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Eric Allen, an associate professor of marine biology,  in his laboratory at Scripps Institution of Oceanography at UC San Diego.

Eric Allen, an associate professor of marine biology, in his laboratory at Scripps Institution of Oceanography at UC San Diego.

Center Projects


Project 1: Sources and sinks of HOC synthesis

Project 1 at the Scripps COHH is headed by Paul Jensen (Project Co-Leader) and William Fenical (Project Co-Leader)

The overall goal of Project 1 is to identify the biological sources of halogenated organic compounds (HOCs) that pose a potential threat to human health in the Southern California Bight. This goal will be accomplished through a comprehensive sampling strategy targeting major biotic groups including plankton, bacteria, benthic algae, and filter feeding invertebrates.  The results will be used to guide subsequent microbial cultivation efforts and cultivation-independent diversity studies.  Metagenomic data generated from Project 2 will provide a complimentary analysis of microbial community composition and insight into the biosynthetic genes associated with HOC production.  New information provided by Project 2 about the biosynthetic genes responsible for the production of these compounds is being used to determine the types of bacteria in which they occur.  HOCs that cannot be identified will be isolated, structurally characterized, and provided to Project 3 for toxicological evaluation.  Select HOCs previously identified from environmental samples will be synthesized to provide baseline toxicological data.  A major effort is being placed on the cultivation of HOC-producing bacteria, as there is considerable preliminary evidence that they represent a poorly understood source of these compounds.  This research represents the first major effort to identify the biological sources and sinks of an increasingly important group of marine pollutants in a major US coastal environment.


Introduction to Project 1 investigators:

Dr. Paul Jensen,  and Project 1 Co-Leader 

Dr. Jensen is a Research Microbiologist at the Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography.  His lab works at the interface of marine microbiology and natural product chemistry addressing questions related to microbial diversity and distributions, chemical ecology, and genomics.  This research is primarily funded through the NSF and NIH.

For more information, see


Dr. William Fenical, Director of CMBB and Project 1 Co-Leader 

Dr. Fenical is distinguished professor of oceanography and director of SIO’s Center for Marine Biotechnology and Biomedicine.  In addition, he is distinguished adjunct professor of pharmaceutical sciences at the Skaggs School of Pharmacy and Pharmaceutical Sciences at UC-San Diego.


Project 2: Microbial biosynthesis and genomics of HOCs

Project 2 at the Scripps COHH is headed by Bradley S. Moore (Project Co-Leader) and Eric E. Allen (Project Co-Leader)

Natural polybrominated organic compounds such as polybrominated diphenyl ethers, dioxins and pyrroles are collectively proposed to be biosynthesized by marine organisms such as cyanobacteria and red algae involving unknown metabolic pathways harboring yet to be discovered bromoperoxidase enzymes. Preliminary data generated by the Moore (biosynthesis) and Allen (genomics) laboratories support that marine bacteria possess the genetic capacity to biosynthesize polybrominated organic compounds, such as pentabromopseudilin and bromophene via a novel branched pathway involving flavin-dependent halogenases and not haloperoxidases as previously proposed. This subtle, yet significant distinction, lays the foundation for our hypothesis that authenticated polybrominated organic compound biosynthetic enzymes from marine bacteria (ie, Pseudoalteromonas and Streptomyces, and other producer microbes discovered as part of the Scripps COHH research) will allow for genetic probes to rationally interrogate marine environmental samples to aid in the discovery and monitoring of important source organisms.


Introduction to Project 2 investigators:

Dr. Bradley S. Moore, Center Director and Project 2 Co-Leader 

Dr. Moore is a professor of Pharmaceutical Sciences at UC San Diego’s Skaggs School of Pharmacy and Pharmaceutical Sciences and is a professor of Oceanography at Scripps. Dr. Moore serves as the Center Director and is responsible for overseeing the entire Center. The Scripps COHH is housed within the Center for Marine Biotechnology and Biomedicine (CMBB), where Dr. Moore is the Associate Director. CMBB is a multidisciplinary marine biomedical research group at SIO with members from the UC San Diego Schools of Pharmacy and Medicine and from other campus biomedical research programs. Dr. Moore is an expert in marine biochemistry, genetics and genomics pertaining to natural product biosynthesis with over a dozen years of uninterrupted NIH-supported research as a PI.

