Insufficient reporting of experimental variables as a cause for nonreproducibility in animal physiology? A case study.

Nonreproducibility in scientific investigations has been explained by inadequately reporting methodology, honest error, and even misconduct. We hypothesized that, within the field of animal physiology, the most parsimonious explanation for nonreproducibility is inadequate reporting of key methodological details. We further hypothesized that implementation of relatively recently released reporting guidelines has positively impacted journal article quality, as measured by completeness of the methodology descriptions. We analyzed 84 research articles published in five primarily organismal animal physiology journals in 2008-2010 (generally before current guidelines) and 2018-2020. Compliance for reporting 34 variables referring to biology, experiments, and data collection was assessed. Reporting compliance was just ∼61% in 2008-2010, rising only slightly to 67.5% for 2018-2020. Only 21% of the reported variables showed significant differences across the period from 2008-2020. We conclude that, despite attempts by societies and journals to promote greater reporting compliance, such efforts have so far been relatively unsuccessful in the field of animal physiology.

Running on empty: recharge dynamics from animal movement data.

Vital rates such as survival and recruitment have always been important in the study of population and community ecology. At the individual level, physiological processes such as energetics are critical in understanding biomechanics and movement ecology and also scale up to influence food webs and trophic cascades. Although vital rates and population-level characteristics are tied with individual-level animal movement, most statistical models for telemetry data are not equipped to provide inference about these relationships because they lack the explicit, mechanistic connection to physiological dynamics. We present a framework for modelling telemetry data that explicitly includes an aggregated physiological process associated with decision making and movement in heterogeneous environments. Our framework accommodates a wide range of movement and physiological process specifications. We illustrate a specific model formulation in continuous-time to provide direct inference about gains and losses associated with physiological processes based on movement. Our approach can also be extended to accommodate auxiliary data when available. We demonstrate our model to infer mountain lion (Puma concolor; in Colorado, USA) and African buffalo (Syncerus caffer; in Kruger National Park, South Africa) recharge dynamics.

Seasonal differences in baseline innate immune function are better explained by environment than annual cycle stage in a year-round breeding tropical songbird.

Seasonal variation in innate immunity is often attributed to either temporal environmental variation or to life-history trade-offs that arise from specific annual cycle stages but decoupling them is difficult in natural populations. Here, we effectively decouple seasonal environmental variation from annual cycle stage effects by exploiting cross-seasonal breeding and moult in the tropical Common Bulbul Pycnonotus barbatus. We test how annual cycle stage interacts with a key seasonal environmental variable, rainfall, to determine immunity at population and individual level. If immune challenge varies with precipitation, we might expect immune function to be higher in the wet season due to increased environmental productivity. If breeding or moult imposes resource constraints on birds, depending on or independent of precipitation, we might expect lower immune indices during breeding or moult. We sampled blood from 818 birds in four annual cycle stage categories: breeding, moult, simultaneous breeding and moulting, or neither. We quantified indices of innate immunity (haptoglobin, nitric oxide (NOx ) and ovotransferrin concentrations, and haemagglutination and haemolysis titres) over two annual cycles of wet and dry seasons. Environment (but not annual cycle stage or interactions between both) explained variation in all immune indices, except NOx . NOx concentration differed between annual cycle stages but not between seasons. However, within the wet season, haptoglobin, NOx , ovotransferrin and haemolysis differed significantly between breeding and non-breeding females. Aside from some recorded inconsistencies, population level results were largely similar to results within individuals that were measured repeatedly. Unexpectedly, most immune indices were higher in the dry season and during breeding. Higher immune indices may be explained if fewer or poorer quality resources force birds to increase social contact, thereby exposing individuals to novel antigens and increased infection risk, independently of environmental productivity. Breeding birds may also show higher immunity if less immune-competent and/or infected females omit breeding. We conclude that seasonal environmental variation impacts immunity more directly in natural animal populations than via resource trade-offs. In addition, immune indices were more often variable within than among individuals, but some indices are characteristic of individuals, and so may offer selective advantages if heritable.

Hair cortisol concentration in Siberian flying squirrels is unrelated to landscape and social factors.

