@article{cooper_sinclair_wawrik_2016, title={Transcriptome Analysis of Scrippsiella trochoidea CCMP 3099 Reveals Physiological Changes Related to Nitrate Depletion}, volume={7}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2016.00639}, abstractNote={Dinoflagellates are a major component of marine phytoplankton and many species are recognized for their ability to produce harmful algal blooms (HABs). Scrippsiella trochoidea is a non-toxic, marine dinoflagellate that can be found in both cold and tropic waters where it is known to produce “red tide” events. Little is known about the genomic makeup of S. trochoidea and a transcriptome study was conducted to shed light on the biochemical and physiological adaptations related to nutrient depletion. Cultures were grown under N and P limiting conditions and transcriptomes were generated via RNAseq technology. De novo assembly reconstructed 107,415 putative transcripts of which only 41% could be annotated. No significant transcriptomic response was observed in response to initial P depletion, however, a strong transcriptional response to N depletion was detected. Among the down-regulated pathways were those for glutamine/glutamate metabolism as well as urea and nitrate/nitrite transporters. Transcripts for ammonia transporters displayed both up- and down-regulation, perhaps related to a shift to higher affinity transporters. Genes for the utilization of DON compounds were up-regulated. These included transcripts for amino acids transporters, polyamine oxidase, and extracellular proteinase and peptidases. N depletion also triggered down regulation of transcripts related to the production of Photosystems I & II and related proteins. These data are consistent with a metabolic strategy that conserves N while maximizing sustained metabolism by emphasizing the relative contribution of organic N sources. Surprisingly, the transcriptome also contained transcripts potentially related to secondary metabolite production, including a homolog to the Short Isoform Saxitoxin gene (sxtA) from Alexandrium fundyense, which was significantly up-regulated under N-depletion. A total of 113 unique hits to Sxt genes, covering 17 of the 34 genes found in C. raciborskii were detected, indicating that S. trochoidea has previously unrecognized potential for the production of secondary metabolites with potential toxicity.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Cooper, Joshua T. and Sinclair, Geoffrey A. and Wawrik, Boris}, year={2016}, month={May} }
 @article{waters_wolcott_kamykowski_sinclair_2015, title={Deep-water seed populations for red tide blooms in the Gulf of Mexico}, volume={529}, ISSN={["1616-1599"]}, DOI={10.3354/meps11272}, abstractNote={Populations of the toxic dinoflagellate Karenia brevis that remain near the benthos in deep shelf water in the Gulf of Mexico could be the source for toxic bloom occurrences near shore. A biophysical dynamic simulation model and migrating drifters were used to assess whether such 'seed populations' could persist in nature. The vertical migration responses of plankton to an exclusively benthic nutrient source and light limitation would result in near-benthic behavioral trapping of a slowly growing population in conditions found on the West Florida Shelf (WFS). The model in- dicated that for a 50 m deep bottom, a 2-m-thick layer of ≥2 µmol NO3 - /NO2 - fluxing from the benthos was the minimum needed to permit growth for dark- adapted K. brevis in an oligotrophic water column. Growth rates depended more on the duration of expo- sure to nutrients than on concentration; a 1-m-thick nutrient layer sustained minimum growth levels inde- pendently of the nutrient distri bution at depths ≤40 m. Field experiments using Autonomous Behaving La- grangian Explorer drifters (ABLEs) that exhibited bio- mimetic vertical migration responses to the external environment demonstrated a benthically-oriented movement pattern in response to natural light and cues correlated with elevated near-benthic nutrients. Aver- age measurements of nutrients and light from the bot- tom 2 m of the water column in a potential bloom- forming region of the WFS were higher than the model-generated requirements for growth, suggesting that coastal nutrient distributions could support a ben- thic population offshore. Under upwelling conditions, such populations could be advected inshore to frontal convergence zones and form toxic 'red tide' blooms.