Publications

Books, chapters and monographs (including on-line publications)

Bootsma, H., E. Jensen, E. B. Young and J. A. Berges [Organizers]. 2005. Cladophora Research and Management in the Great Lakes . Proceedings of a Workshop Held at the Great Lakes WATER Institute, December 8, 2004. University of Wisconsin-Milwaukee. http://www.uwm.edu/Dept/GLWI/cladophora/page_report.html

Harrison, P. J. & J. A. Berges. 2005. Chapter 3. Marine culture media. pp. 21-33. In R. A. Andersen [ed.], Algal Culturing Techniques. Elsevier. PDF Copy

Andersen, R. A., J. A. Berges, P. J. Harrison & M. M. Watanabe. 2005. Appendix A. Recipes for freshwater and seawater media. pp. 429-538. In R. A. Andersen [ed.], Algal Culturing Techniques. Elsevier.

Berges, J. A., I. Joint & C. S. Reynolds. 2003. Microalgal ecology, p. 131-150. In T. A. Norton [ed.], Out of the Past: Collected reviews to celebrate the Jubilee of the British Phycological Society. The British Phycological Socety. PDF Copy

Collos, Y., & J. A. Berges. 2003. Nitrogen metabolism in phytoplankton. In C. M. Duarte [ed.], Encyclopedia of Life Support Systems. EOLSS Publishers (UNESCO). Online: http://www.eolss.net PDF Copy

Refereed journals

PDF Copy

Béchette, A., T. Stojsavljevic, M. Tessmer, J. A. Berges, G. A. Pinter & E. B. Young. 2013. Mathematical modeling of bacteria-virus interactions in Lake Michigan incorporating phosphorus content. J. Great Lakes Res. 39 (4): 646–654. PDF Copy

Berges, J. A., Y. Jiang, R. W. Sterner, G. S. Bullerjahn, N. A. Ivanikova & R. M. L. McKay. 2013. Identification of factors constraining nitrate assimilation in Lake Superior, Laurentian Great Lakes. Hydrobiologia doi:10.1007/s10750-013-1637-z PDF Copy

Frederick, N., J. A. Berges, B. Twining, D. Nuñez-Milland, & F. Hellweger. 2013. Exploring mechanisms of intracellular p heterogeneity in cultured phytoplankton using agent based modeling. Appl. Environ. Microbiol. 79: 4359-68. PDF Copy

Choi, C. J. & J. A. Berges. 2013. New types of metacaspases in phytoplankton reveal diverse origins of cell death proteases. Cell Death and Disease 4: e490. PDF Copy

Gronquist, D. & J. A. Berges. 2013. Effects of aquarium-related stresses on the zebrafish, Danio rerio: a comparison of behavioral, physiological and biochemical indicators. J. Aquat. Anim. Health 25: 53-65.

Xiao, L., E. B. Young, J. A. Berges & Z. He. 2012. Integrated photo-bioelectrochemical system for contaminant removal and bioenergy production. Environ. Sci. Technol. 46: 11459-66. PDF Copy

Choi, C. J., J. A. Berges & E. B. Young. 2012. Rapid effects of diverse toxic water pollutants on chlorophyll a fluorescence: Variable responses among freshwater microalgae. Water Research. 46: 2615-26. PDF Copy

Franklin D. J., R. L. Airs, M. Fernandes, T. G. Bell, R. J. Bongaerts, J. A. Berges & G. Malin. 2012. Identification of senescence and death in Emiliania huxleyi and Thalassiosira pseudonana: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism. Limnol. Oceanogr. 57: 305-317. PDF Copy

Fuhrman, K., G. A. Pinter & J. A. Berges. 2011. Dynamics of a virus-host model with an intrinsic quota. Mathematical and Computer Modeling 53: 716-30. PDF Copy
Franklin, D. J., C. J. Choi, C. J. Hughes,G. Malin & J. A. Berges. 2009. Effect of dead phytoplankton cells on the apparent efficiency of Photosystem II. Mar. Ecol. Prog. Ser. 382: 35-40. PDF Copy

