Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum

Genome-wide analysis reveals the contributors to fast molecular evolution of the Chinese hook snout carp (Opsariichthys bidens)

Variations in molecular evolutionary rate have been widely investigated among lineages and genes. However, it remains an open question whether fast rate of molecular evolution is driven by natural selection or random drift, and how the fast rate is linked to metabolic rate. Additionally, previous studies on fast molecular evolution have been largely restricted to concatenated matrix of genes or a few specifically selected genes, but less is known for individual genes at the genome-wide level. Here we addressed these questions using more than 5000 single-copy orthologous (SCO) genes through comparative genomic and phylogenetic analyses among fishes, with a special focus on a newly-sequenced clupeocephalan fish the Chinese hook snout carp Opsariichthys bidens. We showed O. bidens displays significantly higher mean substitution rate and more fast-evolving SCO genes (2172 genes) than most fishes studied here. The rapidly evolving genes are enriched in highly conserved and very basic functions such as translation and ribosome that are critical for biological fitness. We further revealed that ∼25 % of these fast-evolving genes exhibit a constant increase of substitution rate from the common ancestor down to the present, suggesting a neglected but important contribution from ancestral states. Model fitting showed that ∼85 % of fast-evolving genes exclusive to O. bidens and related species follow the adaptive evolutionary model rather than random-drift model, and 7.6 % of fast-evolving genes identified in O. bidens have experienced positive selection, both indicating the reflection of adaptive selection. Finally, metabolic rate was observed to be linked with substitution rate in a gene-specific manner. Overall, our findings reveal fast molecular evolution of SCO genes at genome-wide level in O. bidens, and uncover the evolutionary and ecological contributors to it.

Harnessing ecological theory to enhance ecosystem restoration

Ecosystem restoration can increase the health and resilience of nature and humanity. As a result, the international community is championing habitat restoration as a primary solution to address the dual climate and biodiversity crises. Yet most ecosystem restoration efforts to date have underperformed, failed, or been burdened by high costs that prevent upscaling. To become a primary, scalable conservation strategy, restoration efficiency and success must increase dramatically. Here, we outline how integrating ten foundational ecological theories that have not previously received much attention - from hierarchical facilitation to macroecology - into ecosystem restoration planning and management can markedly enhance restoration success. We propose a simple, systematic approach to determining which theories best align with restoration goals and are most likely to bolster their success. Armed with a century of advances in ecological theory, restoration practitioners will be better positioned to more cost-efficiently and effectively rebuild the world's ecosystems and support the resilience of our natural resources.

Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla

Bioenergetics and biothermodynamics are valuable tools in research on growth and metabolic processes of a wide range of organisms, including viruses, bacteria, fungi, algae and plants, as is shown by the many publications on this topic in the literature. These studies provide insight into growth and metabolism of individual species, as well as interactions between species, like the virus-host interaction (infection) and virus-virus interaction (competition). However, this approach has not yet been applied to animal species. The universality of biothermodynamics and bioenergetics provides a good motive to apply them in analysis of animals. In this research, we made a bioenergetic, biothermodynamic and kinetic characterization for the first time for an animal species - Anguilla anguilla L. (European eel). We made a comparative analysis on yellow (young adult) and silver (mature adult) phases. Metabolic processes were modeled as chemical reactions with characteristic thermodynamic properties: enthalpy, entropy and Gibbs energy. Moreover, Gibbs energy explained growth rates, through phenomenological equations. This analysis of animal metabolism and growth explained metabolic properties of yellow and silver A. anguilla, including the bioenergetic aspect of life history. Moreover, we compared thermodynamic properties of A. anguilla with those of its main macromolecular components and other organisms. The thermodynamic properties were explained by the structural properties of organisms. This research extends the bioenergetic and biothermodynamic approaches to zoology, which should allow analysis of the energetic aspect of animal metabolic processes, interactions with their environment and interactions with other organisms. Furthermore, it connects the macroscopic perspective of zoology with the microscopic perspectives of biochemistry, bioenergetics and biothermodynamics. This will provide a basis for development of mechanistic models of animal growth and metabolism.

The energetic costs of cellular complexity in evolution

The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.

