Search

What are the future directions of the fields of developmental and comparative immunology? In thinking through this question as I write, I find myself marvelling at the very long ways that we have come since I began as a PhD student some 50 years ago. I think that we cannot know what technical and theoretical advances will emerge in the future, nor will our initial aims survive the realities of what appears in our sights, often from unexpected directions. I feel that we should not allow what we already know about some well-studied systems to blind us to the wide range of possibilities, and that remaining a humble seeker helps the uptake of new realities. Finally, it would be good to try answering the whole range of questions about developmental and comparative immunology, from what to how to why., (Copyright © 2024 The Author. Published by Elsevier Ltd.. All rights reserved.)

Of all the properties of individual animals of interest to comparative physiologists, age and stage of development are among the most consequential. In a natural population of any species, the survivorship curve is an important determinant of the relative abundances of ages and stages of development. Demography, thus, has significant implications for the study of comparative physiology. When Edward Deevey published his influential summary of survivorship in animal populations in the wild seven decades ago, he emphasized “serious deficiencies” because survivorship curves for natural populations at the time did not include data on the earliest life stages. Such data have accumulated over intervening years. We survey, for the first time, empirical knowledge of early-age survivorship in populations of most major animal groups in a state of nature. Despite wide variation, it is almost universally true that > 50% of newly born or hatched individuals die before the onset of sexual maturity, even in species commonly assumed to exhibit high early-age survivorship. These demographic facts are important considerations for studies in comparative and environmental physiology whether physiologists (i) aim to elucidate function throughout the life cycle, including both early stages and adults, or (ii) focus on adults (in which case early-age survivorship can potentially affect adult characteristics through selection or epigenesis). We establish that Deevey’s Type I curve (which applies to species with relatively limited early mortality) has few or no actual analogs in the real, natural world.

Neural function depends on maintaining cellular membrane potentials as the basis for electrical signaling. Yet, in mammals and insects, neuronal and glial membrane potentials can reversibly depolarize to zero, shutting down neural function by the process of spreading depolarization (SD) that collapses the ion gradients across membranes. SD is not evident in all metazoan taxa with centralized nervous systems. We consider the occurrence and similarities of SD in different animals and suggest that it is an emergent property of nervous systems that have evolved to control complex behaviors requiring energetically expensive, rapid information processing in a tightly regulated extracellular environment. Whether SD is beneficial or not in mammals remains an open question. However, in insects, it is associated with the response to harsh environments and may provide an energetic advantage that improves the chances of survival. The remarkable similarity of SD in diverse taxa supports a model systems approach to understanding the mechanistic underpinning of human neuropathology associated with migraine, stroke, and traumatic brain injury.

The diversity of Australia’s theropod fauna from the ‘mid’-Cretaceous (Albian–Cenomanian) is distinctly biased towards the medium-sized megaraptorids, despite the preponderance of abelisauroids in the younger but latitudinally equivalent Patagonian theropod fauna. Here, we present new evidence for the presence of ceratosaurian, and specifically abelisauroid, theropods from the Cenomanian Griman Creek Formation of Lightning Ridge, New South Wales. A partial cervical vertebra is described that bears a mediolaterally concave ventral surface of the centrum delimited by sharp ventrolateral ridges that contact the parapophyses. Among theropods, this feature has been reported only in a cervical vertebra attributed to the noasaurid Noasaurus. We also reappraise evidence recently cited against the ceratosaurian interpretation of a recently described astragalocalcaneum from the upper Barremian–lower Aptian San Remo Member of the upper Strzelecki Group in Victoria. Inclusion of the Lightning Ridge cervical vertebra and Victorian astragalocalcaneum into a revised phylogenetic analysis focused on elucidating ceratosaurian affinities reveals support for placement of both specimens within Noasauridae, which among other characters is diagnosed by the presence of a medial eminence on the ascending process of the astragalus. The Lightning Ridge and Victorian specimens simultaneously represent the first noasaurids reported from Australia and the astragalocalcaneum is considered the earliest known example of a noasaurid in the world to date. The recognition of Australian noasaurids further indicates a more widespread Gondwanan distribution of the clade outside of South America, Madagascar and India consistent with the timing of the fragmentation of the supercontinent.

Background Hydrangea macrophylla var. Maculata ‘Yinbianxiuqiu’ (YB) is an excellent plant species with beautiful flowers and leaves with silvery white edges. However, there are few reports on its leaf color characteristics and color formation mechanism. Results The present study compared the phenotypic, physiological and transcriptomic differences between YB and a full-green leaf mutant (YM) obtained from YB. The results showed that YB and YM had similar genetic backgrounds, but photosynthesis was reduced in YB. The contents of pigments were significantly decreased at the edges of YB leaves compared to YM leaves. The ultrastructure of chloroplasts in the YB leaves was irregular. Transcriptome profiling identified 7,023 differentially expressed genes between YB and YM. The expression levels of genes involved in photosynthesis, chloroplast development and division were different between YB and YM. Quantitative real-time PCR showed that the expression trends were generally consistent with the transcriptome data. Conclusions Taken together, the formation of the silvery white leaf color of H. macrophylla var. maculata was primarily due to the abnormal development of chloroplasts. This study facilitates the molecular function analysis of key genes involved in chloroplast development and provides new insights into the molecular mechanisms involved in leaf coloration in H. macrophylla.