Intact ecosystems are being lost or modified worldwide, and many animal species are now forced to live in altered landscapes. A large amount of scientific studies have focused on understanding direct effects of habitat alterations on species occurrence, abundance, breeding success, and other life history aspects. Much less attention has been placed on understanding how habitat alterations impact on the physiology of species, e.g., via elevated chronic stress when living in an altered landscape. Here, we quantify the effects of individual age and sex, as well as effects of landscape and social factors on chronic stress of an endangered forest specialist species, the Siberian flying squirrel Pteromys volans. We collected hair samples over 2 years from across 192 flying squirrels and quantified their chronic stress response via cortisol concentrations. We then ran statistical models to relate cortisol concentrations with landscape and social factors. We show that cortisol concentrations in flying squirrels are neither affected by habitat amount and connectivity, nor by the density of conspecifics in the area. We however found that cortisol concentration was higher in adults than in pups, and in males compared with females. Lack of an effect of environmental factors on cortisol concentrations may indicate low physiological sensitivity to alterations in the surrounding environment, possibly due to low densities of predators that could induce stress in the study area. Further research should focus on possible effects of varying predator densities, alone and in interaction with landscape features, in shaping chronic stress of this and other species.

Peptides for Skin Protection and Healing in Amphibians.

Amphibian skin is not to be considered a mere tegument; it has a multitude of functions related to respiration, osmoregulation, and thermoregulation, thus allowing the individuals to survive and thrive in the terrestrial environment. Moreover, amphibian skin secretions are enriched with several peptides, which defend the skin from environmental and pathogenic insults and exert many other biological effects. In this work, the beneficial effects of amphibian skin peptides are reviewed, in particular their role in speeding up wound healing and in protection from oxidative stress and UV irradiation. A better understanding of why some species seem to resist several environmental insults can help to limit the ongoing amphibian decline through the development of appropriate strategies, particularly against pathologies such as viral and fungal infections.

Teaching Animal Physiology: a 12-year experience transitioning from a classical to interactive approach with continual assessment and computer alternatives.

In response to the Bologna Declaration and contemporary trends in Animal Physiology education, the Animal Physiology course at the Faculty of Sciences, University of Novi Sad, Serbia, has evolved over a 12-yr period (2001-2012): from a classical two-semester course toward a one-semester course utilizing computer simulations of animal experiments, continual assessment, lectures, and an optional oral exam. This paper presents an overview of student achievement, the impact of reforms on learning outcomes, and lessons that we as educators learned during this process. The reforms had a positive impact on the percentage of students who completed the course within the same academic year. In addition, the percentage of students who completed the practical exam increased from 54% to >95% following the transition to a Bologna-based approach. However, average final grades declined from 8.0 to 6.8 over the same period. Students also appear reluctant to take the optional oral exam, and 82-91% of students were satisfied with the lower final grade obtained from only assessments and tests administered during the semester. In our endeavor to achieve learning outcomes set during the pre-Bologna period, while adopting contemporary teaching approaches, we sought to increase students' motivation to strive toward better performance, while ensuring that the increased quantity of students who complete the course is coupled with increased quality of education and a more in-depth understanding of animal physiology.

Activation of dopaminergic D2/D3 receptors modulates dorsoventral connectivity in the hippocampus and reverses the impairment of working memory after nerve injury.

Dopamine plays an important role in several forms of synaptic plasticity in the hippocampus, a crucial brain structure for working memory (WM) functioning. In this study, we evaluated whether the working-memory impairment characteristic of animal models of chronic pain is dependent on hippocampal dopaminergic signaling. To address this issue, we implanted multichannel arrays of electrodes in the dorsal and ventral hippocampal CA1 region of rats and recorded the neuronal activity during a food-reinforced spatial WM task of trajectory alternation. Within-subject behavioral performance and patterns of dorsoventral neuronal activity were assessed before and after the onset of persistent neuropathic pain using the Spared Nerve Injury (SNI) model of neuropathic pain. Our results show that the peripheral nerve lesion caused a disruption in WM and in hippocampus spike activity and that this disruption was reversed by the systemic administration of the dopamine D2/D3 receptor agonist quinpirole (0.05 mg/kg). In SNI animals, the administration of quinpirole restored both the performance-related and the task-related spike activity to the normal range characteristic of naive animals, whereas quinpirole in sham animals caused the opposite effect. Quinpirole also reversed the abnormally low levels of hippocampus dorsoventral connectivity and phase coherence. Together with our finding of changes in gene expression of dopamine receptors and modulators after the onset of the nerve injury model, these results suggest that disruption of the dopaminergic balance in the hippocampus may be crucial for the clinical neurological and cognitive deficits observed in patients with painful syndromes.