Segovia, M. & J. A. Berges. 2009. Inhibition of caspase-like activities prevents the appearance of reactive oxygen species and dark-induced apoptosis in the unicellular chlorophyte Dunaliella tertiolecta. J. Phycol. 45: 1116-26. PDF Copy

Young, E. B., J. A. Berges & M. J. Dring. 2009. Physiological responses of intertidal marine brown algae to nitrogen deprivation and resupply of nitrate and ammonium. Physiol. Plant. 135: 400-11. PDF Copy

Bowler, C., A. E. Allen, J. H. Badger, J. Grimwood, K. Jabbari, A. Kuo, U. Maheswari, C. Martens, F. Maumus, R. P. Otillar, E. Rayko, A. Salamov, K. Vandepoele, B. Beszteri, A. Gruber, M. Heijde, M. Katinka, T. Mock, K. Valentin, F. Verret, J. A. Berges, C. Brownlee, J. P. Cadoret, A. Chiovitti, C. J. Choi, S. Coesel, A. De Martino, J. C. Detter, C. Durkin, A. Falciatore, J. Fournet, M. Haruta, M. J. J. Huysman, B. D. Jenkins, K. Jiroutova, R. E. Jorgensen, Y. Joubert, A. Kaplan, N. Kroger, P. G. Kroth, J. La Roche, E. Lindquist, M. Lommer, V. Martin-Jezequel, P. J. Lopez, S. Lucas, M. Mangogna, K. McGinnis, L. K. Medlin, A. Montsant, M. P. Oudot-Le Secq, C. Napoli, M. Obornik, M. S. Parker, J. L. Petit, B. M. Porcel, N. Poulsen, M. Robison, L. Rychlewski, T. A. Rynearson, J. Schmutz, H. Shapiro, M. Siaut, M. Stanley, M. R. Sussman, A. R. Taylor, A. Vardi, P. von Dassow, W. Vyverman, A. Willis, L. S. Wyrwicz, D. S. Rokhsar, J. Weissenbach, E. V. Armbrust, B. R. Green, Y. Van De Peer & I. V. Grigoriev. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456:239-44. PDF Copy

Montsant A., Allen A. E., Coesel S., De Martino A., Falciatore A., Mangogna M., Siaut M., Heijde M., Jabbari K., Maheswari U., Rayko E., Vardi A., Apt K. E., Berges J. A., Chiovitti A., Davis A. K., Thamatrakoln K., Hadi M. Z., Lane T. W., Lippmeier J. C., Martinez D., Parker M. S., Pazour G. J., Saito M. A., Rokhsar D. S., Armbrust E. V., and Bowler C. 2007. Identification and comparative genomic analysis of signaling and regulatory components in the diatom Thalassiosira pseudonana. J. Phycol. 43: 585-604. PDF Copy

Ribalet F., Berges J. A., Ianora A., and Cassotti R. 2007. Growth inhibition of cultured marine phytoplankton by toxic algal-derived polyunsaturated aldehydes. Aquat. Toxicol. 85: 219-227. PDF Copy

Young E. B., Dring M. J., and Berges J. A. (2007) Distinct patterns of nitrate reductase activity in brown algae: light and ammonium sensitivity in Laminaria digitata is absent in Fucus species. J. Phycol. 43: 1200-1208. PDF Copy

Young E. B., Dring M. J., Savidge G., Birkett D. A., Berges J. A. 2007. Seasonal variations in nitrate reductase activity and internal N pools in intertidal brown algae are correlated with ambient nitrate concentrations. Plant Cell Environ. 30: 764-774. PDF Copy

Kirkpatrick, A.J., Gerhardt, A., Dick, J.T.A., McKenna, M. & Berges, J.A. 2006. Use of the multispecies freshwater biomonitor to assess behavioral changes of Corophium volutator (Pallas, 1766) (Crustacea, Amphipoda) in response to toxicant exposure in sediment. Ecotoxicol. Environ. Saf. 64: 298-303. PDF Copy

Kirkpatrick, A.J., Gerhardt, A., Dick, J.T.A., Laming, P. & Berges, J.A. 2006. Suitability of Crangonyx pseudogracilis (Crustacea: Amphipoda) as an early warning indicator in the Multispecies Freshwater Biomonitor. Env. Sci. Pollut. Res. 13: 242-250. PDF Copy

