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A recent study from Rachel L. Malison and colleagues at the University of Montana published in Freshwater Science investigated how stoneflies living in thermally stable alluvial aquifers and more variable benthic surface waters differ in their physiological responses to increasing temperatures. The work addresses an important question for freshwater ecology: does exposure to different levels of natural temperature variation influence how species cope with warming?

River floodplains provide a particularly interesting system for studying this question. Benthic stoneflies living in surface waters experience substantial daily and annual temperature fluctuations, while stoneflies inhabiting alluvial aquifers spend much of their lives in comparatively stable groundwater. According to the climate variability hypothesis, species evolving under stable conditions may develop narrower thermal tolerances, potentially making aquifer species more sensitive to warming.

To investigate this, the researchers compared five benthic and three aquifer stonefly species collected from three river floodplains in Montana. Rather than relying on a single measure of thermal tolerance, they combined critical thermal maximum (CT_MAX) measurements with metabolic rate across increasing temperatures.

Central to the metabolic measurements was an 8 chamber Loligo Systems resting respirometry system. Individual stoneflies were placed in glass respirometry chambers, where oxygen consumption was measured using optical oxygen sensors and AutoResp software. Intermittent respirometry measurements were performed at nine temperatures ranging from 6°C to 30°C, providing metabolic profiles across the thermal range.

The results showed a clear difference in acute thermal tolerance. Benthic stoneflies had CT_MAX values approximately 5°C higher than aquifer species, suggesting that species accustomed to greater temperature variability may tolerate acute warming better.

However, the respirometry experiments revealed a more nuanced picture. Despite their difference in CT_MAX, aquifer and benthic stoneflies showed surprisingly similar metabolic responses as temperatures increased. There was no clear difference between the groups in the temperature at which metabolic rates peaked or in the breadth of their metabolic performance curves.

The study highlights why multiple physiological measurements are important when assessing climate vulnerability. CT_MAX provided a clear indication that aquifer stoneflies were more sensitive to acute warming, while respirometry showed that the metabolic responses of the two groups were considerably more similar. Taken together, these measurements provide a more complete understanding of how different freshwater species may respond to rising temperatures.

The paper, “Comparative vulnerability of riverine benthic and aquifer stoneflies as the climate warms,” was published in Freshwater Science and can be found online at https://doi.org/10.1086/742841

Do you want to learn more about the respirometry tools used in this paper?

• Resting respirometry systems
• Witrox oxygen meters
• AutoResp™ respirometry software

A recent study published in Journal of Thermal Biology provides the first experimentally derived thermal optimum for octopus paralarvae and offers new insight into one of the most challenging stages of cephalopod aquaculture. The research focused on the gloomy octopus (Octopus tetricus) and investigated how temperature affects metabolic performance during the first four days after hatching.

The work addresses a fundamental problem in both aquaculture and ecology. Survival during the paralarval stage remains a major bottleneck for octopus culture, while warming ocean temperatures may increasingly affect the early life stages of cephalopods. Temperature influences developmental rate, metabolic demand, yolk utilisation, feeding success, and ultimately survival. Understanding the thermal requirements of paralarvae is therefore essential for improving rearing protocols and assessing how populations may respond to environmental change.

The researchers measured standard metabolic rate (SMR), routine metabolic rate (RMR), maximum metabolic rate (MMR), and aerobic scope (AS) across temperatures ranging from 12°C to 27°C. Aerobic scope is particularly informative because it reflects the metabolic capacity available for oxygen-demanding activities such as swimming, prey capture, and feeding.

The microplate respirometry system enabled high-throughput measurements of individual octopus paralarvae. Researchers placed individual animals into the wells of the microplate, where oxygen consumption could be continuously monitored under controlled temperature conditions. The system allowed simultaneous measurement of multiple animals while accounting for background microbial respiration.

Following initial measurements, paralarvae were exercised to exhaustion and then returned to the sensor plate for post-exercise measurements. This enabled the researchers to quantify maximum metabolic performance and calculate aerobic scope across temperatures.

The results revealed a clear temperature-dependent pattern. Aerobic scope was highest between 15 and 21°C, with a model-derived optimum temperature of approximately 18.98°C. At cooler and warmer temperatures, aerobic scope declined, indicating reduced physiological capacity. The findings suggest that octopus paralarvae possess a relatively narrow thermal window during which performance is maximized.

