Sex in troubled waters: Widespread agricultural contaminant disrupts reproductive behaviour in fish.

Chemical pollution is a pervasive and insidious agent of environmental change. One class of chemical pollutant threatening ecosystems globally is the endocrine disrupting chemicals (EDCs). The capacity of EDCs to disrupt development and reproduction is well established, but their effects on behaviour have received far less attention. Here, we investigate the impact of a widespread androgenic EDC on reproductive behaviour in the guppy, Poecilia reticulata. We found that short-term exposure of male guppies to an environmentally relevant concentration of 17ß-trenbolone-a common environmental pollutant associated with livestock production-influenced the amount of male courtship and forced copulatory behaviour (sneaking) performed toward females, as well as the receptivity of females toward exposed males. Exposure to 17ß-trenbolone was also associated with greater male mass. However, no effect of female exposure to 17ß-trenbolone was detected on female reproductive behaviour, indicating sex-specific vulnerability at this dosage. Our study is the first to show altered male reproductive behaviour following exposure to an environmentally realistic concentration of 17ß-trenbolone, demonstrating the possibility of widespread disruption of mating systems of aquatic organisms by common agricultural contaminants.

Model-guided design of microRNA-based gene circuits supports precise dosage of transgenic cargoes into diverse primary cells.

To realize the potential of engineered cells in therapeutic applications, transgenes must be expressed within the window of therapeutic efficacy. Differences in copy number and other sources of extrinsic noise generate variance in transgene expression and limit the performance of synthetic gene circuits. In a therapeutic context, supraphysiological expression of transgenes can compromise engineered phenotypes and lead to toxicity. To ensure a narrow range of transgene expression, we design and characterize Compact microRNA-Mediated Attenuator of Noise and Dosage (ComMAND), a single-transcript, microRNA-based incoherent feedforward loop. We experimentally tune the ComMAND output profile, and we model the system to explore additional tuning strategies. By comparing ComMAND to two-gene implementations, we highlight the precise control afforded by the single-transcript architecture, particularly at relatively low copy numbers. We show that ComMAND tightly regulates transgene expression from lentiviruses and precisely controls expression in primary human T cells, primary rat neurons, primary mouse embryonic fibroblasts, and human induced pluripotent stem cells. Finally, ComMAND effectively sets levels of the clinically relevant transgenes FMRP1 and FXN within a narrow window. Together, ComMAND is a compact tool well-suited to precisely specify expression of therapeutic cargoes.

Evaluation of physiological stress in free-ranging bears: current knowledge and future directions.

Stress responses, which are mediated by the neurogenic system (NS) and hypothalamic-pituitary-adrenal (HPA) axis help vertebrates maintain physiological homeostasis. Fight-or-flight responses are activated by the NS, which releases norepinephrine/noradrenaline and epinephrine/adrenaline in response to immediate stressors, whilst the HPA axis releases glucocorticoid hormones (e.g. cortisol and corticosterone) to help mitigate allostatic load. There have been many studies on stress responses of captive animals, but they are not truly reflective of typical ranges or the types of stressors encountered by free-ranging wildlife, such as responses and adaptation to environmental change, which are particularly important from a conservation perspective. As stress can influence the composition of age and sex classes of free-ranging populations both directly and indirectly, ecological research must be prioritised towards more vulnerable taxa. Generally, large predators tend to be particularly at risk of anthropogenically driven population declines because they exhibit reduced behavioural plasticity required to adapt to changing landscapes and exist in reduced geographic ranges, have small population sizes, low fecundity rates, large spatial requirements and occupy high trophic positions. As a keystone species with a long history of coexistence with humans in highly anthropogenic landscapes, there has been growing concern about how humans influence bear behaviour and physiology, via numerous short- and long-term stressors. In this review, we synthesise research on the stress response in free-ranging bear populations and evaluate the effectiveness and limitations of current methodology in measuring stress in bears to identify the most effective metrics for future research. Particularly, we integrate research that utilised haematological variables, cardiac monitors and Global Positioning System (GPS) collars, serum/plasma and faecal glucocorticoid concentrations, hair cortisol levels, and morphological metrics (primarily skulls) to investigate the stress response in ursids in both short- and long-term contexts. We found that in free-ranging bears, food availability and consumption have the greatest influence on individual stress, with mixed responses to anthropogenic influences. Effects of sex and age on stress are also mixed, likely attributable to inconsistent methods. We recommend that methodology across all stress indicators used in free-ranging bears should be standardised to improve interpretation of results and that a wider range of species should be incorporated in future studies.