Deep rest: An integrative model of how contemplative practices combat stress and enhance the body's restorative capacity

Engaging in contemplative practice like meditation, yoga, and prayer, is beneficial for psychological and physical well-being. Recent research has identified several underlying psychological and biological pathways that explain these benefits. However, there is not yet consensus on the underlying overlapping physiological mechanisms of contemplative practice benefits. In this article, we integrate divergent scientific literatures on contemplative practice interventions, stress science, and mitochondrial biology, presenting a unified biopsychosocial model of how contemplative practices reduce stress and promote physical health. We argue that engaging in contemplative practice facilitates a restorative state termed "deep rest," largely through safety signaling, during which energetic resources are directed toward cellular optimization and away from energy-demanding stress states. Our model thus presents a framework for how contemplative practices enhance positive psychological and physiological functioning by optimizing cellular energy consumption. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Chronic exposure to environmental temperature attenuates the thermal sensitivity of salmonids

Metabolism, the biological processing of energy and materials, scales predictably with temperature and body size. Temperature effects on metabolism are normally studied via acute exposures, which overlooks the capacity for organisms to moderate their metabolism following chronic exposure to warming. Here, we conduct respirometry assays in situ and after transplanting salmonid fish among different streams to disentangle the effects of chronic and acute thermal exposure. We find a clear temperature dependence of metabolism for the transplants, but not the in-situ assays, indicating that chronic exposure to warming can attenuate salmonid thermal sensitivity. A bioenergetic model accurately captures the presence of fish in warmer streams when accounting for chronic exposure, whereas it incorrectly predicts their local extinction with warming when incorporating the acute temperature dependence of metabolism. This highlights the need to incorporate the potential for thermal acclimation or adaptation when forecasting the consequences of global warming on ecosystems.

Estimating the magnitude and sensitivity of energy fluxes for stickleback hosts and Schistocephalus solidus parasites using the metabolic theory of ecology

Parasites are ubiquitous, yet their effects on hosts are difficult to quantify and generalize across ecosystems. One promising metric of parasitic impact uses the metabolic theory of ecology (MTE) to calculate energy flux, an estimate of energy lost to parasites. We investigated the feasibility of using metabolic scaling rules to compare the energetic burden of parasitism among individuals. Specifically, we found substantial sensitivity of energy flux estimates to input parameters used in the MTE equation when using available data from a model host-parasite system (Gasterosteus aculeatus and Schistocephalus solidus). Using literature values, size data from parasitized wild fish, and a respirometry experiment, we estimate that a single S. solidus tapeworm may extract up to 32% of its stickleback host's baseline metabolic energy requirement, and that parasites in multiple infections may collectively extract up to 46%. The amount of energy siphoned from stickleback to tapeworms is large but did not instigate an increase in respiration rate in the current study. This emphasizes the importance of future work focusing on how parasites influence ecosystem energetics. The approach of using the MTE to calculate energy flux provides great promise as a quantitative foundation for such estimates and provides a more concrete metric of parasite impact on hosts than parasite abundance alone.

Body mass dependence of oxidative phosphorylation efficiency in liver mitochondria from mammals

In eukaryotes, the performances of an organism are dependent on body mass and chemically supported by the mitochondrial production of ATP. Although the relationship between body mass and mitochondrial oxygen consumption is well described, the allometry of the transduction efficiency from oxygen to ATP production (ATP/O) is still poorly understood. Using a comparative approach, we investigated the oxygen consumption and ATP production of liver mitochondria from twelve species of mammals ranging from 5 g to 600 kg. We found that both oxygen consumption and ATP production are mass dependent but not the ATP/O at the maximal phosphorylating state. The results also showed that for sub-maximal phosphorylating states the ATP/O value positively correlated with body mass, irrespective of the metabolic intensity. This result contrasts with previous data obtained in mammalian muscles, suggesting a tissue-dependence of the body mass effect on mitochondrial efficiency.

Are size and mitochondrial power of cells inter-determined?

Mitochondria are the central hub of ATP production in most eukaryotic cells. Cellular power (energy per unit time), which is primarily generated in these organelles, is crucial to our understanding of cell function in health and disease. We investigated the relation between a mitochondrion's power (metabolic rate) and host cell size by combining metabolic theory with the analysis of two recent databases, one covering 109 protists and the other 63 species including protists, metazoans, microalgae, and vascular plants. We uncovered an interesting statistical regularity: in well-fed protists, relatively elevated values of mitochondrion power cluster around the smallest cell sizes and the medium-large cell sizes. In contrast, in starved protists and metazoans, the relation between mitochondrion power and cell size is inconclusive, and in microalgae and plants, mitochondrion power seems to increase from smaller cells to larger ones (where this investigation includes plant cells of volume up to ca. 2.18 × 105 μm3). Using these results, estimates are provided of the number of active ATP synthase molecules and basal uncouplers.

