robertslab.info https://faculty.washington.edu/sr320/ quarto-1.7.32 Thu, 19 Mar 2026 07:00:00 GMT Unlocking the Secrets of Tunicate Stress Responses Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-celeste/ We are thrilled to highlight the incredible work of Celeste Valdivia, who recently defended her Master of Science thesis at the University of Washington’s School of Aquatic and Fishery Sciences. Co-advised by Dr. Alison Gardell and Dr. Steven Roberts, Celeste’s research dives deep into the biology of the globally invasive marine tunicate, Botryllus schlosseri. Her innovative work lays a crucial foundation for overcoming a decades-long hurdle in marine biology: the development of the first immortalized marine invertebrate cell line.

A Unique Strategy for Surviving Toxic Stress To understand the cellular mechanisms that might allow tunicate cells to become immortalized, Celeste first evaluated how whole colonies of B. schlosseri respond to oxidative stress caused by nickel. Astonishingly, she discovered that this species is highly tolerant to nickel toxicity, establishing an acute 24-hour lethal concentration (LC50) of roughly 177 mg/L—among the highest tolerance levels ever recorded for a marine invertebrate in artificial seawater.

Instead of generating a massive, traditional antioxidant response to combat this severe stress, Celeste found that B. schlosseri employs a systemic survival strategy. At high nickel concentrations (100 mg/L), the colonies entered “blastogenic arrest”—halting their weekly asexual reproductive cycle and pausing the development of new buds. Through transcriptomic (RNA-seq) analysis, Celeste revealed that the colonies tightly coordinated this response by modulating developmental signaling pathways, inhibiting apoptosis, and remodeling their extracellular matrix (ECM) and vasculature. By putting reproduction and generational turnover on pause, the colony effectively mitigates its endogenous oxidative burden to survive the toxic environment.

Innovations in Cell Culture and Unexpected Discoveries Translating these findings from the whole organism to a petri dish, Celeste significantly advanced in vitro primary epithelial cell culture methods for the species. She implemented a novel partial desiccation explantation technique that vastly improved tissue adherence to the plastic culture substrate, resulting in highly reliable and consistent epithelial monolayer growth from both zooids and primary buds.

When she challenged these cultured epithelial cells with acute nickel exposure, she made an unexpected discovery: the cultured cells were remarkably unfazed, displaying no morphological changes or increased cell death even at extreme concentrations.

However, this incredible resilience also extended to laboratory chemicals, posing a massive technical hurdle. When Celeste attempted to extract RNA from these cells for transcriptomic analysis, the cells vigorously resisted traditional mechanical and chemical lysis techniques. Under the microscope, she observed that the cultured cells were actively producing fibrous, tunic-like secretions. Because the tunicate “tunic” is primarily composed of cellulose—a rigid structural carbohydrate typically found in plants—Celeste hypothesizes that these miniature biological shields not only protected the cells from the toxic heavy metals but also from laboratory lysis buffers.

Looking Forward Celeste’s findings provide fascinating insights into how colonial marine organisms regulate cell fate and maintain cellular integrity under extreme environmental stress. Her methodological troubleshooting has set the stage for future breakthroughs, with recommendations to incorporate cellulase enzyme treatments to bypass the protective tunic secretions in future transcriptomic workflows.

Supported by an NSF-BSF collaborative grant and conducted with partners at UC Davis and in Israel, Celeste’s thesis perfectly exemplifies the persistence, creativity, and adaptability required to pioneer new model systems in marine biology.

Congratulations, Celeste, on an outstanding Master’s thesis and defense!

Defense Recording

]]> tunicate cell https://faculty.washington.edu/sr320/posts/frontpage/sr320-celeste/ Thu, 19 Mar 2026 07:00:00 GMT Decoding Coral Gene Regulation: Tensor Decomposition and Elastic Nets Meet Marine Epigenetics Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-escience/ Coral reefs are among the most biodiverse ecosystems on the planet, and they are under siege. Rising ocean temperatures and other environmental stressors are reshaping coral communities in real time. But how exactly do corals respond to these changes at the molecular level? And can those responses be passed to future generations?

These are the questions driving the E5 Coral Project, a collaborative effort to predict the phenotypic and eco-evolutionary consequences of environmental-energetic-epigenetic linkages in reef-building corals. This week at the eScience Institute, we presented two computational approaches — developed through the eScience Incubator Program — that are giving us new ways to make sense of complex, multi-species molecular data. You can check out the slidedeck here.

