How it works

AREE is a working pipeline, not a literature summary. It has five connected layers:

1. Study registry and intake. Each public dataset gets a machine-readable registration using controlled vocabularies for phenotypes, stressors, tissues, and life stages, so “heat stress” means the same thing across studies.
2. Standardized reanalysis. Nextflow workflows reprocess RNA-seq, DNA methylation, proteomics, and metabolomics data, either from raw reads or from authors’ published results tables.
3. Cross-study harmonization. Everything lands in one shared evidence schema, with gene identifiers mapped to a common reference and every mapping labeled with an explicit confidence level.
4. Meta-analysis and prioritization. Random-effects meta-analysis pools results across studies, with heterogeneity statistics and a transparent candidate score broken into named components (number of supporting studies, direction agreement, effect size, and more). Hard gates mean no candidate reaches the top tier without independent replication.
5. User-facing outputs. A live dashboard, an in-browser Explore page for querying the evidence tables, per-gene evidence cards, and tools that let AI assistants such as Claude query the evidence directly.

An evidence engine, not a claims engine

The design principle we care most about is honesty. AREE identifies associations and convergence across studies and molecular layers. It never presents a significant hit in a single study as a validated biomarker. A few ways that shows up:

• Resilience is kept separate from stress response. A gene that responds to heat tells you an animal is stressed. A gene that already differs between resilient and susceptible animals before any stress is what a breeder can actually use. AREE labels every candidate by what kind of evidence supports it and keeps these classes apart.
• Disagreement is surfaced, not averaged away. When studies point in opposite directions, that conflict appears on the evidence card.
• Provenance is tracked everywhere. Every result traces back to its source file, checksum, parameters, and workflow version, and published supplementary tables are converted by committed, re-runnable scripts rather than copy and paste.
• Simulated data stays quarantined. Demo datasets used to test the pipeline are clearly labeled and excluded from real findings.
• It says what it doesn’t know. Missing metadata, uncertain identifier mappings, and low replication are recorded and reported. The project even keeps a candid implementation status page that lists what is finished, what is only scaffolded, and what it previously got wrong.

Where things stand

As of a mid-October 2026 snapshot, AREE had registered 30 real public studies with 69 experimental comparisons, and harmonized more than one million evidence records from 16 of those studies across RNA-seq, methylation, and proteomics. That includes our first full raw reanalysis, an OsHV-1 challenge study, in which per-sample viral read QC caught an infected control animal that is now excluded from the analysis. Cross-study pools already exist for oyster disease susceptibility (up to five studies), oyster thermal tolerance, and Manila clam thermal tolerance, with work underway to bring in more mussel and clam species. The dashboard is regenerated from the pipeline’s own outputs on every update, so check it for current numbers.

Why it matters

For breeding programs and hatcheries, a candidate marker that will inform selection decisions needs a paper trail that a skeptical geneticist can follow back to source data. For researchers, AREE means the next public dataset can be added with a registration file and a handful of commands, rather than another one-off reanalysis. And for the field, it turns years of publicly funded sequencing into a shared, growing resource.

Get involved

AREE is open source, and we welcome new datasets, species, and contributors.

• Dashboard and documentation: https://sr320.github.io/AREE/
• Code: https://github.com/sr320/AREE
• Have a public shellfish omics dataset that should be included? The documentation includes a step-by-step guide to adding a study, or just get in touch.

From correlations to mechanism

Most environmental epigenetics studies (including plenty of ours) are correlational: expose animals to a treatment, profile marks, and look for differences that line up with the environment or with gene expression. That approach has been productive, but it leaves the mechanism as a black box.

Led by Holly Moeller and Roger Nisbet at UC Santa Barbara, this work flips the order. We built an individual-based stochastic simulation in which each organism carries a string of genomic “sites” that are either marked or unmarked, and the environment has its own string describing the best-matched epigenetic state. An organism’s stress is simply the fraction of sites that are mismatched with the environment. The more stressed an organism is, the faster it remodels: marks are added and removed site by site, partly at random and partly “preferentially” at sites the organism can tell are wrong. The model is deliberately agnostic about whether a site is a single CpG, a gene, or a cluster of co-regulated marks, and about whether a mark activates or represses expression.

