Appendix IB

Protein Biomarkers.

Cytochrome P450 monooxygenases are a family of proteins involved in biotransformation of organic chemicals. These are often induced by specific hydrocarbon compounds - aromatic (PAH) or halogenated (e.g., PCP) hydrocarbons. These are mainly assayed in fish. Measures include (1) Catalytic (MFO) enzyme activity in fish liver. EROD and AHH activities are selectively induced. (2) Antibodies to P450; these can reveal the cell types where induction occurs, showing route of exposure and (3) DNA probes. A cDNA probe for fish PAH-inducible P450 has been generated. Response of cytochrome P450 monooxygenases is rapid, up to 6 to 24 h after exposure, with decay rate variable from days to weeks. Detection provides a clear sign that exposure to biochemically significant levels of inducer has occurred.

Metallothioneins are metal binding proteins that sequester and metabolize heavy metals. They are induced by both essential and nonessential toxic heavy metals. Their synthesis can be induced by Cd, Cu, Zn, Hg, Co, Ni, Bi and Ag, as well as others. Function of these proteins is poorly known however, so it is not possible to link levels to injury at the cellular level. They are though to be involved in metal detoxification, regulation of Zn and Cu (for nucleic acid metabolism, protein synthesis etc.), donation of metals to metallo proteins. Stress-related increase in metalothioneins occurs, and is mediated by hormones.

This biomarker seems to be more effective in fish than invertebrates as an assay of metal exposure. However, liver metal concentrations in fish around an outfall were low, despite high metal concentrations in sediments and water borne particulates (Brown et al. 1987). There are advantages to studying these metal-binding proteins over measuring tissue concentrations of metals. Knowledge of intracellular metal compartmentation is essential to understanding mechanisms of injury. Typically it is the non-bound metals that are causing the injury, and metallothionein induction is a protective cellular response. Metal toxicity usually only occurs after the protective capacity is exceeded. Assay mechanisms are rather complicated. They include immuno-affinity chromatography/AAS or ICP MS.

Stress/heat shock proteins reflect changes in gene expression in response to environmental variables. They may protect the cell from damage resulting from environmental perturbations or regulate genes, but not much is known about environmental relevance. Inducers can include heat, metals, xenobiotics and anoxia. Heat shock proteins hsp 90 and hsp70 are not considered here, as heat is not an outfall issue. Glucose related proteins may be assayed by protein-specific antibodies or cDNA probes.

Phase II enzymes - act in detoxification and excretion of foreign compounds (ie metabolites from cytochrome P450), linking them to water-soluble endogenous compounds. These include glutathione transferases, epoxide hydrolase (which have little evidence of chemical induction in aquatic species), UDP-Glucuronosyltransferases, and

sulfotransferases. Overall, results are not consistent enough for use of Phase II enzymes as biomarkers.

Oxidant-mediated responses act to enhance production of oxyradicals in cells, causing induction of antioxidant enzymes, changing concentrations of other antioxidants, or producing lesions. Key antioxidant enzymes include superooxide dismutase (SOD), Catalase (CAT), perioxidase (Px), Glutathione reductase (GR) and DT diaphorase. SODs are highly inducible - but use as a biomarker is speculative. There are also biochemical indices of oxidative damage. These incude lipid peroxidation, DNA oxidation, methemoglobinemia and redox status.

Heme/porphyrin synthesis is sensitive to organic and inorganic chemicals. Disruption in the pathway can cause cell injury.

Vitellogenin. Vitellogenin (Vg) is an egg yolk precursor protein that is typically expressed only in female fish and is dormant in male fish. It is synthesized by the liver of oviparous fish in response to estradiol stimulation. The blood carries Vg to the ovary, where it is sequestered by oocytes to form the yolk. The presence of vitellogenin in the plasma is indicative of estrogenic stimulation of the liver. When male fish are exposed to estrogenic endocrine disruptors the Vg gene is expressed in a dose-dependent manner. Thus, Vg gene expression in male fish can be used as a molecular marker of exposure to estrogenic EDCs, which often occur in sewage effluent. In most cases feminization results appear to be irreversible (Rodgers Gray 2001). A reverse transcription quantitative polymerase chain reaction (RT-QPCR) is used to quantify Vg gene expression. To study EDC exposure Vg could be measured in caged fish (e.g., Purdom et al. 1993) or in field caught specimens (Lye et al. 1998), although their migration history would be unknown.

Most of these biomarkers may be best used in combination. There are strong linkages between classes of biomarkers. Understanding the nature of linkage may be essential to evaluating higher-order effects.

