Innate Lymphoid Cells and Interferons Limit Neurologic and Articular Complications of Brucellosis.

Brucellosis is a globally significant zoonotic disease. Human patients with brucellosis develop recurrent fever and focal complications, including arthritis and neurobrucellosis. The current study investigated the role of innate lymphoid cells (ILCs) in the pathogenesis of focal brucellosis caused by Brucella melitensis. After footpad infection, natural killer cells and ILC1 cells both limited joint colonization by Brucella. Mice lacking natural killer cells, and in particular mice lacking all ILCs, also developed marked arthritis after footpad infection. Following pulmonary infection, mice lacking adaptive immune cells and ILCs developed arthritis, neurologic complications, and meningitis. Adaptive immune cells and ILCs both limited colonization of the brain by Brucella following pulmonary infection. Transcriptional analysis of Brucella-infected brains revealed marked up-regulation of genes associated with inflammation and interferon responses, as well as down-regulation of genes associated with neurologic function. Type II interferon deficiency resulted in colonization of the brain by Brucella, but mice lacking both type I and type II interferon signaling more rapidly developed clinical signs of neurobrucellosis, exhibited hippocampal neuronal loss, and had higher levels of Brucella in their brains than mice lacking type II interferon signaling alone. Collectively, these findings indicate ILCs and interferons play an important role in prevention of focal complications during Brucella infection, and that mice with deficiencies in ILCs or interferons can be used to study pathogenesis of neurobrucellosis.

Looking beyond the mean: quantile regression for comparative physiologists.

Statistical analyses that physiologists use to test hypotheses predominantly centre on means, but the tail ends of the response distribution can behave quite differently and underpin important scientific phenomena. We demonstrate that quantile regression (QR) offers a way to bypass some limitations of least squares regression (LSR) by building a picture of independent variable effects across the whole distribution of a dependent variable. We used LSR and QR with simulated and real datasets. With simulated data, LSR showed no change in the mean response but missed significant effects in the tails of the distribution found using QR. With real data, LSR showed a significant change in the mean response but missed a lack of response in the upper quantiles which was biologically revealing. Together, this highlights that QR can help to ask and answer more questions about variation in nature.

Atlantic salmon Salmo salar do not prioritize digestion when energetic budgets are constrained by warming and hypoxia.

During summer, farmed Atlantic salmon (Salmo salar) can experience prolonged periods of warming and low aquatic oxygen levels due to climate change. This often results in a drop in feed intake; however, the physiological mechanism behind this behaviour is unclear. Digestion is a metabolically expensive process that can demand a high proportion of an animal's energy budget and might not be sustainable under future warming scenarios. We investigated the effects of elevated temperature and acute hypoxia on specific dynamic action (SDA; the energetic cost of digestion), and how much of the energy budget (i.e. aerobic scope, AS) was occupied by SDA in juvenile Atlantic salmon. AS was 9% lower in 21°C-acclimated fish compared to fish reared at their optimum temperature (15°C) and was reduced by ~50% by acute hypoxia (50% air saturation) at both temperatures. Furthermore, we observed an increase in peak oxygen uptake rate during digestion which occupied ~13% of the AS at 15°C and ~20% of AS at 21°C, and increased the total cost of digestion at 21°C. The minimum oxygen tolerance threshold in digesting fish was ~42% and ~53% at 15 and 21°C, respectively, and when digesting fish were exposed to acute hypoxia, gut transit was delayed. Thus, these stressors result in a greater proportion of the available energy budget being directed away from digestion. Moderate environmental hypoxia under both optimal and high temperatures severely impedes digestion and should be avoided to limit exacerbating temperature effects on fish growth.

Sublethal consequences of ultraviolet radiation exposure on vertebrates: Synthesis through meta-analysis.