That framework let us ask three questions, each paired with a look at the empirical evidence in marine invertebrates and a clear statement of what is still unknown.

1. Tracking the environment requires site-level information

Without any information about which sites are mismatched, organisms never do better than chance: stress hovers around 0.5, the expectation for a random epigenome. Give them that information, and populations drop to roughly 15% mismatch within about 100 time steps, spike when the environment shifts, and then recover. The more an organism can separate preferential from random mark removal, the better it does.

This lines up with patterns we and others have seen. Pteropods (Limacina antarctica) lose DNA methylation after acute low pH exposure and return to baseline within 6 days. Heat-stressed Acropora cervicornis methylation profiles diverge and then become indistinguishable from controls 8 days after the stress ends. Oysters, geoduck, and corals all show methylation shifts with acidification. What we still lack is the mechanism: how does an animal translate an environmental cue into a targeted change at the right sites?

2. Adding and removing marks must be coupled

If mark addition and removal get out of balance, an organism either strips its genome bare or marks everything, and either way ends up badly mismatched. Using a simple evolutionary algorithm (the most stressed individual dies, the least stressed reproduces, removal tendencies occasionally mutate), we found that higher addition tendencies always require proportionally higher removal tendencies. The exact balance depends on the environment: settings that call for few marks favor stronger removal.

Biochemically, addition and removal are handled by different enzymes (DNMTs versus TETs for DNA methylation; HATs, HDACs, and histone demethylases for histone marks), and both cost energy. How organisms coordinate these pools is an open question, and one we think ties epigenetics directly to an animal’s energetic state.

3. Epigenetic tracking only works in some environments

We then let the environment shift in predictable ways, varying both how often it changes and how much. Organisms with good environmental information can follow infrequent changes, even big ones (“abrupt jumps”), and frequent changes if they are small (“slow and steady”). Frequent, large changes push stress back toward random.

This leads to a prediction we are excited to test: lineages from highly variable habitats (intertidal zones, estuaries) should lean more heavily on epigenetic regulation than close relatives from stable ones. Oysters are a natural system for this, with Eastern and Pacific oysters living in fluctuating estuaries while relatives such as Crassostrea nippona occupy more stable coastal waters. We also argue that the environmental changes most likely to select for epigenetic responses are reversible ones that recur on the order of a generation or two.

Where the field goes next

The paper closes with a call for experiments designed around mechanism rather than endpoints:

• High-resolution time series after a defined stressor, measuring physiology, gene expression, and epigenetic state together, repeated across lineages and species.
• Quantifying the epigenetic machinery (DNMT, TET, HAT, HDAC, and HDM abundance and activity) to see how addition and removal are coupled.
• Phylogenetically controlled comparisons of lineages from stable versus variable environments, using common garden and reciprocal transplant designs.

For our lab, this is a roadmap. It pushes us toward designs that manipulate the timing and predictability of environmental change, measure mark removal as carefully as mark addition, and follow individuals through time rather than relying on single snapshots.

A collaborative effort

This paper came out of the NSF Understanding the Rules of Life: Epigenetics program, bringing together modelers and empiricists: Holly Moeller and Roger Nisbet (UC Santa Barbara), Hollie Putnam (University of Rhode Island), Ross Cunning (Shedd Aquarium), Jose Eirin-Lopez (Florida International University), and our group at the UW School of Aquatic and Fishery Sciences. Bringing explicit mathematical frameworks together with empirical data is, we argue, exactly what the field needs to move forward.

Learn more

• Full paper (open access): https://doi.org/10.1093/eep/dvag032
• Model code: https://doi.org/10.5281/zenodo.23108257
• Summary video and more: Genefish post
• Preprint: https://doi.org/10.64898/2026.01.08.698487

Figures reproduced from Moeller et al. (2026) under a CC BY-NC 4.0 license.