2

Acronym & Definition List

ADCP – Acoustic Doppler Current ProfilerBACI – Before/After Control/ImpactBOD – Biochemical Oxygen DemandBRI – Benthic Response IndexCFU – Colony Forming Units CTD – Instrument that measures conductivity, temperature, and depthDIC – Disolved Inorganic CarbonDNA – Deoxyribonucleic AcidEC – Enterococci EPA – Environmental Protection AgencyFC – Fecal Coliforms FIB – Fecal Indicator Bacteria FIB – Fecal Indicator BacteriaFVCOM – Finite Volume Calculation Ocean ModelGPS – Global Positioning SystemITI – Infaunal Trophic IndexMDS – Multivariate Multidimensional Scaling NDBC – National Data Buoy CenterMGD – Millions of Gallons per DayMMS – Minerals Management Service MPN – Most Probable Numbers MST – Microbial Source Tracking NCEX – Nearshore Canyon ExperimentNOAA – National Oceanic and Atmosphere AdministrationNPDES – National Pollution Discharge Elimination SystemOCSD – Orange County Sewage DistrictPAHS – Polyaromatic HydrocarbonsPCBs – Polychlorinated BiphenylsPCR – Polymerase Chain ReactionPLOO – Point Loma Ocean OutfallPOM – Princeton Oceanographic ModelPycnocline – A region of the water column that has a strong vertical density gradientRNA – Ribonucleic AcidROMS – Regional Ocean Modeling SystemSBC–SMB – Santa Barbara Channe –Santa Maria Basin SBOO – South Bay Ocean Outfall SCB – Southern California BightSCCWRP – Southern California Coastal Water Resources ProjectSDCOOS – San Diego Coastal Ocean Observing SystemSICS – Sand Island Ocean Outfall Chlorination StudySIO – Scripps Institution of OceanographySWRCB - State Water Resources Control Board TCV – Total Coliforms TN – Total Nitrogen

1

TOC – Total Organic Carbon T-S– Temperature–SalinityZID – Zone of Initial Dilution

2

References

Alexander, C. R., & Venherm, C. (2003). Modern sedimentary processes in the

Santa Monica, California continental margin: Sediment accumulation, mixing and

budget. Marine Environmental Research, 56, 177—204.

Alexander, C. R., Nittrouer, C. A., & DeMaster, D. J. (1991). Sediment

accumulation in a modern epicontinental shelf setting: The Yellow Sea. Marine Geology,

98, 5172.

Bayona, J.M., N. Chalaux, J.H. Dachs, C. Maldonado, M.I. Venkatesan, & J.

Albaiges. (1997). Use of trialkylamines as a marker of sewage addition into the marine

environment. pp261-275. In Eganhouse, R.P. (ed. ) Molecular markers in Environmental

Geochemistry. American Chemical Society.

Bergen, M., Cadien, D., Dalkey, A., Montagne, D., Smith, R., Stull, J., Velarde,

R., Weisberg, S. (1999) Assessment of benthic infauna on the mainland shelf of Southern

California. in Southern California Coastal Water Research Project Annual Report 1997–

1998, eds. S. B. Weisberg and D. Hallock, 143–154.

Bernhard, A. E., & Field, K. G. (2000a). A PCR assay to discriminate human and

ruminant feces on the basis of host differences in Bacteroides–Prevotella genes encoding

16S rRNA. Applied and Environmental Microbioliology, 66, 4571–4574.

Bernhard, A. E., & Field, K. G. (2000b). Identification of nonpoint sources of

fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic

markers from fecal anaerobes. Applied and Environmental Microbioliology, 66, 1587–

1594.

Blackstone, G. M., Nordstrom, J. L., Vickery, M. C. L., Bowen, M. D., Meyer, R.

F. & DePaola. A. (2003). Detection of pathogenic Vibrio parahaemolyticus in oyster

enrichments by real time PCR. Journal of Microbiological Methods, 53, 149–155.

Boehm, A. B., Grant, S. B., Kim, J. H., Mowbray, S. L., McGee, C. D. Clark, C.

D. Foley, D. M., & Wellman. D. E. (2002). Decadal and shorter period variability of surf

zone water quality at Huntington Beach, California. Environmental Science &

Technology, 36, 3885–3892.

1

Brasher, C. W., De Paola, A., Jones, D. D., & Bej, A. K. (1998). Detection of

microbial pathogens in shellfish with multiplex PCR. Current Microbiology, 37, 101–

107.