A matrigel-free method for culture of pancreatic endocrine-like cells in defined protein-based hydrogels.

The transplantation of pancreatic endocrine islet cells from cadaveric donors is a promising treatment for type 1 diabetes (T1D), which is a chronic autoimmune disease that affects approximately nine million people worldwide. However, the demand for donor islets outstrips supply. This problem could be solved by differentiating stem and progenitor cells to islet cells. However, many current culture methods used to coax stem and progenitor cells to differentiate into pancreatic endocrine islet cells require Matrigel, a matrix composed of many extracellular matrix (ECM) proteins secreted from a mouse sarcoma cell line. The undefined nature of Matrigel makes it difficult to determine which factors drive stem and progenitor cell differentiation and maturation. Additionally, it is difficult to control the mechanical properties of Matrigel without altering its chemical composition. To address these shortcomings of Matrigel, we engineered defined recombinant proteins roughly 41 kDa in size, which contain cell-binding ECM peptides derived from fibronectin (ELYAVTGRGDSPASSAPIA) or laminin alpha 3 (PPFLMLLKGSTR). The engineered proteins form hydrogels through association of terminal leucine zipper domains derived from rat cartilage oligomeric matrix protein. The zipper domains flank elastin-like polypeptides whose lower critical solution temperature (LCST) behavior enables protein purification through thermal cycling. Rheological measurements show that a 2% w/v gel of the engineered proteins display material behavior comparable to a Matrigel/methylcellulose-based culture system previously reported by our group to support the growth of pancreatic ductal progenitor cells. We tested whether our protein hydrogels in 3D culture could derive endocrine and endocrine progenitor cells from dissociated pancreatic cells of young (1-week-old) mice. We found that both protein hydrogels favored growth of endocrine and endocrine progenitor cells, in contrast to Matrigel-based culture. Because the protein hydrogels described here can be further tuned with respect to mechanical and chemical properties, they provide new tools for mechanistic study of endocrine cell differentiation and maturation.

Supercoiling-mediated feedback rapidly couples and tunes transcription.

Transcription induces a wave of DNA supercoiling, altering the binding affinity of RNA polymerases and reshaping the biochemical landscape of gene regulation. As supercoiling rapidly diffuses, transcription dynamically reshapes the regulation of proximal genes, forming a complex feedback loop. However, a theoretical framework is needed to integrate biophysical regulation with biochemical transcriptional regulation. To investigate the role of supercoiling-mediated feedback within multi-gene systems, we model transcriptional regulation under the influence of supercoiling-mediated polymerase dynamics, allowing us to identify patterns of expression that result from physical inter-gene coupling. We find that gene syntax-the relative ordering and orientation of genes-defines the expression profiles, variance, burst dynamics, and inter-gene correlation of two-gene systems. Furthermore, supercoiling can enhance or weaken biochemical regulation. Our results suggest that supercoiling couples behavior between neighboring genes, providing a regulatory mechanism that tunes transcriptional variance in engineered gene networks and explains the behavior of co-localized native circuits.

Genetically Programmable Microbial Assembly.

Engineered microbial communities show promise in a wide range of applications, including environmental remediation, microbiome engineering, and synthesis of fine chemicals. Here we present methods by which bacterial aggregates can be directed into several distinct architectures by inducible surface expression of heteroassociative protein domains (SpyTag/SpyCatcher and SynZip17/18). Programmed aggregation can be used to activate a quorum-sensing circuit, and aggregate size can be tuned via control of the amount of the associative protein displayed on the cell surface. We further demonstrate reversibility of SynZip-mediated assembly by addition of soluble competitor peptide. Genetically programmable bacterial assembly provides a starting point for the development of new applications of engineered microbial communities in environmental technology, agriculture, human health, and bioreactor design.

Transcriptome-wide changes associated with the reproductive behaviour of male guppies exposed to 17α-ethinyl estradiol.