Hannah Nowers — Cracking the case of the wasting sea stars 🌟

Sea star wasting disease has wiped out 20+ species from Alaska to Baja, melting animals into goo. The obvious hypothesis: maybe the susceptible species just don’t have enough immune genes. Hannah put that idea to the test, combing through annotated sea star genomes and sorting immune genes into functional categories. The plot twist? Gene count isn’t the answer. Susceptible and resistant species carry similar immune gene arsenals — so the real story is about how those genes are switched on and off, not how many there are. One clean result, and suddenly the whole field is asking a better question.

Download Hannah’s capstone presentation (PDF) · Read Hannah’s capstone paper (PDF) · GitHub repo

Noah Ozguner — Do oysters get stressed when you shake them? 🦪

Oyster farmers “tumble” their oysters to sculpt prettier shells — but is it secretly stressing the animals out? Noah grabbed two sizes of oyster seed, gave them a 20-minute shake, and tracked their metabolism for a week with a color-changing assay. Tiny oysters? Totally unbothered. But the big ones threw a delayed metabolic curveball — no reaction at first, then a dramatic spike a full week later (p = 0.0006). Turns out bigger oysters carry a hidden energetic hangover, and it shows up on a timer.

Download Noah’s poster (PDF)

Hazel Abrahamson-Amerine — What a heatwave does to an oyster’s fuel tank 🔥

Oysters bank energy as glycogen — their cellular savings account. Hazel asked what happens to that account during a marine heatwave. Using a glow-in-the-dark glycogen assay, they cranked oysters to 32 °C for 48 hours and watched the reserves crash. The hopeful part: give them a break from the heat, and they slowly rebuild the stash. Recovery is real — it just takes time. Next up: where in the body it happens, and whether oysters toughen up for round two.

Download Hazel’s presentation (PDF)

Christina Zhang — Can oysters be trained to take the heat? 🌡️

If a heatwave hits twice, does surviving the first one help with the second? Christina tested whether oysters can be “primed” — toughened up by an earlier non-lethal heat exposure. She gave Pacific oyster seed different thermal histories (cool or hot, then cool or hot again) and read out their metabolism across a temperature gradient. The verdict: priming changes the game. Below 35 °C, primed oysters ran a calmer, lower metabolic response — a sign of tolerance — while unprimed oysters spiked. But push past 37 °C and the stress response overrides any priming benefit, and mortality climbs. Oysters can learn to take the heat, but only up to a point.

Download Christina’s poster (PDF)

Four students, four big swings, four home runs. Congrats Hannah, Noah, Hazel, and Christina — the lab is lucky to have you. 🎉

Defense Recording

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.

The Early Response: Turning Up the Cellular Machinery

At 8 hours, snow crab were already responding at the molecular level.

Across both moderate and severe acidification treatments, genes involved in:
• mitochondrial metabolism
• electron transport
• protein refolding (heat shock proteins)
• cuticle maintenance
• immune modulation

were strongly activated.

The response was especially pronounced under severe acidification.

Figure 3. Short-term differential gene expression (8 hours) (Spencer et al. 2026)

The volcano plots show a clear pattern: severe acidification triggers a broader and stronger transcriptional response than moderate acidification. Mitochondrial and protein homeostasis pathways dominate.

This is not a passive response. Snow crab rapidly increase energy production and activate cellular repair systems. Tolerance, in this case, appears to be an energetically expensive strategy.

⸻

Moderate vs. Severe: Adjustment or Damage Control?

The distinction between moderate and severe acidification is not simply one of degree — it is one of strategy.

Under moderate OA (pH 7.8), gene expression emphasized:
• ion and osmotic regulation
• solute transport
• endocrine coordination

This resembles regulatory adjustment — maintaining balance through coordinated physiological control.

Under severe OA (pH 7.5), expression shifted toward:
• DNA repair
• RNA processing and splicing
• heat shock proteins
• oxidative stress pathways
• chitin remodeling

This profile reflects cellular damage mitigation rather than fine-tuned regulation.

In other words:
• Moderate OA → compensation
• Severe OA → cellular defense

⸻

The Quiet Period Before Mortality

At 88 days — still well before survival diverged — gene expression patterns between moderate and severe treatments were already clearly different.