Brown, D.A., Bay, S.M., Greenstein, D.J., Szalay, P., Hershelman, G.P., Ward,

C.F., Westcott, A.M., & Cross, J.N. (1987). Municipal wastewater contamination in the

Southern California Bight: Part II. Cystolic distribution of contaminants and biochemical

effects in fish livers. Marine Environmental Research, 21:135-161.

Cabelli, V. J. (1983a). Health effects criteria for marine recreational waters.

Environmental Protection Agency, 600/1-84-004, 7.

Cabelli, V. J. (1983b). A marine recreational water quality criterion consistent

with indicator concepts and risk analysis. Journal of the Water Pollution Control

Federation, 55, 1306–1314.

Cabelli, V. J., Dufour, A. P., Levin, M. A., & McCabe, L. J. (1982). Swimming-

associated gastroenteritis and water quality. American Journal of Epidemiology, 115,

606–616.

Campbell, M. S., & Wright, A. C. (2003). Real-time PCR analysis of Vibrio

vulnificus from oysters. Applied and Environmental Microbiology, 69, 7137–7144.

Chadwick, D. B., & Largier, J. L. (1999). Tidal exchange at the bay–ocean

boundary. Journal of Geophysical Research, 104(C12), 29,901–29,919.

City of San Diego Metropolitan Wastewater and Southern California Coastal

Water Research Project. (2004). San Diego sediment mapping study: Workplan for

generating scientifically defensible maps of sediment condition in the San Diego region.

San Diego, CA: City of San Diego.

Clarke, K. R., & Ainsworth, M. (1993). A method of linking multivariate

community structure to environmental variables. Marine Ecology Progress Series, 92,

205–219.

Csanady, G. T. (1983a). Dispersal by randomly varying currents. Journal of Fluid

Mechanics, 132, 375–394.

Csanady, G. T. (1983b). Advection, diffusion, and particle settling. In E. P. Myers

& E. T. Harding (Eds.), Ocean disposal of municipal wastewater: Impacts on the coastal

environment (pp. 177–246). Cambridge, MA: The MIT Press.

2

Dayton P. K., Tegner, M. J., Parnell, P. E., & Edwards. P. B. (1992). Temporal

and spatial patterns of disturbance and recovery in a kelp forest community. Ecological

Monographs 62:421-445

Dayton, P. K., Tegner, M. J., Edwards, P. B., & Riser, K. L. (1999).Temporal and

spatial scales of kelp demography: The role of oceanographic climate. Ecological

Monographs vol. 69:2, 219-250.

de Besten, P.J. (1998). Concepts for the implementation of biomarkers in

environmental monitoring. Marine Environmental Research, 46:253-256.

DeMaster, D. J., Brewster, D. C., McKee, B. A., Nittrouer, C. A. (1991). Rates of

particle scavenging, sediment reworking, and longitudinal ripple formation at the

HEBBLE site based on measurements of 234Th and 210Pb. Marine Geology, 99:423-444

Desmond, J., Williams, G., James, M., Johnson, J., Callaway, J., Zedler, J. (1999).

Tijuana River National Estuarine Research Reserve: Annual report on ecosystem

monitoring. Report to NOAA National Ocean Service, Sanctuaries and Programs

Division

Dever, E. P., M. C. Hendershott, et al. (1998). "Statistical aspects of surface

drifter observations of circulation in the Santa Barbara Channel." Journal of Geophysical

Research-Oceans 103(C11): 24781-24797.

DiBacco, C., & Chadwich, C., (2001). Assessing the dispersal and exchange of

brachyuran larvae between regions of San Diego Bay, California and nearshore coastal

habitats using elemental fingerprinting. Journal of Marine Research, 59(1), 53–78.

Dorman, C. E., & C. D. Winant, (2000). The structure and variability of the

marine atmosphere around the Santa Barbara Channel, Mon. Weather Review, Vol. 128,

No. 2, 261-282.

Dufour, A. P. (1984). Bacterial indicators of recreational water quality. Canadian

Journal of Public Health, 75, 49–56.

3

Dunbar, S. A., Vander Zee, C. A., Oliver, K. G., Karem, K. L., & Jacobson, J. W.

(2003). Quantitative, multiplexed detection of bacterial pathogens: DNA and protein

applications of the Luminex LabMAP (TM) system. Journal of Microbiological Methods,

53, 245–252.

Eaton, A. D., Clesceri, L. S., & Greenberg, A. E. (Eds.). (1998). Standard

methods for the examination of water and wastewater (20th ed.). Baltimore, MD:

American Public Health Association, American Water Works Association, Water

Environment Federation.