Ultraviolet radiation (UVR) from the sun is a natural daytime stressor for vertebrates in both terrestrial and aquatic ecosystems. UVR effects on the physiology of vertebrates manifest at the cellular level, but have bottom-up effects at the tissue level and on whole-animal performance and behaviours. Climate change and habitat loss (i.e. loss of shelter from UVR) could interact with and exacerbate the genotoxic and cytotoxic impacts of UVR on vertebrates. Therefore, it is important to understand the range and magnitude of effects that UVR can have on a diversity of physiological metrics, and how these may be shaped by taxa, life stage or geographical range in the major vertebrate groups. Using a meta-analytical approach, we used 895 observations from 47 different vertebrate species (fish, amphibian, reptile and bird), and 51 physiological metrics (i.e. cellular, tissue and whole-animal metrics), across 73 independent studies, to elucidate the general patterns of UVR effects on vertebrate physiology. We found that while UVR's impacts on vertebrates are generally negative, fish and amphibians were the most susceptible taxa, adult and larvae were the most susceptible life stages, and animals inhabiting temperate and tropical latitudes were the most susceptible to UVR stress. This information is critical to further our understanding of the adaptive capacity of vulnerable taxon to UVR stress, and the wide-spread sublethal physiological effects of UVR on vertebrates, such as DNA damage and cellular stress, which may translate up to impaired growth and locomotor performance. These impairments to individual fitness highlighted by our study may potentially cause disruptions at the ecosystem scale, especially if the effects of this pervasive diurnal stressor are exacerbated by climate change and reduced refuge due to habitat loss and degradation. Therefore, conservation of habitats that provide refuge to UVR stress will be critical to mitigate stress from this pervasive daytime stressor.

Carryover effects from environmental change in early life: An overlooked driver of the amphibian extinction crisis?

Ecological carryover effects, or delayed effects of the environment on an organism's phenotype, are central predictors of individual fitness and a key issue in conservation biology. Climate change imposes increasingly variable environmental conditions that may be challenging to early life-history stages in animals with complex life histories, leading to detrimental physiological and fitness effects in later life. Yet, the latent nature of carryover effects, combined with the long temporal scales over which they can manifest, means that this phenomenon remains understudied and is often overlooked in short-term studies limited to single life-history stages. Herein, we review evidence for the physiological carryover effects induced by elevated ultraviolet radiation (UVR; 280-400 nm) as a potential contributor to recent amphibian population declines. UVR exposure causes a suite of molecular, cellular and physiological consequences known to underpin carryover effects in other taxa, but there is a lack of research linking embryonic and larval UVR exposures to fitness consequences post-metamorphosis in amphibians. We propose that the key impacts of UVR on disease-related amphibian declines are facilitated through carryover effects that bridge embryonic and larval UVR exposure with potential increased disease susceptibility post-metamorphosis. We conclude by identifying a practical direction for the study of ecological carryover effects in amphibians that could guide future ecological research in the broader field of conservation physiology. Only by addressing carryover effects can many of the mechanistic links between environmental change and population declines be elucidated.

Through the looking glass: attempting to predict future opportunities and challenges in experimental biology.

To celebrate its centenary year, Journal of Experimental Biology (JEB) commissioned a collection of articles examining the past, present and future of experimental biology. This Commentary closes the collection by considering the important research opportunities and challenges that await us in the future. We expect that researchers will harness the power of technological advances, such as '-omics' and gene editing, to probe resistance and resilience to environmental change as well as other organismal responses. The capacity to handle large data sets will allow high-resolution data to be collected for individual animals and to understand population, species and community responses. The availability of large data sets will also place greater emphasis on approaches such as modeling and simulations. Finally, the increasing sophistication of biologgers will allow more comprehensive data to be collected for individual animals in the wild. Collectively, these approaches will provide an unprecedented understanding of 'how animals work' as well as keys to safeguarding animals at a time when anthropogenic activities are degrading the natural environment.

Thermal compensation reduces DNA damage from UV radiation.