Although many pharmaceutical compounds (and their metabolites) can induce harmful impacts at the molecular, physiological and behavioural levels, their underlying mechanistic associations have remained largely unexplored. Here, we utilized RNA-Seq to build a whole brain transcriptome profile to examine the impact of a common endocrine disrupting pharmaceutical (17α-ethinyl estradiol, EE2) on reproductive behaviour in wild guppies (Poecilia reticulata). Specifically, we annotated 16,791 coding transcripts in whole brain tissue in relation to the courtship behaviour (i.e. sigmoid display) of EE2 exposed (at environmentally relevant concentration of 8 ng/L for 28-days) and unexposed guppies. Further, we obtained 10,960 assembled transcripts matching in the non-coding orthologous genomes. Behavioural responses were assessed using a standard mate choice experiment, which allowed us to disentangle chemical cues from visual cues. We found that a high proportion of the RNAseq reads aligned back to our de novo assembled transcriptome with 80.59% mapping rate. Behavioural experiments showed that when males were presented only with female visual cues, there was a significant interaction between male treatment and female treatment in the time spent in the preference zone. This is one of the first studies to show that transcriptome-wide changes are associated with the reproductive behaviour of fish: EE2 exposed male guppies that performed high levels of courtship had a gene profile that deviated the most from the other treatment groups, while both non-courting EE2 and control males had similar gene signatures. Using Gene Ontology pathway analysis, our study shows that EE2-exposed males had gene transcripts enriched for pathways associated with altered immunity, starvation, altered metabolism and spermatogenesis. Our study demonstrates that multiple gene networks orchestrate courting behaviour, emphasizing the importance of investigating impacts of pharmaceuticals on gene networks instead of single genes.

Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales.

Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates as a highly dynamic feedback control system. Recent experimental techniques have provided increasingly detailed data that revise and augment the relatively static, hierarchical view of genomic architecture with an understanding of how dynamic processes drive organization. Here, we review how novel technologies from sequencing, imaging, and synthetic biology refine our understanding of chromatin structure and function and enable chromatin engineering. Finally, we discuss opportunities to use these tools to enhance understanding of the dynamic interrelationship of chromatin structure and function.

The endocrine disruptor, 17α-ethinyl estradiol, alters male mate choice in a freshwater fish.

Among the handful of studies on the behavioural effects of endocrine disrupting chemicals (EDCs), only a few have set out to disentangle the mechanisms underpinning behavioural changes. In fish, previous studies have shown that both visual and chemical cues play an important role in mate choice. As such, contaminant-induced changes in either transmission or perception of mate choice cues could have direct implications for individual's fitness. One widespread contaminant of environmental concern is 17α-ethinyl estradiol (EE2), a synthetic estrogen used in the contraceptive pill. Here, we investigated the impacts of EE2 exposure (28 days; measured concentration 14 ng/L) on visual and chemical communication in wild guppies (Poecilia reticulata). Using a standard dichotomous mate choice assay, we first gave individual males (either control or EE2-exposed) the opportunity to court two size-matched females (one control and one EE2-exposed) using only visual cues. We then introduced chemical cues of females (control and EE2-exposed) to the trial tank. We found that there was no significant effect of EE2-treatment on total time males spent associating with the females, when given only visual cues. There was, however, a significant effect on male courtship behaviour, with both control and EE2-exposed males spending more time performing 'sigmoid' displays towards the visual cues of control females compared to EE2-exposed females. When males were presented with both visual and chemical female cues simultaneously, we found that males spent more time courting control females that were paired with EE2-chemical cues. Not only does our study uncover a previously unknown behavioural impact of EE2-exposure on chemical cues, but demonstrates that EE2-exposure can exert complex effects on visual and chemical communication in a mate choice context. Finally, we contribute to the discussion of intraspecific variability by providing data on the potential trade-offs underpinning contaminant-induced behavioural changes.

Behavioural effects of psychoactive pharmaceutical exposure on European perch (Perca fluviatilis) in a multi-stressor environment.