Ionic Current Variability and Functional Stability in the Nervous System.

Identified neurons in different animals express ionic currents at highly variable levels (population variability). If neuronal identity is associated with stereotypical function, as is the case in genetically identical neurons or in unambiguously identified individual neurons, this variability poses a conundrum: How is activity the same if the components that generate it-ionic current levels-are different? In some cases, ionic current variability across similar neurons generates an output gradient. However, many neurons produce very similar output activity, despite substantial variability in ionic conductances. It appears that, in many such cells, conductance levels of one ionic current vary in proportion to the conductance levels of another current. As a result, in a population of neurons, these conductances appear to be correlated. Here, I review theoretical and experimental work that suggests that neuronal ionic current correlation can reduce the global ionic current variability and can contribute to functional stability.

Electrical Signaling in Motile and Primary Cilia.

Cilia are highly conserved for their structure and also for their sensory functions. They serve as antennae for extracellular information. Whether the cilia are motile or not, they respond to environmental mechanical and chemical stimuli and signal to the cell body. The information from extracellular stimuli is commonly converted to electrical signals through the repertoire of ion-conducting channels in the ciliary membrane resulting in changes in concentrations of ions, especially Ca2+, in the cilia. These changes, in turn, affect motility and signaling pathways in the cilia and cell body to carry on the signal transduction. We review here the activities of ion channels in cilia from protists to vertebrates.

What can an ecophysiological approach tell us about the physiological responses of marine invertebrates to hypoxia?

Hypoxia (low O2) is a common and natural feature of many marine environments. However, human-induced hypoxia has been on the rise over the past half century and is now recognised as a major problem in the world's seas and oceans. Whilst we have information on how marine invertebrates respond physiologically to hypoxia in the laboratory, we still lack understanding of how they respond to such stress in the wild (now and in the future). Consequently, here the question 'what can an ecophysiological approach tell us about physiological responses of marine invertebrates to hypoxia' is addressed. How marine invertebrates work in the wild when challenged with hypoxia is explored using four case studies centred on different hypoxic environments. The recent integration of the various -omics into ecophysiology is discussed, and a number of advantages of, and challenges to, successful integration are suggested. The case studies and -omic/physiology integration data are used to inform the concluding part of the review, where it is suggested that physiological responses to hypoxia in the wild are not always the same as those predicted from laboratory experiments. This is due to behaviour in the wild modifying responses, and therefore more than one type of 'experimental' approach is essential to reliably determine the actual response. It is also suggested that assuming it is known what a measured response is 'for' can be misleading and that taking parodies of ecophysiology seriously may impede research progress. This review finishes with the suggestion that an -omics approach is, and is becoming, a powerful method of understanding the response of marine invertebrates to environmental hypoxia and may be an ideal way of studying hypoxic responses in the wild. Despite centring on physiological responses to hypoxia, the review hopefully serves as a contribution to the discussion of what (animal) ecophysiology looks like (or should look like) in the 21st century.

Follistatin controls the number of murine teeth by limiting TGF-ß signaling.

Supernumerary teeth are common developmental anomalies of dentition. However, the factors and mechanisms driving their formation remain largely unknown. Here, we report that conditional knockout of Fst, encoding an antagonist for the transforming growth factor ß (TGF-ß) signaling pathway, in both oral epithelium and mesenchyme of mice (Fst CKO ) led to supernumerary upper incisor teeth, arising from the lingual dental epithelium of the native teeth and preceded by an enlarged and split lingual cervical loop. Fst-deficiency greatly activated TGF-ß signaling in developing maxillary incisor teeth, associated with increased epithelium cell proliferation. Moreover, Fst CKO teeth exhibited increased expression of Tbx1, Sp6, and Sox2, which were identified as direct targets of TGF-ß/SMAD2 signaling. Finally, we show that upregulation of Tbx1 in response to Fst-deficiency was largely responsible for the formation of extra teeth in Fst CKO mice. Taken together, our investigation indicates a novel role for Fst in controlling murine tooth number by restricting TGF-ß signaling.