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Waters, Linda G. and Wolcott, Thomas G. and Kamykowski, Dan and Sinclair, Geoff}, year={2015}, month={Jun}, pages={1–16} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2009, title={LIPID CLASS, CAROTENOID, AND TOXIN DYNAMICS OF KARENIA BREVIS (DINOPHYCEAE) DURING DIEL VERTICAL MIGRATION}, volume={45}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2008.00627.x}, abstractNote={The internal lipid, carotenoid, and toxin concentrations of Karenia brevis (C. C. Davis) Gert Hansen and Moestrup are influenced by its ability to use ambient light and nutrients for growth and reproduction. This study investigated changes in K. brevis toxicity, lipid class, and carotenoid concentrations in low‐light, nitrate‐replete (250 μmol quanta · m−2 · s−1, 80 μM NO3); high‐light, nitrate‐replete (960 μmol quanta · m−2 · s−1, 80 μM NO3); and high‐light, nitrate‐reduced (960 μmol quanta · m−2 · s−1, <5 μM NO3) mesocosms. Reverse‐phase HPLC quantified the epoxidation state (EPS) of the xanthophyll‐cycle pigments diadinoxanthin and diatoxanthin, and a Chromarod Iatroscan thin layer chromatography/flame ionization detection (TLC/FID) system quantified changes in lipid class concentrations. EPS did not exceed 0.20 in the low‐light mesocosm, but increased to 0.65 in the high‐light mesocosms. Triacylglycerol and monogalactosyldiacylglycerol (MGDG) were the largest lipid classes consisting of 9.3% to 48.7% and 37.3% to 69.7% of total lipid, respectively. Both lipid classes also experienced the greatest concentration changes in high‐light experiments. K. brevis increased EPS and toxin concentrations while decreasing its lipid concentrations under high light. K. brevis may mobilize its toxins into the surrounding environment by reducing lipid concentrations, such as sterols, limiting competition, or toxins are released because lipids are decreased in high light, reducing any protective mechanism against their own toxins.}, number={1}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward}, year={2009}, month={Feb}, pages={154–163} }
 @article{sinclair_kamykowski_2008, title={Benthic-pelagic coupling in sediment-associated populations of Karenia brevis}, volume={30}, ISSN={["1464-3774"]}, DOI={10.1093/plankt/fbn042}, abstractNote={Nutrient delivery to populations of Karenia brevis in oligotrophic water columns in the Gulf of Mexico remains uncertain. Aggregations of K. brevis near the sediment-water interface suggest that cells derive nutrients from the sediment. Video of cells near the sediment suggest that cells either access nutrients that flux out of the sediment or migrate into the sediment pores where higher nutrient concentrations exist. Experiments tested K. brevis' ability to migrate into the sediment using chambers divided by a 100 μm mesh overlain with a thin layer of sediment. Since the diel vertical migration of K. brevis typically displays a nocturnal descent, experiments tested migration response at night in response to sub-sediment nutrient sources. The experiments suggest that while the sediment affects the progress of descending cells, migration occurs through thin layers of sediment and increases in response to elevated nutrient concentrations below the sediment. Since all cells found below the sediment had significantly higher C/N ratios than those remaining above the sediment, migration appears related to a cell's internal biochemical state. The vertical migration behavior of K. brevis may help alleviate bottom-up controls and permit populations to persist as vegetative cells near the sediment-water interface.}, number={7}, journal={JOURNAL OF PLANKTON RESEARCH}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel}, year={2008}, month={Jul}, pages={829–838} }
 @article{schaeffer_kamykowski_mckay_sinclair_milligan_2007, title={A comparison of photoresponse among ten different Karenia brevis (Dinophyceae) isolates}, volume={43}, ISSN={["1529-8817"]}, DOI={10.1111/j.1529-8817.2007.00377.x}, abstractNote={Many laboratories have solely used the Wilson isolate to physiologically characterize the harmful algal bloom (HAB) dinoflagellate Karenia brevis (C. C. Davis) G. Hansen et Moestrup. However, analysis of one isolate may lead to misinterpretations when extrapolating measurements to field populations. In this study, pulse‐amplitude‐modulated chlorophyll fluorometer (PAM‐FL) relative electron transport rate (ETR), Fv/Fm, and chl were compared with traditional techniques, such as 14C photosynthesis versus irradiance (P–E) curves, DCMU [3‐(3′,4′‐dichlorophenyl)‐1,1‐dimethyl