Comparative Analysis of Heart Regeneration: Searching for the Key to Heal the Heart-Part II: Molecular Mechanisms of Cardiac Regeneration

Cardiovascular diseases are the leading cause of death worldwide, among which ischemic heart disease is the most representative. Myocardial infarction results from occlusion of a coronary artery, which leads to an insufficient blood supply to the myocardium. As it is well known, the massive loss of cardiomyocytes cannot be solved due the limited regenerative ability of the adult mammalian hearts. In contrast, some lower vertebrate species can regenerate the heart after an injury; their study has disclosed some of the involved cell types, molecular mechanisms and signaling pathways during the regenerative process. In this 'two parts' review, we discuss the current state-of-the-art of the main response to achieve heart regeneration, where several processes are involved and essential for cardiac regeneration.

The Relevance of Time in Biological Scaling

Various phenotypic traits relate to the size of a living system in regular but often disproportionate (allometric) ways. These "biological scaling" relationships have been studied by biologists for over a century, but their causes remain hotly debated. Here, I focus on the patterns and possible causes of the body-mass scaling of the rates/durations of various biological processes and life-history events, i.e., the "pace of life". Many biologists have regarded the rate of metabolism or energy use as the master driver of the "pace of life" and its scaling with body size. Although this "energy perspective" has provided valuable insight, here I argue that a "time perspective" may be equally or even more important. I evaluate various major ways that time may be relevant in biological scaling, including as (1) an independent "fourth dimension" in biological dimensional analyses, (2) a universal "biological clock" that synchronizes various biological rates/durations, (3) a scaling method that uses various biological time periods (allochrony) as scaling metrics, rather than various measures of physical size (allometry), as traditionally performed, (4) an ultimate body-size-related constraint on the rates/timing of biological processes/events that is set by the inevitability of death, and (5) a geological "deep time" approach for viewing the evolution of biological scaling patterns. Although previously proposed universal four-dimensional space-time and "biological clock" views of biological scaling are problematic, novel approaches using allochronic analyses and time perspectives based on size-related rates of individual mortality and species origination/extinction may provide new valuable insights.

Gene and protein expression and metabolic flux analysis reveals metabolic scaling in liver ex vivo and in vivo

Metabolic scaling, the inverse correlation of metabolic rates to body mass, has been appreciated for more than 80 years. Studies of metabolic scaling have largely been restricted to mathematical modeling of caloric intake and oxygen consumption, and mostly rely on computational modeling. The possibility that other metabolic processes scale with body size has not been comprehensively studied. To address this gap in knowledge, we employed a systems approach including transcriptomics, proteomics, and measurement of in vitro and in vivo metabolic fluxes. Gene expression in livers of five species spanning a 30,000-fold range in mass revealed differential expression according to body mass of genes related to cytosolic and mitochondrial metabolic processes, and to detoxication of oxidative damage. To determine whether flux through key metabolic pathways is ordered inversely to body size, we applied stable isotope tracer methodology to study multiple cellular compartments, tissues, and species. Comparing C57BL/6 J mice with Sprague-Dawley rats, we demonstrate that while ordering of metabolic fluxes is not observed in in vitro cell-autonomous settings, it is present in liver slices and in vivo. Together, these data reveal that metabolic scaling extends beyond oxygen consumption to other aspects of metabolism, and is regulated at the level of gene and protein expression, enzyme activity, and substrate supply.