Summer fades, deer change: Photoperiodic control of cellular seasonal acclimatization of skeletal muscle.

We found major seasonal changes of polyunsaturated fatty acids (PUFAs) in muscular phospholipids (PL) in a large non-hibernating mammal, the red deer (Cervus elaphus). Dietary supply of essential linoleic acid (LA) and α-linolenic acid (ALA) had no, or only weak influence, respectively. We further found correlations of PL PUFA concentrations with the activity of key metabolic enzymes, independent of higher winter expression. Activity of the sarcoplasmic reticulum (SR) Ca++-ATPase increased with SR PL concentrations of n-6 PUFA, and of cytochrome c oxidase and citrate synthase, indicators of ATP-production, with concentrations of eicosapentaenoic acid in mitochondrial PL. All detected cyclic molecular changes were controlled by photoperiod and are likely of general relevance for mammals living in seasonal environments, including humans. During winter, these changes at the molecular level presumably compensate for Arrhenius effects in the colder peripheral body parts and thus enable a thrifty life at lower body temperature.

What happens when the lights are left on? Transcriptomic and phenotypic habituation to light pollution.

Artificial light at night (ALAN) is a ubiquitous pollutant worldwide. Exposure can induce immediate behavioral and physiological changes in animals, sometimes leading to severe health consequences. Nevertheless, many organisms persist in light-polluted environments and may have mechanisms of habituating, reducing responses to repeated exposure over time, but this has yet to be tested experimentally. Here, we tested whether zebra finches (Taeniopygia guttata) can habituate to dim (0.3 lux) ALAN, measuring behavior, physiology (oxidative stress and telomere attrition), and gene expression in a repeated measures design, over 6 months. We present evidence of tolerance to chronic exposure, persistent behavioral responses lasting 8 weeks post-exposure, and attenuation of responses to re-exposure. Oxidative stress decreased under chronic ALAN. Changes in the blood transcriptome revealed unique responses to past exposure and re-exposure. Results demonstrate organismal resilience to chronic stressors and shed light on the capacity of birds to persist in an increasingly light-polluted world.

Regulation of interstitial fluid flow in adventitia along vasculature by heartbeat and respiration.

Converging studies showed interstitial fluid (ISF) adjacent to blood vessels flows in adventitia along vasculature into heart and lungs. We aim to reveal circulatory pathways and regulatory mechanism of such adventitial ISF flow in rat model. By MRI, real-time fluorescent imaging, micro-CT, and histological analysis, ISF was found to flow in adventitial matrix surrounded by fascia and along systemic vessels into heart, then flow into lungs via pulmonary arteries and back to heart via pulmonary veins, which was neither perivascular tissues nor blood or lymphatic vessels. Under physiological conditions, speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, became pulsative during heavy breathing. During cardiac or respiratory cycle, each dilation or contraction of heart or lungs can generate to-and-fro adventitial ISF flow along femoral veins. Discovered regulatory mechanisms of adventitial ISF flow along vasculature by heart and lungs will revolutionize understanding of cardiovascular system.

Behavioral, metabolic, and lipidomic characterization of the 5xFADxTg30 mouse model of Alzheimer's disease.

Alzheimer's disease (AD) is associated with both extracellular amyloid-ß (Aß) plaques and intracellular tau-containing neurofibrillary tangles (NFT). We characterized the behavioral, metabolic and lipidomic phenotype of the 5xFADxTg30 mouse model which contains overexpression of both Aß and tau. Our results independently reproduce several phenotypic traits described previously for this model, while providing additional characterization. This model develops many aspects associated with AD including frailty, decreased survival, initiation of aspects of cognitive decline and alterations to specific lipid classes and molecular lipid species in the plasma and brain. Notably, some sex-specific differences exist in this model and motor impairment with aging in this model does compromise the utility of the model for some movement-based behavioral assessments of cognitive function. These findings provide a reference for individuals interested in using this model to understand the pathology associated with elevated Aß and tau or for testing potential therapeutics for the treatment of AD.

The importance of animal specificity in animal experimentation, part II: Physiological challenges and opportunities in relation to pediatric urology.