With the ability to resist biodegradation and exert therapeutic effects at low concentrations, pharmaceutical contaminants have become environmental stressors for wildlife. One such contaminant is the anxiolytic oxazepam, a psychoactive pharmaceutical that is frequently detected in surface waters globally. Despite growing interest in understanding how wildlife respond to anxiolytics, synergistic effects of pharmaceuticals and other abiotic (e.g. temperature) and biotic (e.g. predation risk) stressors remain unclear. Here, using a multi-stressor approach, we investigated effects of 7-day oxazepam exposure (6.5 µg/L) on anxiety-related behaviours in juvenile European perch (Perca fluviatilis). The multi-stressor approach was achieved by exposing perch to oxazepam at two temperatures (10 °C and 18 °C), and at two predation risk regimes-generated using chemical cues from the northern pike (Esox lucius). Our exposures resulted in a successful uptake of the drug from the water, i.e., oxazepam was measured in perch muscle tissue at 50 ±â€¯17 ng/g (mean ±â€¯SD). We found significant oxazepam-induced effects on boldness, with 76.7% of the treated fish entering the white background (i.e. 'exposed' area where exposure to presumed risks are higher) within the first 5 min, compared to 66.6% of the control fish. We also found a significant effect of temperature on total time spent freezing (i.e. staying motionless). Specifically, fish in the low temperature treatments (oxazepam, predation) froze for longer than fish in high temperatures. Our multi-stressor study is the first to uncover how anxiety-related behaviours in wild juvenile fish are altered by changes in water temperature and perceived predation risk. Importantly, our findings highlight the need to focus on multiple stressors to improve understanding of how organisms not only survive, but adapt to, human-induced environmental change.

Field-realistic exposure to the androgenic endocrine disruptor 17ß-trenbolone alters ecologically important behaviours in female fish across multiple contexts.

The capacity of pharmaceutical pollution to alter behaviour in wildlife is of increasing environmental concern. A major pathway of these pollutants into the environment is the treatment of livestock with hormonal growth promotants (HGPs), which are highly potent veterinary pharmaceuticals that enter aquatic ecosystems via effluent runoff. Hormonal growth promotants are designed to exert biological effects at low doses, can act on physiological pathways that are evolutionarily conserved across taxa, and have been detected in ecosystems worldwide. However, despite being shown to alter key fitness-related processes (e.g., development, reproduction) in various non-target species, relatively little is known about the potential for HGPs to alter ecologically important behaviours, especially across multiple contexts. Here, we investigated the effects of exposure to a field-realistic level of the androgenic HGP metabolite 17ß-trenbolone-an endocrine-disrupting chemical that has repeatedly been detected in freshwater systems-on a suite of ecologically important behaviours in wild-caught female eastern mosquitofish (Gambusia holbrooki). First, we found that 17ß-trenbolone-exposed fish were more active and exploratory in a novel environment (i.e., maze arena), while boldness (i.e., refuge use) was not significantly affected. Second, when tested for sociability, exposed fish spent less time in close proximity to a shoal of stimulus (i.e., unexposed) conspecific females and were, again, found to be more active. Third, when assayed for foraging behaviour, exposed fish were faster to reach a foraging zone containing prey items (chironomid larvae), quicker to commence feeding, spent more time foraging, and consumed a greater number of prey items, although the effect of exposure on certain foraging behaviours was dependent on fish size. Taken together, these findings highlight the potential for exposure to sub-lethal levels of veterinary pharmaceuticals to alter sensitive behavioural processes in wildlife across multiple contexts, with potential ecological and evolutionary implications for exposed populations.

Use of erythrocyte indicators of health and condition in vertebrate ecophysiology: a review and appraisal.

We review evidence for and against the use of erythrocyte indicators of health status and condition, parasite infection level and physiological stress in free-living vertebrates. The use of indicators that are measured directly from the blood, such as haemoglobin concentration, haematocrit and erythrocyte sedimentation rate, and parameters that are calculated from multiple measured metrics, such as mean cell volume, mean cell haemoglobin content or mean cell haemoglobin concentration is evaluated. The evidence for or against the use of any given metric is equivocal when the relevant research is considered in total, although there is sometimes strong support for using a particular metric in a particular taxon. Possibly the usefulness of these metrics is taxon, environment or condition specific. Alternatively, in an uncontrolled environment where multiple factors are influencing a metric, its response to environmental change will sometimes, but not always, be predictable. We suggest that (i) researchers should validate a metric's utility before use, (ii) multiple metrics should be used to construct an overall erythrocyte profile for an individual or population, (iii) there is a need for researchers to compile reference ranges for free-living species, and (iv) some metrics which are useful under controlled, clinical conditions may not have the same utility or applicability for free-living vertebrates. Erythrocyte metrics provide useful information about health and condition that can be meaningfully interpreted in free-living vertebrates, but their use requires careful forethought about confounding factors.

A 20-year investigation of declining leatherback hatching success: implications of climate variation.