Mechanistic evaluations of processes that underlie organism-level physiology often require reductionist approaches. Dermal fibroblasts offer one such approach. These cells are easily obtained from minimally invasive skin biopsy, making them appropriate for the study of protected and/or logistically challenging species. Cell culture approaches permit extensive and fine-scale sampling regimes as well as gene manipulation techniques that are not feasible in vivo. Fibroblast isolation and culture protocols are outlined here for primary cells, and the benefits and drawbacks of immortalization are discussed. We show examples of physiological metrics that can be used to characterize primary cells (oxygen consumption, translation, proliferation) and readouts that can be informative in understanding cell-level responses to environmental stress (lactate production, heat shock protein induction). Importantly, fibroblasts may display fidelity to whole animal physiological phenotypes, facilitating their study. Fibroblasts from Antarctic Weddell seals show greater resilience to low temperatures and hypoxia exposure than fibroblasts from humans or rats. Fibroblast oxygen consumption rates are not affected by temperature stress in the heat-tolerant camel, whereas similar temperature exposures depress mitochondrial metabolism in fibroblasts from rhinoceros. Finally, dermal fibroblasts from a hibernator, the meadow jumping mouse, better resist experimental cooling than a fibroblast line from the laboratory mouse, with the hibernator demonstrating a greater maintenance of homeostatic processes such as protein translation. These results exemplify the parallels that can be drawn between fibroblast physiology and expectations in vivo, and provide evidence for the power of fibroblasts as a model system to understand comparative physiology and biomedicine.

Meta-analysis is a powerful tool used to generate quantitatively informed answers to pressing global challenges. By distilling data from broad sets of research designs and study systems into standardised effect sizes, meta-analyses provide physiologists with opportunities to estimate overall effect sizes and understand the drivers of effect variability. Despite this ambition, research designs in the field of comparative physiology can appear, at the outset, as being vastly different to each other because of ‘nuisance heterogeneity’ (e.g. different temperatures or treatment dosages used across studies). Methodological differences across studies have led many to believe that meta-analysis is an exercise in comparing ‘apples with oranges’. Here, we dispel this myth by showing how standardised effect sizes can be used in conjunction with multilevel meta-regression models to both account for the factors driving differences across studies and make them more comparable. We assess the prevalence of nuisance heterogeneity in the comparative physiology literature – showing it is common and often not accounted for in analyses. We then formalise effect size measures (e.g. the temperature coefficient, Q10) that provide comparative physiologists with a means to remove nuisance heterogeneity without the need to resort to more complex statistical models that may be harder to interpret. We also describe more general approaches that can be applied to a variety of different contexts to derive new effect sizes and sampling variances, opening up new possibilities for quantitative synthesis. By using effect sizes that account for components of effect heterogeneity, in combination with existing meta-analytic models, comparative physiologists can explore exciting new questions while making results from large-scale data sets more accessible, comparable and widely interpretable.

Comparative phylogenetic studies of adaptation are uncommon in biomechanics and physiology. Such studies require data collection from many species, a challenge when this is experimentally intensive. Moreover, researchers struggle to employ the most biologically appropriate phylogenetic tools for identifying adaptive evolution. Here, we detail an established but greatly underutilized phylogenetic comparative framework – the Ornstein–Uhlenbeck process – that explicitly models long-term adaptation. We discuss challenges in implementing and interpreting the model, and we outline potential solutions. We demonstrate use of the model through studying the evolution of thermal physiology in treefrogs. Frogs of the family Hylidae have twice colonized the temperate zone from the tropics, and such colonization likely involved a fundamental change in physiology due to colder and more seasonal temperatures. However, which traits changed to allow colonization is unclear. We measured cold tolerance and characterized thermal performance curves in jumping for 12 species of treefrogs distributed from the Neotropics to temperate North America. We then conducted phylogenetic comparative analyses to examine how tolerances and performance curves evolved and to test whether that evolution was adaptive. We found that tolerance to low temperatures increased with the transition to the temperate zone. In contrast, jumping well at colder temperatures was unrelated to biogeography and thus did not adapt during dispersal. Overall, our study shows how comparative phylogenetic methods can be leveraged in biomechanics and physiology to test the evolutionary drivers of variation among species.