Eganhouse, R.P. (ed.) (1997). Molecular markers in Environmental

Geochemistry. American Chemical Society.

Esser, B., Volpe, A. (2002). At-sea high-resolution trace element mapping: San

Diego Bay and its plume in the adjacent coastal ocean. Environmental Science &

Technology, 36(13):2826-2832.

Fairey, R., Roberts, C., Jacobi, M., Lamerdin, S., Clark, R., Downing, J.,

Long, E., Hunt, J., Anderson, B., Newman, J., Tjeerdema, R., Stephenson, M., &

Wilson, C. (1998). Assessment of sediment toxicity and chemical concentrations in the

San Diego Bay region, California, USA. Environmental Toxicology and Chemistry,

SETAC Press. Toxicology and Chemistry, 17(8)1570-1581

Field, K. G., Bernhard, A. E., & Brodeur, T. J. (2003). Molecular approaches to

microbiological monitoring: Fecal source detection. Environmental Monitoring and

Assessment, 81, 313–326.

Fricker, E. J., & Fricker, C. R. (1994). Application of the polymerase chain

reaction to the identification of Escherichia coli and coliforms in water. Letters in

Applied Microbiology, 19, 44–46.

Gardner J. V., Butman, P. B., Mayer, L. A., & Clarke J. H. (1998). Mapping U.S. continental shelves. Sea Technology, 39 (6), 10–17.

Gersberg, R. M., Trindade, F., & Nordby, C. (1989). Heavy metals in sediments

and fish of the Tijuana Estuary. Journal of Border Health, 5, 5–15.

Griffin, D. W. (2001). Microbial public health indicators in the marine

environment. pp. 541-558. In J. H. Paul (ed.), Methods in Microbiology, Marine

Microbiology, vol. 30. Academic Press.

4

Griffin, D. W., Donaldson, K. A., Paul, J. H., & Rose, J. B. (2003). Pathogenic

human viruses in coastal waters. Clinical Microbiology Reviews, 16, 129–143.

Griffin, D. W., Lipp, E. K., McLaughlin, M. R., & Rose, J. B. (2001). Marine

recreation and public health microbiology: Quest for the ideal indicator. BioScience, 51,

817–825.

Griffith, J. F., Weisberg, S. B., & McGee, C. D. (2003). Evaluation of microbial

source tracking methods using mixed fecal sources in aqueous test samples. Journal of

Water and Health, 01.4, 141–151.

Harms, S. & C. D. Winant,. (1998). Characteristic patterns of the circulation in

the Santa Barbara Channel, J. Geophys. Res. 103(C2), 3041-3065.

Haile, R. W., Witte, J. S., Gold, M., Cressey, R., McGee, C., Millikan, R. C.,

Glasser, A., Harawa, N., Ervin, C., Harmon, P., Harper, J., Dermand, J., Alamillo, J.,

Barrett, K., Nides, M., & Wang, G. Y. (1999). The health effects of swimming in ocean

water contaminated by storm drain runoff. Epidemiology, 10, 355–363.

Hsu, F. C., Shieh, Y. S. C., Vanduin, J., Beekwilder, M. J., & Sobsey, M. D.

(1995). Genotyping male-specific RNA coliphages by hybridization with oligonucleotide

probes. Environmental Microbiology, 61, 3960–3966.

Huggett, R., Kimrle, P., Mehrle, P., & Bergman, H. (eds.). (1992). Biomarkers:

Biochemical, Physiological and Histological Markers of Anthropogenic Stress. Lewis

Publications.

Inman, D. (1976). Man’s impact on the California coastal zone. Dept. of

Navigation and Ocean Development, State of California – The Resources Agency.

Jiang, S. (2001). Vibrio cholerae in recreational beach waters and tributaries of

Southern California. Hydrobiologia, 460, 157–164.

Jiang, S., Chu, W. P., & Fu, W. X. (2003). Prevalence of cholera toxin genes

(ctxA and zot) among non-O1/O139 Vibrio cholerae strains from Newport Bay,

California. Applied and Environmental Microbiology, 69, 7541–7544.

Jiang, S., Noble, R., & Chui, W. (2001). Human adenoviruses and coliphages in

urban runoff-impacted coastal waters of Southern California. Applied and Environmental

Microbiology, 67, 179–184.

5

Jiang, S. C., & Fu, W. (2001). Seasonal abundance and distribution of Vibrio

cholerae in coastal waters quantified by a 16S-23S intergenic spacer probe. Microbial

EcolOgy, 42, 540–548.

Kaufman, G. E., Myers, M. L., Pass, C. L., Bej, A. K., & Kaysner, C. A. (2002).