Temperature variability and metabolic adaptation in terrestrial and aquatic ectotherms

Thermodynamics is a major factor determining rates of energy expenditure, rates of biochemical dynamics, and ultimately the biological and ecological processes linked with resilience to global warming in ectothermic organisms. Nonetheless, whether ectothermic organisms exhibit general adaptive metabolic responses to cope with worldwide variation in thermal conditions has remained as an open question. Here we combine a model comparison approach with a global dataset of standard metabolic rates (SMR), including 1,160 measurements across 788 species of aquatic invertebrates, insects, fishes, amphibians and reptiles, to investigate the association between metabolic rates and environmental temperatures in their respective habitats. Our analyses suggest that variation in SMR after removing allometric and thermodynamic effects is best explained by the temperature range encountered across seasons, which always provided a better fit than the average temperature for the hottest and coldest month and mean annual temperatures. This pattern was consistent across taxonomic groups and robust to sensitivity analyses. Nonetheless, aquatic and terrestrial lineages responded differently to seasonality, with SMR declining - 6.8% °C^-1 of thermal range across seasons in aquatic organisms and increasing 2.8% °C^-1 in terrestrial organisms. These responses may reflect alternative strategies to mitigate the impact of increments in warmer temperatures on energy expenditure, either by means of metabolic reduction in thermally homogeneous water bodies or effective behavioral thermoregulation to exploit temperature heterogeneity on land.

Ontogenetic changes in root and shoot respiration, fresh mass and surface area of Fagus crenata

BACKGROUND AND AIMS

To date, studies on terrestrial plant ecology and evolution have focused primarily on the trade-off patterns in the allocation of metabolic production to roots and shoots in individual plants and the scaling of whole-plant respiration. However, few empirical studies have investigated the root : shoot ratio by considering scaling whole-plant respiration at various sizes throughout ontogeny.

METHODS

Here, using a whole-plant chamber system, we measured the respiration rates, fresh mass and surface area of entire roots and shoots from 377 Fagus crenata individuals, from germinating seeds to mature trees, collected from five different Japanese provenances. Non-linear regression analysis was performed for scaling of root and shoot respiration, fresh mass and surface area with body size.

KEY RESULTS

Whole-plant respiration increased rapidly in germinating seeds. In the seedling to mature tree size range, the scaling of whole-plant respiration to whole-plant fresh mass was expressed as a linear trend on the log-log coordinates (exponent slightly greater than 0.75). In the same body size range, root and shoot respiration vs. whole-plant fresh mass were modelled by upward-convex (exponent decreased from 2.35 to 0.638) and downward-convex trends (exponent increased from -0.918 to 0.864), respectively. The root fraction in whole-plant respiration, fresh mass and surface area shifted continuously throughout ontogeny, increasing in smaller seedlings during early growth stages and decreasing in larger trees.

CONCLUSIONS

Our results suggest a gradual shift in allocation priorities of metabolic energy from roots in seedlings to shoots in mature trees, providing insights into how roots contribute to shoot and whole-plant growth during ontogeny. The models of root : shoot ratio in relation to whole-plant physiology could be applied in tree growth modelling, and in linking the different levels of ecological phenomena, from individuals to ecosystems.

Metabolic rate, sleep duration, and body temperature in evolution of mammals and birds: the influence of geological time of principal groups divergence

This study contains an analysis of basal metabolic rate (BMR) in 1817 endothermic species. The aim was to establish how metabolic scaling varies between the main groups of endotherms during evolution. The data for all the considered groups were combined and the common exponent in the allometric relationship between the BMR and body weight was established as b = 0.7248. Reduced to the common slope, the relative metabolic rate forms the following series: Neognathae – Passeriformes – 1.00, Neognathae – Non-Passeriformes – 0.75, Palaeognathae – 0.53, Eutheria – 0.57, Marsupialia – 0.44, and Monotremata – 0.26. The main finding is that the metabolic rate in the six main groups of mammals and birds consistently increases as the geological time of the group’s divergence approaches the present. In parallel, the average body temperature in the group rises, the duration of sleep decreases and the duration of activity increases. BMR in a taxon correlates with its evolutionary age: the later a clade diverged, the higher is its metabolic rate and the longer is its activity period; group exponents decrease as group divergence nears present times while with increase metabolic rate during activity, they not only do not decrease but can increase. Sleep duration in mammals was on average 40% longer than in birds while BMR, in contrast, was 40% higher in birds. The evolution of metabolic scaling, body temperature, sleep duration, and activity during the development of endothermic life forms is demonstrated, allowing for a better understanding of the underlying principles of endothermy formation.

OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases

Patients with primary mitochondrial oxidative phosphorylation (OxPhos) defects present with fatigue and multi-system disorders, are often lean, and die prematurely, but the mechanistic basis for this clinical picture remains unclear. By integrating data from 17 cohorts of patients with mitochondrial diseases (n = 690) we find evidence that these disorders increase resting energy expenditure, a state termed hypermetabolism. We examine this phenomenon longitudinally in patient-derived fibroblasts from multiple donors. Genetically or pharmacologically disrupting OxPhos approximately doubles cellular energy expenditure. This cell-autonomous state of hypermetabolism occurs despite near-normal OxPhos coupling efficiency, excluding uncoupling as a general mechanism. Instead, hypermetabolism is associated with mitochondrial DNA instability, activation of the integrated stress response (ISR), and increased extracellular secretion of age-related cytokines and metabokines including GDF15. In parallel, OxPhos defects accelerate telomere erosion and epigenetic aging per cell division, consistent with evidence that excess energy expenditure accelerates biological aging. To explore potential mechanisms for these effects, we generate a longitudinal RNASeq and DNA methylation resource dataset, which reveals conserved, energetically demanding, genome-wide recalibrations. Taken together, these findings highlight the need to understand how OxPhos defects influence the energetic cost of living, and the link between hypermetabolism and aging in cells and patients with mitochondrial diseases.

The energetic cost of allostasis and allostatic load

Chronic psychosocial stress increases disease risk and mortality, but the underlying mechanisms remain largely unclear. Here we outline an energy-based model for the transduction of chronic stress into disease over time. The energetic model of allostatic load (EMAL) emphasizes the energetic cost of allostasis and allostatic load, where the "load" is the additional energetic burden required to support allostasis and stress-induced energy needs. Living organisms have a limited capacity to consume energy. Overconsumption of energy by allostatic brain-body processes leads to hypermetabolism, defined as excess energy expenditure above the organism's optimum. In turn, hypermetabolism accelerates physiological decline in cells, laboratory animals, and humans, and may drive biological aging. Therefore, we propose that the transition from adaptive allostasis to maladaptive allostatic states, allostatic load, and allostatic overload arises when the added energetic cost of stress competes with longevity-promoting growth, maintenance, and repair. Mechanistically, the energetic restriction of growth, maintenance and repair processes leads to the progressive wear-and-tear of molecular and organ systems. The proposed model makes testable predictions around the physiological, cellular, and sub-cellular energetic mechanisms that transduce chronic stress into disease risk and mortality. We also highlight new avenues to quantify allostatic load and its link to health across the lifespan, via the integration of systemic and cellular energy expenditure measurements together with classic allostatic load biomarkers.

Variable metabolic scaling breaks the law: from 'Newtonian' to 'Darwinian' approaches

Life's size and tempo are intimately linked. The rate of metabolism varies with body mass in remarkably regular ways that can often be described by a simple power function, where the scaling exponent (b, slope in a log-linear plot) is typically less than 1. Traditional theory based on physical constraints has assumed that b is 2/3 or 3/4, following natural law, but hundreds of studies have documented extensive, systematic variation in b. This overwhelming, law-breaking, empirical evidence is causing a paradigm shift in metabolic scaling theory and methodology from ‘Newtonian’ to ‘Darwinian’ approaches. A new wave of studies focuses on the adaptable regulation and evolution of metabolic scaling, as influenced by diverse intrinsic and extrinsic factors, according to multiple context-dependent mechanisms, and within boundary limits set by physical constraints.

Eukaryotic gene regulation at equilibrium, or non?

Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory-theory that prescribes rather than just describes-in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.

How Metabolic Rate Relates to Cell Size

Simple Summary

The metabolic conversion of resources into living structures and processes is fundamental to all living systems. The rate of metabolism (‘fire of life’) is critical for supporting the rates of various biological processes (‘pace of life’), but why it varies considerably within and among species is little understood. Much of this variation is related to body size, but such ‘metabolic scaling’ relationships also vary extensively. Numerous explanations have been offered, but no consensus has yet been reached. Here, I critically review explanations concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Numerous lines of evidence suggest that cell size and growth can affect metabolic rate at any given body mass, as well as how it changes with increasing body mass during growth or evolution. Mechanisms causing negative associations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, but more research is needed. A cell-size perspective not only helps to explain some (but not all) variation in metabolic rate and its body-mass scaling, but may also foster the conceptual integration of studies of ontogenetic development and body-mass scaling.

