Following is a list of publications resulting from research conducted in the ONR Coastal Benthic Optical Properties (CoBOP) program. When the article title is highlighted it means that a pdf version of the paper is freely available at the publisher's web site, reached by the link.
1999
Fux, E., and C. H. Mazel, 1999. Unmixing coral fluorescence emission spectra and predicting new spectra under different excitation conditions. Appl. Opt., 38:486-494.
Decho, A.W., 1999. Imaging an alginate polymer gel matrix using atomic-force microscopy. Carbohydr. Res., 315: 330-333.
Decho, A.W., and T. Kawaguchi. 1999. Confocal Imaging of in situ natural microbial communities and their extracellular polymeric secretions using Nanoplast resin. BioTechniques 27: 1246-1252.
Decho, A.W. 1999. Microbial biofilms in intertidal systems: an overview. Cont. Shelf Res. 20: 1257-1273.
2000
Lesser, M. P., C. H. Mazel, D. Phinney and C. S. Yentsch, 2000. Light absorption and utilization by colonies of the congeneric hermatypic corals, Montastraea faveolata and Montastraea cavernosa. Limnol. Oceanogr., 45:76-86.
Gorbunov, M.Y., P. G. Falkowski and Z. Kolber, 2000. Measurement of photosynthetic parameters in benthic organisms in situ using a SCUBA-based fast repetition rate fluorometer. Limnol. Oceanogr. 45: 242-245.
Lombardi, M. R., M. P. Lesser and M. Y. Gorbunov, 2000. Fast repetition rate (FRR) fluorometry: variability of chlorophyll a fluorescence yields in colonies of the corals, Montastraea faveolata (w.) and Diploria labyrinthiformes (h.) recovering from bleaching. Journal of Experimental Marine Biology and Ecology, 252:75-84.
K. J. Voss, A. Chapin, M. Monti, and H. Zhang, 2000. An instrument to measure the bi-directional reflectance distribution function (BRDF) of surfaces. Appl. Opt., 39:6197 - 6206.
Kawaguchi, T. and A.W. Decho, 2000. Biochemical characterization of cyanobacterial extracellular polymers (EPS). Prep. Biochem. BioTechnol. 30: 321-330.
Hoffman, M., and A.W. Decho, 2000. Proteolytic enzymes in the marine bacterium Pseudoalteromonas atlantica: post-secretional activation and effects of environmental conditions. Aquat. Microb. Ecol. 23: 29-39.
2001
Gorbunov, M. Y., Z. S. Kolber, M. P. Lesser, and P. G. Falkowski, 2001. Photosynthesis and photoprotection in symbiotic corals. Limnol. Oceanogr. 46:75-85.
Lesser, M. P., and M. Y. Gorbunov, 2001. Diurnal and bathymetric changes in chlorophyll fluorescence yields of reef corals measured in situ with a fast repetition rate fluorometer. Mar. Ecol. Prog. Ser., 212:69-77.
VanDuin, E.H.S., G. Bloom, F.J. Los, R. Maffione, R. Zimmerman, C. Cerco, M. Dortch, and E.P.H. Best, 2001. Modeling underwater light climate in relation to sedimentation, resuspension, water quality and autotrophic growth. Hydrobiologia, 44:25-42.
Zaneveld, R., E. Boss and C. Moore, 2001. A diver operated optical and physical profiling system. Jour. of Atmospheric and Oceanic Technology, 18:1421-1427.
Fuchs, E., 2001. Separating the fluorescence and reflectance components of coral spectra. Appl. Opt., 40:3614-3621.
Carder, K. L., D.K. Costello, H. Warrior, L.C. Langebrake, W. Hou, J.T. Patton, and E. Kaltenbacher., 2001. Ocean science mission needs: real-time AUV data for command, control, and model inputs. IEEE Journal of Ocean Engineering 26(4):742-751.
Leathers, R. A., T. V. Downes, and C. D. Mobley, 2001. Self-shading correction for upwelling sea-surface radiance measurements made with buoyed instruments. Optics Express, 8(10):561-570
Kawaguchi, T., and A.W. Decho. 2001. In situ microspatial imaging using two-photon and confocal laser scanning microscopy of bacteria and their extracellular polymeric secretions (EPS). Marine BioTechnol. 4: 127-131.