For more information, see


Dr. Eric E. Allen, Project 2 Co-Leader 

Dr. Allen is an assistant professor with joint faculty appointments in the Marine Biology Research Division at Scripps and in Molecular Biology in UC San Diego’s Department of Biological Sciences. Dr. Allen serves as Project 2 Co-Leader. He is an expert in marine metagenomics, bioinformatic analysis of genome sequence information, and bacterial genetics.

For more information, see


Project 3: Diversity and distribution of HOCs

Project 2 at the Scripps COHH is headed by Lihini I. Aluwihare  (Project  Co-Leader) and Eunha Hoh (Project Co-Leader)

Natural polybrominated organic compounds such as polybrominated diphenyl ethers (PBDE), dioxins and bipyrroles have been previously detected in a variety of marine organisms. Although several of these compounds have been linked to natural sources there is still significant uncertainty with regards to their origin and how they are acquired and metabolized. In this project we focus on the Southern California Bight region and aim to provide a comprehensive, non-targeted, compilation of the halogenated compounds present in apex marine predators (e.g. dolphins, and apex predators that are consumed by humans) and their prey. By focusing our study regionally (inshore and offshore) we have observed some patterns in the distribution of natural halogenated organic compounds, detected congeners that have not been previously reported and tentatively identified some unknown compounds that may be of natural origin. The non-targeted approach that was applied further enabled us to examine the biota-specific distribution of both halogenated anthropogenic contaminants that are currently in use as well as and the vast array of legacy pollutants and their degradation products. For this study P3 investigators are collaborating with Nathan Dodder and Keith Maruya of the Southern California Coastal Water Resources Project and the Ceatacean ecology group at the South West Fisheries Science Center in La Jolla, including Dave Weller and Kerri Danil.

Using such a non-targeted approach P3 investigators will also examine breast milk from Southern California mothers to establish the “contaminome” of this population. In addition, a more targeted approach coupled with seafood consumptions surveys will be used to systematically examine dietary pathways by which these various halogenated organic compounds enter human populations. This project will further seek to apply stable isotope and natural abundance radiocarbon studies on pooled breast milk samples to definitively establish the ultimate source of compounds (natural or anthropogenic) such as methoxylated polybrominated diphenyl ethers and other PBDE derivatives. For this work P3 investigators are collaborating with Drs. Jae Kim, Christina Chambers, and Michelle Leff in the UCSD School of Medicine, as well as Jenny Quintana and Mel Hovell at the SDSU School of Public Health.

The final component of this project includes an investigation of both the metabolism and potential toxicity of specific brominated compounds of proposed natural origin. Initial studies will be conduced with both in-vitro and in-vivo bioassays and will target endocrine disruption pathways as well as detoxification mechanisms. This investigation will use compounds that have been chemically synthesized by William Fenical’s groups (Project 1) and biosynthesized by bacteria under investigation by Bradley Moore’s group (Project 2). Current collaborators for this work include Alvina Mehinto and Keith Maruya of the Southern California Coastal Water Resources Project.

Introduction to Project 3 investigators:

Dr. Lihini I. Aluwihare, Project 3 Co-Leader. 

Dr. Aluwihare is associate professor of Marine Chemistry at UC San Diego’s Scripps Institution of Oceanography. Dr. Aluwihare also serves as the Center Co-Director and the Director for the Center’s Analytical Facility. Dr. Aluwihare’s expertise is in marine organic biogeochemistry and isotope geochemistry and her work is primarily funded by NSF_OCE. 

For more information see


Dr. Eunha Hoh is a Project 2 Co-Leader.

Dr. Hoh is associate professor of Environmental Health at the SDSU School of Public Health. Her expertise is in environmental chemistry focusing on fate and exposure assessment of organic contaminants and discovery of novel contaminants in environments.

For more information, see

Other P3 participants include Nellie Shaul, an SIO graduate students who’s initial work in this areas formed the basis for this Center, Susie Mackintosh, a post doc who has expertise in analysis of organic contaminants including PBDEs in various matrices.