Abstract

Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and supporting data) concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Cell size and growth may affect size-specific metabolic rate, as well as the vertical elevation (metabolic level) and slope (exponent) of metabolic scaling relationships. Mechanistic causes of negative correlations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, related to decreased surface area per volume, larger intracellular resource-transport distances, lower metabolic costs of ionic regulation, slower cell multiplication and somatic growth, and larger intracellular deposits of metabolically inert materials in some tissues. A cell-size perspective helps to explain some (but not all) variation in metabolic rate and its body-mass scaling and thus should be included in any multi-mechanistic theory attempting to explain the full diversity of metabolic scaling. A cell-size approach may also help conceptually integrate studies of the biological regulation of cellular growth and metabolism with those concerning major transitions in ontogenetic development and associated shifts in metabolic scaling.

Metabolic Scaling in Birds and Mammals: How Taxon Divergence Time, Phylogeny, and Metabolic Rate Affect the Relationship between Scaling Exponents and Intercepts

Simple Summary

This study is based on a large dataset and re-evaluates data on the metabolic rate, providing new insights into the similarities and differences across different groups of birds and mammals. We compared six taxonomic groups of mammals and birds according to their energetic characteristics and the geological time of evolutionary origin. The overall metabolic rate of a taxonomic group increases with the geological time of evolutionary origin. The terrestrial mammals and flightless birds have almost equal metabolic levels. The higher the metabolic rate in a group, the less it increases within increasing body size in this group.

Abstract

Analysis of metabolic scaling in currently living endothermic animal species allowed us to show how the relationship between body mass and the basal metabolic rate (BMR) has evolved in the history of endothermic vertebrates. We compared six taxonomic groups according to their energetic characteristics and the time of evolutionary divergence. We transformed the slope of the regression lines to the common value and analyzed three criteria for comparing BMR of different taxa regardless of body size. Correlation between average field metabolic rate (FMR) of the group and its average BMR was shown. We evaluated the efficiency of self-maintenance in ordinary life (defined BMR/FMR) in six main groups of endotherms. Our study has shown that metabolic scaling in the main groups of endothermic animals correlates with their evolutionary age: the younger the group, the higher the metabolic rate, but the rate increases more slowly with increasing body weight. We found negative linear relationship for scaling exponents and the allometric coefficient in five groups of endotherms: in units of mL O₂/h per g, in relative units of allometric coefficients, and also in level or scaling elevation. Mammals that diverged from the main vertebrate stem earlier have a higher “b” exponent than later divergent birds. A new approach using three criteria for comparing BMR of different taxa regardless of body mass will be useful for many biological size-scaling relationships that follow the power function.

Gill area explains deviations from body size-metabolic rate relationship in teleost fishes

Whether gill area constrains fish metabolism through oxygen limitation is a debated topic. Here, the authors provide insights into this question by analysing mass-specific metabolic rates across 44 teleost fishes extracted from FishBase. They explore whether species deviations from metabolic rates predicted by body mass can be explained by species gill area. They show that the gill area explains c. 26%-28% of species-level deviations from mass-specific metabolic rates. Their findings suggest that gill area might indeed be one of the factors limiting metabolic rate in fishes.

Climatic conditions and prevalence of melanistic snakes-contrasting effects of warm springs and mild winters

Climate change is one of the greatest challenges that wildlife is facing. Rapid shifts in climatic conditions may accelerate evolutionary changes in populations as a result of strong selective pressure. Most studies focus on the impact of climatic conditions on phenologies and annual cycles, whereas there are fewer reports of empirical support for climate-driven changes in the phenotypic variability of free-living populations. We investigated whether climatic variables explain the prevalence of colour polymorphism in a population of the grass snake (Natrix natrix) with two morphotypes, the melanistic and non-melanistic ones, in the period 1981-2013. We found that the prevalence of the black phenotype was negatively related to spring temperature and winter harshness, expressed as the number of snow days. According to the thermal melanism hypothesis, a high predation rate during warmer springs may override relaxed thermal benefits and vice versa, i.e. black individuals may perform better than typical ones when thermal conditions in spring are unfavourable. In turn, because they are smaller, melanistic individuals may be exposed to a higher risk of winter mortality, particularly during longer winters. We highlight the need for more studies on the effects of climatic conditions on temporal variation in melanism prevalence in other populations and species as well as in various geographic regions.

AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size

Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.