August Krogh (1874–1949) was amongst the most influential physiologists in the first part of the 20th century. This was an era when physiology emerged as a quantitative research field and when many of the current physiological disciplines were defined; Krogh can rightfully be viewed as having introduced comparative physiology, epithelial transport and – together with Johannes Lindhard – exercise physiology as independent disciplines. With a unique ability to design and construct equipment, Krogh could address novel questions in both human and animal physiology with unprecedented precision. Krogh would characteristically focus on a given physiological problem over a couple of years, delineate the focal mechanisms, provide a solution to the major problems, and then move onto new academic ground. For each of his major research areas (respiratory gas exchange, capillary function, osmoregulation), he wrote comprehensive books or monographs that remain important resources for scholars today ( Krogh, 1916 ; Krogh, 1922 ; Krogh, 1939 ; Krogh, 1941 ), and he engaged in the writing of physiology textbooks for the Danish high school. Krogh's research appears to have been driven by curiosity to understand how animals (including humans) work, but he did not hesitate to apply his insight to societal and clinical problems throughout his long academic career.

Objectives Ambient temperature impinges on energy metabolism in a body size dependent manner. This has implications for the housing temperature at which mice are best compared to humans. In 2013, we suggested that, for comparative studies, solitary mice are best housed at 23–25 °C, because this is 3–5 °C below the mouse thermoneutral zone and humans routinely live 3–5 °C below thermoneutrality, and because this generates a ratio of DEE to BMR of 1.6–1.9, mimicking the ratio found in free-living humans. Methods Recently, Fischer et al. (2017) challenged this estimate. By studying mice at 21 °C and at 30 °C (but notably not at 23–25 °C) they concluded that 30 °C is the optimal housing temperature. Here, we measured energy metabolism of C57BL/6 mice over a range of temperatures, between 21.4 °C and 30.2 °C. Results We observed a ratio of DEE to BMR of 1.7 at 27.6 °C and of 1.8 at 25.5 °C, suggesting that this is the best temperature range for housing C57BL/6 mice to mimic human thermal relations. We used a 24 min average to calculate the ratio, similar to that used in human studies, while the ratio calculated by Fisher et al. dependent on short, transient metabolic declines. Conclusion We concur with Fisher et al. and others that 21 °C is too cool, but we continue to suggest that 30 °C is too warm. We support this with other data. Finally, to mimic living environments of all humans, and not just those in controlled Western environments, mouse experimentation at various temperatures is likely required., Graphical abstract Image 1, Highlights • Translation from mice to man is best done at comparable metabolic conditions. • ‘Western’ humans metabolize at 1.7 to 1.8x BMR and are below thermoneutrality. • Thermoneutrality of solitary housed C57BL/6 laboratory mice commences above 28 °C. • 1.7x - 1.8x BMR for solitary housed C57BL/6 lab mice is between 25.5 °C - 27.6 °C. • Neither 21 °C nor 30 °C are suitable housing temperatures for translation.

August Krogh’s 1929 principle is referenced as the cornerstone of comparative physiology (CP). However, there are diverse views as to what type of research falls under the CP approach. This study had three aims: 1) determine how CP is defined through an online survey (OS) of physiologists and a systematic review (SR), 2) put forth an updated definition of CP by summarizing OS and SR results, and 3) outline the numerous CP research approaches. Professional physiology societies ( n = 54) were invited to share the OS with their members, and a SR was conducted, which yielded 197 and 70 definitions, respectively. The three most common words in descending order in the OS definitions were “different,” “animals,” and “species” and in the SR definitions, “animals,” “species,” and “organisms.” The three most prevalent themes from the OS and SR definitions were comparing/differences/diversity across species (78% and 51%, respectively), response to the environment/ecology (28% and 43%, respectively), and included evolution or adaptation (24% and 60%, respectively). Ten research approaches were identified, which include broad comparison (i.e., many species generalization), specific comparison (e.g., 2 species; for traits that are different, exaggerated, extreme, missing, or not induced), or comparison while considering evolution (i.e., evolutionary physiology), ecology (i.e., ecophysiology), or human physiology/medicine. Only 5% and 33% of OS and SR definitions described or mentioned Krogh’s principle. In conclusion, CP can best be defined as a compilation of research approaches that utilize different types of comparisons to elucidate physiological mechanisms and not simply comparing physiologies as the name implies.

‘Omics’ methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into ‘fishing expeditions’ and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.

