Monterey Bay Aquarium Research Institute
Environmental Sample Processor
 

Publications listed alphabetically by first author

Anderson, D.M., D.M. Kulis, B.A. Keafer, K.E. Gribble, R.Marin and C.A. Scholin.  2005.  Identification and enumeration of Alexandrium spp. from the Gulf of Maine using molecular probes.  Deep-Sea Research II  52: 2467-2490. [pdf]

Ayers K, Rhodes L, Tyrrell J, Gladstone M, Scholin C.  2005.  International accreditation of sandwich hybridisation assay format DNA probes for micro-algae.  New Zealand J. Marine and Freshwater Res. 39: 1225–1231. [pdf]

Babin, M., J.J. Cullen, C.S. Roesler, P.L. Donaghay, G.J. Doucette, M. Kahru, M.R. Lewis, C.A. Scholin, M.E. Sieracki, and H.M. Sosik.  2005.  New approaches and technologies for observing harmful algal blooms.  Oceanography 18: 210-227. [pdf]

Bates, S.S., Scholin, C.A., Ferguson, M. & Leger, C.  1999.  Application of ribosomal RNA-targeted probes to detect Pseudo-nitzschia multiseries and P. pungens in Atlantic Canadian waters.  Canandian Techechnical Reports of Fisheries and Aquatic Sciences  2261:63-67.

Cangelosi, G.A., A.M. Hamlin, R. Marin III, C.A. Scholin.  Detection of stable pre-rRNA in toxigenic Pseudo-nitzschia species.  1997.  Applied and Environmental Microbiology 63: 4859-4865.

Doucette, G.J., Mikulski, C.M., Jones K.L., King, K.L., Greenfield D.I., Marin III R., Jensen S., , Roman B., Elliott C.T., Scholin, CA.  2009.  Remote, subsurface detection of the algal toxin domoic acid onboard the Environmental Sample Processor: assay development and initial field trials.  Harmful Algae 8:880-888. [pdf]

Goffredi, S.K., W. Jones, C. Scholin, R. Marin, S. Hallam, R.C. Vrijenhoek.  2006.  Molecular detection of marine larvae.  Marine Biotechnology 8: 149-160. [pdf]

Greenfield, D., R. Marin III, G.J. Doucette, C. Mikulski, S. Jensen, B. Roman, N. Alvarado, C.A. Scholin.  2008.  Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007.  Limnology and Oceanography: Methods 6: 667-679. [pdf]

Greenfield, D.I., R. Marin III, S. Jensen, E. Massion, B. Roman, J. Feldman, C. Scholin.  2006. Application of the Environmental Sample Processor (ESP) methodology for quantifying Pseudo-nitzschia australis using ribosomal RNA-targeted probes in sandwich and fluorescent in situ hybridization.  Limnology and Oceanography: Methods 4: 426-435. [pdf]

Haywood, A.J., C.A. Scholin, R. Marin III, K. Petrik, R. Pigg, M. Garrett, K. A. Steidinger, and C. Heil. 2009.  Detection of Karenia brevis in Florida coastal waters using sandwich hybridization assays in two formats. p 95-100. In: Proceedings of the 6th International Conference on Molluscan Shellfish Safety. Royal Society of New Zealand Miscellaneous Series 71. Blenheim, Marlborough, New Zealand. 355 pp.

Haywood, A.J., C. A. Scholin, R. Marin III, K. A. Steidinger, C. A. Heil and J. Ray.  2007.  Molecular detection of the brevetoxin-producing dinoflagellate Karenia brevis (Dinophyceae) and closely related species using ribosomal RNA probes and a semi-automated sandwich hybridization assay.  Journal of Phycology 43:1271–1286. [pdf]

John Paul, Chris Scholin, Ger van den Engh, Mary Jane Perry.  2007.  In situ Instrumentation.  Oceanography 20: 58-66. [pdf]

Jones, W.J., C. Preston, R. Marin III, C. Scholin, R. Vrijenhoek  2007.  A Robotic Molecular Method for in situ Detection of Marine Invertebrate Larvae.  Molecular Eclology Notes (in press; available on-line doi: 10.1111/j.1471-8286.2007.02021.x [pdf]

Judge, B.S., C.A. Scholin and D. M. Anderson.  1993.  RFLP analysis of the large-subunit ribosomal RNA gene of globally distributed populations of the toxic dinoflagellate AlexandriumBiological Bulletin 185: 329-330.