Figure 4. Differential expression at Day 88 (Spencer et al. 2026)

Under chronic severe acidification, genes involved in:

• RNA processing
• protein refolding
• DNA repair
• oxidative stress defense
• acid–base regulation

remained elevated.

Physiologically, the crabs appeared normal. Molecularly, however, a sustained stress signature persisted.

The companion long-term experiment showed that mortality under severe acidification began after ~250 days.

The molecular data suggest why: chronic cellular maintenance carries an energetic cost that accumulates over time.

Eventually, that cost may become unsustainable — particularly during molting, a process that demands substantial energy and structural remodeling.

⸻

A Molecular Early-Warning Signal

Among the genes elevated under long-term severe acidification, one stood out: carbonic anhydrase 7 (CA7).

Figure 5. Expression patterns of candidate genes (Spencer et al. 2026)

Carbonic anhydrases regulate acid–base balance. CA7 expression was specifically elevated under chronic severe acidification, making it a promising biomarker of ongoing OA stress.

If validated in field populations, CA7 could provide an early indicator of physiological strain before mortality increases.

⸻

Variability as Resilience?

Principal component analysis revealed another intriguing pattern: transcriptional variability increased under severe acidification.

Rather than shutting down metabolism — as seen in more sensitive species such as red king crab — snow crab maintained broad transcriptional activity.

This suggests that resilience may involve maintaining flexibility rather than suppressing activity. Transcriptional breadth could represent an adaptive strategy for coping with environmental change.

Figure 2. Global expression patterns (Spencer et al. 2026)

The PCA illustrates separation among treatments and highlights the stress-response and metabolic pathways driving that variation.

⸻

What This Means

Snow crab are not simply tolerant or sensitive. They are tolerant — up to a point.

Short-term exposure activates powerful metabolic and repair systems. Moderate acidification can be compensated for through regulatory adjustments. Severe acidification, however, induces sustained cellular stress that precedes visible effects by months.

This study reinforces a critical lesson:

Absence of early physiological change does not mean absence of impact.

Sublethal molecular stress can accumulate long before survival declines.

As high-latitude oceans continue to acidify, identifying these hidden thresholds becomes essential for predicting the future of snow crab populations and the fisheries that depend on them.

⸻

Citation

Spencer LH, Spies IB, Gardner JL, Roberts SB, Long WC (2026). Short-term mechanisms, long-term consequences: molecular effects of ocean acidification on juvenile snow crab. bioRxiv preprint 

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.

🌊 Introduction

Ocean acidification (OA) poses one of the most pressing threats to marine calcifiers. As CO₂ dissolves into seawater, pH declines and carbonate saturation drops — creating a chemical environment that makes it harder for larval shellfish to build and maintain shells. Early life stages, from embryos to D-veligers, are especially vulnerable.

A new paper by Emma Timmins-Schiffman et al. (2025) presents hopeful evidence that maternal signaling—the physiological messages passed from mothers to offspring—can help larvae weather these conditions. The study, published in Aquaculture, demonstrates that broodstock conditioning under low-pH conditions can increase larval survival and developmental success under ocean acidification.

👉 Read the paper here →

🧬 Study Overview

Overview of the experimental design. Adult broodstock clams were exposed to low or ambient pH for 78 days, which included the main gametogenic period. Broodstock pH response was assessed and clams were spawned, with eggs collected to measure maternal effects. Larvae were reared in a full factorial design, with larvae resulting from each broodstock treatment raised at both ambient and low pH.

The research team conducted a two-stage experiment:

1. Broodstock conditioning: Adult bivalves were exposed to either ambient or low-pH seawater for several weeks prior to spawning.
   
2. Larval challenge: Offspring from each broodstock treatment were reared under both ambient and acidified conditions.

This design allowed the authors to test for maternal carry-over effects — whether the experience of parents could influence offspring performance under stress.