Franklin, D.J., Brussaard, C.P.D. & Berges, J.A. 2006. What is the role and nature of programmed cell death in phytoplankton ecology? Eur. J. Phycol. 41: 1-14. PDF Copy

Young, E.B., Lavery, P.S., van Elven, B., Dring, M.J. & Berges, J.A. 2005. Nitrate reductase activity in macroalgae and its vertical distribution in macroalgal epiphytes of seagrasses. Mar. Ecol. Prog. Ser. 288: 103-114. PDF Copy

Segovia, M. & Berges, J.A. 2005. Effect of inhibitors of protein synthesis and DNA replication on the induction of proteolytic activities, caspase-like activities and cell death in the unicellular chlorophyte Dunaliella tertiolecta. Eur. J. Phycol. 40: 21-30. PDF Copy

Tomas, J., Geffen, A.J., Allen, I.S. & Berges, J.A. 2004. Analysis of the soluble matrix of vaterite otoliths of juvenile herring (Clupea harengus): do crystalline otoliths have less protein? Comp. Biochem. Physiol. A Comp. Physiol. 139: 301-308. PDF Copy

Franklin, D. J., & J. A. Berges. 2004. Mortality in cultures of the dinoflagellate Amphidinium carterae during culture senescence and darkness. Proc. R. Soc. Lond. B. 271: 2099-2107. PDF Copy

Armbrust, E.V., Berges, J.A., Bowler, C., Green, B.R., Martinez, D., Putnam, N.H., Zhou, S., Allen, A.E., Apt, K.E., Bechner, M., Brzezinski, M.A., Chaal, B.K., Chiovitti, A., Davis, A.K., Demarest, M.S., Detter, J.C., Glavina, T., Goodstein, D., Hadi, M.Z., Hellesten, U., Hildebrand, M., Jenkins, B.D., Jurka, J., Kapitonov, V.V., Kroger, N., Lau, W.W.Y., Lane, T.W., Larimer, F.W., Lippmeier, J.C., Lucas, S., Medina, M., Monstant, A., Obornik, M., Parker, M.S., Palenik, B., Pazour, G.J., Richardson, P.M., Rynearson, T.A., Saito, M.A., Schwartz, D.C., Thamatrakoln, K., Valentin, K., Vardi, A., Wilkerson, F.P. & Rokhsar, D.S. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution and metabolism. Science (Washington, D.C.). 306: 79-86. PDF Copy

Montagnes, D. J. S. & J. A. Berges. 2004. Determining parameters of the numerical response. Microb. Ecol. 48: 139-144. PDF Copy

Wilson, S., C. Blake, J. A. Berges, & C. A. Maggs. 2004. Environmental tolerances of free-living coralline algae (maerl): implications for European marine conservation. Biological Conservation. 120: 283-293. PDF Copy

Franklin, D. J., O. Hoegh-Guldberg, R. J. Jones & J. A. Berges. 2004. Cell death and degeneration in the symbiotic dinoflagellates of the Stylophora pistillata (Esper) in response to the combined effects of elevated temperature and light. Mar. Ecol. Prog. Ser. 272: 117-130. PDF Copy

Berges, J. A., C. E. Gibson & B. M. Stewart. 2004. Physiological responses of phytoplankton communities in the Irish Sea to simulated upwelling. Hydrobiologia 517: 121-132. PDF Copy

Segovia, M., L. Haramaty, J. A. Berges, & P. G. Falkowski. 2003. Caspases and cell death in a unicellular chlorophyte alga: the evolution of apoptosis. Plant Physiol. 132: 95-105. PDF Copy

Perez-Llorens, J. L., E. Benitez, J. J. Vergara & J. A. Berges. 2003. Characterization of proteolytic enzyme activities in macroalgae. Eur. J. Phycol. 38: 55-64. PDF Copy

Berges, J. A., D. E. Varela & P. J. Harrison. 2002. Effects of temperature on growth rate, composition and nitrogen metabolism in the marine diatom Thalassiosira pseudonana (Bacillariophyceae). Mar. Ecol. Prog. Ser. 225: 139-146. PDF Copy