This graphical review highlights a focused application of a key principle (‘Krogh Principle’) identified by Nobel-prize winning physiologist Professor August Krogh (1874 – 1949) that states "for many problems there is an animal on which it can be most conveniently studied". We apply the Krogh Principle to human physiology by proposing that "for many problems there is a unique group of humans on which it can be most conveniently studied". As such, we present 5 unique human case studies. Case 1 discusses whether signals from exercising muscles cause blood pressure to rise using a patient with a spinal cord lesion. Case 2 investigates the role of the sympathetic nervous system in the blood pressure response to exercise using patients who have undergone sympathectomy for hypertension. Case 3 asks whether increases in blood lactate are necessary for the non-linear increase in breathing with heavy exercise using patients with McArdle’s disease. Case 4 applies fundamental scaling principles from comparative physiology to elite athletes to investigate the role of body size on maximal aerobic capacity. Finally, Case 5 describes our recent work that investigates whether a left shift in the oxygen hemoglobin dissociation curve can facilitate hypoxic exercise using patients with left-shifted hemoglobinopathies. In summary, we have expanded the inter-species message of the August Krogh Principle and highlighted the need to search for odd examples and experiments of nature. In this context, observations from unusual humans are a source of insights into physiology, which may be translated into therapeutic approaches for disease.

There are some historical divisions in methods, rationales, and purposes between studies on comparative cognition and behavioural ecology. In turn, the interaction between these two branches and studies from mathematics, computation, and neuroscience is not usual. In this short piece, we attempt to build bridges among these disciplines. We present a series of interconnected vignettes meant to illustrate what a more interdisciplinary approach looks like when successful, and its advantages. Concretely, we focus on a recent topic, namely animal rhythms in interaction, studied under different approaches. We showcase 5 research efforts, which we believe successfully link 5 particular scientific areas of rhythm research conceptualised as the following: social neuroscience, detailed rhythmic quantification, ontogeny, computational approaches, and spontaneous interactions. Our suggestions will hopefully spur a "comparative rhythms in interaction" field, which can integrate and capitalize on knowledge from zoology, comparative psychology, neuroscience, and computation. (PsycInfo Database Record (c) 2020 APA, all rights reserved).

B-cells are key to humoral immunity, are found in multiple lymphoid organs, and have the unique ability to mediate the production of antigen-specific antibodies in the presence of pathogens. The marsupial immunoglobulin (Ig) heavy (H) chain locus encodes four constant region isotypes, IgA, IgG, IgM and IgE, but no IgD, and there are two light (L) chain isotypes, lambda (Igλ) and kappa (Igκ). To gain an understanding of the marsupial humoral immune system, B-cell transcriptomes generated by single-cell RNA sequencing from gray short-tailed opossum (Monodelphis domestica) splenocytes, and peripheral blood mononuclear cells were analysed. The cells used were from a single unimmunized animal and the majority of B-cells were transcribing IgM heavy chains. The ratio of Ig light chain use was roughly 2:1, Igλ:Igκ in this individual. This was not predicted due to Igκ being the more complex of the two L chain loci. The variable (V) gene segment pairs used in individual B-cells confirm greater diversity provided by the L chain V. This study is the first to report on using single cell analysis to investigate Ig repertoires in a marsupial and confirms a number of prior hypothesis, as well as revealing some surprises.

For almost 100 years, biologists have made fundamental discoveries using a handful of model organisms that are not representative of the rich diversity found in nature. The advent of CRISPR genome editing now opens up a wide range of new organisms to mechanistic investigation. This increases not only the taxonomic breadth of current research but also the scope of biological problems that are now amenable to study, such as population control of invasive species, management of disease vectors such as mosquitoes, the creation of chimeric animal hosts to grow human organs and even the possibility of resurrecting extinct species such as passenger pigeons and mammoths. Beyond these practical applications, work on non-model organisms enriches our basic understanding of the natural world. This special issue addresses a broad spectrum of biological problems in non-model organisms and highlights the utility of genome editing across levels of complexity from development and physiology to behaviour and evolution.

A new family of paratanaoidean Tanaidacea – Paranarthrurellidae fam. nov. – is erected to accommodate two genera without family classification (Paratanaoidea incertae sedis), namely Armatognathia Kudinova-Pasternak, 1987 and Paranarthrurella Lang, 1971. Seven new species of Paranarthrurella and two of Armatognathia are described from material taken in different deep-sea areas of the Atlantic and Pacific oceans. The type species of Paranarthrurella — P. caudata (Kudinova-Pasternak, 1965) — is redescribed based on the paratype. The genus Cheliasetosatanais Larsen and Araújo-Silva, 2014 originally classified within Colletteidae is synonymised with Paranarthrurella, and Arthrura shiinoi Kudinova-Pasternak, 1973 is transferred to Armatognathia. Amended diagnoses of Armatognathia and Paranarthrurella genera are given. Choosing characters for distinguishing and defining both genera was supported by Principal Component Analysis. Designation of the new family is supported by molecular phylogenetic analysis of COI and 18S datasets. The distribution of all species currently included in the new family was visualised and their bathymetric distribution analysed.