📈 Key Findings

G and H show the reaction norms for larval survival at 7 and 14 days post-fertilization in larval ambient and low pH conditions, respectively. Panel I shows the percent normal shells for larvae reared in ambient conditions (left panel) versus low pH conditions (right panel) for days 2, 7 and 14 post-fertilization.

• Enhanced survival: Larvae from OA-conditioned parents showed higher survival under acidified conditions compared to larvae from ambient parents.
  
• Improved shell development: Morphological assessments indicated partial rescue of calcification deficits in OA-exposed larvae.
  
• Maternal provisioning: The authors suggest that biochemical or molecular cues—such as lipids, RNAs, or epigenetic marks—mediate this resilience.

Together, these results underscore the potential of broodstock conditioning as an applied tool for aquaculture and restoration.

⚗️ Mechanisms and Implications

Maternal signaling could occur via: - Differential energy or lipid provisioning to oocytes
- Altered mRNA or non-coding RNA content in eggs
- Epigenetic modifications that influence early developmental gene expression

Such carry-over effects represent a non-genetic inheritance mechanism that can modulate offspring performance in a changing ocean.

🐚 Relevance for Aquaculture and Restoration

For hatcheries and conservation programs, these findings offer practical guidance:

• Broodstock priming: Conditioning adults in mildly stressful environments could pre-adapt larvae to future ocean conditions.
  
• Selective breeding integration: Maternal conditioning could complement genetic selection programs.
  
• Ecosystem resilience: Field validation may help determine whether these benefits persist in natural, variable environments.

🔬 Future Directions

This study opens up rich avenues for follow-up research:

1. Molecular dissection: Use transcriptomics, lipidomics, and DNA methylation profiling to identify specific maternal signals.
   
2. Multi-stressor interactions: Test if benefits extend under warming, hypoxia, or nutrient stress.
   
3. Transgenerational persistence: Determine whether resilience carries into F₂ and beyond.
   
4. Trade-offs: Evaluate broodstock fecundity and energy costs associated with preconditioning.
   
5. Applied implementation: Assess the cost-benefit of maternal conditioning for commercial hatchery production.

💡 Broader Perspective

This work builds upon a growing body of literature demonstrating transgenerational plasticity in marine organisms.
It also resonates with ongoing efforts to integrate epigenetic and physiological tools into aquaculture resilience frameworks.

As the authors succinctly show, sometimes the best defense against future oceans lies in the memories mothers pass on.

📚 Reference

Timmins-Schiffman, E., et al. (2025). Maternal signaling boosts larval resilience under ocean acidification conditions. Aquaculture, Article 12748.
https://doi.org/10.1016/j.aquaculture.2025.12748

🌊 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

Why Germ Cells Matter for Aquaculture

Germ cells give rise to gametes (eggs and sperm) and are the cellular “gatekeepers” of reproduction. For marine aquaculture, the ability to reliably produce sterile animals is essential for:

• Preventing genetic introgression of hatchery lines into wild populations
• Minimizing ecological risk of non-native stock
• Improving meat quality and energy allocation in culture
• Increasing thermal and stress resilience during grow-out

Triploidy has been the only scalable sterility tool used in oysters to date, but its performance declines under environmental stress. This work opens the door to next-generation sterility strategies based on targeted disruption of germ cell formation — an approach already used successfully in some finfish species.

What the Team Discovered

Using droplet-based single-cell transcriptomics, the team tracked more than 29,000 embryonic cells across the earliest developmental stages. Dr. Gavery and Dr. Vandepas identified:

Importantly, the study not only confirmed known germline markers (vasa, nanos) but uncovered new PGC-associated genes unique to bivalves — now high-value candidates for future sterility research.

Gene Atlas

Their work bridges NOAA’s applied aquaculture mission and UW’s expertise in molluscan developmental genomics, resulting in the first single-cell molecular map of oyster development prior to the trochophore stage — a foundational resource for both aquaculture innovation and evolutionary developmental biology.

