remediated with reasonable cost and acceptable certainty using thermal remediation techniques. Thermal techniques have been used by several industries and in many countries to provide a permanent solution to problems that would otherwise persist for centuries. Prior arguments that there is not technology capable of removing heavier than water liquids from the subsurface have been negated, giving fresh impetus to the push for aggressive environmental cleanup by regulatory agencies.

The Berkeley research, under NIEHS funding, lead to a very successful full scale demonstration of Steam Enhanced Extraction at Lawrence Livermore National Laboratory and then to a showcase industrial application at the Visalia Pole Yard in Visalia, California one of the first sites placed on the National Proiority List. That project has been considered to be a break-through application of remediation technology, thus earning the first and only EPA Remediation Technology Development Award for “for technical excellence in the development of in situ thermal treatment technologies”. The application of Steam Enhanced Extraction at that site decreased the financial liability of the site by $85 million for a cost of about $15 million, showing a clear financial incentive for publicly owned corporations to take a more aggressive approach to environmental restoration.

The transfer of NIEHS supported thermal technology has continued with growing applications at Superfund sites and other sites of National interest. Specifically, the use of Steam Enhanced Extraction was included as the selected cleanup remedy in the record of decision for Wyckhoff Superfund site adjacent to Eagle Harbor near Seattle. A pilot test of the technology, consisting of about 10 injection and 10 extraction wells is now underway. The technology is also being considered for the remediation of the Baxter and McCormick Superfund site near Stockton, California with a full scale design completed in sufficient detail for costing purposes. The project now is under funding consideration by EPA. This site is one on the largest wood treating chemical spills in the country and defies all other techniques for remediation in any reasonable time frame.

Steam injection was also applied at Cape Canaveral at Launch Complex 34. This site is particularly important in that the steam technology is the third technique to be demonstrated in adjacent plots. The use of steam injection at that site is also unique in its application through the co-injection of air with the steam. This approach, first considered by researchers at the University of Stuttgart in Germany for the removal of semi-volatile non-aqueous phase liquids in the vadose zone, was extended for application to volatile non-aqueous phase liquids found in the saturated zone through NIEHS funding. That research developed the theoretical underpinning of the value of air co-injection with the steam in the elimination of accumulation of the non-aqueous phase liquid at the steam condensation front. Such accumulation has been shown to be the requisite step leading to uncontrolled downward migration of the non-aqueous phase liquid during thermally enhanced cleanup operations. In principal, the co-injection of air provides conditions where the NAPL vapors do not condense with the steam at the condensation front. Instead, the non-aqueous phase liquid vapors remain in the gaseous phase to percolate upward into the vadose zone where they are pulled to vapor extraction wells. In all cases, including controlled two dimensional laboratory experiments, the simultaneous injection of air and steam increases the NAPL compound removal rate beyond that which could be achieved by either pure steam injection or pure air sparging.

Of near equal importance is a project initiated at Loring Air Force Base in Maine where steam is to be injected into fractured rock which is contaminated by  non-aqueous phase liquids trapped in the fractures. This is a large project where both State of Maine and EPA are actively engaged in the application and evaluation of the potential of steam enhanced extraction to remediate fractured geologies. NIEHS contributes to that project through the transfer of the steam injection technology expertise to the multi-agency consortium of stakeholders to ensure that the most current engineering knowledge is applied to the contaminants and  media of interest at that site.

International application has also been gaining momentum. Expertise from NIEHS funded work has been applied to a PCE and kerosene site in Denmark with success, and Steam Enhanced Extraction is being used routinely in the Czech Republic, including the first successful remediation of a fractured bedrock site. Also of interest is the successful pilot demonstration of the technology at the Pancevo site in the former Yugoslavia, now Serbia, which experienced a catastrophic release of millions of pounds of the highly toxic chemical, 1,2 DCA due to the NATO bombings in 1999.