LaGier, M.J., C.A. Scholin, J.W. Fell, J.Wang and K.D. Goodwin.  2005.  An electrochemical RNA hybridization assay for detection of the fecal indicator bacterium Escherichia coliMarine Pollution Bulletin 50: 1251-1261. [pdf]

Lenaers, G., C. A. Scholin, Y. Bhaud, D. Saint-Hilaire and M. Herzog. 1991.  A molecular phylogeny of dinoflagellate protists (Pyrrhophyta) inferred from the sequence of the 24S rRNA divergent domains D1 and D8.  Journal of Molecular Evolution 32: 53-63.

Lundholm, N., Ø. Moestrup, Y. Kotaki, C. Scholin, P. Miller.  2006.  Inter- and intraspecific variation of the Pseudo-nitzschia delicatissima-complex (Bacillariophyceae) illustrated by rRNA probes, morphological data and phylogenetic analyses identification of P. decipiens and P. dolorosa spp. Nov.  Journal of Phycology 42: 464-481. [pdf]

Marin III, R., and C. Scholin. 2010  Sandwich Hybridization. In: Microscopic and molecular methods for quantitative phytoplankton analysis (Chapter 12). Karlson, B., Cusack, C. and Bresnan, E. (editors). IOC Manuals and Guides, no. 55. (IOC/2010/MG/55)  Paris, UNESCO. 110 pages. [pdf]

Matweyou, J.A., D.A. Stockwell, C.A. Scholin, S. Hall, V.L. Trainer, J.D. Ray, T.E. Whitledge, A.R. Childers, F.G. Plumley.  2004.  Use of Alexandrium rRNA targeted probes to predict PSP events on Kodiak Island, Alaska.  In: K. A. Steidinger, J. H. Landsberg, C. R. Tomas and G. A. Vargo (eds.) Harmful Algae 2002, pp. 267-269.  Florida Fish and Wildlife Conservation Commission, Florida Institute of Oceanography, and Intergovernmental Oceanographic Commission of UNESCO. St. Petersburg, Florida, USA.

Metfies, K., K. Töbe, C. Scholin, and L.K. Medlin.  2006.  Laboratory and field applications of ribosomal RNA probes to aid the detection and monitoring of harmful algae.  In: Ecology of Harmful Algae (Granéli, E., and Turner, J.T. eds), pp. 311-325.  Springer Verlag, Berlin, Heidelberg, New York.

Mikulski, C.M., Y.T. Park, K.L. Jones, C.K. Lee, W.A. Lim, C.A. Scholin, G.J. Doucette.  2008.  Development and filed application of rRNA-targeted probes for the detection of Cochlodinium ploykrikoides in Korean coastal waters using whole cell and sandwich hybridization formats.  Harmful Algae 7: 347–359. [pdf]

Miller, P.E., R. Marin III, C. Scholin, J.C. Goldman, G. Doucette, C. Powell.  2004. Variation in reactivity of rRNA-targeted probes towards Pseudo-nitzschia multiseries grown in nitrate- and silicate-limited continuous cultures. In K. A. Steidinger, J. H. Landsberg, C. R. Tomas and G. A. Vargo (eds.) Harmful Algae 2002, pp. 270-272. Florida Fish and Wildlife Conservation Commission, Florida Institute of Oceanography, and Intergovernmental Oceanographic Commission of UNESCO. St. Petersburg, Florida, USA.

Miller, P.E. and C.A. Scholin.  2000.  On detection of Pseudo-nitzschia species using rRNA-targeted probes: sample fixation and stability.  Journal of Phycology 36: 238-250.

Miller, P.E. and C.A. Scholin.  1998.  Identification and enumeration of cultured and wild Pseudo-nitzschia (Bacillariophyceae) using species-specific LSU rRNA-targeted fluorescent probes and filter-based whole cell hybridization.  Journal of Phycology 34: 371-382. [pdf]

Miller, P.E. and C.A. Scholin.  1996.  Identification of cultured Pseudo-nitzschia (Bacillariophyceae) using species-specific LSU rRNA-targeted fluorescent probes.  Journal of Phycology 32: 646-655.