Increases in ultraviolet radiation (UVR) correlate spatially and temporally with global amphibian population declines and interact with other stressors such as disease and temperature. Declines have largely occurred in high-altitude areas associated with greater UVR and cooler temperatures. UVR is a powerful mutagenic harming organisms largely by damaging DNA. When acutely exposed to UVR at cool temperatures, amphibian larvae have increased levels of DNA damage. Amphibians may compensate for the depressive effects of temperature on DNA damage through acclimatisation, but it is unknown whether they have this capacity. We reared striped marsh frog larvae (Limnodynastes peronii) in warm (25 °C) and cool (15 °C) temperatures under a low or moderate daily dose of UVR (10 and 40 µW cm-2 UV-B for 1 h at midday, respectively) for 18-20 days and then measured DNA damage resulting from an acute high UVR dose (80 µW cm-2 UV-B for 1.5 h) at a range of temperatures (10, 15, 20, 25, and 30 °C). Larvae acclimated to 15 °C and exposed to UVR at 15 °C completely compensated UVR-induced DNA damage compared with 25 °C acclimated larvae exposed to UVR at 25 °C. Additionally, warm-acclimated larvae had higher DNA damage than cold-acclimated larvae across test temperatures, which indicated a cost of living in warmer temperatures. Larvae reared under elevated UVR levels showed no evidence of UVR acclimation resulting in lower DNA damage following high UVR exposure. Our finding that thermal acclimation in L. peronii larvae compensated UVR-induced DNA damage at low temperatures suggested that aquatic ectotherms living in cool temperatures may be more resilient to high UVR than previously realised. We suggested individuals or species with less capacity for thermal acclimation of DNA repair mechanisms may be more at risk if exposed to changing thermal and UVR exposure regimes.

The Mutant Mouse Resource and Research Center (MMRRC): the NIH-supported National Public Repository and Distribution Archive of Mutant Mouse Models in the USA.

The Mutant Mouse Resource and Research Center (MMRRC) Program is the pre-eminent public national mutant mouse repository and distribution archive in the USA, serving as a national resource of mutant mice available to the global scientific community for biomedical research. Established more than two decades ago with grants from the National Institutes of Health (NIH), the MMRRC Program supports a Consortium of regionally distributed and dedicated vivaria, laboratories, and offices (Centers) and an Informatics Coordination and Service Center (ICSC) at three academic teaching and research universities and one non-profit genetic research institution. The MMRRC Program accepts the submission of unique, scientifically rigorous, and experimentally valuable genetically altered and other mouse models donated by academic and commercial scientists and organizations for deposition, maintenance, preservation, and dissemination to scientists upon request. The four Centers maintain an archive of nearly 60,000 mutant alleles as live mice, frozen germplasm, and/or embryonic stem (ES) cells. Since its inception, the Centers have fulfilled 13,184 orders for mutant mouse models from 9591 scientists at 6626 institutions around the globe. Centers also provide numerous services that facilitate using mutant mouse models obtained from the MMRRC, including genetic assays, microbiome analysis, analytical phenotyping and pathology, cryorecovery, mouse husbandry, infectious disease surveillance and diagnosis, and disease modeling. The ICSC coordinates activities between the Centers, manages the website (mmrrc.org) and online catalog, and conducts communication, outreach, and education to the research community. Centers preserve, secure, and protect mutant mouse lines in perpetuity, promote rigor and reproducibility in scientific experiments using mice, provide experiential training and consultation in the responsible use of mice in research, and pursue cutting edge technologies to advance biomedical studies using mice to improve human health. Researchers benefit from an expansive list of well-defined mouse models of disease that meet the highest standards of rigor and reproducibility, while donating investigators benefit by having their mouse lines preserved, protected, and distributed in compliance with NIH policies.

Fire and rain: A systematic review of the impacts of wildfire and associated runoff on aquatic fauna.