Activities funded in part by NIEHS technology transfer money included participation in the expert panel to set the future research agenda for the SERDP program. That agenda now includes expanded consideration of the science and applicability of thermal remediation technologies – thermally enhanced extraction processes in particular.  Additional input to the national policy debate on appropriate technologies for source removal has been solicited and provided to EPA. That effort was documented in a expert panel recommendation report completed in September, 2002.

Arsenic is a major environmental carcinogen

Project Investigator: Allan H. Smith

The revelation that arsenic is a major environmental carcinogen is largely due to the work of epidemiologist Dr. Allan Smith’s group at Berkeley, whose research provided definitive evidence that arsenic in drinking water causes bladder, lung, and other internal cancers. Their arsenic research activities began more than ten years ago with a risk assessment focusing mainly on cancer. This work, on which Superfund Director Dr Martyn Smith was also a co-author led to the conclusion that the cancer risks from inorganic arsenic in drinking water were potentially very high. The Arsenic Health Effects Research Program was then started with funding from the Superfund Basic Research Program to study the health risks from exposure to inorganic arsenic (Project 3 in this program). Currently it involves international research projects including studies and investigations in Argentina, Chile, India, Bangladesh as well as projects in California and Nevada in the United States.

Employing novel biomarkers developed in Dr. Martyn Smith’s laboratory (Project 1), the research team showed effects on bladder epithelium occur at or around the U.S. drinking water standard of 50 ppb. The Superfund-sponsored epidemiological studies in Nevada, Argentina, and Chile, made clear the need for better understanding of arsenic-related cancers, and led to the award of R01 support to investigate the dose-response relationship in greater detail. Dr. Allan Smith and Dr. John Wiencke (also of Project 1) both serve on the National Academy of Sciences Subcommittee on Arsenic in Drinking Water set up by the Board on Environmental Studies and Toxicology, National Research Council. Dr. Smith has also served as a Consultant to the World Health Organization on the Arsenic problems in Bangladesh including five visits to Bangladesh and preparation of three reports.

The following is a list of accomplishments:

  1. Provided definitive evidence (from studies conducted in Argentina and Chile) that arsenic is a potent cause of human bladder cancer.
  2. Provided definitive evidence (from studies conducted in Argentina and Chile) that arsenic in drinking water is a potent cause of human lung cancer.
  3. Demonstrated that epidemiological and experimental human data do not support that arsenic methylation protects from low dose effects.
  4. Showed that with exposure to water containing around 600 ug/L, 1 in 10 adult deaths may be due to arsenic-caused cancers, the highest environmental cancer risk ever reported.
  5. Identified a dose-response relationship between arsenic exposure and bladder cell micronuclei, a genotoxic biomarker of early effect.
  6. Identified a preliminary dose-response relationship between arsenic concentration in well water in India and the occurrence of keratoses and hyperpigmentation.
  7. Studies currently underway in India, Chile and the US, will allow projection of cancer risks with individual exposure data.
  8. Studies are currently underway to identify nutritional and genetic suceptibility to arsenic effects.

This research has reduced uncertainty in the risk assessment for arsenic and impacted the regulation of this important environmental contaminant.

Notable Innovation
Adding air during steam injection prevents downward spreading of toxic contaminants

Project Investigator: Kent S. Udell

Basic research on coupled thermo-fluid interactions of toxic liquid/water and gas phases in soils being heated to the boiling point of water has lead to a finding that air added to steam which is being injected into contaminated soils can eliminate the potential of downward spreading on the toxic liquid during thermal remediation operations. This finding served as the foundation for divergent research into the basic mechanisms responsible for this positive result, leading to the development of basic theory to predict the optimum air/steam ratio. With this basic understanding, steam injection projects currently in planning stages were modified to operate with air co-injection . Four projects benefited greatly from this simple modification and a new generation of thermal remediation technologies came into being. This change has eliminated the most problematic feature of steam injection and has revolutionized the remediation industry. The range of contaminated sites that can be cleaned-up has grown substantially, and the EPA has aggressively promoted this new incarnation of thermally enhanced remediation technology.