Monterey Bay Aquarium Research Institute
Environmental Sample Processor
 

Publications listed by publication year

2011
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).

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

2010
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]

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

2009
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]

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.

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]

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]

2008
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]

Mikulski, C.M., Y.T. Park, K.L. Jones, C.K. Lee, W.A. Lim, C.A. Scholin, G.J. Doucette.  2008.  Development and field 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]

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.

2007
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: 70-78. [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]

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.

2006
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.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]

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]

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.

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]

2005
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]

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]

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]

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]

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]

2004
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.

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.

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.

2003
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).

2002
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]

2001
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.

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.

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.

2000
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.

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.

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]

1999
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.

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.

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]

1998
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]

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.

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.

1997
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.

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.

1996
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.

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.

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.

1995
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.

1994
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.

1993
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.

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.

1991
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.

1988
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.

Selected Contributions

Roman, B., C. Scholin, S. Jensen, R. Marin III, E. Massion, and J. Feldman.  The 2nd generation environmental sample processor: Evolution of a robotic underwater biochemical laboratory.  Proceedings, OCEANS 2005 MTS/IEEE Conference. Washington, D.C. 2004.  Marine Technology Society, Columbia, MD.  ISBN CD-ROM 0-933957-33-5.

Scholin, C. S. Jensen, B. Roman, E. Massion, R. Marin, C. Preston, D. Greenfield, W. Jones, K. Wheeler.  2006.  The Environmental Sample Processor (ESP) – An Autonomous Robotic Device for Detecting Microorganisms Remotely using Molecular Probe Technology.  Proceedings, OCEANS 2006 MTS/IEEE Conference. Boston, MA.  Marine Technology Society, Columbia, MD.

Selected Reports

Scholin, C.A.  2003.  Molecular Biological Technologies Applicable to Autonomous and Lagrangian Platforms (invited white paper presented at the Autonomous and Lagrangian Platforms and Sensors (ALPS) workshop, Scripps Institute of Oceanography, March ’03; available at: http://www.geo-prose.com/ALPS/white_papers.html).

Littaker, W., C. Scholin, G.R. Vasta.  2000.  Molecular approaches for identification and environmental detection of Pfiesteria piscicida and Pfiesteria-like dinoflagellates.  Workshop held at the Center of Marine Biotechnology September 1999, Baltimore, MD.

Scholin, C.A., N. Wainwright and G.M. Hallegraeff.  1994.  Feasibility of developing a rapid diagnostic test for toxic dinoflagellates in ships' ballast water. Report for the Australian Quarantine and Inspection Service.

Patents
Anderson, D.M., and Scholin, C.A.  1996.  Genetic markers and methods of identifying Alexandrium (Dinophyceae) species.  US Pat. No. 5582983.

Scholin, C.A., Haydock, P., and Cangelosi, G.  1999.  Detection of toxigenic marine pennate diatoms of the genus Pseudo-nitzschia US Pat. No. 5958689.

Scholin, C.A., Massion, E.I., Wright, D.K., Cline, D.E., Mellinger, E., Brown, M.  2001.  Aquatic autosampler device. US Pat. No. 6187530.

Tyrrell, J.V., Scholin, C.A., Bergquist, P., and Bergquist, P.  2004.  Compostion and methods for detecting Raphidophytes. US Pat. No. 6787648

 

 

Last updated: Oct. 30, 2012