Climate and land-use changes are expected to increase the future occurrence of wildfires, with potentially devastating consequences for freshwater species and ecosystems. Wildfires that burn in close proximity to freshwater systems can significantly alter the physicochemical properties of water. Following wildfires and heavy rain, freshwater species must contend with complex combinations of wildfire ash components (nutrients, polycyclic aromatic hydrocarbons, and metals), altered light and thermal regimes, and periods of low oxygen that together can lead to mass mortality events. However, the responses of aquatic fauna to wildfire disturbances are poorly understood. Here we provide a systematic review of available evidence on how aquatic animals respond to and recover from wildfire disturbance. Two databases (Web of Science and Scopus) were used to identify key literature. A total of 83 studies from across 11 countries were identified to have assessed the risk of wildfires on aquatic animals. We provide a summary of the main ecosystem-level changes associated with wildfires and the main responses of aquatic fauna to such disturbances. We pay special focus to physiological tools and biomarkers used to assess how wildfires impact aquatic animals. We conclude by providing an overview of how physiological biomarkers can further our understanding of wildfire-related impacts on aquatic fauna, and how different physiological tools can be incorporated into management and conservation plans and serve as early warning signs of wildfire disturbances.

Se espera que el cambio climático y el cambio en el uso de suelo aumentaran la ocurrencia de incendios forestales, con consecuencias potencialmente devastadoras para las especies de agua dulce y los ecosistemas. Los incendios forestales que arden cerca de los sistemas de agua dulce pueden alterar significativamente las propiedades fisicoquímicas del agua. Después de los incendios forestales y llueves fuertes, las especies de agua dulce lidian con combinaciones complejas de componentes de cenizas de incendios forestales (nutrientes, sedimentos, hidrocarburos aromáticos policíclicos y metales), regímenes de luz y térmicos alterados y períodos de bajo oxígeno que, en conjunto, pueden conducir a eventos de mortalidad masiva. Sin embargo, las respuestas de la fauna acuática a las perturbaciones de los incendios forestales son poco conocidas. Aquí proporcionamos una revisión sistemática de la evidencia disponible sobre cómo los animales acuáticos responden y se recuperan de la perturbación de los incendios forestales. Se utilizaron dos bases de datos (Web of Science y Scopus) para identificar la literatura clave. Se identificaron un total de 83 estudios de 11 países que habían evaluado el riesgo de incendios forestales en animales acuáticos. Proporcionamos un resumen de los principales cambios a nivel de ecosistema asociados con los incendios forestales y las principales respuestas de la fauna acuática a tales perturbaciones. Prestamos especial atención a las herramientas fisiológicas y los biomarcadores que se utilizan para evaluar cómo los incendios forestales afectan a los animales acuáticos. Concluimos proporcionando una descripción general de cómo los biomarcadores fisiológicos pueden mejorar nuestra comprensión de los impactos relacionados con los incendios forestales en la fauna acuática, y cómo se pueden incorporar diferentes herramientas fisiológicas en los planes de gestión y conservación y servir como señales de alerta temprana de las perturbaciones de los incendios forestales.

The role of environmental calcium in the extreme acid tolerance of northern banjo frog (Limnodynastes terraereginae) larvae.

Many aquatically respiring animals acutely exposed to low pH waters suffer inhibition of ion uptake and loss of branchial (gill) epithelial integrity, culminating in a fatal loss of body Na+. Environmental calcium levels ([Ca2+]e) are pivotal in maintaining branchial junction integrity, with supplemental Ca2+ reversing the negative effects of low pH in some animals. Tolerance of some naturally acidic environments by aquatic animals is further complicated by low [Ca2+]e, yet many of these environments are surprisingly biodiverse. How animals overcome the damaging actions of low pH and low environmental Ca2+ remains unknown. We examined the effects of [Ca2+]e on the response to low pH in larvae of the highly acid-tolerant frog Limnodynastes terraereginae. Acute exposure to low pH water in the presence of low (5 µmol l-1) [Ca2+]e increased net Na+ efflux. Provision of additional [Ca2+]e reduced net Na+ efflux, but the effect was saturable. Acclimation to both low and high (250 µmol l-1) [Ca2+]e improved the resistance of larvae to Na+ efflux at low pH. Exposure to the Ca2+ channel inhibitor ruthenium red resulted in an abrupt loss of tolerance in low pH-acclimated larvae. Acclimation to acidic water increased branchial gene expression of the intracellular Ca2+ transport protein calbindin, consistent with a role for increased transcellular Ca2+ trafficking in the tolerance of acidic water. This study supports a role for [Ca2+]e in promoting branchial integrity and highlights a potential mechanism via the maintenance of transcellular Ca2+ uptake in the acid tolerance of L. terraereginae larvae.