Researchers and practitioners are increasingly using comparative assessments of critical thermal and physiological limits to assess the relative vulnerability of ectothermic species to extreme thermal and aridity conditions occurring under climate change. In most assessments of vulnerability, critical limits are compared across taxa exposed to different environmental and developmental conditions. However, many aspects of vulnerability should ideally be compared when species are exposed to the same environmental conditions, allowing a partitioning of sources of variation such as used in quantitative genetics. This is particularly important when assessing the importance of different types of plasticity to critical limits, using phylogenetic analyses to test for evolutionary constraints, isolating genetic variants that contribute to limits, characterizing evolutionary interactions among traits limiting adaptive responses, and when assessing the role of cross generation effects. However, vulnerability assessments based on critical thermal/physiological limits also need to take place within a context that is relevant to field conditions, which is not easily provided under controlled environmental conditions where behavior, microhabitat, stress exposure rates and other factors will differ from field conditions. There are ways of reconciling these requirements, such as by taking organisms from controlled environments and then testing their performance under field conditions (or vice versa). While comparisons under controlled environments are challenging for many taxa, assessments of critical thermal limits and vulnerability will always be incomplete unless environmental effects within and across generations are considered, and where the ecological relevance of assays measuring critical limits can be established.

Animal models can reproduce some model-specific aspects of human diseases, but some animal models translate poorly or fail to translate to the corresponding human disease. Here, we develop a strategy to systematically compare human and mouse tissues, and conduct a proof-of-concept experiment to identify molecular similarities and differences using patients with idiopathic pulmonary fibrosis and a bleomycin-induced fibrosis mouse model. Our novel approach employs high-throughput tissue microarrays (TMAs) of humans and mice, high-resolution matrix-assisted laser desorption/ionization-Fourier transform-ion cyclotron resonance-mass spectrometry imaging (MALDI-FT-ICR-MSI) to spatially resolve mass spectra at the level of specific metabolites, and hierarchical clustering and pathway enrichment analysis to identify functionally similar/different molecular patterns and pathways in pathological lesions of humans and mice. We identified a large number of common molecules (n=1366) and fewer exclusive molecules in humans (n=83) and mice (n=54). Among the common molecules, the 'ascorbate and aldarate metabolism' pathway had the highest similarity in human and mouse lesions. This proof-of-concept study demonstrates that our novel strategy employing a reliable and easy-to-perform experimental design accurately identifies pathways and factors that can be directly compared between animal models and human diseases.

Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity. Initial studies showed that the Mollusca (second largest animal phylum), and invertebrates in general, possess innate defenses but lack the lymphocytic immune system that characterizes vertebrate immunology. Recognizing the reality of both common and taxon-specific immune features, and applying up-to-date cell and molecular research capabilities, in-depth studies of a select number of bivalve and gastropod species continue to reveal novel aspects of molluscan immunity. The genomics era heralded a new stage of comparative immunology; large-scale efforts yielded an initial set of full molluscan genome sequences that is available for analyses of full complements of immune genes and regulatory sequences. Next-generation sequencing (NGS), due to lower cost and effort required, allows individual researchers to generate large sequence datasets for growing numbers of molluscs. RNAseq provides expression profiles that enable discovery of immune genes and genome sequences, reveal distribution and diversity of immune factors across molluscan phylogeny. Although computational de novo sequence assembly will benefit from continued development and automated annotation may require some experimental validation, NGS is a powerful tool for comparative immunology, especially increasing coverage of the extensive molluscan diversity. To date, immunogenomics revealed new levels of complexity of molluscan defense by indicating sequence heterogeneity in individual snails and bivalves, and members of expanded immune gene families are expressed differentially to generate pathogen-specific defense responses.

Comparative physiologists are often interested in adaptive physiological phenomena found in unconventional model organisms; however, research on these species is frequently constrained by the limited availability of investigative tools. Here, we propose that induced pluripotent stem cells (iPSCs) from unconventional model organisms may retain certain species-specific features that can consequently be investigated in depth in vitro; we use hibernating mammals as an example. Many species (including ground squirrels, bats and bears) can enter a prolonged state of physiological dormancy known as hibernation to survive unfavorable seasonal conditions. Our understanding of the mechanisms underpinning the rapid transition and adaptation to a hypothermic, metabolically suppressed winter torpor state remains limited partially because of the lack of an easily accessible model. To address the fascinating unanswered questions underlying hibernation biology, we have developed a powerful model system: iPSCs from a hibernating species, the thirteen-lined ground squirrel (Ictidomys tridecemlineatus). These stem cells can potentially be differentiated into any cell type, and can be used for the analysis of cell-autonomous mechanisms that facilitate adaptation to hibernation and for comparisons with non-hibernators. Furthermore, we can manipulate candidate molecular and cellular pathways underlying relevant physiological phenomena by pharmacological or RNAi-based methods, and CRISPR/Cas9 gene editing. Moreover, iPSC strategies can be applied to other species (e.g. seals, naked mole rats, humming birds) for in vitro studies on adaptation to extreme physiological conditions. In this Commentary, we discuss factors to consider when attempting to generate iPSCs from unconventional model organisms, based on our experience with the thirteen-lined ground squirrel.