Beyond aquaculture, the findings have broader ecological significance. The authors note that higher ocean temperatures and marine heatwaves could expose early-life stages to conditions outside their optimal physiological range, potentially affecting feeding success, survival, and recruitment. The ability to identify thermal optima through respirometry therefore provides an important tool for evaluating how cephalopods may respond to future environmental change.

The paper titled Thermal sensitivity and aerobic scope in paralarvae of Octopus tetricus is published Journal of Thermal Biology and can be found online at https://doi.org/10.1016/j.jtherbio.2026.104561

Do you want to learn more about the Respirometry system used in this paper?

• Microplate respirometry system
• MicroResp ™: Automated microplate respirometry software
• More papers published using the Microplate system

A recent study from the Mokalled lab at Washington University School of Medicine investigated one of the central questions in regenerative biology: why zebrafish can recover function after spinal cord injury while mammals exhibit limited repair. The researchers identified the gene tcim as an important regulator of macrophage function during regeneration and demonstrated how efficient debris clearance contributes to recovery after injury.

A major challenge following spinal cord injury is the accumulation of cellular and myelin debris. In mammals, inefficient clearance of this material contributes to prolonged inflammation and impaired recovery. In contrast, zebrafish rapidly remove debris following injury, creating a more permissive environment for regeneration. The authors found that macrophages are central to this process and that their depletion significantly reduced both anatomical and functional recovery.

The study used a comprehensive experimental approach to examine the role of TCIM. Comparative transcriptomics first identified tcim as a gene enriched in regenerative zebrafish macrophages. The researchers then generated tcim knockout fish, overexpressed human TCIM, performed immune-cell transplantation studies, and investigated lipid metabolism and phagocytic activity using multiple independent assays.

Throughout the project, swimming performance served as an important functional readout. Swim endurance was measured using a Loligo 5 L swim tunnel system, allowing the researchers to track recovery after spinal cord injury. Fish lacking macrophages or tcim showed markedly reduced swimming performance during recovery, while expression of human TCIM accelerated the return of swim capacity. These measurements demonstrated that the molecular and cellular changes translated into meaningful improvements in swimming performance.

The study revealed that TCIM promotes phagocytosis and lipid metabolism in macrophages. Loss of tcim reduced debris engulfment and resulted in the persistence of lipid-rich deposits after injury. In contrast, TCIM expression increased lipid clearance and enhanced phagocytic capacity in both zebrafish and mouse macrophages. The authors further demonstrated that stimulating lipid breakdown could rescue many of the defects observed in tcim mutants, supporting lipid metabolism as a central component of the regenerative response.

Together, these findings suggest that efficient clearance of lipid-rich debris is a key component of successful spinal cord repair. By combining sophisticated molecular approaches with whole-animal performance testing, the study provides new insight into how immune cells support regeneration and highlights the value of swim tunnel assays for measuring functional recovery in zebrafish models of neurological injury.

The paper, "Elevated phagocytic capacity directs innate spinal cord repair", was published in Cell Reports in 2026 and can be found at https://doi.org/10.1016/j.celrep.2026.117482.

Do you want to learn more about the Swim Tunnel system used in this paper?

• Swim Tunnel Performance System
• AutoSwim 2: Computerized and automated water velocity control
• More papers published using our Swim Tunnels

Unlike zebrafish (Danio rerio), medaka (Oryzias latipes) have been considered to be incapable of cardiac regeneration. In a new comparative study, Miguel Angel Garitagoitia-Romero, María Galardi-Castilla, Miguel Torres and Nadia Mercader put this assumption to the test by performing a detailed side-by-side analysis of heart regeneration in medaka and zebrafish following cardiac cryoinjury. Their findings reveal that medaka possess a far greater regenerative capacity than previously recognized.

The researchers identified many of the same regenerative processes seen in zebrafish, including cardiomyocyte proliferation, transient blood vessel formation, regression of fibrotic scar tissue, and recovery of cardiac function in a subset of animals. While these responses were generally slower or less complete than in zebrafish, they demonstrate that medaka do not entirely lack a regenerative response as previously believed.

Importantly, the study extended beyond tissue-level measurements to assess how heart injury affects whole-animal performance. Using a Swimming tunnel from Loligo® Systems, the authors measured critical swimming speed (Ucrit) in both species during recovery. Despite a measurable decline in cardiac function after injury, swimming performance was unaffected in either medaka or zebrafish, indicating that the regenerative process preserves overall exercise capacity.