urea] Fv/Fm, and extracted chl. The DCMU and PAM‐FL values of Fv/Fm (r2 = 0.51) and chl (r2 = 0.58) were in good agreement. There was no correlation between 14C and PAM‐FL α, Pmax, and β parameters because PAM‐FL ETR was only a relative measurement. The PAM‐FL techniques were then used to investigate P–E curves, quantum yield of PSII (Fv/Fm), and chl from 10 K. brevis isolates to determine whether one or all isolates would better represent the species. Comparisons were made with a radial photosynthetron, which allowed for controlled conditions of light and temperature. Isolate α, Pmax, and β varied between 0.097 and 0.204 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, 80.41 and 241 μmol e− · m−2 · s−1, and 0.005 and 0.160 μmol e− · m−2 · s−1 · (μmol quanta · m−2 · s−1)−1, respectively. Either carbon limitation and/or bacterial negative feedback were implicated as the cause of the P–E parameter variability. Furthermore, these results directly contradicted some literature suggestions that K. brevis is a low‐light‐adapted dinoflagellate. Results showed that K. brevis was more than capable of utilizing and surviving in light conditions that may be present on cloudless days off Florida.}, number={4}, journal={JOURNAL OF PHYCOLOGY}, author={Schaeffer, Blake A. and Kamykowski, Daniel and McKay, Laurie and Sinclair, Geoff and Milligan, Edward J.}, year={2007}, month={Aug}, pages={702–714} }
 @article{mckay_kamykowski_milligan_schaeffer_sinclair_2006, title={Comparison of swimming speed and photophysiological responses to different external conditions among three Karenia brevis strains}, volume={5}, ISSN={["1878-1470"]}, DOI={10.1016/j.hal.2005.12.001}, abstractNote={Behavior, growth, and production are integral in the life history of Karenia brevis, an autotrophic, dinoflagellate HAB species, and are important variables in modeling blooms in the Gulf of Mexico. This study compares swimming speeds, growth rates, and photosynthetic responses of recent isolates of K. brevis (specifically the Apalachicola – APA, Manasota – MAN, and Jacksonville – JAX strains) over a range of light intensities and temperatures. Strain swimming speeds were similar and remained fairly constant from 17 to 30 °C, but decreased markedly at 13 °C. Photosynthetic responses of the strains to different acclimated temperatures had opposite trends with APA exhibiting higher electron transport rates (ETR) at higher temperatures and MAN exhibiting higher ETR at lower temperatures. In the light experiments, the cells’ internal physiological state (represented by photosynthetic yield, ETR, and neutral lipid reserves) and swimming capabilities were examined in the dark after 6 h incubations in the radial photosynthetron. For all strains, at initial incubation light intensities swimming speed decreased and ETR increased. As incubation light intensities increased, ETR decreased and swimming speed increased. At the highest incubation light intensities, ETR and swimming speed decreased. Neutral lipids followed a pattern similar to ETR, only lipids peaked after ETR at a light intensity that corresponded to the increase in swimming speed. The results suggest that cells may partition energy selectively depending on the needs of the cell. Information was combined to characterize a generalized species response to light and temperature ranges.}, number={6}, journal={HARMFUL ALGAE}, author={McKay, Laurie and Kamykowski, Daniel and Milligan, Ed and Schaeffer, Blake and Sinclair, Geoff}, year={2006}, month={Dec}, pages={623–636} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. I. Influences of prior environmental exposure and biochemical state on diel uptake of nitrate}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328117}, abstractNote={The ability of a Karenia brevis population to persist in an oligotrophic water column depends on how cell physiology and cell behavior contribute to the acquisition of light and nutrients that often are separated in space. We hypothesized that an aggregation of K. brevis, observed under- going a diel vertical migration (DVM) in the bottom half of a 22 m water column on the West Florida Shelf, used the sediments as a nutrient source. We tested how the physiology of K. brevis contributed to the acquisition of nitrate by evaluating how nitrate uptake changed with prior environmental exposure. The experimental conditions simulated the extremes that cells might endure during DVM when migrating up into an oligotrophic water column versus cells that remained near the