Loss-of-function technologies, such as morpholino- and RNAi-mediated gene knockdown, and TALEN- and CRISPR/Cas9-mediated gene knockout, are widely used to investigate gene function and its physiological significance. Here, we provide a general overview of the various knockdown and knockout technologies commonly used in comparative physiology and discuss the merits and drawbacks of these technologies with a particular focus on research conducted in zebrafish. Despite their widespread use, there is an ongoing debate surrounding the use of knockdown versus knockout approaches and their potential off-target effects. This debate is primarily fueled by the observations that, in some studies, knockout mutants exhibit phenotypes different from those observed in response to knockdown using morpholinos or RNAi. We discuss the current debate and focus on the discrepancies between knockdown and knockout phenotypes, providing literature and primary data to show that the different phenotypes are not necessarily a direct result of the off-target effects of the knockdown agents used. Nevertheless, given the recent evidence of some knockdown phenotypes being recapitulated in knockout mutants lacking the morpholino or RNAi target, we stress that results of knockdown experiments need to be interpreted with caution. We ultimately argue that knockdown experiments should not be discontinued if proper control experiments are performed, and that with careful interpretation, knockdown approaches remain useful to complement the limitations of knockout studies (e.g. lethality of knockout and compensatory responses).

Vascular resistance and conductance are reciprocal indices of vascular tone that are often assumed to be interchangeable. However, in most animals in vivo, blood flow (i.e. cardiac output) typically varies much more than arterial blood pressure. When blood flow changes at a constant pressure, the relationship between conductance and blood flow is linear, whereas the relationship between resistance and blood flow is non-linear. Thus, for a given change in blood flow, the change in resistance depends on the starting point, whereas the attendant change in conductance is proportional to the change in blood flow regardless of the starting conditions. By comparing the effects of physical activity at different temperatures or between species – concepts at the heart of comparative cardiovascular physiology – we demonstrate that the difference between choosing resistance or conductance can be marked. We also explain here how the ratio of conductance in the pulmonary and systemic circulations provides a more intuitive description of cardiac shunt patterns in the reptilian cardiovascular system than the more commonly used ratio of resistance. Finally, we posit that, although the decision to use conductance or resistance should be made on a case-by-case basis, in most circumstances, conductance is a more faithful portrayal of cardiovascular regulation in vertebrates.

Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host–microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host–microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables – including sampling regime, environmental parameters, host metadata and analytical methods – can influence experimental outcomes in host–microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host–microbiome interactions among a broad range of metazoans, including humans.

We investigated the physiological and proteomic changes in the leaves of three Lolium perenne genotypes, one Iranian putative self-pollinating genotype named S10 and two commercial genotypes of Vigor and Speedy, subjected to drought stress conditions. The results of this study indeed showed higher RWC (relative water content), SDW (shoot dry weight), proline, ABA (abscisic acid), nitrogen and amino acid contents, and antioxidant enzymes activities of S10 under drought stress in comparison with the two other genotypes. A total of 915 proteins were identified using liquid chromatography-mass spectrometry (LC/MS) analysis, and the number of differentially abundant proteins between normal and stress conditions was 467, 456, and 99 in Vigor, Speedy, and S10, respectively. Proteins involved in carbon and energy metabolism, photosynthesis, TCA cycle, redox, and transport categories were up-regulated in the two commercial genotypes. We also found that some protein inductions, including those involved in amino acid and ABA metabolisms, aquaporin, HSPs, photorespiration, and increases in the abundance of antioxidant enzymes, are essential responses of the two commercial genotypes to drought stress. In contrast, we observed only slight changes in the protein profile of the S10 genotype under drought stress. Higher homozygosity due to self-pollination in the genetic background of the S10 genotype may have led to a lower variation in response to drought stress conditions.

Comparative endocrinology has traditionally focused on studies of the evolution of endocrine systems, regulation of hormone actions in animals, development of model systems, and the role of the environment in controlling hormone functions related to major life-history events. Comparative endocrinology also has made important contributions to basic research and clinical endocrinology. In recent years there has been a shift to a focus on anthropogenic chemical factors and their alteration of major life history events through endocrine disruption. During the 21st century, environmental comparative endocrinologists must play an important role in the identification and assessment of endocrine disruption on vertebrate and invertebrate animals and their environment as well as in monitoring remediation. All comparative biologists are encouraged to communicate their understanding of threats to biological systems to non-scientists to facilitate their understanding of the human impacts of various kinds of pollution and habitat destruction on wildlife and ecosystems as well as their long-term consequences.