Kawaguchi, T., and A.W. Decho. 2001. Potential roles of extracellular polymeric secretions (EPS) in regulating calcification. Thalassas 17: 11-19.
2002
Gorbunov, M. Y., and P. G. Falkowski, 2002. Photoreceptors in the cnidarian hosts allow symbiotic corals to sense blue moonlight. Limnol. Oceanogr. 47:309-315.
Davis, C. O., J. Bowles, R. A. leathers, D. Korwan, T. V. Downes, W. A. Snyder, W. J. Rhea, W. Chen, J. Fisher, W. P. Bissett and R. A. Reisse, 2002. Ocean PHILLS hyperspectral imager: design, characterization, and calibration. Optics Express, 10(4):210-221.
Burdige, D.J., and R.C. Zimmerman. 2002. Impact of sea grass density on carbonate dissolution in Bahamian sediments. Limnol. Oceanogr. 47:1751-1763.
Yentsch, C. S., C. M. Yentsch, J. J. Cullen, B. Lapointe, D. A. Phinney and S. W. Yentsch. 2002. Sunlight and water transparency: cornerstones in coral research. Journal of Experimental Marine Biology and Ecology, 268:171-183..
Wheatcroft, R.A. 2002. In situ measurements of near-surface porosity in shallow-water marine sands. IEEE Journal of Oceanic Engineering, 27:561-570.
Louchard, E. M., R. P. Reid, C. F. Stephens, C. O. Davis, R. A. Leathers, T. V. Downes, and R. A. Maffione, 2002. Derivative analysis of absorption features in hyperspectral remote sensing data of carbonate sediments. Optics Express, 10(26):1573-1584.
Kawaguchi, T. and A.W. Decho. 2002. A laboratory investigation of cyanobacterial extracellular polymeric secretions in CaCO3 polymorphism. J. Crystal Growth 240: 230-235.
Kawaguchi, T. and A.W. Decho. 2002. Isolation and biochemical characterization of extracellular polymers (EPS) and their inhibitory effect on CaCO3 precipitation. Prep. Biochem. BioTechnol. 32: 51-63.
Kawaguchi, T. and A.W. Decho. 2002. In situ analysis of carboxyl- and sulfhydral- groups of extracellular polymeric secretions by confocal scanning microscopy. Anal. BioChem. 304: 266-267.
2003
Ackleson, Steven G., 2003. Light in shallow waters: A brief research review. Limnol. Oceanogr. 48:323-328.
Mobley, Curtis D., and Lydia K. Sundman, 2003. Effects of optically shallow bottoms on upwelling radiances: Inhomogeneous and sloping bottoms. Limnol. Oceanogr. 48:329-336.
Mobley, Curtis D., Hao Zhang, and Kenneth J. Voss, 2003. Effects of optically shallow bottoms on upwelling radiances: Bidirectional reflectance distribution function effects. Limnol. Oceanogr. 48:337-345.
Boss, Emmanuel, and J. Ronald V. Zaneveld, 2003. The effect of bottom substrate on inherent optical properties: Evidence of biogeochemical processes. Limnol. Oceanogr. 48:346-354.
Carder, Kendall L., Cheng-Chien Liu, Zhongping Lee, David C. English, James Patten, F. Robert Chen, James E. Ivey, and Curtiss O. Davis, 2003. Illumination and turbidity effects on observing faceted bottom elements with uniform Lambertian albedos. Limnol. Oceanogr. 48:355-363.
Voss, Kenneth J., Curtis D. Mobley, Lydia K. Sundman, James E. Ivey, and Charles H. Mazel, 2003. The spectral upwelling radiance distribution in optically shallow waters. Limnol. Oceanogr. 48:364-373.
Zaneveld, J. Ronald V., and Emmanuel Boss, 2003. The influence of bottom morphology on reflectance: Theory and two-dimensional geometry model. Limnol. Oceanogr. 48:374-379.