Why Standard Tools Fall Short

If you work in genomics, you are probably familiar with tools like DESeq2 and edgeR for differential gene expression analysis. These are workhorses of the field, but they are built for pairwise comparisons: treatment vs. control, timepoint A vs. timepoint B. Our coral data has a richer structure — expression measured across multiple genes, multiple species, and multiple samples over time — that these tools cannot natively capture.

We needed methods that could discover coordinated expression patterns spanning all three of those dimensions simultaneously.

Barnacle: Sparse Tensor Decomposition for Multi-Species Expression

Enter Barnacle, a sparse tensor decomposition tool originally developed for marine metatranscriptomics. The idea is elegant: instead of flattening your data into a two-dimensional matrix, you represent it as a 3D tensor (Gene x Taxon x Sample) and decompose it into a small number of sparse components. Each component captures a distinct co-expression program — a group of genes that behave similarly across species and conditions.

The critical tuning decisions are:

  • How many components (rank)? Too few and you miss real signals; too many and you start fitting noise. We use a cross-validation strategy — fit on half the data, test reconstruction on the held-back half — to find the sweet spot.
  • How sparse? Sparsity controls which genes are assigned to each component. We use split-half reproducibility: if both halves of a random split identify the same core genes for a component, the sparsity threshold is keeping real members.

Applied to our E5 coral timeseries data, Barnacle revealed biologically meaningful components. One component, for example, aligned closely with known calcification genes — a result that would be difficult to extract from traditional pairwise analyses.

With these components in hand, we now have groups of co-regulated genes that we can interrogate for epigenetic regulatory patterns and use to test hypotheses about how environmental stress propagates through molecular networks.

The Epigenetic Layer: More Than One Regulator

Epigenetics — heritable changes in gene activity that do not alter the DNA sequence itself — is central to our project. In marine invertebrates, the epigenetic landscape includes:

  • DNA methylation — In contrast to mammals, marine invertebrate methylation is mosaic and concentrated in gene bodies rather than promoters.
  • Long non-coding RNA (lncRNA) — Regulatory RNA molecules numbering in the tens of thousands.
  • MicroRNA (miRNA) — Short regulatory RNAs that target messenger RNA for degradation or translational repression.

Each of these layers can influence gene expression, and they likely interact with each other. Simple pairwise correlations between a single epigenetic mark and expression only tell part of the story. We wanted a model that could integrate all three layers and identify which features — and which combinations — actually drive expression.

Elastic Net Regression: Predicting Expression from Epigenetics

This is where Elastic Net regression comes in. Elastic Net is a regularized regression method that blends two complementary penalties:

  • Lasso (the “harsh editor”) drives coefficients to exactly zero, performing feature selection by removing irrelevant predictors.
  • Ridge (the “compromiser”) shrinks correlated predictors together rather than arbitrarily choosing one, handling multicollinearity gracefully.

Our predictor space is formidable: roughly 50 miRNAs, 10,000 lncRNAs, and 20,000 gene-body methylation features, all predicting expression across approximately 40 samples per species. This is a classic p >> n problem, and Elastic Net is well suited for it.

We trained models using 80/20 train/test splits repeated across 50 replicates, validated predictions using noise injection (if the model is real, adding noise to predictors should degrade performance), and applied stability selection (Faletto and Bien 2022) to focus on features that are consistently selected across resampled datasets rather than artifacts of any single split.

Video

What We Found

The results are striking and represent, to our knowledge, the first integrated picture of multi-layer epigenetic regulation of gene expression in a marine invertebrate system:

  • Per-gene regulatory profiles reveal that individual genes differ substantially in which epigenetic features predict their expression. Some are primarily methylation-driven, others lncRNA-driven, and many are regulated by a combination.
  • High-level type compositions show systematic patterns in how regulatory strategies are distributed across the genome.
  • Regulatory network maps capture how epigenetic features interact, suggesting coordinated regulatory programs rather than independent, isolated effects.

Looking Ahead

This work is a starting point. The tensor decomposition framework can be extended to incorporate additional data types (e.g., lncRNA expression, genes found in fewer than all species), and the elastic net models can be refined as more samples and species are added. The broader goal — understanding how environmental stress rewires epigenetic regulation and whether those changes can be inherited — remains one of the most important questions in coral biology and climate adaptation.

We are grateful to the eScience Incubator Program and particularly to Vaughn Iverson for pushing us to think about our data in new ways. The combination of domain expertise in marine biology with data science methods has opened analytical doors that neither community would have found alone.

For more information, visit the E5 project and Barnacle documentation.