O’Halloran, C., M.W. Silver, T.R. Holman and C.A. Scholin.  2006.  Heterosigma akashiwo in Central California Waters.  Harmful Algae 5: 124-132. [pdf]

Parsons, M.L., C. Scholin, G. Doucette, G.A. Fryxell, Q. Dortch and T.M. Soniat.  1999.  Pseudo-nitzschia species (Bacillariophyceae) in Louisiana coastal waters: molecular probe field trials, genetic variability and domoic acid analyses. Journal of Phycology 35: 1368-1378.

Peperzak, L., B. Sandee, C. Scholin, P. Miller and L. Van Nieuwerburgh.  2001.  Appliction and flow cytometric detection of antibody and rRNA probes to Gymnodinium mikimotoi (Dinophyceae) and Pseudo-nitzschia multiseries (Bacillariophyceae).  In: G. M. Hallegraeff, S. I. Blackburn, C. J. Bolch and R. J. Lewis [Eds.]. Harmful Algal Blooms 2000, pp 206-209.  Intergovernmental Oceanographic Commission of UNESCO.

Preston, C., R. Marin III, S. Jenson, J. Feldman, E. Massion, E. DeLong, M. Suzuki, K. Wheeler, D. Cline, N. Alvarado, and C. Scholin.  2009.  Near real-time, autonomous detection of marine bacterioplankton on a coastal mooring in Monterey Bay, California, using rRNA-targeted DNA probes.  Environmental Microbiology 11:1168-1180. [pdf]

Rhodes, L., A. Haywood, J. Adamson, K. Ponikla, C. Scholin. 2004.  DNA probes for the rapid detection of Karenia species in New Zealand's coastal waters. In K. A. Steidinger, J. H. Landsberg, C. R. Tomas and G. A. Vargo (eds.) Harmful Algae 2002, pp. 273-275. Florida Fish and Wildlife Conservation Commission, Florida Institute of Oceanography, and Intergovernmental Oceanographic Commission of UNESCO. St. Petersburg, Florida, USA.

Rhodes, L., C.A. Scholin, J.V. Tyrrell, J. Adamson and K. Todd, K.  2001.  The integration of DNA probes into New Zealand’s routine phytoplankton monitoring programs. In: G. M. Hallegraeff, S. I. Blackburn, C. J. Bolch and R. J. Lewis (eds). Harmful Algal Blooms 2000, pp. 429-432. Intergovernmental Oceanographic Commission of UNESCO.

Rhodes, L.L., J. Adamson, and C. Scholin.  2000.  Pseudo-nitzschia multistriata (Bacillariophyceae) in New Zealand.  New Zealand Journal of Marine and Freshwater Research 34:463-467.

Rhodes, L., C. Scholin and I Garthwaite.  1998.  Pseudo-nitzschia in New Zealand and the role of DNA probes and immunoassays in refining marine biotoxin monitorring programmes.  Natural Toxins 6: 105-111.

Rhodes, L., C. Scholin, I. Garthwaite, A. Haywood and A. Thomas.  1998.  Domoic acid-producing Pseudo-nitzschia species educed by whole cell DNA probe-based and immunochemical assays.  In: Regura, B., Blanko, J., Fernandez, M.L. and Wyatt, T [Eds.], Harmful Algae.  Xunta de Galicia and Intergovernmental Ocenaographic Commission of UNESCO pp. 274-277.

Roman, B., C. Scholin, S. Jensen, E. Massion, R, Marin III, C. Preston, D. Greenfield, W. Jones, and K. Wheeler.  2007.  Controlling a Robotic Marine Water Sampler with the Ruby Scripting Language.  Journal of American Laboratory Automation 12: 56-61.

Ryan,J.,  D. Greenfield, R. Marin III, C. Preston, B. Roman, S. Jensen, D. Pargett, J. Birch, C. Mikulski, G. Doucette and C. Scholin.  2011.  Harmful phytoplankton ecology studies using an autonomous molecular analytical and ocean observing network.  Limnology and Oceanography (in press).