Unprecedented increases in air temperature and erratic precipitation patterns are predicted throughout the twenty-first century as a result of climate change. A recent global analysis of leatherback turtle hatchling output predicts that the nesting site at Sandy Point National Wildlife Refuge (SPNWR) will experience the most significant regional climate alterations. We aimed to identify how local air temperatures and precipitation patterns influenced within-nest mortality and overall hatchling output at this site between 1990 and 2010. We show that while the greatest mortality occurred during the latest stages of development (stage three), the rate of embryo mortality was highest during the initial stages (stage zero) of development (approx. 3.8 embryos per day per clutch). Increased mortality at stage three was associated with decreased precipitation and increased temperature during this developmental period, whereas precipitation prior to, and during stage zero had the greatest influence on early mortality. There was a significant decline in overall hatching success (falling from 74% to 55%) and emergence rate (calculated from the number of hatchlings that emerged from the nest as a percentage of hatched eggs) which fell from 96% to 91%. However, there was no trend observed in local temperature or precipitation during this timeframe, and neither variable was related to hatching success or emergence rate. In conclusion, our findings suggest that despite influencing within-nest mortality, climatic variability does not account for the overall decline in hatchling output at SPNWR from 1990 to 2010. Further research is therefore needed to elicit the reasons for this decline.

Impacts of the antidepressant fluoxetine on the anti-predator behaviours of wild guppies (Poecilia reticulata).

Chemical pollution from pharmaceuticals is increasingly recognised as a major threat to aquatic communities. One compound of great concern is fluoxetine, which is one of the most widely prescribed psychoactive drugs in the world and frequently detected in the environment. The aim of this study was to investigate the effects of 28-d fluoxetine exposure at two environmentally relevant levels (measured concentrations: 4ng/L and 16ng/L) on anti-predator behaviour in wild guppies (Poecilia reticulata). This was achieved by subjecting fluoxetine-exposed and unexposed guppies to a simulated bird strike and recording their subsequent behavioural responses. We found that exposure to fluoxetine affected the anti-predator behaviour of guppies, with exposed fish remaining stationary for longer (i.e. 'freezing' behaviour) after the simulated strike and also spending more time under plant cover. By contrast, control fish were significantly more active and explored the tank more, as indicated by the distance covered per minute over the period fish spent swimming. Furthermore, behavioural shifts were sex-dependent, with evidence of a non-monotonic dose-response among the fluoxetine-exposed fish. This is one of the first studies to show that exposure to environmentally relevant concentrations of fluoxetine can alter the anti-predator behaviour of adult fish. In addition to the obvious repercussions for survival, impaired anti-predator behaviour can have direct impacts on fitness and influence the overall population dynamics of species.

Characterisation of the transcriptome of male and female wild-type guppy brains with RNA-Seq and consequences of exposure to the pharmaceutical pollutant, 17α-ethinyl estradiol.

Waterways are increasingly being contaminated by chemical compounds that can disrupt the endocrinology of organisms. One such compound is 17α-ethinyl estradiol (EE2), a synthetic estrogen used in the contraceptive pill. Despite considerable research interest in the effects of EE2 on reproduction and gene expression, surprisingly, only a few studies have capitalised on technologies, such as next-generation sequencing (NGS), to uncover the molecular pathways related to EE2 exposure. Accordingly, using high-throughput sequencing technologies, the aim of our study was to explore the effects of EE2 on brain transcriptome in wild-type male and female guppy (Poecilia reticulata). We conducted two sets of experiments, where fish were exposed to EE2 (measured concentrations: 8ng/L and 38ng/L) in a flow-through system for 21days. The effects on the brain transcriptome on both males and females were assessed using Illumina sequencing (MiSeq and HiSeq) platform followed by bioinformatics analysis (edgeR, DESeq2). Here, we report that exposure to EE2 caused both up- and downregulation of specific transcript abundances, and affected transcript abundance in a sex-specific manner. Specifically, we found 773 transcripts, of which 60 were male-specific, 61 female-specific and 285 treatment-specific. EE2 affected expression of 165 transcripts in males, with 88 downregulated and 77 upregulated, while in females, 120 transcripts were affected with 62 downregulated and 58 upregulated. Finally, RT-qPCR validation demonstrated that expression of transcripts related to transposable elements, neuroserpin and heat shock protein were significantly affected by EE2-exposure. Our study is the first to report brain transcriptome libraries for guppies exposed to EE2. Not only does our study provide a valuable resource, it offers insights into the mechanisms underlying the feminizing effects on the brains of organisms exposed to environmentally realistic concentrations of EE2.