When performing animal experimentation in Pediatric Urology studies, it is important to be aware of physiological differences between species and to understand when relevant disease models are available. Diseased animal models may be more relevant in many cases, rather than performing studies in healthy and normally developed animals. For example, they may be more appropriate for the study of congenital malformations, to investigate the secondary effects of prenatal urinary obstruction, to study the effect of prenatal exposure to endogenous or exogenous factors which may lead to disease, or in testing bioengineered structures. In this short educational article, we aim to describe some disease models that have been used to simulate human pathologies and how, if properly designed, these studies can lead to important new knowledge for human translation. In addition, we also highlight the importance of formulating a research question(s) before deciding on the animal experimental model and species to choose.

Long-term intermittent hypoxia in mice induces inflammatory pathways implicated in sleep apnea and steatohepatitis in humans.

Obstructive sleep apnea (OSA) induces intermittent hypoxia (IH), an independent risk factor for non-alcoholic fatty liver disease (NAFLD). While the molecular links between IH and NAFLD progression are unclear, immune cell-driven inflammation plays a crucial role in NAFLD pathogenesis. Using lean mice exposed to long-term IH and a cohort of lean OSA patients (n = 71), we conducted comprehensive hepatic transcriptomics, lipidomics, and targeted serum proteomics. Significantly, we demonstrated that long-term IH alone can induce NASH molecular signatures found in human steatohepatitis transcriptomic data. Biomarkers (PPARs, NRFs, arachidonic acid, IL16, IL20, IFNB, TNF-α) associated with early hepatic and systemic inflammation were identified. This molecular link between IH, sleep apnea, and steatohepatitis merits further exploration in clinical trials, advocating for integrating sleep apnea diagnosis in liver disease phenotyping. Our unique signatures offer potential diagnostic and treatment response markers, highlighting therapeutic targets in the comorbidity of NAFLD and OSA.

In vivo techniques for assessment of insulin sensitivity and glucose metabolism.

Metabolic tests are vital to determine in vivo insulin sensitivity and glucose metabolism in preclinical models, usually rodents. Such tests include glucose tolerance tests, insulin tolerance tests, and glucose clamps. Although these tests are not standardized, there are general guidelines for their completion and analysis that are constantly being refined. In this review, we describe metabolic tests in rodents as well as factors to consider when designing and performing these tests.

Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin.

Zebrafish regenerate their fins which involves a component of cell plasticity. It is currently unclear how regenerate cells divide labor to allow for appropriate growth and patterning. Here, we studied lineage relationships of fluorescence-activated cell sorting-enriched epidermal, bone-forming (osteoblast), and (non-osteoblast) blastemal fin regenerate cells by single-cell RNA sequencing, lineage tracing, targeted osteoblast ablation, and electron microscopy. Most osteoblasts in the outgrowing regenerate derive from osterix+ osteoblasts, while mmp9+ cells reside at segment joints. Distal blastema cells contribute to distal osteoblast progenitors, suggesting compartmentalization of the regenerating appendage. Ablation of osterix+ osteoblasts impairs segment joint and bone matrix formation and decreases regenerate length which is partially compensated for by distal regenerate cells. Our study characterizes expression patterns and lineage relationships of rare fin regenerate cell populations, indicates inherent detection and compensation of impaired regeneration, suggests variable dependence on growth factor signaling, and demonstrates zonation of the elongating fin regenerate.

KLF4 promotes milk fat synthesis by regulating the PI3K-AKT-mTOR pathway and targeting FASN activation in bovine mammary epithelial cells.

Milk fat is an important indicator for evaluating the quality of cow's milk. In this study, we used bovine mammary epithelial cells (BMECs) to investigate the role and molecular mechanism of KLF4 in the regulation of milk fat synthesis. The results showed that KLF4 was more highly expressed in mammary tissues of high-fat cows compared with low-fat cows. KLF4 positively regulated the expression of genes related to milk fat synthesis in BMECs, increasing intracellular triglycerides content, and KLF4 promoted milk fat synthesis by activating the PI3K-AKT-mTOR signaling pathway. Furthermore, the results of animal experiments also confirmed that knockdown of KLF4 inhibited milk fat synthesis. In addition, yeast one-hybrid assays and dual-luciferase reporter gene assays confirmed that KLF4 directly targets and binds to the fatty acid synthase (FASN) promoter region to promote FASN transcription. These results demonstrate that KLF4 is a key transcription factor for milk fat synthesis in BMECs.