Single-cell transcriptional heterogeneity of early C. gigas embryos increases with developmental time. (A) Sampling design: cleavage-stage embryos were pooled into a single sample representing all cleavage stages. A sample of blastula-stage embryos were collected and sequenced in a separate library to allow the identification of the developmentally oldest cells in the pool. Gastrula-stage embryos sampled at 10 hpf for reference. (B) UMAP visualization of single-cell clustering of the cleavage (pre-blastula) + blastula stage (cb) that revealed 10 putative clusters. (C) UMAP visualization of single-cell clustering of the gastrula stage. Twenty-seven putative clusters representing broad cell types were resolved using UMAP clustering analysis (Cil, ciliated cells; Circ, circulatory system-related; Mes, undefined mesodermal derivatives; Mus, muscle-related; Neu, neuronal; PGC, primordial germ cell; SF, shell field; Un, undefined)

What Comes Next

This atlas now enables targeted functional studies of early germline pathways — the next step toward non-triploid sterility methods for sustainable shellfish aquaculture. The open-access dataset will also support comparative evo-devo research across molluscs and other invertebrates.

Source: Gavery, M.R., Vandepas, L.E., Saunders, L.M., Vadopalas, B., Luckenbach, J.A., Trapnell, C., & Roberts, S.B. (2025). Primordial germ cell specification and early developmental cell states in Pacific oyster. BMC Genomics 26:951.

Building Connections Through Art and Science

Working in small groups, students wrote, directed, photographed, and edited a geo-located guided walk through Golden Gardens Park, designed to reveal what remains hidden at high tide. Their final piece, The Golden Hour, is now publicly available on the Echoes app for anyone to experience—on-site or remotely.

To celebrate the culmination of the program, students led family and community members on their guided walk at Golden Gardens. This showcase not only highlighted their new knowledge but also allowed them to teach their families about the shoreline environment, reinforcing connections across generations.

Alongside the student projects, the team developed a flexible art + science curriculum, including community-building activities, photography and sound recording methods, and editing techniques. This content has already been shared at national conferences, sparking dialogue on how to integrate creativity and environmental learning.

Lasting Impact on Students and Community

The program’s impact can be seen in three ways:

• Student empowerment – Students gained literacy and comfort in their local environment, transforming initial unfamiliarity into curiosity and pride.
• Community engagement – Families participated enthusiastically in the showcase, with students confidently leading and teaching.
• Interdisciplinary learning – The program demonstrated how art can deepen science learning and strengthen environmental connection.

Feedback from both students and families revealed a surprising outcome: parents expressed interest in participating alongside their children. Future iterations will explore opportunities to involve families more directly.

What We Learned

EarthLab’s support made this interdisciplinary experiment possible. We learned how to foster curiosity in high school students outside of traditional grading systems, how to effectively blend art and science as teaching tools, and how to build trust and community in creative learning spaces.

For future rounds, we plan to lengthen the program, weave art and science even more tightly together, and expand opportunities for community members to take part. Continued mentorship with Garfield High School students is already underway, with plans to build on their intertidal research and experiential learning credits in spring 2025.

Looking Ahead

Deliverables from Intertidal Innovators will continue to grow. In addition to the Echoes guided walk, an ArcGIS StoryMap and a complete open-source curriculum will be available by early 2026, along with a media library of student-created photos, videos, and recordings.

We are grateful to EarthLab for supporting this innovative project, and to our collaborators—UW School of Aquatic and Fishery Sciences, UW DXARTS, Black in Marine Science, and Sea Potential—for making this work possible. Together, we’ve shown how art and science can inspire the next generation of environmental stewards.

Why This Matters

Marine ecosystems are on the front lines of climate change. From corals to clams, invertebrates must constantly adjust to stressors like heat waves, hypoxia, and ocean acidification. The paper highlights how metabolic and lipidomic tools can:

• Detect subtle but critical energy shifts before mortality occurs.

• Reveal differences in resilience between species, populations, and even sexes.

• Provide early biomarkers of stress tolerance that can inform conservation and aquaculture.

A Framework for Best Practices

Recognizing that metabolomic and lipidomic studies are still emerging in marine biology, Venkataraman and Huffmyer provide a roadmap for experimental design and analysis. Their recommendations include:

• Careful sampling and preservation to prevent artifacts.