Roberts, D., H. M. Moore, J. Berges, J. W. Patching, M. W. Carton & D. F. Eardly, 2001, Sediment distribution, hydrolytic enzyme profiles and bacterial activities in the guts of Oneirophanta mutabilis, Psychropotes longicauda and Pseudostichopus villosus: what do they tell us about digestive strategies of abyssal holothurians? Prog. Oceanogr. 50: 443-458. PDF Copy

Berges, J. A., D. J. Franklin & P. J. Harrison. 2001. Evolution of an artificial seawater medium: Improvements in enriched seawater, artificial water over the last two decades. J. Phycol. 37: 1138-1145. PDF Copy

Boyd, P. W., N. D. Sherry, J. A. Berges, J. K. B. Bishop, S. E. Calvert, M. A. Charette, S. J. Giovannoni, R. Goldblatt, P. J. Harrison, S. B. Moran, S. Roy, M. Soon. 1999. Transformations of biogenic particulates from the pelagic to the deep ocean realm. Deep-Sea Research 46: 2761-2792. PDF Copy

Boyd, P., Berges, J. & Harrison, P. 1998. In vitro iron enrichment experiments at iron-rich and -poor sites in the NE subarctic Pacific. J. Exp. Mar. Biol. Ecol. 227: 133-151. PDF Copy

Vergara, J.J., Berges, J.A. & Falkowski, P.G. 1998. Diel periodicity of nitrate reductase activity and protein levels in the marine diatom Thalassiosira weissflogii (Bacillariophyceae). J. Phycol. 34: 952-961. PDF Copy

Berges, J. A. & P. G. Falkowski. 1998. Physiological stress and cell death in marine phytoplankton: induction of proteases in reponse to nitrogen- or light-limitation. Limnol. Oceanogr. 43: 129-135. PDF Copy

Berges, J.A. 1997. Algal nitrate reductases. Eur. J. Phycol. 32: 3-8. PDF Copy

Berges, J.A. 1997. Ratios, regression statistics, and ”spurious” correlations. Limnol. Oceanogr. 42: 1006-1007. PDF Copy

Berges, J. A., & P. G. Falkowski. 1996. Cell-associated proteolytic enzymes from marine phytoplankton. J. Phycol. 32: 566-574. PDF Copy

Berges, J. A., D. O. Charlebois, D. C. Mauzerall, & P. G. Falkowski. 1996. Differential effects of nitrogen limitation on photosynthetic efficiency of Photosystems I and II in microalgae. Plant. Physiol. 110: 689-696. PDF Copy

Fisher, A. E., J. A. Berges, & P. J. Harrison. 1996. Does light quality affect the sinking rate of marine diatoms? J. Phycol. 32: 353-360. PDF Copy

Hurd, C. L., J. A. Berges, J. Osborne & P. J. Harrison. 1995. An in vitro nitrate reductase assay for marine macroalgae: optimization and characterization of the enzyme for Fucus gardneri (Phaeophyta). J. Phycol. 31: 835-843. PDF Copy

Berges, J. A., W. P. Cochlan, & P. J. Harrison. 1995. Laboratory and field responses of algal nitrate reductase to diel periodicity in irradiance, nitrate exhaustion, and the presence of ammonium. Mar. Ecol. Prog. Ser. 124: 259-269. PDF Copy

Berges, J. A., & P. J. Harrison. 1995a. Nitrate reductase activity quantitatively predicts the rate of nitrate incorporation under steady-state light limitation: a revised assay and characterization of the enzyme in 3 species of marine phytoplankton. Limnol. Oceanogr. 40: 82-93. PDF Copy

Berges, J. A., & P. J. Harrison. 1995b. Relationships between nitrate reductase activity and rates of growth and nitrate incorporation under steady-state light or nitrate limitation in the marine diatom Thalassiosira pseudonana (Bacillariophyceae). J. Phycol. 31: 85-95. PDF Copy

Berges, J. A., D. J. S. Montagnes, C. L. Hurd, & P. J. Harrison. 1994. Fitting ecological and physiological data to rectangular hyperbolae: a comparison of methods using Monte Carlo simulations. Mar. Ecol. Prog. Ser. 114: 175-183. PDF Copy