Ryan, J.P., H.M. Dierssen, R.M. Kudela, C.A. Scholin, K. S. Johnson, J.M. Sullivan, A.M. Fisher, E.V., Rienecker, P.R. McEnany, and F.P. Chavez.  2005.  Coastal Ocean Physics and red tides: an example from Monterey Bay, California.  Oceanography 18: 246-255. [pdf]

Scholin, C.  2010.  What are “ecogenomic sensors?” A review and thoughts for the future.  Ocean Science 6: 51-60. [pdf]

Scholin, C, G. Doucette, S. Jensen, B. Roman, D. Pargett, R. Marin III, C. Preston, W. Jones, J. Feldman, C. Everlove, A. Harris, N. Alvarado, E. Massion, J. Birch, D. Greenfield, R. Vrijenhoek, C. Mikulski, K. Jones.  2009.  Remote detection of marine microbes, small invertebrates, harmful algae and biotoxins using the Environmental Sample Processor (ESP).  Oceanography 22:158-167. [pdf]

Scholin, C.A., G.J. Doucette, and A.D. Cembella.  2008.  Prospects for developing automated systems for in situ detection of harmful algae and their toxins.  In: M. Babin, C.S. Roesler and J.J. Cullen (eds.) Real-Time Coastal Observing Systems for Ecosystem Dynamics and Harmful Algal Blooms, pp 413-462, UNESCO Publishing, Paris, France

Scholin, C.A., E. Vrieling, L. Peperzak, L. Rhodes and P. Rublee.  2003.  Detection of HAB species using lectin, antibody and DNA probes.  In:  G.M. Hallegraeff,  D.M. Anderson  A.D. Cembella (eds), Manual on Harmful Marine Microalgae, pp. 131-64. Paris, Intergovernmental Oceanographic Commission, UNESCO. (Vol. 11. Second Edition).

Scholin, C.A., F. Gulland, G. Doucette and others.  2000.  Mortality of sea lions along the central California coast linked to a toxic diatom bloom.  Nature 403: 80-84. [pdf]

Scholin, C., R, Marin, P. Miller, G. Doucette, C. Powell, J. Howard., P. Haydock and J. Ray.  1999.  Application of DNA probes and a receptor binding assay for detection of Pseudo-nitzschia (Bacillariophyceae) species and domoic acid activity in cultured and natural samples.  Journal of Phycology 35: 1356-1367. [pdf]

Scholin, C., G. Massion, E. Mellinger, M. Brown, D. Wright and D. Cline.  1998.  The development and application of molecular probes and novel instrumentation for detection of harmful algae.  Ocean Community Conference ’98 Proceedings, Marine Technology Society, Vol. 1 pp. 367-370.

Scholin, C.A. and D.M. Anderson.  1998.  Detection and quantification of HAB species using antibody and DNA probes: progress to date and future research objectives. In: Regura, B., Blanko, J., Fernandez, M.L. and Wyatt, T [Eds.], Harmful Algae.  Xunta de Galicia and Intergovernmental Ocenaographic Commission of UNESCO pp. 253-257.

Scholin, C.A.  Development of nucleic acid probe-based diagnostics for identifying and enumerating harmful algal bloom species.  1998.  In: Anderson, D.M., Hallegraeff, G.M. and Cembella A.D. [Eds.], The Physiological Ecology of Harmful Algal Blooms.  NATO Advanced Study Institute Series.  Springer-Verlag, Heidelberg pp. 337-349.

Scholin, C.A.  Morphological, genetic and biogeographic relationships of Alexandrium tamarense, A. catenella and A. fundyense.  1998.  In: Anderson, D.M., Hallegraeff, G.M.          and Cembella A.D. [Eds.], The Physiological Ecology of Harmful Algal Blooms.  NATO Advanced Study Institute Series. Springer-Verlag, Heidelberg. pp 13-27.

Scholin, C.A., P. Miller, K. Buck, F. Chavez, P. Harris, P. Haydock, J. Howard and G. Cangelosi.  1997.  Detection and quantification of Pseudo-nitzschia australis in cultured and natural populations using LSU rRNA-targeted probes.  Limnology and Oceanography 42: 1265-1272.