Molecular analysis of Vibrio parahaemolyticus isolated from human patients and

shellfish during U.S. Pacific north-west outbreaks. Letters in Applied Microbiology,

34,155–161.

Kim, J. H., & Grant, S. B. (2004). Public mis-notification of coastal water quality:

A probabilistic evaluation of posting errors at Huntington Beach, California.

Environmental Science & Technology, 38, 2497–2504.

Kloepper-Sams, P. J., & Stegeman, J. J. (1992). Effects of temperature

acclimation on the expression of hepatic cytochrome P450 1A mRNA and protein in the

fish Fundulus heteroclitus. Archives of BiochemIstry and Biophysics, 299, 38–46.

Lam, P. K. S., & Gray, J. (2003). The use of biomarkers in environmental

monitoring programmes. Marine Pollution Bulletin, 46, , 182–186.

Largier, J., Rasmussen, L., Carter, M., & Scearce, C., in prep. Evaluation of the

South Bay International Wastewater Treatment Plant receiving water quality monitoring

program to determine its ability to identify source(s) of recorded bacterial exceedences,

EPA, Region IX, San Francisco, CA

Leeming, R., Latham V., Rayner, M. & Nichols, P. (1997). Detecting and

distinguishing sources of sewage pollution in Australian inland and coastal waters and

sediments. pp. 306-319 In Eganhouse, R.P. (ed. )1997. Molecular markers in

Environmental Geochemistry. American Chemical Society.

Lennert-Cody, C. E., & Franks, P. J. S. (1999). Plankton patchiness in high-

frequency internal waves. Marine Ecology—Progress Series, 186, 59–66.

Lucena, F., Araujo, R., & Jofre, J. (1996). Usefulness of bacteriophages infecting

Bacteroides fragilis as index microorganisms of remote fecal pollution. Water Research,

30, 2812–2816.

Lye, C.M., Frid C. L. J., & Gill, M. E. (1998). Seasonal reproductive health of

flounder Platichthys flesus exposed to sewage effluent ,MEPS 170:249-260.

6

Lyne, V. D., Butman, B., & Grant, W. D. (1987). Sediment movement along the

U.S. east coast continental shelf: II. Modeling suspended sediment concentration and

transport rate during storms. Continental Shelf Research, 10, 429–461.

Lyon, W. J. (2001). TaqMan PCR for detection of Vibrio cholerae O1, O139,

non-O1, and non-O139 in pure cultures, raw oysters and synthetic seawater. Applied and

Environmental Microbiology , 67, 4685–4693.

Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of

microorganisms. Upper Saddle River, NJ: Prentice Hall.

McCain, B., Chan, S., Krahn, M., Brown, D., Myers, M., Landahl, J., Pierce, S.,

Clark, R., & Varanasi, U. (1992). Chemical contamination and associated fish diseases

in San Diego Bay. Environmental Science & Technology, 26(4)725-733.

McKenney, C.L., Weber D.E., Celestial, D., & MacGregor, M.A. (1998). Altered

growth and metabolism of an estuarine shrimp, Palaemonetes pugio, during and after

metamorphosis onto fenvalerate-laden sediment. Arch. Environmental Contamination

and Toxicology, 35:464-471.

Mearns, A. J., M. Matta, G., Shigenaka, D., MacDonald, M., Buchman, H.,

Harris, J., Golas, & Lauenstein, G. (1991). Contaminant trends in the Southern California

Bight: Inventory and assessment. NOAA Technical Memorandum NOS ORCA 62.

Meyer, S. F., & Gersberg, R. M. (1997). Heavy metals and acid-volatile sulfides

in sediments of the Tijuana Estuary. Bulletin of Environmental Contamination and

Toxicology, 59, 113–119.

Miyagi, K., Omura, K., Ogawa, A., Hanafusa, M., Nakano, Y., Morimatsu, S., &

Sano, K. (2001). Survival of Shiga toxin-producing Escherichia coli O157 in marine

water and frequent detection of the Shiga toxin gene in marine water samples from an

estuary port. Epidemiology & Infection, 126, 129–133.

Morris, J. G., Jr. (2003). Cholera and other types of vibriosis: A story of human

pandemics and oysters on the half shell. Clinical Infectious Diseases, 37, 272–280.

Mourino-Perez, R. R., Worden, A. Z., & Azam. F. (2003). Growth of Vibrio

cholerae O1 in red tide waters off California. Applied and Environmental Microbiology,

69, 6923–6931.

