Berger
Cory A.
Berger
Cory A.
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ArticleDe novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression(Elsevier, 2021-01-29) Berger, Cory A. ; Steinberg, Deborah K. ; Copley, Nancy ; Tarrant, Ann M.Copepods are small crustaceans that dominate most zooplankton communities in terms of both abundance and biomass. In the polar oceans, a subset of large lipid-storing copepods occupy central positions in the food web because of their important role in linking phytoplankton and microzooplankton with higher trophic levels. In this paper, we generated a high-quality de novo transcriptome for Rhincalanus gigas, the largest—and among the most abundant—of the Southern Ocean copepods. We then conducted transcriptional profiling to characterize the developmental transition between late-stage juveniles and adult females. We found that juvenile R. gigas substantially upregulate lipid synthesis and glycolysis pathways relative to females, as part of a developmental gene expression program that also implicates processes such as muscle growth, chitin formation, and ion transport. This study provides the first transcriptional profile of a developmental transition within Rhincalanus gigas or any endemic Southern Ocean copepod, thereby extending our understanding of copepod molecular physiology.
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ArticleSensory conflict disrupts circadian rhythms in the sea anemone Nematostella vectensis(eLife Sciences Publications, 2023-04-06) Berger, Cory A. ; Tarrant, Ann M.Circadian clocks infer time of day by integrating information from cyclic environmental factors called zeitgebers, including light and temperature. Single zeitgebers entrain circadian rhythms, but few studies have addressed how multiple, simultaneous zeitgeber cycles interact to affect clock behavior. Misalignment between zeitgebers ('sensory conflict') can disrupt circadian rhythms, or alternatively clocks may privilege information from one zeitgeber over another. Here, we show that temperature cycles modulate circadian locomotor rhythms in, a model system for cnidarian circadian biology. We conduct behavioral experiments across a comprehensive range of light and temperature cycles and find that's circadian behavior is disrupted by chronic misalignment between light and temperature, which involves disruption of the endogenous clock itself rather than a simple masking effect. Sensory conflict also disrupts the rhythmic transcriptome, with numerous genes losing rhythmic expression. However, many metabolic genes remained rhythmic and in-phase with temperature, and other genes even gained rhythmicity, implying that some rhythmic metabolic processes persist even when behavior is disrupted. Our results show that a cnidarian clock relies on information from light and temperature, rather than prioritizing one signal over the other. Although we identify limits to the clock's ability to integrate conflicting sensory information, there is also a surprising robustness of behavioral and transcriptional rhythmicity.
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Working PaperFinal cruise report and post-cruise sample processing R/V Gulf Challenger “GC Mixo 23-02”(Woods Hole Oceanographic Institution, 2023-11-28) Alatalo, Philip ; Gast, Rebecca J. ; Tarrant, Ann M. ; Zuñiga, Rodrigo ; Berger, Cory A.A primary topic of interest in the field of biological oceanography is the role of planktonic productivity in the global carbon cycle. Over the past 20+ years, the traditional food web of algal production, zooplanktonic consumers and higher trophic level predators has been undergoing revision with a stronger understanding of the contributions made within the microbial loop. Of particular interest has been mixotrophy, the blurring of trophic mode assignments within the The overall goal of this cruise was to obtain a snapshot of the prevalence of mixotrophy within the Gulf of Maine and the potential contributions of mixotrophs to copepod diets. We proposed to accomplish this goal by sampling water and zooplankton from 3 stations.
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ThesisExploring circadian rhythms, food intake, and their interactions in marine invertebrates(Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, 2024-02) Berger, Cory A. ; Tarrant, Ann M.Circadian rhythms and energy metabolism are critical and interconnected components of animal physiology. Metabolic inputs like time of feeding modulate circadian clocks and behavioral and molecular rhythms. In turn, circadian clocks regulate metabolic processes, allowing animals to optimize energy usage on daily timescales. On longer timescales, animals require physiological responses to tolerate variation in food availability. Most of our mechanistic knowledge of these processes comes from terrestrial mammals and insects, while there are major knowledge gaps for marine invertebrates. My dissertation focuses on the interactions of circadian rhythms and metabolism in three marine invertebrate systems using a combination of behavioral, molecular, and bioinformatic approaches. In Chapter 2, to understand how sensory signals are integrated into circadian clocks, I test the effects of various light and temperature regimes on circadian rhythms in the sea anemone Nematostella vectensis. Misaligned light and temperature cycles severely disrupt behavioral rhythms and substantially alter the rhythmic transcriptome, particularly the expression of genes mediating metabolic processes. This illustrates how interactions between environmental cues shape circadian behavior and physiology. In Chapter 3, I develop a high-throughput behavioral system to study diel vertical migration (DVM) in the copepod Acartia tonsa. DVM is driven by tradeoffs related to food availability, but we do not fully understand how food availability affects this circadian process. Using high-resolution tracking software, I find that Acartia possesses group-level DVM-like circadian rhythms in the lab, and that these swimming rhythms are altered by time-restricted feeding. This illustrates that food availability can impact DVM via effects on circadian clocks. In Chapter 4, I analyze how polar copepods respond to starvation at the molecular level. I find that two species with distinct dietary strategies partially share a genetic toolkit to respond to starvation, whereas differences in their starvation responses may reflect different modes of lipid storage. I also use evolutionary analyses to show that starvation response genes are under selective constraint, underlining their importance to organismal fitness. In aggregate, this thesis provides insights into the circadian rhythms of marine organisms, explores how metabolism modulates circadian rhythms, and sheds lights on the physiological consequences of food availability in zooplankton.
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ArticleComparative analysis of the molecular starvation response of Southern Ocean copepods(Wiley, 2024-05-09) Berger, Cory A. ; Steinberg, Deborah K. ; Copeman, Louise A. ; Tarrant, Ann M.Large lipid-storing copepods dominate mesozooplankton biomass in the polar oceans and form a critical link between primary production and higher trophic levels. The ecological success of these species depends on their ability to survive periods of food deprivation in a highly seasonal environment, but the molecular changes that mediate starvation tolerance in these taxa are unknown. We conducted starvation experiments for two dominant Southern Ocean copepods, Calanoides acutus and Calanus propinquus, allowing us to compare the molecular starvation response between species. These species differ in life history, diet and metabolic traits, and expressed overlapping but distinct transcriptomic responses to starvation. Most starvation-response genes were species-specific, but we identified a conserved core set of starvation-response genes related to RNA and protein metabolism. We used phylotranscriptomics to place these results in the context of copepod evolution and found that starvation-response genes are under strong purifying selection at the sequence level and stabilizing selection at the expression level, consistent with their role in mediating essential biological functions. Selection on starvation-response genes was especially strong in our focal lipid-storing lineage relative to other copepod taxa, underscoring the significance of starvation tolerance for these species. We also found that certain key lipid enzymes (elongases and desaturases) have experienced diversification and positive selection in lipid-storing lineages, reflecting the unique lipid storage needs of these animals. Our results shed light on the molecular adaptations of high-latitude zooplankton to variable food conditions and suggest that starvation-response genes are under particularly strong sequence and expression constraints.