Scholin, C.A. and D.M. Anderson.  1996.  LSU rDNA-based RFLP assays for discriminating species and strains of Alexandrium (Dinophyceae).  Journal of Phycology 32: 1022-1035.

Scholin, C. and D.M. Anderson.  1996.  Identification of Alexandrium species and strains using RFLP analysis of PCR-amplified LSU rDNA.  In: Oshima, Y and Fukuyo, Y [Eds.] Harmful and Toxic Algal Blooms,Intergovernmental Oceanographic Commission of UNESCO, Paris.  pp 451-454.

Scholin, C., P. Miller, K. Buck, F. Chavez, G. Cangelosi, P. Haydock, J. Howard and P. Harris.  1996.  DNA Probe-based detection of harmful algal species using Pseudo-nitzschia species as models.  In: Oshima, Y and Fukuyo, Y [Eds.] Harmful and Toxic Algal Blooms,Intergovernmental Oceanographic Commission of UNESCO, Paris.  pp 439-442.

Scholin, C.A., K.R. Buck, T. Britschgi, J. Cangelosi and F.P. Chavez.  1996.  Identification of Pseudo-nitzschia australis (Bacillariophyceae) using rRNA-targeted probes in whole cell and sandwich hybridization formats.  Phycologia 35: 190-197.

Scholin, C.A., G.M. Hallegraeff and D.M. Anderson.  1995.  Molecular evolution of the Alexandrium tamarense "species complex" (Dinophyceae): dispersal in the North American and West Pacific regions.  Phycologia 34: 472-485.

Scholin, C.A. and D.M. Anderson.  1994.  Identification of species and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae).  I.  RFLP analysis of SSU rRNA genes.  Journal of Phycology 30: 744-754.

Scholin, C.A., M. Herzog, M.L. Sogin and D.M Anderson.  1994.  Identification of group and strain-specific genetic markers for globally distributed Alexandrium (Dinophyceae).  II. Sequence analysis of a fragment of the LSU rRNA gene.  Journal of Phycology 30: 999-1011.

Scholin, C.A., M.C. Villac, K.R. Buck, J.M. Krupp, D.A. Powers, G.A. Fryxell and F.P. Chavez.  1994.  Ribosomal DNA sequences discriminate among toxic and non-toxic Pseudonitzschia species.  Natural Toxins 2: 152-165.

Scholin, C.A. and D.M. Anderson.  1993.  Population analysis of toxic and non-toxic Alexandrium species using ribosomal RNA signature sequences.  In: Smayda, T.J., and Shimizu, Y. [Eds.], Toxic Phytoplankton Blooms in the Sea.  Elsevier, New York, pp. 95-102.

Scholin, C.A., D.M. Anderson and M. Sogin.  1993.  The existence of two distinct small-subunit rRNA genes in the toxic dinoflagellate Alexandrium fundyenseJournal of Phycology 29: 209-216

Tyrrell, J.V., L.B. Connell and C.A. Scholin.  2002. Monitoring for Heterosigma akashiwo using a sandwich hybridization assay.  Harmful Algae 1:205-214. [pdf]

Tyrrell, J.V., C.A. Scholin, P.R. Berguist and P.L. Berguist.  2001.  Detection and enumeration of Heterosigma akashiwo and Fibrocapsa japonica (Raphidophyceae) using rRNA-targeted oligonucleotide probes.  Phycologia 40: 457-467.

Vrieling, E., R. Koeman, C. Scholin, P. Scheerman, L. Peperzak, M. Veenhuis and W. Gieskes.  1996.  Detection of a domoic acid-producing Pseudo-nitzschia species in the Dutch Wadden Sea by electron microscopy and molecular probes.  European Journal of Phycology 31: 333-340.

Yoch, D.C., J. Li, C-Z. Hu and C.A. Scholin.  1988.  Ammonia switch-off of nitrogenase from Rhodobacter sphaeroides and Methylosinus trichosporium: no evidence for Fe protein modification.  Archives of Microbiology 150: 1-5.

Zehr, J.P., J. Robidart and C. Scholin. 2011.  Marine microorganisms, biogeochemical cycles, and global climate change.  Microbe 6(4) (in press)

 

 

Last updated: Sep. 10, 2012