7

Mouzin, E., Mascola, L., Tormey, M. P., & Dassey, D. E. (1997). Prevention of

Vibrio vulnificus infections—Assessment of regulatory educational strategies. The

Journal of American Medical Association, 278, 576–578.

NCEX, http://science.whoi.edu/users/elgar/NCEX/ncex.html

Nittrouer, C. A., Sternberg, R. W., Carpenter, R., & Bennett, J. T. (1979). The use

of 210Pb geochronology as a sedimentological tool: Application to the Washington

continental shelf. Marine Geology., 31, 297–316.

Nittrouer, C. A., DeMaster, D. J., McKee, B. A., Cheng, G., & Qian, J. (1983).

Formation of sedimentary strata in the East China Sea. InSedimentation on the

continental shelf with special reference to the East China Sea (pp. 696–704). New York:

Springer-Verlag.

Noda, Edward K. & Associates, Inc., (1999). Sand Island Chlorination Study,

Sand Island Ocean Outfall, O'ahu, Hawai'i, Prepared for the City and County of

Honolulu, Dept. of Wastewater Management.

Noble, R. T., & Fuhrman, J. A. (2001). Enteroviruses detected by reverse

transcriptase polymerase chain reaction from the coastal waters of Santa Monica Bay,

California: Low correlation to bacterial indicator levels. Hydrobiologia, 460, 175–184.

Noble, R. T., Moore, D. F., Leecaster, M. K., McGee, C. D., & Welsberg, S. B.

(2003). Comparison of total coliform, fecal coliform, and enterococcus bacterial indicator

response for ocean recreational water quality testing. Water Research, 37, 1637–1643.

Noble, R. T., Weisberg, S. B., Leecaster, M. K., McGee, C. D., Ritter, K. Walker,

K. O., & Vainik, P. (2003). Comparison of beach bacterial water quality indicator

measurement methods. Environmental Monitoring and Assessment, 81, 301–312.

Oberdorster, E., & Cheek, A. O. (2000). Gender benders at the beach: Endocrine

disruption in marine and estuarine organisms. Environmental Toxicology and Chemistry,

20, 23–36.

Oey, L.-Y., Wang, D.-P., Hayward, T., Winant, C., & Hendershott, M. (2001).

Upwelling and cyclonic regimes of the near-surface circulation in the Santa Barbara

Channel. Journal of Geophysical Research, 106(C5), 9213–9222

8

Oey, L.-Y., C. Winant, E. Dever, W. Johnson & D. P. Wang (2004). A model of

the near-surface circulation of the Santa Barbara Channel: comparison with observations

and dynamical interpretation. J. Phys. Oceanogr., 34(1), 23 – 43.

Parnell, P.E. (2001). The distribution of estuarine and oceanic water masses on

the southern shore of O'ahu, Hawai'i: Ecological and coastal management implications,

and novel methodology. Limnology and Oceanography, 46(6):1468-1485.

Parnell, P. E. (2003). The effects of sewage discharge on water quality and

phytoplankton of Hawai'ian coastal waters. Marine Environmental Research, 55(4):293-

311.

Parnell, P., Lennert-Cody, C., & Dayton, P. in prep. Recommendations for a

marine reserve in La Jolla based on spatial patterns of habitat, diversity, and

oceanographic climate.

Penland, R. L., Boniuk, M., & Wilhelmus, K. R. (2000). Vibrio ocular infections

on the U.S. Gulf Coast. Cornea, 19, 26–29.

Petrenko, A. A., Jones, B. H., Dickey, T. D., et al. (1997). Effects of a sewage

plume on the biology, optical characteristics, and particle size distributions of coastal

waters. Journal of Geophysical Research—Oceans, 102 (C11), 25061–25071.

Petrenko, A. A., Jones, B. H., Dickey, T. D., et al. (2000). Internal tide effects on

a sewage plume at Sand Island, Hawaii. Continental Shelf Research, 20(1), 1–13.

Phillips, C.R., Venkatesan , M. I. & Bowen, R.. (1997). Interpretations of

contaminant sources to San Pedro Shelf sediments using molecular markers and principal

component analysis. pp. 242-260 In. Eganhouse, R.P. (ed. ) (1997). Molecular markers in

Environmental Geochemistry. American Chemical Society.

Pineda, J. (1994). Internal tide bores in the nearshore—Warm-water fronts,

seaward gravity currents and the onshore transport of neustonic larvae. Journal of Marine

Research, 52(3), 427–458.

Pineda, J. (1999). Circulation and larval distribution in internal tidal bore warm

fronts. Limnology and Oceanography, 44(6), 1400–1414. 