Montagnes, D. J. S., J. A. Berges, F. J. R. Taylor, & P. J. Harrison. 1994. Estmating carbon, nitrogen, protein and chlorophyll a from cell volume in marine phytoplankton: a comparison of optical and electronic particle counting techniques and the effect of fixation with Lugol’s iodine. Limnol. Oceanogr. 39: 1044-1060. PDF Copy

Berges, J. A., & C. Virtanen. 1993. Expanding the capabilities of laboratory instruments using built-in microprocessors and serial interfaces: adapting an LKB Ultrospec II UV spectrophotometer for scanning and enzyme kinetic analyses. Comput. Biol. Med. 23: 131-141. PDF Copy

Berges, J. A., & P. J. Harrison. 1993. Relationship between nucleoside diphosphate kinase activity and light-limited growth rate in the marine diatom Thalassiosira pseudonana (Bacillariophyceae). J. Phycol. 29: 45-53. PDF Copy

Berges, J. A., A. E. Fisher, & P. J. Harrison. 1993. A comparison of Lowry, Bradford, and Smith protein assays using different protein standards and protein purified from the marine diatom Thalassiosira pseudonana. Mar. Biol. (Berl.) 115: 187-193. PDF Copy

Berges, J. A., J. C. Roff, & J. S. Ballantyne. 1993. Enzymatic indexes of respiration and ammonia excretion: relationships to body size and food levels. J. Plankton Res. 15: 239-254. PDF Copy

Berges, J. A., & J. S. Ballantyne. 1991. Size-scaling of whole-body maximal enzyme activities in aquatic crustaceans. Can J. Fish. Aquat. Sci. 48: 2385-2394. PDF Copy

Ballantyne, J.S. & Berges, J.A. 1991. Enzyme activities of gill, hepatopancreas, mantle, and adductor muscle of the oyster (Crassostrea virginica) after changes in diet and salinity. Can. J. Fish. Aquat. Sci. 48: 1117-1123. PDF Copy

Berges, J. A., J. C. Roff, & J. S. Ballantyne. 1990. Relationship between body size, growth rate, and maximal enzyme activities in the brine shrimp, Artemia franciscana. Biol. Bull. 179: 287-296. PDF Copy

Hopcroft, R. R., J. C. Roff, & J. A. Berges. 1990. Size-fractionated sedimentation in a tropical neritic ecosystem near Kingston, Jamaica. Cont. Shelf Res. 10: 795-806. PDF Copy

Berges, J. A., & J. S. Ballantyne. 1989. 3-Hydroxy-3-methylglutaryl coenzyme A lyase from tissues of the oyster, Crassostrea virginica, the little skate, Raja erinacea and the lake charr, Salvelinus namaycush: a simplified spectrophotometric assay. Comp. Biochem. Physiol. B 93: 583-588. PDF Copy

Non-refereed publications

Andersen, R. A., and J. A. Berges. 2001. Meeting Report: 7th International Phycological Congress, Thessaloniki, Greece, August 18-25, 2001. Protist 152: 249-253. PDF Copy

Benitez, E., J. J. Vergara, J. A. Berges, and J. L. Perez-Llorens. 2001. Actividades proteolíticas en macroalgas marinas, p. 378. In F. M. Canovas and F. J. Florencio, [eds.], Anvances en el metabolismo del nitrogeno: biouímica, fisiología y biología molecular. Universidad de Málaga.

Berges, J. A. 1996. Book Review: Round & Chapman 1995. Eur. J. Phycol. 31: 291-292. PDF Copy

Berges, J. A. 1999. Book review: Cooksey 1998. Eur. J. Phycol. 34: 317-318. PDF Copy

Vergara, J. J., J. A. Berges, and P. G. Falkowski. 2001. Ciclos diarios de la nitrato reductasa en la diatomea marina Thalassiosira weissflogii, p. 215-223. In F. M. Canovas and F. J. Florencio, [eds.], Anvances en el metabolismo del nitrogeno: biouímica, fisiología y biología molecular. Universidad de Málaga.