This work provides new insight into the diversity of regenerative responses among teleost fishes and suggests that medaka occupy an intermediate position between highly regenerative and poorly regenerative species. The study establishes medaka as an important comparative model for understanding the cellular and physiological mechanisms that govern heart repair.

The paper titled Comparison of cardiac regeneration capacity between zebrafish and medaka reveals a regenerative response in both teleost species is published in npj Regenerative Medicine and can be found online at https://doi.org/10.1038/s41536-026-00482-x

Do you want to learn more about the Swim Tunnel system used in this paper?

• Swim Tunnel System
• AutoSwim 2: Computerized and automated water velocity control
• More papers published using our Swim Tunnels

Linking Biomarkers to Function in Zebrafish

Research in animal disease models require physiological readouts to translate genetic and molecular changes into a functional context.

Modern analytical methods can identify many potential biomarkers, but it is often unclear which are relevant, as disease markers or targets for treatment. Functional assays are needed to validate findings and focus the downstream work.

Zebrafish models provide a strong platform, combining short development time, well annotated genomes, and multiple physiological assays across life stages.

Swim tunnels as a functional platform

Swim tunnels provide an established platform to measure physiological endpoints in zebrafish. The controlled environment of a swim tunnel enables the exploration and validation of molecular biomarkers and treatment effects.

They provide two primary functions. First, they enable flexible exercise protocols to study physical activity as an intervention, the endpoint being upper critical swimming speed (Ucrit) or swimming endurance. Second, they provide quantitative measurements of oxygen consumption rate as a proxy for aerobic metabolism with endpoints like max MO2, aerobic scope, cost of transport, etc.

Measure of whole-organism physiology

The range of swimming assay measurements provide a system-level view of the physiological state by integrating muscle performance, cardiovascular capacity, and metabolic needs.
Key metrics include swimming endurance, swimming distance, critical swimming speed (Ucrit), and oxygen consumption rate (MO2).

The continuous nature of these metrics supports quantitative analysis and improves biomarker identification through integration with other datasets.

Swimming assays are broadly applied

Zebrafish are established as gold standard model animals due to their regenerative capacity, well mapped genomes, and proven translatability to human biology. Swimming assays provide functional measurements across all these systems.

Swim tunnels are used across a broad range of disease models, including exercise, metabolic disease, cardiology, and muscle disorders. (Heinkele 2021, Buerger 2022, Chen 2025, Wen 2023, Harji 2025) In these studies, swimming assays either provide quantitative measures of recovery or are used directly as controlled exercise interventions

There are several groups working on spinal-cord regeneration in which the swimming endurance assay is a central part of the research. (Lafouasse 2026, Cigliola 2023, Burris 2021) Crucially, they found that early swimming performance at can predict later regeneration outcomes, with measurements at 2 weeks predicting cellular regeneration at 8 weeks. (Jensen 2023)

Conclusion

Swim tunnel assays directly link molecular changes and whole-organism physiology in zebrafish disease models. Through the combination of controlled experimental conditions and quantitative measurements, they enable reproducible assessments of physiological state and treatment effects.

As zebrafish models continue to be used alongside high-throughput analytical methods, swim tunnel assays provide a practical way to connect biological findings to functional outcomes.

How do I get started?

There are excellent published protocols that can walk you through many of the different assays that are discussed in this article.

• Swimming assays in Cardiomyopathy models (Ma 2021)
• Behaviour and swimming endurance in zebrafish models (Burris 2021)
• Spinal cord regeneration (Burris 2024)
• Exercise regiments and oxygen consumption (Castro-Sepulveda 2025)

You are always welcome to reach out to us, and we will guide you on what equipment to get based on the assays that you want to run.

Our Performance Swim Tunnel Systems can be found here: Core Performance Swim Tunnels

Our Respirometry Swim Tunnel Systems can be found here: Core Respirometry Swim Tunnels

The Giacomotto lab (GRIDD/Griffith University) used our swim tunnel system to study the behavioural and physical effects of removing neurexin (nxrn) genes, which are associated with neurodevelopmental and mental disorders.

Here they generated the first complete set of zebrafish knockouts for the neuroxin gene family (NRXN1, NRXN2, NRXN3). Allowing them to study the impact of losing each gene during development and adulthood.

Using a comprehensive battery of developmental and behavioural tests, which includes our swim tunnel system, they found that during early development, loss of neurexin had no obvious impact on embryonic development, brain morphology, or early life behaviour.  In adulthood, however, significant behavioural changes emerged.