]]> machine learning ai https://faculty.washington.edu/sr320/posts/frontpage/sr320-escience/ Thu, 12 Mar 2026 07:00:00 GMT Epigenomics in Chile Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-epiaqua/ Last week I traveled to Chile to teach at the Austral Summer Institute and spend time with collaborators at the University of Concepción through our ongoing INCAR2 partnership. It was one of those trips that reminds me why I enjoy this work so much—bringing together students, colleagues, and real-world systems to explore how molecular biology connects to environmental change and aquaculture sustainability.

At the Summer Institute, I taught Epigenomics in Aquaculture (EpiAqua) to an outstanding group of graduate students and postdoctoral researchers from across South America. The course focused on how epigenetic mechanisms—especially DNA methylation and non-coding RNAs—mediate organismal responses to stress, and how these tools can be applied in aquaculture and climate resilience research.

Professor Rick Goetz giving lecture on phenotypic variation in trout.

What stood out most was the energy in the room. Students came from diverse backgrounds spanning ecology, physiology, genomics, and applied aquaculture, which led to thoughtful discussions about experimental design, data integration, and how to move from sequencing data to actionable insight. These kinds of exchanges are incredibly motivating—and they’re exactly how new collaborations and ideas begin.

After the course, I spent time at the University of Concepción continuing work with INCAR2 colleagues. Together we moved forward on several exciting new directions, including:

• Penguin epigenetics, exploring how environmental exposure may be reflected in epigenomic variation in wild populations.

• Sea lice sex determination, aimed at understanding molecular mechanisms that could inform management strategies in salmon aquaculture.

• Presence–absence variation (PAV) in trout ecomorphs, investigating how structural genomic differences may contribute to ecological specialization.

Each of these projects fits into our broader goal of linking genomics and epigenomics to physiology, performance, and resilience in aquatic organisms.

Following the academic portion of the trip, I also had the opportunity to visit salmon farms in southern Chile. Seeing production systems firsthand always adds important perspective—connecting lab-based molecular work to the environmental realities faced by farmers and managers. These visits reinforced why translational research matters: our models and datasets ultimately need to work in complex, real-world settings.

Visiting salmon farms in Puerto Montt

Overall, the trip was a great reminder of the value of international partnerships and immersive training environments. Teaching at the Austral Summer Institute and collaborating with INCAR2 continues to strengthen a shared vision around environmental memory, aquaculture sustainability, and training the next generation of scientists.

I’m grateful to our host, Dr. Cristian Gallardo and collaborators in Chile for their generosity and enthusiasm—and I’m excited to build on these new projects in the months ahead.

]]> teaching aquaculture https://faculty.washington.edu/sr320/posts/frontpage/sr320-epiaqua/ Fri, 30 Jan 2026 08:00:00 GMT Can Oyster Parents Prepare Their Offspring for What’s Next? Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-polyic/ New research from the Roberts Lab reveals that immune “training” in adult oysters can reshape how their offspring grow, metabolize energy, and survive extreme heat.

Marine heatwaves and disease outbreaks are increasingly hitting oyster farms and wild populations at the same time. For Pacific oysters (Magallana gigas), this deadly combination often shows up as summer mortality events, when up to 90% of animals can die in a matter of days. But what if oyster parents could “prepare” their offspring for these stressful conditions before they are even born?

A new study from our lab, led by Madeline Baird and Ariana Huffmyer provides exciting evidence that they can.

Training oyster parents’ immune systems

In this study, adult Pacific oysters were briefly exposed to Poly(I:C), a harmless synthetic molecule that mimics viral infection and activates the oyster immune system. This kind of immune priming has been shown to increase disease resistance in oysters—but here we asked a different question:

Does immune priming in parents change how their offspring handle heat and metabolic stress?

After the exposure, oysters were spawned, and their larvae were reared in commercial hatchery conditions and then grown into seed oysters over several months. These offspring were later tested for growth, survival under heat stress, and metabolic performance.

Faster growth in primed families

The first surprise was growth.

Although offspring from primed parents were slightly smaller early on, they grew faster over time and ended up larger than controls by 236 days post-fertilization. In other words, immune priming in parents altered how energy was allocated during development—suggesting a shift in developmental strategy.

This matters for hatcheries, where faster-growing seed often perform better during nursery and grow-out phases.

Heat survival depends on how hot it gets

Next, the team exposed oysters to temperatures ranging from normal conditions to extreme heat (up to 45°C) and measured survival.