Although placental diversity in mammals received growing attention in the 1600s through the early 1800s, placentation was not documented in reptiles until the mid-19th century. In his classic 1855 study on a viviparous lizard, Cesare Studiati (University of Pisa) described a structural/functional arrangement of fetal and maternal tissues that meets contemporary criteria for recognition of placentation. Through the fortuitous selection of a highly placentotrophic species, Chalcides chalcides, Studiati recognized the functional role of placental tissues in provision of oxygen as well as nutrients. Although Studiati worked in a pre-evolutionary milieu and without the benefits of histological techniques, his findings revealed that viviparous reptiles could exhibit placental specializations that paralleled those of mammals. Accordingly, his classic paper initiated a highly productive body of research that has continued to the present and highlighted specializations of a species that has figured importantly in placental research.

This review explores challenges and opportunities in developmental physiology outlined by a symposium at the 2014 American Physiological Society Intersociety Meeting: Comparative Approaches to Grand Challenges in Physiology. Across animal taxa, adverse embryonic/fetal environmental conditions can alter morphological and physiological phenotypes in juveniles or adults, and capacities for developmental plasticity are common phenomena. Human neonates with body sizes at the extremes of perinatal growth are at an increased risk of adult disease, particularly hypertension and cardiovascular disease. There are many rewarding areas of current and future research in comparative developmental physiology. We present key mechanisms, models, and experimental designs that can be used across taxa to investigate patterns in, and implications of, the development of animal phenotypes. Intraspecific variation in the timing of developmental events can be increased through developmental plasticity (heterokairy), and could provide the raw material for selection to produce heterochrony — an evolutionary change in the timing of developmental events. Epigenetics and critical windows research recognizes that in ovo or fetal development represent a vulnerable period in the life history of an animal, when the developing organism may be unable to actively mitigate environmental perturbations. ‘Critical windows’ are periods of susceptibility or vulnerability to environmental or maternal challenges, periods when recovery from challenge is possible, and periods when the phenotype or epigenome has been altered. Developmental plasticity may allow survival in an altered environment, but it also has possible long-term consequences for the animal. “Catch-up growth” in humans after the critical perinatal window has closed elicits adult obesity and exacerbates a programmed hypertensive phenotype (one of many examples of “fetal programing”). Grand challenges for developmental physiology include integrating variation in developmental timing within and across generations, applying multiple stressor dosages and stressor exposure at different developmental timepoints, assessment of epigenetic and parental influences, developing new animal models and techniques, and assessing and implementing these designs and models in human health and development.

In jawed vertebrates, the crosstalk between immune and endocrine system as well as many fundamental mechanisms of T cell development are evolutionary conserved. Oestrogens affect mammalian thymic function and plasticity, but the mechanisms of action and the oestrogen receptors involved remain unclear. To corroborate the oestrogenic regulation of thymic function in teleosts and to identify the implicated oestrogen receptor subtypes, we examined the distribution of nuclear and membrane oestrogen receptors within the thymus of the European Sea bass, Dicentrarchus labrax, in relation to its morpho-functional organisation. Immunohistological analysis specified thymus histology and organisation in teleosts and described, for the first time, Hassall's corpuscle like structures in the medulla of sea bass. All oestrogen receptors were expressed at the transcript and protein level, both in T cells and in stromal cells belonging to specific functional areas. These observations suggest complex regulatory actions of oestrogen on thymic function, notably through the stromal microenvironment, comprising both, genomic and non-genomic pathways that are likely to affect T cell maturation and trafficking processes. Comparison with birds, rodents and humans supports the thymic localization of oestrogen receptors and suggests that oestrogens modulate T cell maturation in all gnathostomes. (C) 2017 Elsevier Ltd. All rights reserved. ANR [ANR-15-CE32-0014] FR CNRS 3730 SCALE info:eu-repo/semantics/publishedVersion

The ecological processes that are crucial to an animal's growth, survival, and reproductive fitness have energetic costs. The imperative for an animal to meet these costs within the energetic constraints of the environment drives many aspects of animal ecology and evolution, yet has largely been overlooked in traditional ecological paradigms. The field of 'ecological energetics' is bringing comparative physiology out of the laboratory and, for the first time, is becoming broadly accessible to field ecologists addressing real-world questions at many spatial and temporal scales. In an era of unprecedented global environmental challenges, ecological energetics opens up the tantalising prospect of a more predictive, mechanistic understanding of the drivers of threatened species decline, delivering process-based modelling approaches to natural resource management.