Portillo-López, A., & M. L. Lizárraga-Partida. (1997). Detection of Vibrio

cholerae 01 in different habitats of Todos Santos Bay, Baja California, Mexico. Ciencias

Marinas 23:435-447.9

Purdom, C.E., Hardiman, P.A., Bye, V.J., Eno, N.C., Tyler, C.R. & Sumpter, J.P.

(1994). Estrogenic effects of the effluent from sewage treatment works. Chemistry and

Ecology, 8: 275-285.Portillo-López, A., & Lizárraga-Partida, M. L. (1997). Detection of

Vibrio cholerae 01 in different habitats of Todos Santos Bay, Baja California, Mexico.

Ciencias Marinas, 23, 435–447.

Pringle, J. M., & Riser, K. (2003). Remotely forced nearshore upwelling in

Southern California. Journal of Geophysical Research, 108, 3131.

Reemtsma, T., I. Savric, C. Hartig, & M. Jekel. (1997). Linear

alkylbenzenesulfonates and polychlorinated biphenyls as indicators of accumulation,

biodegradation and transport processes in sewage farm soils. ch. 14 pp 213-230 IN:

Eganhouse, R.P. (ed. ) Molecular markers in Environmental Geochemistry. American

Chemical Society.

Rehnstam, A.-S., Backman, S., Smith, D. C., Azam, F., & Hagstrom, A. (1993).

Blooms of sequence-specific culturable bacteria in the sea. FEMS Microbiology Ecology,

102, 161–166.

Rhoads, D. C., & Young, D. K. (1970). The influence of deposit-feeding

organisms on sediment stability and community trophic structure. Journal of Marine

Research, 28, 150–178.

Roberts, P. J. W. (1999a). Modeling the Mamala Bay outfall plumes: I. Near field.

Journal of Hydraulic Engineering, 125, 564–573.

Roberts, P. J. W. (1999b.) Modeling the Mamala Bay outfall plumes: II. Far field.

Journal of Hydraulic Engineering, 125, 574–583.

Roberts, P. J. W., Snyder, W. H., & Baumgartner, D. J. (1989a). Ocean outfalls: I.

Submerged wastefield formation. Journal of Hydraulic Engineering, 115, 1–25.

Roberts, P. J. W., Snyder, W. H., & Baumgartner, D. J. (1989b). Ocean outfalls:

II. Evolution of submerged wastefield. Journal of Hydraulic Engineering, 115, 26–48.

Rodgers-Gray T.P., Jobling, S. , Kelly, C., Morris, S., Brighty, G., Waldock, M.

J., Sumpter, J.P., & Tyler, C. R. (2001). Exposure of juvenile roach (Rutilus rutilus) to

treated sewage effluent induces dose-dependent and persistent disruption in gonadal duct

development. Environal Science & Technology. 35(3): 462-70.

10

Roszak, D. B., & Colwell, R. R. (1987). Survival strategies of bacteria in the

natural environment. Microbial Review, 51, 531–538.

San Diego Bay Interagency Water Quality Control Board. (1994). San Diego Bay

1992 Annual Report. AB 158. Technical Rpt., California State Water Resources Control

Board.

Science Applications International Corporation. (2001). Strategic process study

No. 1: Plume tracking—Ocean currents. Final Report to Orange County Sanitation

District.

Science Applications International Corporation. (2002). Nearfield and particle

tracking model report. Report submitted to Orange County Sanitation District.

Schiff, K., Allen, M., Zeng, E., & Bay, S. (2000). Southern California. Marine

Pollution Bulletin, 41(1-6):76-93.

Smith, C.R., Pope, R.H., DeMaster, D.J., & Magaard, L. (1992). Age-dependent

mixing of deep-sea sediments. Geochemica Cosmochimica Acta, 57:1473-1488.

Smith, A. W., Skilling, D. E., Cherry, N., Mead, J. H., & Matson, D. O. (1998).

Calicivirus emergence from ocean reservoirs: Zoonotic and interspecies movements.

Emerging Infectious Diseases,4:13-20.

Smith, C. R. (1992). Factors controlling bioturbation in deep-sea sediments and

their relation to models of carbon diagenesis. In G. T. Rowe & V. Pariente (eds.). Deep-

sea food chains and the global carbon cycle (pp. 375–393). New York: Kluwer.

Southern California Coastal Water Research Project,

http://www.sccwrp.org/about/rspln2004-2005.html#e1

Southern California Coastal Water Research Project, 1990, Annual Report

1989-1990.