Early exposure to UV radiation causes telomere shortening and poorer condition later in life.

Determining the contribution of elevated ultraviolet-B radiation (UVBR; 280-315 nm) to amphibian population declines is being hindered by a lack of knowledge about how different acute UVBR exposure regimes during early life-history stages might affect post-metamorphic stages via long-term carryover effects. We acutely exposed tadpoles of the Australian green tree frog (Litoria caerulea) to a combination of different UVBR irradiances and doses in a multi-factorial laboratory experiment, and then reared them to metamorphosis in the absence of UVBR to assess carryover effects in subsequent juvenile frogs. Dose and irradiance of acute UVBR exposure influenced carryover effects into metamorphosis in somewhat opposing manners. Higher doses of UVBR exposure in larvae yielded improved rates of metamorphosis. However, exposure at a high irradiance resulted in frogs metamorphosing smaller in size and in poorer condition than frogs exposed to low and medium irradiance UVBR as larvae. We also demonstrate some of the first empirical evidence of UVBR-induced telomere shortening in vivo, which is one possible mechanism for life-history trade-offs impacting condition post-metamorphosis. These findings contribute to our understanding of how acute UVBR exposure regimes in early life affect later life-history stages, which has implications for how this stressor may shape population dynamics.

Temperature causes species-specific responses to UV-induced DNA damage in amphibian larvae.

Anthropogenic ozone depletion has led to a 2-5% increase in ultraviolet B radiation (UVBR) levels reaching the earth's surface. Exposure to UVBR causes harmful DNA damage in amphibians, but this is minimized by DNA repair enzymes such as thermally sensitive cyclobutane pyrimidine dimer (CPD)-photolyase, with cool temperatures slowing repair rates. It is unknown whether amphibian species differ in the repair response to a given dose of UVBR across temperatures. We reared larvae of three species (Limnodynastes peronii, Limnodynastes tasmaniensis and Platyplectrum ornatum) at 25°C and acutely exposed them to 80 µW cm-2 UVBR for 2 h at either 20°C or 30°C. UVBR-mediated DNA damage was measured as larvae repaired damage in photoreactive light at their exposure temperatures. Cool temperatures increased DNA damage in two species and slowed DNA repair rate in P. ornatum. The magnitude of DNA damage incurred from UVBR was species-specific. Platyplectrum ornatum had the lowest CPDs and DNA repair rates, and the depressive effects of low temperature on photorepair were greater in L. tasmaniensis. Considering the susceptibility of most aquatic organisms to UVBR, this research highlighted a need to consider the complexity of species-specific physiology when forecasting the influence of changing UVBR and temperature in aquatic ecosystems.

Can slowing the rate of water temperature decline be utilized to reduce the impacts of cold water pollution from dam releases on fish physiology and performance?