Key Points Zoonotic viruses pose a serious threat to human and animal health. Studying the immune response to zoonotic pathogens in the natural reservoir hosts, rather than traditional animal models, offers important insights into control strategies.Comparative studies in natural host systems have provided key information and improved our understanding of co-evolution of hosts and pathogens. This could lead to the discovery of novel immune mechanisms that control viral replication.Understanding the differences between the immune systems of domesticated and wild animal hosts and comparing them to the human immune system is crucial for unravelling the complex disease mechanisms involved in zoonotic infections and for developing new strategies for disrupting their transmission to humans.The use of non-traditional animal models for research poses many challenges. These include the need for specialist high-biosecurity containment facilities, a lack of species-specific reagents for immunology studies, and complex husbandry, ethics and welfare issues.Whole-genome sequencing and comparative analysis of host species have provided key insights into how different immune responses are made to the same pathogen.The identification of key differences in immune pathways between susceptible and non-susceptible hosts might offer clues for developing disease intervention strategies, including new antiviral vaccines and therapies, and disease-resistant animals. Supplementary information The online version of this article (doi:10.1038/nri3551) contains supplementary material, which is available to authorized users., Immunology is traditionally viewed as a science of 'mice and men'. However, key insights can come from the study of immune responses in livestock or wild animals. The fact that the most deadly pathogens of humans are often zoonotic in nature lends further weight to the importance of this research. The authors discuss the benefits of, and challenges posed by, these studies. Supplementary information The online version of this article (doi:10.1038/nri3551) contains supplementary material, which is available to authorized users., Zoonotic viruses that emerge from wildlife and domesticated animals pose a serious threat to human and animal health. In many instances, mouse models have improved our understanding of the human immune response to infection; however, when dealing with emerging zoonotic diseases, they may be of limited use. This is particularly the case when the model fails to reproduce the disease status that is seen in the natural reservoir, transmission species or human host. In this Review, we discuss how researchers are placing more emphasis on the study of the immune response to zoonotic infections in the natural reservoir hosts and spillover species. Such studies will not only lead to a greater understanding of how these infections induce variable disease and immune responses in distinct species but also offer important insights into the evolution of mammalian immune systems. Supplementary information The online version of this article (doi:10.1038/nri3551) contains supplementary material, which is available to authorized users.

A successful immune response against invading pathogens relies on the efficient activation of host defense mechanisms and a timely return to immune homeostasis. Despite their importance, these mechanisms remain ill-defined in most animal groups. This study focuses on the acute inflammatory response of chickens, important both as an avian model with a unique position in evolution as well as an increasingly notable target of infectious zoonotic diseases. We took advantage of an in vivo self-resolving intra-abdominal challenge model to provide an integrative view of leukocyte responses during the induction and resolution phases of acute inflammation. Our results showed rapid leukocyte infiltration into the abdominal cavity post zymosan challenge (significant increase as early as 4 h), which was dominated by heterophils. Peak leukocyte infiltration and ROS production reached maximum levels at 12 h post challenge, which was significantly earlier than comparative studies in teleost fish and mice. Both heterophils and monocyte/macrophages contributed to ROS production. Local leukocyte infiltration was preceded by an increase in peripheral leukocytes and a drop in the number of bone marrow leukocytes. The proportion of apoptotic leukocytes increased following peak of acute inflammation, rising to significant levels within the abdominal cavity by 48 h, consistent with other indicators for the resolution of inflammation. Importantly, comparison of chicken phagocytic responses with those previously shown in agnathan, teleost and murine models suggested a progressive evolutionary shift towards an increased sensitivity to pro-inflammatory pathogen-derived particles and decreased sensitivity towards homeostatic stimuli. Thus, while significant conservation can be noted across the immune systems of endotherms, this study highlights additional unique features that govern the induction and resolution of acute inflammation in the avian system, which may be relevant to disease susceptibility and performance.

Investigation of the effects of various cycles of compression and decompression on the alveolar volumes of the excised lungs of sea lions and dogs. The results obtained include the finding that, in comparison to dog lungs, sea lion lungs empty more completely on mild compression and much more completely on severe compression. These findings support Scholander's (1940) hypothesis that some marine mammals are protected from decompression sickness by cartilaginous reinforcement of the small airways which permits alveolar emptying during a dive, so isolating compressed gas from pulmonary capillary blood.

The MHC is a highly polymorphic genomic region that encodes the transplantation and immune regulatory molecules. It receives special attention for genetic investigation because of its important role in the regulation of innate and adaptive immune responses and its strong association with numerous infectious and/or autoimmune diseases. The MHC locus was first discovered in the mouse and for the past 50 years it has been studied most intensively in both mice and humans. However, in recent years the macaque species have emerged as some of the more important and advanced experimental animal models for biomedical research into MHC with important human immunodeficiency virus/simian immunodeficiency virus and transplantation studies undertaken in association with precise MHC genotyping and haplotyping methods using Sanger sequencing and next-generation sequencing. Here, in this special issue on 'Macaque Immunology' we provide a short review of the genomic similarities and differences among the human, macaque and mouse MHC class I and class II regions, with an emphasis on the association of the macaque class I region with MHC polymorphism, haplotype structure and function.