The results were strikingly temperature-specific:

  • At 40°C, offspring from primed parents were 35% more likely to survive than controls 

  • At 42°C, however, those same primed offspring were more likely to die than controls 

This shows that immune priming doesn’t simply make oysters “tougher”—it reshapes where their thermal limits lie. In a warming ocean, that nuance matters.

Metabolism tells the story

Why did primed offspring survive better at 40°C but worse at 42°C? The answer appears to lie in their metabolism.

Using a high-throughput resazurin assay, the team measured how quickly oysters processed energy under different temperatures  .

They found:

  • At 36°C, primed offspring had 43% higher metabolic activity than controls

  • At 40°C, primed offspring showed lower metabolic activity than controls 

This pattern suggests that immune priming increases metabolic flexibility—the ability to ramp metabolism up under moderate stress and suppress it when conditions become extreme. That flexibility is likely what allows primed oysters to survive better at 40°C by entering a kind of protective metabolic slowdown, a known survival strategy in stressed marine invertebrates.

A form of environmental memory

These effects persisted for more than seven months after fertilization, long after early maternal provisioning should have faded. This points to deeper mechanisms of environmental memory, potentially involving:

  • altered maternal lipid and energy provisioning

  • immune-related transcripts passed into eggs

  • changes in microbiomes

  • epigenetic regulation (DNA methylation, non-coding RNAs) 

Together, these mechanisms may allow oysters to transmit information about parental stress environments directly to the next generation.

What does this mean for aquaculture?

This research opens the door to a new idea:

Hatcheries could condition broodstock before spawning to improve offspring performance.

Because Poly(I:C) can be delivered by simple immersion, it could be integrated into existing hatchery workflows as a scalable, non-invasive treatment. When paired with selective breeding, immune priming might help produce oyster seed that is more resilient to heatwaves and disease—two of the biggest threats to modern shellfish farming.

At the same time, the study makes clear that priming is not a magic bullet. Benefits depended strongly on temperature, and extreme heat erased them. Field trials and longer-term studies are needed before these tools can be used widely.

Why this matters

As oceans warm and pathogens spread, oysters are being pushed toward their physiological limits. This study shows that parents matter—and that immune experiences in one generation can shape how the next generation grows, survives, and uses energy.

That’s environmental memory in action.

And it may become one of our most powerful tools for building climate-resilient aquaculture in the decades ahead.

📚 Reference

Baird M, Huffmyer AS, Ozguner N, Roberts SB. Parental immune priming reshapes offspring growth, metabolism, and thermal tolerance in the Pacific Oyster. bioRxiv. https://doi.org/10.64898/2025.12.10.693539

]]> oyster aquaculture https://faculty.washington.edu/sr320/posts/frontpage/sr320-polyic/ Sun, 11 Jan 2026 08:00:00 GMT From Blue to Pink Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-pink/ In a new preprint titled From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters, Ariana S. Huffmyer and colleagues demonstrate a powerful yet elegant way to measure how oysters breathe, grow, and cope with stress — by watching a color change.

🌊 A New Colorful Window into Oyster Metabolism

Resazurin, a redox-sensitive dye used for decades in biomedical and microbial assays, shifts from blue to pink as it’s reduced by metabolic activity. Huffmyer et al. adapted this dye-based reaction — familiar to many cell biologists — to whole oysters, showing that fluorescence intensity closely tracks oxygen consumption and reflects metabolic performance at the organismal level .

The team developed a standardized, scalable protocol using multi-well plates and fluorometric readings to quantify metabolic rate across hundreds of individuals at once. This makes it one of the first high-throughput metabolic assays for live shellfish, an enormous advance for aquaculture and climate resilience research.

You can explore their detailed methods and ongoing assay development at the Roberts Lab Resazurin Assay Development site.

🔥 Metabolism Under Pressure: What the Color Shift Reveals

By exposing oysters (Crassostrea gigas and C. virginica) to temperature gradients and acute heat shocks, the researchers observed predictable “thermal performance curves” — metabolism peaked near 36 °C before declining sharply at higher temperatures. Notably, oysters that suppressed metabolism under extreme stress were more likely to survive, suggesting that metabolic depression is a hallmark of thermal resilience.

The assay also captured family-level differences in metabolic response, indicating that some oyster lineages are genetically predisposed to handle stress better than others. In a large-scale breeding experiment at the Virginia Institute of Marine Science, metabolic rates measured by resazurin correlated with predicted survival performance in selectively bred oyster families .