• Strategic use of targeted, semi-targeted, or untargeted analyses.

• Embracing time series designs to capture dynamic shifts.

• Integrating molecular data with physiological and phenotypic metrics.

They also call for multi-omic integration—combining metabolomics and lipidomics with gene expression, epigenetics, and physiology—to link molecular mechanisms with whole-organism outcomes

Looking Ahead

The Perspective synthesizes findings from 68 studies published between 1993 and 2025, showing both how far the field has come and where opportunities lie. Importantly, it underscores that the marine science community must embrace metabolic complexity if we are to anticipate and mitigate the impacts of climate change on ecosystems.

By providing this framework, Venkataraman and Huffmyer hope to spark more rigorous, reproducible, and integrative research—work that can help answer one of the defining questions of our time: how will marine life persist in a rapidly changing ocean?

👉 Read the full article here: Interrogating Metabolic Plasticity in Marine Organisms: A Framework for Best Practices Using Metabolomic and Lipidomic Approaches

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.

A Scalable, Gene-Silencing Alternative to Triploidy

While triploidization and genetic modification have been explored for sterility induction, both come with drawbacks—triploid fish can still be partially fertile, and GM fish face regulatory and public acceptance hurdles.

Instead, Dr. Yanagitsuru and collaborators used a Morpholino oligomer (MO) attached to a Vivo transporter to silence the dead end (dnd) gene—a critical regulator of primordial germ cell formation. The innovation lies in delivering this compound through a simple bath immersion, rather than invasive microinjection or genetic alteration.

Results: A Step Toward Sterile, Sustainable Farming

In controlled hatchery trials, sablefish eggs treated with the dnd-MO-Vivo compound before fertilization produced a subset of individuals that were completely sterile (8%) or had drastically reduced numbers of reproductive cells (18%). Importantly, sterile individuals developed normally in all other respects: they showed no major differences in growth, sex steroid hormone levels, or survival under semi-commercial rearing conditions.

Key findings include:

• Target specificity: dnd expression was limited to gonads and unfertilized eggs, confirming its value as a marker for germ cell presence.

• No adverse health effects: Sterile fish were physiologically indistinguishable from fertile fish in terms of somatic growth and overall condition.

• Higher efficacy pre-fertilization: The sterility induction was more effective when the treatment was applied before fertilization, likely due to increased permeability of the egg chorion.

Why It Matters

This method opens a new path for scalable, publicly acceptable sterility induction in marine finfish aquaculture. By eliminating the reproductive capability of escapees, it reduces ecological risk and helps safeguard the genetic integrity of wild populations—while also offering potential gains in growth efficiency and product quality for farmers.

Sablefish, already known for its rich flavor and high omega-3 content, now also stands to become a model species for innovative, sustainable aquaculture practices.

What’s Next?

The authors emphasize that further optimization is needed to improve sterility rates and ensure consistent results across large-scale operations. Future research will likely explore different concentrations, immersion times, and additional species to assess broader applicability.

But for now, this work—driven by Dr. Yanagitsuru’s leadership—marks an important milestone in the development of non-GMO solutions to one of aquaculture’s biggest challenges.

Citation:

Yanagitsuru, Y.R., Hayman, E.S., Fairgrieve, W.T., Zohar, Y., Wong, T-T., & Luckenbach, J.A. (2025). Proof-of-concept for sterility induction in sablefish (Anoplopoma fimbria) via a scalable immersion-based gene silencing approach. Aquaculture, 609, 742945. https://doi.org/10.1016/j.aquaculture.2025.742945

Podcast Episode featuring work: https://podcasts.apple.com/us/podcast/gene-pooling/id1802677296?i=1000718173868

🦪 Genevieve Buchanan: Thermal Tolerance in a Stressful World

Genevieve’s project, “Effects of Salinity and Ocean Acidification Stress on Pacific Oyster (Magallana gigas) Thermal Tolerance”, examined how prior exposure to low salinity and acidic conditions influences oyster survival during subsequent heat stress. Pacific oysters are economically vital to aquaculture industries and ecologically foundational to coastal ecosystems, yet they face increasing threats from climate change-induced stressors.

