Developmental and comparative immunology single-cell transcriptome analysis of the B-cell repertoire reveals the usage of immunoglobulins in the gray short-tailed opossum (Monodelphis domestica).

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.

Experiments of nature and within species comparative physiology.

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.

Comparative physiological and proteomic analysis indicates lower shock response to drought stress conditions in a self-pollinating perennial ryegrass.

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.

Integrative systematics and ecology of a new deep-sea family of tanaidacean crustaceans.

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.

[Cell therapy in muscular disorders: the future lies in comparisons of progenitors]. / Thérapie cellulaire des maladies musculaires - Un avenir à l'aune d'une comparaison des progéniteurs.

Cell therapy approaches dedicated to the treatment of dystrophinopathies and involving essentially myoblasts and mesoangioblasts have produced mitigated clinical results. If several types of alternative progenitors have been developed, no standardized comparison has been carried out yet to investigate their regenerative efficacy in vivo, at least at a local level. A comparative study has therefore been designed recently aiming at giving a new impetus to this therapeutic field.

TITLE: Thérapie cellulaire des maladies musculaires - Un avenir à l'aune d'une comparaison des progéniteurs. ABSTRACT: Les approches de thérapie cellulaire des dystrophinopathies basées sur l'utilisation de myoblastes ou de mésoangioblastes se sont traduites par des résultats cliniques mitigés. De nombreux candidats cellulaires alternatifs ont été décrits, mais aucune comparaison standardisée n'a pu encore établir leurs efficacités, ne serait-ce qu'en vue d'une régénération musculaire localisée. Une étude comparative a donc été décidée récemment et pourrait permettre de donner un nouvel élan à cette approche.

Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing?

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).

Comparative studies of critical physiological limits and vulnerability to environmental extremes in small ectotherms: How much environmental control is needed?

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.

Molecular similarities and differences from human pulmonary fibrosis and corresponding mouse model: MALDI imaging mass spectrometry in comparative medicine.

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.

A place for host-microbe symbiosis in the comparative physiologist's toolbox.

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.

Evolutionary Medicine: The Ongoing Evolution of Human Physiology and Metabolism.

The field of evolutionary medicine uses evolutionary principles to understand changes in human anatomy and physiology that have occurred over time in response to environmental changes. Through this evolutionary-based approach, we can understand disease as a consequence of anatomical and physiological "trade-offs" that develop to facilitate survival and reproduction. We demonstrate how diachronic study of human anatomy and physiology is fundamental for an increased understanding of human health and disease.

COMPARATIVE GUT PHYSIOLOGY SYMPOSIUM: Comparative physiology of digestion.

The digestive systems of all species have been shaped by environmental pressures over long evolutionary time spans. Nevertheless, all digestive systems must achieve the same end points, the ingestion of biological material and its conversion to molecules that serve as energy substrates and structural components of tissues. A range of strategies to extract nutrients, including for animals reliant primarily on foregut fermentation, hindgut fermentation, and enzymatic degradation, have evolved. Moreover, animals have adapted to different foodstuffs as herbivores (including frugivores, folivores, granivores, etc.), carnivores, and omnivores. We present evidence that humans have diverged from other omnivores because of the long history of consumption of cooked or otherwise prepared food. We consider them to be cucinivores. We present examples to illustrate that the range of foodstuffs that can be efficiently assimilated by each group or species is limited and is different from that of other groups or species. Differences are reflected in alimentary tract morphology. The digestive systems of each group and of species within the groups are adaptable, with constraints determined by individual digestive physiology. Although overall digestive strategies and systems differ, the building blocks for digestion are remarkably similar. All vertebrates have muscular tubular tracts lined with a single layer of epithelial cells for most of the length, use closely related digestive enzymes and transporters, and control the digestive process through similar hormones and similarly organized nerve pathways. Extrapolations among species that are widely separated in their digestive physiologies are possible when the basis for extrapolation is carefully considered. Divergence is greatest at organ or organismal levels, and similarities are greatest at the cell and molecular level.

COMPARATIVE GUT PHYSIOLOGY SYMPOSIUM: Comparative physiology of glucagon-like peptide-2: Implications and applications for production and health of ruminants.

Glucagon-like peptide-2 (GLP-2) is a 33-amino acid peptide derived from proteolytic cleavage of proglucagon by prohormone convertase 1/3 in enteroendocrine L cells. Studies conducted in humans, in rodent models, and in vitro indicate that GLP-2 is secreted in response to the presence of molecules in the intestinal lumen, including fatty acids, carbohydrates, amino acids, and bile acids, which are detected by luminal chemosensors. The physiological actions of GLP-2 are mediated by its G protein-coupled receptor expressed primarily in the intestinal tract on enteric neurons, enteroendocrine cells, and myofibroblasts. The biological activity of GLP-2 is further regulated by dipeptidyl peptidase IV, which rapidly cleaves the N-terminus of GLP-2 that is responsible for GLP-2 receptor activation. Within the gut, GLP-2 increases nutrient absorption, crypt cell proliferation, and mesenteric blood flow and decreases gut permeability and motility, epithelial cell apoptosis, and inflammation. Outside the gut, GLP-2 reduces bone resorption, can suppress appetite, and is cytoprotective in the lung. Thus, GLP-2 has been studied intensively as a therapeutic to improve intestinal function of humans during parenteral nutrition and following small bowel resection and, more recently, as a treatment for osteoporosis and obesity-related disorders and to reduce cellular damage associated with inflammation of the gut and lungs. Recent studies demonstrate that many biological actions and properties of GLP-2 in ruminants are similar to those in nonruminants, including the potential to reduce intestinal nitro-oxidative stress in calves caused by parasitic diseases such as coccidiosis. Because of its beneficial impacts on nutrient absorption, gut healing, and normal gut development, GLP-2 therapy offers significant opportunities to improve calf health and production efficiency. However, GLP-2 therapies require an extended time course to achieve desired physiological responses, as well as daily administration because of the hormone's short half-life. Thus, practical means of administration and alternative strategies to enhance basal GLP-2 secretion (e.g., through specific feed additives), which are more likely to achieve consumer acceptance, are needed. Opportunities to address these challenges are discussed.