🧬 Why This Matters

Metabolic rate is one of the most fundamental indicators of animal health and stress, but it’s historically been difficult and time-consuming to measure in shellfish. The resazurin assay overcomes that bottleneck, offering:

  • High-throughput capability: hundreds of oysters per run

  • Low cost and minimal equipment (a simple plate reader suffices)

  • Compatibility with live animals — no lethal sampling required

  • Potential for integration with breeding and monitoring programs

These advantages make it a game-changer for aquaculture, ecology, and conservation, enabling rapid screening of stress resilience across populations and environments.

🌍 Toward Smarter, More Resilient Aquaculture

As marine ecosystems face intensifying heatwaves and acidification, tools like the resazurin assay can help hatcheries, farmers, and researchers identify the oysters most likely to thrive under stress. The study’s message is clear: color can tell a powerful physiological story.

Blue means rest. Pink means life. And somewhere between those hues lies the key to building a more resilient future for oysters — and the people who depend on them.

📘 Citation

Huffmyer, A. S., Ozguner, N., Baird, M., Elvrum, C., Kounellas, C., Dicksion, D., White, S. J., Plough, L., Gavery, M. R., Krebs, N., Walton, W., Small, J., Pitsenbarger, M., Ealy-Whitfield, H., & Roberts, S. (2025). From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters. bioRxiv. https://doi.org/10.1101/2025.11.06.686367

]]> oyster aquaculture resazurin https://faculty.washington.edu/sr320/posts/frontpage/sr320-pink/ Tue, 11 Nov 2025 08:00:00 GMT Building Resilient Oysters: Launching the SORMI Project Steven Roberts https://faculty.washington.edu/sr320/posts/frontpage/sr320-sormi/ We are excited to share that our proposal, Development of SORMI (Summer Oyster Resilience and Mortality Index): A Quantitative Tool for Improving Field Survival, has been funded through the Western Regional Aquaculture Center. This multi-institutional effort will address one of the most pressing challenges in shellfish aquaculture—recurrent summer mortality in Pacific oysters.

The Challenge

For decades, oyster growers across the West Coast have faced sudden, large-scale summer die-offs linked to rising seawater temperatures, disease, and other stressors. These events threaten farm productivity and the economic stability of the shellfish industry. Despite years of research, a single cause has never been identified. Instead, we are taking a new approach: focusing on why oysters survive rather than why they die.

What Is SORMI?

SORMI—the Summer Oyster Resilience and Mortality Index—will be a generalized stress resilience index for Pacific oysters. By integrating a suite of physiological and metabolic assays, the index will help predict which oyster families are most resilient under real-world conditions. This tool will directly support breeding programs and hatcheries, providing a practical way to select for survival and reduce the frequency of catastrophic summer mortality events .

Our Role at UW

At the Roberts Lab, our team will be leading development of innovative, high-throughput stress assays, including a new resazurin-based metabolic assay we have been refining as a cost-effective, scalable way to measure oyster metabolism. We will also work closely with partners to analyze stress resilience across hundreds of oyster families and link these traits to field survival outcomes. Our focus is on providing growers and breeding programs with actionable, science-based tools that are accessible and easy to implement.

Project Leadership and Partners

This project is led by Bobbi Hudson, Executive Director of the Pacific Shellfish Institute (PSI). The collaborative team brings together expertise and resources from across the region, including:

  • University of Washington (Roberts Lab) – stress physiology and assay development

  • USDA Agricultural Research Service (Neil Thompson, Pacific Oyster Genomic Selection project) – breeding program integration and genetic analysis

  • NOAA Fisheries (Mackenzie Gavery) – environmental physiology and genomics

  • California Sea Grant (Kevin Johnson, Cal Poly) – aquaculture extension and grower engagement

  • Industry partners – Goose Point Oyster Company (WA) and Hog Island Oyster Company (CA)

This broad coalition ensures the project is grounded in industry needs while pushing forward fundamental science .

Implications for the Shellfish Industry

The ultimate goal of SORMI is to give oyster growers a practical decision-making tool. With a reliable index, farmers could anticipate when their stocks are stressed and take proactive measures—harvesting before a mortality event, adjusting management practices, or prioritizing resilient broodstock. For breeding programs, SORMI will add a measurable, heritable trait that can accelerate development of hardier oyster lines.

In short, this project will help secure the future of West Coast oyster farming by turning science into survival.

]]> aquaculture stress https://faculty.washington.edu/sr320/posts/frontpage/sr320-sormi/ Fri, 05 Sep 2025 07:00:00 GMT