Through a carefully controlled experiment using oysters from the Point Whitney Shellfish Hatchery, Genevieve tested whether low pH or reduced salinity exposure would compound mortality under acute thermal stress. Her findings showed that, surprisingly, these prior stressors did not significantly impact thermal tolerance. This suggests that Pacific oysters may be energetically adapted to the variable conditions of the Pacific Northwest, offering a glimmer of hope for aquaculture resilience in the face of climate extremes.

🔗 Watch Genevieve’s full presentation on YouTube

📄 Download Genevieve’s Presentation Slides (PPTX)

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🧵 Henry Berg: Mussel Threads and Climate Stress

Henry’s capstone, “Physiological Markers Associated with Byssus Attachment Following Environmental Perturbations in Marine Mussels”, focused on the byssal threads that mussels use to anchor themselves to surfaces—an essential trait for survival and aquaculture yield.

Comparing Mytilus trossulus and Mytilus galloprovincialis, Henry exposed mussels to ocean acidification, warming, and hypoxia, then measured thread production and metabolic rates. His results were striking: ocean acidification increased thread production in both species, while warming favored M. galloprovincialis. Hypoxia, however, drastically reduced thread output, particularly in M. galloprovincialis. These species-specific responses highlight the complexity of climate resilience and point to potential physiological markers that could inform aquaculture site selection and selective breeding strategies.

🔗 Watch Henry’s full presentation on YouTube

📄 Download Henry’s Presentation Slides (PPTX)

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A Proud Moment for Undergraduate Research

Projects were conducted under the guidance of Ariana Huffmyer and Matt George, respectively, and reflect the high caliber of undergraduate research in our lab. We are incredibly proud of Genevieve and Henry—not only for their scientific contributions but also for their clarity, creativity, and commitment to advancing our understanding of marine organism resilience in a changing world.

Please take a moment to view their presentations and join us in celebrating their accomplishments.

Zachary Bengtsson – NW CASC Fellow

Zach has been awarded a Northwest Climate Adaptation Science Center (NW CASC) Fellowship, joining a distinguished cohort of graduate researchers from institutions across the Northwest. His project, titled Developing computational tools for genetic risk assessment of Olympia oyster (Ostrea lurida) populations in the Puget Sound, focuses on advancing genetic tools that help guide the sustainable restoration of Washington’s native oyster.

Zach’s research integrates environmental drivers of local adaptation, hatchery management, and climate resilience to evaluate how restoration practices affect the genetic diversity of wild oyster populations. The selection committee praised his proposal for its clear relevance to stakeholder needs—highlighted by strong support from the Washington Department of Fish and Wildlife—and his deep commitment to co-produced, actionable science. His work will provide valuable tools for conservation managers as they balance ecological recovery with long-term resilience in Puget Sound estuaries.

Kathleen Durkin – Smithsonian Fellow

Kathleen has received a fellowship to conduct groundbreaking research at the Smithsonian National Museum of Natural History, where she will pioneer the use of nanopore sequencing to map DNA methylation in archival coral specimens. Her project represents one of the first efforts to explore historical DNA methylation (hDNA) in invertebrates using museum collections.

Drawing from coral samples that span over a century of collection history, Kathleen’s work will assess how epigenetic changes—particularly DNA methylation—can offer insights into coral stress responses and environmental resilience over time. By applying Oxford Nanopore Technology’s direct sequencing platform, she aims to overcome the limitations of traditional bisulfite sequencing in degraded DNA and establish a robust method for tracking historical epigenomic signatures.

This innovative research will not only advance our understanding of coral adaptation during a period of unprecedented climate change but also expand the utility of natural history collections for modern genomic and conservation science.

These fellowships reflect the drive and creativity that Zach and Kathleen bring to their work, and we are excited to watch their projects unfold over the coming year. Their success exemplifies the kind of interdisciplinary, forward-thinking science that will shape the future of marine conservation and climate adaptation.

Please join us in congratulating Zachary and Kathleen on these outstanding achievements!