Development and application of a multiroute physiologically based pharmacokinetic model for oxytetracycline in dogs and humans.

Oxytetracycline (OTC) is a commonly used tetracycline antibiotic in veterinary and human medicine. To establish a quantitative model for predicting OTC plasma and tissue exposure, a permeability-limited multiroute physiologically based pharmacokinetic model was developed in dogs. The model was calibrated with plasma pharmacokinetic data in beagle dogs following single intravenous (5 mg/kg), oral (100 mg/kg), and intramuscular (20 mg/kg) administrations. The model predicted other available dog data well, including drug concentrations in the liver, kidney, and muscle after repeated exposure, and data in the mixed-breed dog. The model was extrapolated to humans and the human model adequately simulated measured plasma OTC concentrations after intravenous (7.14 mg/kg) and oral exposures (6.67 mg/kg). The dog model was applied to predict 24-h OTC area-under-the-curve after three therapeutic treatments. Results were 27.75, 51.76, and 64.17 µg/mL*h in the plasma, and 120.93, 225.64, and 279.67 µg/mL*h in the kidney for oral (100 mg/kg), intravenous (10 mg/kg), and intramuscular (20 mg/kg) administrations, respectively. This model can be used to predict plasma and tissue concentrations to aid in designing optimal therapeutic regimens with OTC in veterinary, and potentially, human medicine; and as a foundation for scaling to other tetracycline antibiotics and to other animal species. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:233-243, 2015.

A systematic evaluation of the use of physiologically based pharmacokinetic modeling for cross-species extrapolation.

Transfer of knowledge along the different phases of drug development is a fundamental process in pharmaceutical research. In particular, cross-species extrapolation between different laboratory animals and further on to first-in-human trials is challenging because of the uncertain comparability of physiological processes. Physiologically based pharmacokinetic (PBPK) modeling allows translation of mechanistic knowledge from one species to another by specifically considering physiological and biochemical differences in between. We here evaluated different knowledge-driven approaches for cross-species extrapolation by systematically incorporating specific model parameter domains of a target species into the PBPK model of a reference species. Altogether, 15 knowledge-driven approaches were applied to murine and human PBPK models of 10 exemplary drugs resulting in 300 different extrapolations. Statistical analysis of the quality of the different extrapolations revealed not only species-specific physiology as the key determinant in cross-species extrapolation but also identified a synergistic effect when considering both kinetic rate constants and gene expression profiles of relevant enzymes and transporters. Moreover, we show that considering species-specific physiology, plasma protein binding, enzyme and transport kinetics, as well as tissue-specific gene expression profiles in PBPK modeling increases accuracy of cross-species extrapolations and thus supports first-in-human trials based on prior preclinical knowledge.

Mapping circuits beyond the models: integrating connectomics and comparative neuroscience.

The brain has been shaped by evolution, and its connectome reflects that history. Comparative neuroscience research, framed by evolutionary relationships, is key to interpreting connectome organization and can address fundamental circuit questions that are not accessible through single-species connectomics efforts.

A critical evaluation of automated blood gas measurements in comparative respiratory physiology.

Precise measurements of blood gases and pH are of pivotal importance to respiratory physiology. However, the traditional electrodes that could be calibrated and maintained at the same temperature as the experimental animal are increasingly being replaced by new automated blood gas analyzers. These are typically designed for clinical use and automatically heat the blood sample to 37°C for measurements. While most blood gas analyzers allow for temperature corrections of the measurements, the underlying algorithms are based on temperature-effects for human blood, and any discrepancies in the temperature dependency between the blood sample from a given species and human samples will bias measurements. In this study we review the effects of temperature on blood gases and pH and evaluate the performance of an automated blood gas analyzer (GEM Premier 3500). Whole blood obtained from pythons and freshwater turtles was equilibrated in rotating Eschweiler tonometers to a variety of known P(O2)'s and P(CO2)'s in gas mixtures prepared by Wösthoff gas mixing pumps and blood samples were measured immediately on the GEM Premier 3500. The pH measurements were compared to measurements using a Radiometer BMS glass capillary pH electrode kept and calibrated at the experimental temperature. We show that while the blood gas analyzer provides reliable temperature-corrections for P(CO2) and pH, P(O2) measurements were substantially biased. This was in agreement with the theoretical considerations and emphasizes the need for critical calibrations/corrections when using automated blood gas analyzers.

What is biodiversity? Stepping forward from barcoding to understanding biological differences.

This opinion paper gives personal views of the direction that cataloguing biodiversity should be going in. Although molecular taxonomy enables rapid and high throughput identification of species, it needs to be anchored to traditional taxonomy, because without information of actual biological properties of species, DNA barcoding just reports differences in selected DNA sequences, which need not have anything to do with the biological properties of the organisms, and the reasons for the development of the species. Since functional differences are the most common reason behind species differences, the future of cataloguing biodiversity and biodiversity research is, in my opinion, in trying to integrate genomic research to comparative physiology in order to be able to evaluate which functional properties have likely been important in generating biodiversity. This task is overwhelming, and requires forgetting the traditional disciplines. Further, major problems associated with the present-day treatment of genomic data are presented from my viewpoint.