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 Profiler
BACI – Before/After Control/Impact
BOD – Biochemical Oxygen Demand
BRI – Benthic Response Index
CFU – Colony Forming Units
CTD – Instrument that measures conductivity, temperature, and depth
DIC – Disolved Inorganic Carbon
DNA – Deoxyribonucleic Acid
EC – Enterococci
EPA – Environmental Protection Agency
FC – Fecal Coliforms
FIB – Fecal Indicator Bacteria
FIB – Fecal Indicator Bacteria
FVCOM – Finite Volume Calculation Ocean Model
GPS – Global Positioning System
ITI – Infaunal Trophic Index
MDS – Multivariate Multidimensional Scaling
NDBC – National Data Buoy Center
MGD – Millions of Gallons per Day
MMS – Minerals Management Service
MPN – Most Probable Numbers
MST – Microbial Source Tracking
NCEX – Nearshore Canyon Experiment
NOAA – National Oceanic and Atmosphere Administration
NPDES – National Pollution Discharge Elimination System
OCSD – Orange County Sewage District
PAHS – Polyaromatic Hydrocarbons
PCBs – Polychlorinated Biphenyls
PCR – Polymerase Chain Reaction
PLOO – Point Loma Ocean Outfall
POM – Princeton Oceanographic Model
Pycnocline – A region of the water column that has a strong vertical density gradient
RNA – Ribonucleic Acid
ROMS – Regional Ocean Modeling System
SBC–SMB – Santa Barbara Channe –Santa Maria Basin
SBOO – South Bay Ocean Outfall
SCB – Southern California Bight
SCCWRP – Southern California Coastal Water Resources Project
SDCOOS – San Diego Coastal Ocean Observing System
SICS – Sand Island Ocean Outfall Chlorination Study
SIO – Scripps Institution of Oceanography
SWRCB - State Water Resources Control Board
TCV – Total Coliforms
TN – Total Nitrogen
1
TOC – Total Organic Carbon
T-S– Temperature–Salinity
ZID – 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). Swimmingassociated 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 highfrequency 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):293311.
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.). Deepsea 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
Systems, 36, 51–74.
12
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 19791980, 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.
13