Reproductive investment compromises maternal health in three species of freshwater turtle.

Life-history theory predicts that a trade-off in the allocation of resources between different physiological systems exists because resources are finite. As a result, females investing heavily in reproduction may compromise their future health. We used hematology, serum biochemistry, mass, and morphometric measurements as indicators of physiological health state to investigate whether reproductive investment altered subsequent maternal health in three Australian freshwater turtles: the oblong turtle (Chelodina oblonga; n = 12), the Macquarie turtle (Emydura macquarii; n = 9), and the eastern long-necked turtle (Chelodina longicollis; n = 8). Maternal health was impaired in turtles that produced larger and heavier eggs and clutches. In C. oblonga and E. macquarii, increased reproductive investment generally resulted in negative changes to the hematology and serum biochemistry profile of maternal blood. Generally, increases in heterophil/lymphocyte ratio, aspartate transaminase, creatine kinase, calcium/phosphorus ratio, and albumin/globulin ratio were observed following reproduction, in addition to a decrease in glucose and total protein. These findings agree with the physiological constraint hypothesis and highlight the connection between life-history evolution and animal physiology by documenting, for the first time, how measures of physiological health state relate to reproductive investment in Australian freshwater turtles. Additionally, our findings suggest that body condition, a readily used morphological biomarker, is a poor predictor of health in turtles. Our results emphasize the need to investigate how maternal health is influenced by the reproductive process in different species.

Does habitat fragmentation cause stress in the agile antechinus? A haematological approach.

Although the vertebrate stress response is essential for survival, frequent or prolonged stress responses can result in chronic physiological stress, which is associated with a suite of conditions that can impair survivorship and reproductive output. Anthropogenic habitat fragmentation and degradation are potential stressors of free-living vertebrates, and in theory could result in chronic stress. To address this issue, we compared haematological indicators of stress and condition in agile antechinus (Antechinus agilis) populations in 30 forest fragments and 30 undisturbed, continuous forest sites (pseudofragments) in south-eastern Australia over 2 years. In peripheral blood, the total leucocyte count was lower and the neutrophil/lymphocyte ratio and percentage of eosinophils in the total leucocyte population was higher in fragment than pseudofragment populations, indicating that fragment populations were probably experiencing higher levels of stress hormone-mediated and/or parasite infection-related chronic physiological stress. The total erythrocyte count and haematocrit were higher and mean erythrocyte haemoglobin content was lower in fragment than pseudofragment populations. This suggests that fragment populations showed possible signs of regenerative anaemia, a syndrome associated with elevated hypothalamus-pituitary-adrenal axis mediated stress. However, mean erythrocyte volume was also lower in fragments, and red blood cell distribution width did not differ between the study populations, findings which were not consistent with this diagnosis. Whole blood and mean cell haemoglobin concentrations were similar in fragment and pseudofragment populations. We suggest that where anthropogenic activity results in habitat fragmentation and degradation, chronic stress could contribute to a decline in agile antechinus populations. The broader implication is that chronic stress could be both symptomatic of, and contributing to, decline of some vertebrate populations in anthropogenically fragmented and degraded habitats.

Interpreting indices of physiological stress in free-living vertebrates.

When vertebrate physiological ecologists use the terms 'stress' or 'physiological stress', they typically mean the level of hypothalamus-pituitary-adrenal (HPA-) axis activation. Measurements of stress hormone concentrations (e.g. glucocorticoids in blood, urine or faeces), leukocytes (e.g. the neutrophil-lymphocyte ratio or heterophil equivalent), immunofunction (e.g. innate, cell-mediated or humoral immunity measures) and regenerative anaemia (e.g. mean erythrocyte volume and red blood cell distribution width) have all been used to estimate HPA-axis activity in free-living vertebrates. Stress metrics have provided insights into aspects of autecology or population regulation that could not have been easily obtained using other indices of population wellbeing, such as body condition or relative abundance. However, short- and long-term stress (often problematically termed acute and chronic stress, respectively) can interact in unpredictable ways. When animals experience trapping and handling stress before blood, faeces and/or urine is sampled, the interaction of short- and long-term stress can confound interpretation of the data, a fact not always acknowledged in studies of stress in free-living vertebrates. This review examines how stress metrics can be confounded when estimates of HPA-axis activation are collected for free-living vertebrates and outlines some approaches that can be used to help circumvent the influence of potentially confounding factors.