Zhang, Hao, Kenneth J. Voss, R. Pamela Reid, and Eric M. Louchard, 2003. Bidirectional reflectance measurements of sediments in the vicinity of Lee Stocking Island, Bahamas. Limnol. Oceanogr. 48:380-389.
Mazel, Charles H., and Eran Fuchs, 2003. Contribution of fluorescence to the spectral signature and perceived color of corals. Limnol. Oceanogr. 48:390-401.
Mazel, Charles H., Michael P. Lesser, Maxim Y. Gorbunov, Thomas M. Barry, Julianne H. Farrell, Kevin D. Wyman, and Paul G. Falkowski, 2003. Green-fluorescent proteins in Caribbean corals. Limnol. Oceanogr. 48:402-411.
Zawada, David G., and Jules S. Jaffe, 2003. Changes in the fluorescence of the Caribbean coral Montastraea faveolata during heat-induced bleaching. Limnol. Oceanogr. 48:412-425.
Decho, Alan W., Tomohiro Kawaguchi, Mead A. Allison, Eric M. Louchard, R. Pamela Reid, F. Carol Stephens, Kenneth J. Voss, Robert A. Wheatcroft, and Brenton B. Taylor, 2003. Sediment properties influencing upwelling spectral reflectance signatures: The “biofilm gel effect”. Limnol. Oceanogr. 48:431-443.
Dierssen, Heidi M., Richard C. Zimmerman, Robert A. Leathers, T. Valerie Downes, and Curtiss O. Davis, 2003. Ocean color remote sensing of seagrass and bathymetry in the Bahamas Banks by high resolution airborne imagery. Limnol. Oceanogr. 48:444-455.
Drake, Lisa A., Fred C. Dobbs, and Richard C. Zimmerman, 2003. Effects of epiphyte load on optical properties and photosynthetic potential of the seagrasses Thalassia testudinum Banks ex König and Zostera marina L. Limnol. Oceanogr. 48:456-463.
Louchard, Eric M., R. Pamela Reid, F. Carol Stephens, Curtiss O. Davis, Robert A. Leathers, and T. Valerie Downes, 2003. Optical remote sensing of benthic habitats and bathymetry in coastal environments at Lee Stocking Island, Bahamas: A comparative spectral classification approach. Limnol. Oceanogr. 48:511-521.
Mazel, Charles H., Michael P. Strand, Michael P. Lesser, Michael P. Crosby, Bryan Coles, and Andrew J. Nevis, 2003. High resolution determination of coral reef bottom cover from multispectral fluorescence laser line scan imagery. Limnol. Oceanogr. 48:522-534.
Stephens, F. Carol, Eric M. Louchard, R. Pamela Reid, and Robert A. Maffione, 2003. Effects of microalgal communities on reflectance spectra of carbonate sediments in subtidal optically shallow marine environments. Limnol. Oceanogr. 48:535-546.
Zimmerman, Richard C., 2003. A biooptical model of irradiance distribution and photosynthesis in seagrass canopies. Limnol. Oceanogr. 48:568-585.
Cummings, M., and R. Zimmerman, 2003. Light harvesting and the package effect in the seagrasses Thalassia testudinum Banks ex König and Zostera marina L.: optical constraints on photoacclimation. Aquatic Botany 75(3):261-274.
Kawaguchi, T., H. Al-Sayegh, A.W. Decho. 2003. Development of an indirect competitive enzyme-linked immunosorbent assay to detect extracellular substances (EPS). J. Immunoassay Immunochem. 24: 29-39.
2004
Mazel, C. H., T. W. Cronin, R. L. Caldwell, and N. J. Marshall. 2004. Fluorescent Enhancement of Signaling in a Mantis Shrimp. Science 303:51.
Lesser, M. P., C. H. Mazel, M. Y. Gorbunov, and P. G. Falkowski. 2004. Discovery of Symbiotic Nitrogen-Fixing Cyanobacteria in Corals. Science 305:997-1000.
Dobbs, F.C., R.C. Zimmerman, and L.A. Drake. 2004. Widespread occurrence of previously unreported intracellular crystals in Thalassia testudinum Banks ex König. Aquatic Botany 80:23-28.