Cold water pollution (CWP) is caused by releases of unseasonably cold water from large, thermally stratified dams. Rapid and prolonged decreases in water temperature can have depressive effects on the metabolism, growth and swimming performance of fish. However, it is unknown if reducing the rate of temperature decrease could mitigate these negative effects by allowing thermal acclimation/acclimatization to occur. This study investigated the rate of temperature decrease as a potential CWP mitigation strategy in juvenile Murray cod Maccullochella peelii. M. peelii were exposed to a gradual, intermediate or rapid temperature decrease from 24 to 14°C. Energetic costs, locomotor performance, growth and survival were measured to determine if the initial thermal regime affected the thermal acclimation capacity of M. peelii. Cold exposure had significant acute and lasting depressive effects regardless of the rate of temperature decrease, although M. peelii showed varying degrees of thermal compensation in swimming performance and metabolism after 8 weeks of exposure to low temperatures. The short-term effects of CWP-like reductions in temperature are significant, but over time M. peelii can offset some of the depressive effects of CWP through thermal plasticity. This study highlights the importance of understanding physiological responses of fish to inform management and conservation. We conclude that rate of water temperature decline cannot be used to mitigate the sublethal effects of CWP on juvenile M. peelii but may still be useful for managing the negative effects in other native Australian fish species.

Role of perivascular nerve and sensory neurotransmitter dysfunction in inflammatory bowel disease.

Inflammatory bowel disease (IBD) is associated with both impaired intestinal blood flow and increased risk of cardiovascular disease, but the functional role of perivascular nerves that control vasomotor function of mesenteric arteries (MAs) perfusing the intestine during IBD is unknown. Because perivascular sensory nerves and their transmitters calcitonin gene-related peptide (CGRP) and substance P (SP) are important mediators of both vasodilation and inflammatory responses, our objective was to identify IBD-related deficits in perivascular sensory nerve function and vascular neurotransmitter signaling. In MAs from an interleukin-10 knockout (IL-10-/-) mouse model, IBD significantly impairs electrical field stimulation (EFS)-mediated sensory vasodilation and inhibition of sympathetic vasoconstriction, despite decreased sympathetic nerve density and vasoconstriction. The MA content and EFS-mediated release of both CGRP and SP are decreased with IBD, but IBD has unique effects on each transmitter. CGRP nerve density, receptor expression, hyperpolarization, and vasodilation are preserved with IBD. In contrast, SP nerve density and receptor expression are increased, and SP hyperpolarization and vasodilation are impaired with IBD. A key finding is that blockade of SP receptors restores EFS-mediated sensory vasodilation and enhanced CGRP-mediated vasodilation in MAs from IBD but not Control mice. Together, these data suggest that an aberrant role for the perivascular sensory neurotransmitter SP and its downstream signaling in MAs underlies vascular dysfunction with IBD. We propose that with IBD, SP signaling impedes CGRP-mediated sensory vasodilation, contributing to impaired blood flow. Thus, substance P and NK1 receptors may represent an important target for treating vascular dysfunction in IBD.NEW & NOTEWORTHY Our study is the first to show that IBD causes profound impairment of sensory vasodilation and inhibition of sympathetic vasoconstriction in mesenteric arteries. This occurs alongside decreased SP-containing nerve density and increased expression of NK1 receptors for SP. In contrast, CGRP dilation, nerve density, and receptor expression are unchanged. Blocking NK1 receptors restores sensory vasodilation in MAs and increases CGRP-mediated vasodilation, indicating that SP interference with CGRP signaling may underlie impaired sensory vasodilation with IBD.

The gut microbiome of laboratory mice: considerations and best practices for translational research.

Just as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.

Diving in hot water: a meta-analytic review of how diving vertebrate ectotherms will fare in a warmer world.