Southern California Coastal Water Research Project, 1992, Annual Report

1991-92

State Water Resources Control Board. (1995). State mussel watch program:

1987-1993 data report. California Environmental Protection Agency, Sacramento, CA

11

Stegeman, J., Brouwer, M., Digiulio, R.T., Forlin, L., Fowler, B.A., Sanders, B.,

& VanVeld, P. (1992). Molecular responses to environmental contamination: enzyme and

protein systems as indicators of chemical exposure and effect. In: Biomarkers:

Biochemical, Physiological and Histological Markers of Anthropogenic Stress. R.

Huggett, R. Kimerle, P. Mehrle, & H. Bergman (eds.). Lewis Publications.

Stoll, J.M.A, Poiger, T.F., Lotter, A.F., Sturm, M., & Giger, W. (1997).

Fluorescent whitening agents as molecular markers for domestic wastewater in recent

sediments of Greifensee, Switzerland. pp. 231-241 IN Eganhouse, R.P. (ed. ) Molecular

markers in Environmental Geochemistry. American Chemical Society.

Strom, M. S., & Paranjpye, R. N. (2000). Epidemiology and pathogenesis of

Vibrio vulnificus. Microbes & Infection, 2, 177–188.

Stull, J.K. (1995). Two decades of marine biological monitoring, Palos Verdes,

California, 1972 to 1992. Bulletin of the Southern California Academy of Sciences,

94(1):21–45.

Takada, H., Satoh, F., Bothner, M.H., Tripp, B.W., Johnson, C.G. & Farrington,

J.W. (1997). Anthropogenic molecular markers: Tools to identify the sources and

transport pathways of pollutants. P178-195 In. Eganhouse, R.P. (ed.) (1997). Molecular

markers in Environmental Geochemistry. American Chemical Society.

Thompson, B. & Bergen, M. (1993). Population biology of the brittlestar

Amphiodia urtica. In: Southern California Coastal Water Research Project Annual

Report (1992-93).

Thompson, B. E., Tsukada, D. & O’Donohue, D. (1993). 1990 Reference Survey

(Contribution No. 355). Southern California Coastal Water Research Project,

Westminster, California.

Vetter, E. W. & Dayton, P. K. (1999). Organic enrichment by macrophyte detritus,

and abundance patterns of megafaunal populations in submarine canyons. Marine

Ecology Progress Series, 186, 137–148.

Volpe, A. M. & Esser, B. K. (2002). Real-time ocean chemistry for improved

biogeochemical observation in dynamic coastal environments. Journal of Marine

12

Systems, 36, 51–74.

Wagner, P. D., Evans, S. D., Dunlap, J., & Ballon-Landa, G. (1995). Necrotizing

fasciitis and septic shock caused by Vibrio cholerae acquired in San Diego. Western

Journal of Medicine, 163, 375–378.

Wheatcroft, R. A., & Martin, W. R. (1996). Spatial variation in short-term

(super(234)Th) sediment bioturbation intensity along an organic-carbon gradient. Journal

of Marine Research, 54(4), 763–792.

Winant, C.D., Alden, D.J., Dever, E.P., Edwards, K.A. & Hendershott, M.C.

(1999) Near-surface trajectories off central and southern California, J. Geophys. Res.

104(C7): 15,713-15,726.

Winant, C. D., Dever, E. P. & Hendershott, M. C. (2003). Characteristic patterns

of shelf circulation at the boundary between central and southern California. Journal of

Geophysical Research, 108(C2), 3021.

Word, J. (1978). The infaunal trophic index. In Coastal Water Research Project

annual report, ed. W. Bascom, pp. 19-39. Southern California Coastal Water Research

Project.

Word, J. (1980). Classification of benthic invertebrates into infaunal trophic index

feeding groups. In: Coastal Water Research Project, biennial report for the years 1979-

1980, W. Bascom (ed.), pp.103-121. Southern California Coastal Water Research Project.

Wu, Y., Washburn, L. & Jones, B. H. (1994). Buoyant plume dispersion in a

coastal environment: Observations of plume structure and dynamics. Continental Shelf

Research 14:1001-1023.

Yang, L., Tran, D. K., & Wang, X. (2001). BADGE, BeadsArray for the detection

of gene expression, a high-throughput diagnostic bioassay. Genome Research, 11, 1888–

1898.

Yavzori, M., Porath, N. Ochana, O., Dagan, R., Orniwasserlauf, R., & Cohen, D.

(1998). Detection of enterotoxigenic Escherichia coli in stool specimens by polymerase

chain reaction. Diagnostic Microbiology and Infectious Disease, 31, 503–509.

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