sediment- water interface. The first culture, representing cells that attained the maximum apex of their migra- tion away from the sediments, was grown under relatively high light (350 μmol quanta m -2 s -1 ) and reached nitrate-depleted conditions (<0.5 μM NO3 - ) prior to the experiment. The second culture, rep- resenting cells that remained near the sediment-water interface, was grown under relatively low light (60 μmol quanta m -2 s -1 ) and nitrate-replete conditions (~20 μM NO3 - ) prior to the experiment. Cells exposed to nitrate-depleted environments for 12 h prior to the experiment enhanced nocturnal uptake compared to cells continuously exposed to nitrate-replete conditions. Changes in cell physi- ology may contribute to nitrate acquisition after descent from oligotrophic environments to areas with elevated nitrate concentrations.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={117–124} }
 @article{sinclair_kamykowski_milligan_schaeffer_2006, title={Nitrate uptake by Karenia brevis. II. Behavior and uptake physiology in a nitrate-depleted mesocosm with a bottom nutrient source}, volume={328}, ISSN={["1616-1599"]}, DOI={10.3354/meps328125}, abstractNote={Karenia brevis may optimize growth by alternately maximizing exposure to light, migrating up into an oligotrophic water column during the day, and to nutrients (nitrate), by migrat- ing down to the sediment-water interface at night. Understanding how cell behavior contributes to the acquisition of light and nutrients that are separated in space is critical to understanding how K. brevis populations persist in oligotrophic environments. In response to previous modeling efforts that parameterized cell physiology and behavior in nitrate-replete conditions, we examined similar cellular characteristics in a stratified 1.5 m deep mesocosm. The upper 2/3 of the mesocosm, encom- passing the surface and middle samples, was nitrate depleted (<0.5 µM NO3 - ) and simulated an oligotrophic water column. The lower 1/3 of the mesocosm contained 10 µM NO3 - corresponding to elevated nutrient levels near the sediment-water interface. We sampled uptake rates at 3 depths during the day at light levels of 350, 125 and 60 µmol quanta m -2 s -1 and again at night in the dark. Nocturnal uptake of nitrate in the mesocosm was significantly less than diurnal uptake. Nocturnal uptake rates in the mesocom were intermediate between cells exposed to prolonged nitrate-depleted and nitrate-replete conditions. Both migration, as indicated by diel aggregation patterns, and cell physiology indicate that descent to regions of higher nutrient concentrations were sufficient to main- tain average growth rates of 0.3 div d -1 . Thus, both the physiology and behavior of K. brevis may sup- port populations near the sediment-water interface, where they may grow undetected in offshore oligotrophic water columns.}, journal={MARINE ECOLOGY PROGRESS SERIES}, author={Sinclair, Geoffrey A. and Kamykowski, Daniel and Milligan, Edward and Schaeffer, Blake}, year={2006}, pages={125–131} }
 @article{sinclair_kamykowski_2006, title={The effects of physiology and behaviour on the near-bottom distributions of Karenia brevis on the West Florida shelf: a numerical study}, volume={28}, ISSN={["1814-2338"]}, DOI={10.2989/18142320609504178}, abstractNote={The distribution of near-bottom populations of Karenia brevis depends on both cell physiology and behaviour. The migration distance of cells, and the subsequent exposure to light, may vary as a result of the nocturnal uptake of nitrate. The adaptive advantage of higher nocturnal uptake rates and upward migration is evident in clear deep (90m) water columns as well as in shallower (30m), more turbid water columns. In deeper offshore environments, migrating cells with high nocturnal uptake rates are able to access light levels needed to compensate growth, whereas migrating cells with slow nocturnal uptake rates or non-migrating cells cannot access the minimum light levels needed for growth. In shallow, more turbid environments, migrating cells access between 35% and 67% of the light needed to saturate growth, whereas cells that do not migrate are only exposed to 6% of the light needed to saturate growth. Vertical migration may not only extend the depth distribution of K. brevis but also provide an adaptation to persist in more turbid nearshore waters.}, number={2}, journal={AFRICAN JOURNAL OF MARINE SCIENCE}, author={Sinclair, G. A. and Kamykowski, D.}, year={2006}, month={Sep}, pages={361–364} }