Diving ectothermic vertebrates are an important component of many aquatic ecosystems, but the threat of climate warming is particularly salient to this group. Dive durations typically decrease as water temperatures rise; yet, we lack an understanding of whether this trend is apparent in all diving ectotherms and how this group will fare under climate warming. We compiled data from 27 studies on 20 ectothermic vertebrate species to quantify the effect of temperature on dive durations. Using meta-analytic approaches, we show that, on average, dive durations decreased by 11% with every 1°C increase in water temperature. Larger increases in temperature (e.g. +3°C versus +8-9°C) exerted stronger effects on dive durations. Although species that respire bimodally are projected to be more resilient to the effects of temperature on dive durations than purely aerial breathers, we found no significant difference between these groups. Body mass had a weak impact on mean dive durations, with smaller divers being impacted by temperature more strongly. Few studies have examined thermal phenotypic plasticity (N=4) in diving ectotherms, and all report limited plasticity. Average water temperatures in marine and freshwater habitats are projected to increase between 1.5 and 4°C in the next century, and our data suggest that this magnitude of warming could translate to substantial decreases in dive durations, by approximately 16-44%. Together, these data shed light on an overlooked threat to diving ectothermic vertebrates and suggest that time available for underwater activities, such as predator avoidance and foraging, may be shortened under future warming.

Low light intensities increase avoidance behaviour of diurnal fish species: implications for use of road culverts by fish.

Inadequately designed culverts can be physical barriers to fish passage if they increase the velocity of water flow in the environment, alter natural turbulence patterns or fail to provide adequate water depth. They may also act as behavioural barriers to fish passage if they affect the willingness of fish species to enter or pass through the structure due to altered ambient light conditions. To understand how reduced light intensity might affect fish behaviour in culverts, the authors performed a behavioural choice experiment quantifying the amount of time individual fish spent in dark and illuminated areas of a controlled experimental channel. They found that behavioural responses were largely reflective of the species' diel activity patterns; the diurnal species Craterocephalus stercusmuscarum and Retropinna semoni preferred illuminated regions, whereas the nocturnal/crepuscular Macquaria novemaculeata preferred the darkened region of the channel. Bidyanus bidyanus were strongly rheotactic, and their behaviour was influenced more by water flow direction than ambient light level. The authors then determined that a threshold light intensity of only c. 100-200 lx (cf. midday sunlight c. 100,000 lx) was required to overcome the behavioural barrier in c. 70% of the diurnally active C. stercusmuscarum and R. semoni tested. When these values were placed into an environmental context, 15 road-crossing (3.4-7.0 m long) box (c. 1 m × 1 m, height × width) and pipe (c. 1 m diameter) culverts sampled in Brisbane, Australia, recorded light intensities in the centre of the structure that were below the threshold for C. stercusmuscarum and R. semoni movement and could potentially be a barrier to their passage through the structure. Attention is required to better understand the impacts of low light intensity in culverts on fish passage and to prioritize restoration.

Cooler temperatures slow the repair of DNA damage in tadpoles exposed to ultraviolet radiation: Implications for amphibian declines at high altitude.

Ultraviolet B radiation (UVBR) damages the DNA of exposed cells, causing dimers to form between adjacent pyrimidine nucleotides. These dimers block DNA replication, causing mutations and apoptosis. Most organisms utilize biochemical or biophysical DNA repair strategies to restore DNA structure; however, as with most biological reactions, these processes are likely to be thermally sensitive. Tadpoles exposed to elevated UVBR at low environmental temperatures have significantly higher rates of mortality and developmental deformities compared with tadpoles exposed to the same levels of UVBR at higher environmental temperatures. We hypothesized that low environmental temperatures impair the primary enzymatic (photolyase) DNA repair pathway in amphibians, leading to the accumulation of DNA damage. To test this hypothesis, we compared DNA repair rates and photolyase gene expression patterns in Limnodynastes peronii. Tadpoles were acutely exposed to UVBR for 1 hr at either 20 or 30°C, and we measured DNA damage and photolyase expression levels at intervals following this exposure. Temperature had a significant effect on the rate of DNA repair, with repair at 30°C occurring twice as fast as repair at 20°C. Photolyase gene expression (6-4 PP and CPD) was significantly upregulated by UVBR exposure, with expression levels increasing within 6 hr of UVBR exposure. CPD expression levels were not significantly affected by temperature, but 6-4 PP expression was significantly higher in tadpoles in the 30°C treatment within 12 hr of UVBR exposure. These data support the hypothesis that DNA repair rates are thermally sensitive in tadpoles and may explain why enigmatic amphibian declines are higher in montane regions where UVBR levels are naturally elevated and environmental temperatures are lower.

Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation.

BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, environmental variables, and interactions with the GM is exceedingly difficult. We previously observed significant differences in intestinal adenoma multiplicity between C57BL/6 J-ApcMin (B6-Min/J) from The Jackson Laboratory (JAX), and original founder strain C57BL/6JD-ApcMin (B6-Min/D) from the University of Wisconsin. METHODS: To resolve genetic and environmental interactions and determine their contributions we utilized two genetically inbred, independently isolated ApcMin mouse colonies that have been separated for over 20 generations. Whole genome sequencing was used to identify genetic variants unique to the two substrains. To determine the influence of genetic variants and the impact of differences in the GM on phenotypic variability, we used complex microbiota targeted rederivation to generate two Apc mutant mouse colonies harboring complex GMs from two different sources (GMJAX originally from JAX or GMHSD originally from Envigo), creating four ApcMin groups. Untargeted metabolomics were used to characterize shifts in the fecal metabolite profile based on genetic variation and differences in the GM. RESULTS: WGS revealed several thousand high quality variants unique to the two substrains. No homozygous variants were present in coding regions, with the vast majority of variants residing in noncoding regions. Host genetic divergence between Min/J and Min/D and the complex GM additively determined differential adenoma susceptibility. Untargeted metabolomics revealed that both genetic lineage and the GM collectively determined the fecal metabolite profile, and that each differentially regulates bile acid (BA) metabolism. Metabolomics pathway analysis facilitated identification of a functionally relevant private noncoding variant associated with the bile acid transporter Fatty acid binding protein 6 (Fabp6). Expression studies demonstrated differential expression of Fabp6 between Min/J and Min/D, and the variant correlates with adenoma multiplicity in backcrossed mice. CONCLUSIONS: We found that both genetic variation and differences in microbiota influences the quantitiative adenoma phenotype in ApcMin mice. These findings demonstrate how the use of metabolomics datasets can aid as a functional genomic tool, and furthermore illustrate the power of a multi-omics approach to dissect complex disease susceptibility of noncoding variants.

Thermal acclimation offsets the negative effects of nitrate on aerobic scope and performance.

Rising temperatures are set to imperil freshwater fishes as climate change ensues unless compensatory strategies are employed. However, the presence of additional stressors, such as elevated nitrate concentrations, may affect the efficacy of compensatory responses. Here, juvenile silver perch (Bidyanus bidyanus) were exposed to current-day summer temperatures (28°C) or a future climate-warming scenario (32°C) and simultaneously exposed to one of three ecologically relevant nitrate concentrations (0, 50 or 100 mg l-1). We measured indicators of fish performance (growth, swimming), aerobic scope (AS) and upper thermal tolerance (CTmax) to test the hypothesis that nitrate exposure would increase susceptibility to elevated temperatures and limit thermal compensatory responses. After 8 weeks of acclimation, the thermal sensitivity and plasticity of AS and swimming performance were tested at three test temperatures (28, 32, 36°C). The AS of 28°C-acclimated fish declined with increasing temperature, and the effect was more pronounced in nitrate-exposed individuals. In these fish, declines in AS corresponded with poorer swimming performance and a 0.8°C decrease in CTmax compared with unexposed fish. In contrast, acclimation to 32°C masked the effects of nitrate; fish acclimated to 32°C displayed a thermally insensitive phenotype whereby locomotor performance remained unchanged, AS was maintained and CTmax was increased by ∼1°C irrespective of nitrate treatment compared with fish acclimated to 28°C. However, growth was markedly reduced in 32°C-acclimated compared with 28°C-acclimated fish. Our results indicate that nitrate exposure increases the susceptibility of fish to acute high temperatures, but thermal compensation can override some of these potentially detrimental effects.