The findings revealed clear differences between neurexin family members. Loss of NRXN1 primarily affected social behaviour and aggression, while NRXN2 loss produced severe anxiety-like behaviour, reduced exploration, freezing episodes, and increased susceptibility to seizure-like events.

They observed that NRXN1 and NRXN2 mutants responded in opposite ways to environmental context. Conditions that reduced anxiety-like behaviour in NRXN2 mutants exacerbated abnormal behaviour in NRXN1 mutants, suggesting these genes may regulate how the brain interprets and responds to environmental cues.

The study confirms the value of zebrafish for investigating the biological foundations of psychiatric disorders. By combining genetics, behaviour, and physiological assays researchers explore how genetic changes lead to adult behavioural outcomes, and support future drug discovery efforts.

If you want to read the article in full, or learn more about Loligo Systems swim tunnels and other tools, please visit the link in the comment below.

The paper titled Towards modelling mental disorders in zebrafish. Neurexins severely modulate anxiety, affiliative social behaviour and aggression is published in Molecular psychiatry and can be found online at https://doi.org/10.1038/s41380-026-03721-1

Do you want to learn more about the Swim Tunnel system used in this paper?

• Swim Tunnel System
• AutoResp™ 3: Computerized intermittent respirometry
• More papers published using our Swim Tunnels

Our office will be closed for the summer holiday from 20th - 31st of July (both days included).

We wish everyone a lovely summer!

The Loligo^® team

A recent study from the Killen lab (SBOHVM, Glasgow) made novel use of our swim tunnels to study how social hierarchies affect the ingestion of microplastics in static or flowing conditions.

Using European minnows (Phoxinus phoxinus) they tested the ingestion behaviour of different dominance social hierarchies during static water and controlled flow conditions.

They found that steep hierarchies with highly dominant individuals demonstrated increased ingestion of microplastic in the most dominant individual, but swallow rates were only increased in the flow condition.
Interestingly, the less dominant fish in groups with steep hierarchies were more effective at rejecting microplastics. At the overall group level, the total microplastic ingestion was unchanged compared to the other conditions, highlighting how concentrated the microplastic exposure was in the most dominant individual.

The findings demonstrate how traits that are usually associated with success can increase the pollution risk from microplastics and other contaminants. Potentially, leading to changes in group dynamics as the individuals and groups are affected to different degrees depending on both the social and physical environments that they live in.

The paper titled Intraspecific behavioural and environmental contexts influence collective risk of microplastic ingestion in a social fish is published in Proceedings B and can be found online at https://doi.org/10.1098/rspb.2026.0384

Do you want to learn more about the Swim Tunnel system used in this paper?

• Swim Tunnel System
• AutoResp™ 3: Computerized intermittent respirometry
• More papers published using our Swim Tunnels

Our swim tunnel respirometry system was used by the Brandt lab (University of Connecticut, USA) to investigate how a warmer climate alters the effect of PFAS contamination in fish.

Sheepshead minnows were exposed to environmentally relevant concentrations of a PFAS mixture (PFOS + PFOA) across present-day and future temperature scenarios, the study combined ecotoxicology with whole-organism physiology to better understand the effects of combined exposures.

Our Loligo swim tunnels facilitated robust measurement of oxygen consumption and metabolic performance, through metrics such as standard metabolic rate (SMR), maximum metabolic rate (MMR), aerobic scope, and critical swimming rate (Ucrit).

Based on the results fish can compensate for PFAS exposure by increasing both oxygen demand and supply at moderate warming while maintaining the aerobic scope. However, at higher temperatures, this compensation fails and the MMR and aerobic scope declines. Suggesting that the animals will have reduced ability to support activities that require a lot of energy such as predator avoidance and foraging.

The combination of precise respirometry with toxicology provides deeper insight into how climate change amplifies contaminant effects, revealing metabolic limitations that may ultimately shape fish resilience and population health.

The paper titled Temperature Modulates PFAS Accumulation and Effects on Metabolic Performance in Sheepshead Minnows is published in Environmental Science & Technology and can be found online at: https://pubs.acs.org/doi/10.1021/acs.est.5c15140

Do you want to learn more about the Swim tunnel and respirometry system used in this paper?

• Swim Tunnel System – For Respirometry and Swimming Performance
• AutoResp™ v3 – Computerized Respirometry Software
• More papers published using the Swimming Tunnel systems