Biology subjects

Timmins-Schiffman, E. B.

Publications and source records attributed to Timmins-Schiffman, E. B..

4 recordsLinked to original sources

bioRxiv2025

Proteomic insights into the photobiology of the Hawaiian rice coral Montipora capitata in response to decreased light intensity

Reef-building corals are sessile marine organisms that inhabit a wide range of light habitats along depth gradients. As coral biology is often studied in the context of global change and changing temperatures, knowledge gaps persist in our understanding of the molecular and cellular pathways involved in the responses to other factors than temperature, such as light intensity, which decreases exponentially in the water column and gradually changes the environment. To fill this gap, we tested the response of the Hawaiian rice coral Montipora capitata to decreased light intensity in a field experiment in K[a]neohe Bay, Oahu, Hawaii, using Data-Independent Acquisition (DIA) proteomics. There was a significant effect of light intensity on both the coral and zooxanthellae proteomes. In the M. capitata host, 69 proteins differed significantly in abundance between light levels after two years. The 50 proteins identified as significantly more abundant in the control condition were mostly involved in mRNA and RNA processing, pointing toward a positive correlation between metabolic activity, growth rates and increased light levels. The 19 proteins identified as significantly more abundant in the shade treatment were associated with calcium transport and with the structure of key cellular components, such as cell membrane and cytoskeleton. By contrast, zooxanthellae showed only minor changes in protein abundances, with photosynthesis proteins more abundant in the shade treatment and enzymes involved in fatty acid metabolism more abundant in the control treatment. Overall, these findings establish a baseline for our understanding of the cellular and metabolic processes driving Montipora capitatas acclimatization potential to different light intensities.

ecology↗

bioRxiv2024

Resilience in a time of stress: revealing the molecular underpinnings of coral survival following thermal bleaching events

Coral bleaching events from thermal stress are increasing globally in duration, frequency, and intensity. Bleaching occurs when a corals algal symbionts are expelled, resulting in a loss of color. Some coral colonies survive bleaching, reacquire their symbionts and recover. In this study, we experimentally bleached Montipora capitata colonies to examine molecular and physiological signatures of intrinsic differences between corals that recover (resilient) compared to those that die (susceptible). All colonies were collected from the same bay and monitored for eight months post-bleaching to identify specific colonies exhibiting long-term resilience and survival. Using an integrated systems-biology approach that included quantitative mass spectrometry-based proteomics, 16S rRNA of the microbiome, total lipids, symbiont density and diversity, we explored molecular-level mechanisms of tolerance in pre- and post-bleached colonies and found biomarkers of resilience that can confidently identify resilient and susceptible corals before thermal-induced bleaching events. Prior to thermal stress, resilient corals were characterized by a more diverse microbiome and increased abundances of proteins involved in multiple carbon and nitrogen acquisition strategies, symbiont retention and acquisition, and pathogen resistance. Susceptible corals had early signs of symbiont rejection and had resorted to utilizing urea uptake pathways for carbon and nitrogen. Further, molecular signatures identified prior to bleaching were amplified after bleaching, suggesting these pathways may be deterministic in a colonys fate. Our results have important implications for the future of reefs, revealing molecular factors necessary for survival through thermally-induced bleaching events and providing diagnostic biomarkers for coral reef management. Significance statementCorals are being negatively impacted by the increase in the number and duration of thermal-induced bleaching events. There are, however, some individuals within a single species that will bleach and, after time, reacquire symbionts and physiologically recover while neighboring colonies will die. Here, we used a multidisciplinary approach to understand the biochemical details of the physiological changes of resilient and susceptible Montipora capitata to thermal-induced bleaching. Resilient corals were characterized by their use of multiple carbon and nitrogen acquisition strategies, metabolically active symbiont relationships, abundant antiviral proteins, and a diverse microbiome. We reveal a multi-factor molecular-level approach for confidently identifying resilient and susceptible coral colonies so that environmental managers can rapidly select quality candidates for propagation while in the field.

ecology↗

bioRxiv2019

Dynamic Response in the Larval Geoduck Clam Proteome to Elevated pCO2

Pacific geoduck clams (Panopea generosa) are found along the Northeast Pacific coast where they are significant components of coastal and estuarine ecosystems and the basis of a growing and highly profitable aquaculture industry. The Pacific coastline, however, is also the sight of rapidly changing ocean habitat, including significant reductions in pH. The impacts of ocean acidification on invertebrate bivalve larvae have been widely documented and it is well established that many species experience growth and developmental deficiencies when exposed to low pH. As a native of environments that have historically lower pH than the open ocean, it is possible that geoduck larvae are less impacted by these effects than other species. Over two weeks in larval development (days 6-19 post-fertilization) geoduck larvae were reared at pH 7.5 or 7.1 in a commercial shellfish hatchery. Larvae were sampled at six time points throughout the period for a in-depth proteomics analysis of developmental molecular physiology. Larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development. Competency for settlement was also delayed in larvae from the low pH conditions. A comparison of proteomic profiles over the course of development reveal that these differing phenotypic outcomes are likely due to environmental disruptions to the timing of molecular physiological events as suites of proteins showed differing profiles of abundance between the two pH environments. Ocean acidification likely caused an energetic stress on the larvae at pH 7.1, causing a shift in physiological prioritization with resulting loss of fitness.

molecular biology↗

bioRxiv2016

Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation

Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product along the eastern Pacific coast from Baja California, Mexico to Alaska. These long-lived clams are highly fecund, though sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. Development of assays of gonad physiology could indicate sex and maturation stage, as well as be used to assess the status of natural populations. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data dependent acquisition (DDA) of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data was used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to determine geoduck gonad maturation status. Application of SRM in hemolymph samples demonstrates this procedure could effectively be used to assess reproductive status in marine mollusks in a non-lethal manner.

physiology↗