Measurement(s)	metabolic rate quantification • body mass • brain size
Technology Type(s)	metabolic rate measurement • body mass quantification • brain mass brain volume

On the rules of life and Kleiber's law: the macroscopic relationship between materials and energy

Efforts to accommodate the growth in global energy consumption within a fragile biosphere are primarily focused on managing the transition towards a low-carbon energy mix. We show evidence that a more fundamental problem exists through a scaling relation, akin to Kleiber's Law, between society's energy consumption and material stocks. Humanity's energy consumption scales at 0.78 of its material stocks, which implies predictable environmental pressure regardless of the energy mix. If true, future global energy scenarios imply vast amounts of materials and corresponding environmental degradation, which have not been adequately acknowledged. Thus, limits to energy consumption are needed regardless of the energy mix to stabilize human intervention in the biosphere.

Evolution of prudent predation in complex food webs

Prudent predators catch sufficient prey to sustain their populations but not as much as to undermine their populations' survival. The idea that predators evolve to be prudent has been dismissed in the 1970s, but the arguments invoked then are untenable in the light of modern evolution theory. The evolution of prudent predation has repeatedly been demonstrated in two-species predator-prey metacommunity models. However, the vigorous population fluctuations that these models predict are not widely observed. Here we show that in complex model food webs prudent predation evolves as a result of consumer-mediated ('apparent') competitive exclusion of resources, which disadvantages aggressive consumers and does not generate such fluctuations. We make testable predictions for empirical signatures of this mechanism and its outcomes. Then we discuss how these predictions are borne out across freshwater, marine and terrestrial ecosystems. Demonstrating explanatory power of evolved prudent predation well beyond the question of predator-prey coexistence, the predicted signatures explain unexpected declines of invasive alien species, the shape of stock-recruitment relations of fish, and the clearance rates of pelagic consumers across the latitudinal gradient and 15 orders of magnitude in body mass. Specific research to further test this theory is proposed.

Calorimetric Measurements of Biological Interactions and Their Relationships to Finite Time Thermodynamics Parameters

A description and examination of the potential for calorimetry for use in exploring the entropy flows in biological and or reacting systems is presented. A calorimeter operation background is provided, and two case studies are investigated using a transient numerical simulation. The first case describes a single cell calorimeter containing a single phase material excited by heat generation source function such as joule heating. The second case is a reacting system. The basic observation parameter, the temperature, cannot be used to separate the entropy property changes and the rate of entropy production in the second case. The calculated transient response can be further analyzed to determine the equilibrium constant once the reaction equation and stoichiometric constants are specified which allows entropy property changes and the rate of entropy production to be determined. In a biological community, the equivalent of the reaction equation and a definition of an equilibrium constant are not available for all systems. The results for the two cases illustrate that using calorimetry measurements to identify the entropy flows in biological community activities requires further work to establish a framework similar to that chemical reacting systems that are based on an equilibrium type parameter.

Scaling laws in enzyme function reveal a new kind of biochemical universality

Known examples of life all share the same core biochemistry going back to the last universal common ancestor (LUCA), but whether this feature is universal to other examples, including at the origin of life or alien life, is unknown. We show how a physics-inspired statistical approach identifies universal scaling laws across biochemical reactions that are not defined by common chemical components but instead, as macroscale patterns in the reaction functions used by life. The identified scaling relations can be used to predict statistical features of LUCA, and network analyses reveal some of the functional principles that underlie them. They are, therefore, prime candidates for developing new theory on the “laws of life” that might apply to all possible biochemistries.

All life on Earth is unified by its use of a shared set of component chemical compounds and reactions, providing a detailed model for universal biochemistry. However, this notion of universality is specific to known biochemistry and does not allow quantitative predictions about examples not yet observed. Here, we introduce a more generalizable concept of biochemical universality that is more akin to the kind of universality found in physics. Using annotated genomic datasets including an ensemble of 11,955 metagenomes, 1,282 archaea, 11,759 bacteria, and 200 eukaryotic taxa, we show how enzyme functions form universality classes with common scaling behavior in their relative abundances across the datasets. We verify that these scaling laws are not explained by the presence of compounds, reactions, and enzyme functions shared across known examples of life. We demonstrate how these scaling laws can be used as a tool for inferring properties of ancient life by comparing their predictions with a consensus model for the last universal common ancestor (LUCA). We also illustrate how network analyses shed light on the functional principles underlying the observed scaling behaviors. Together, our results establish the existence of a new kind of biochemical universality, independent of the details of life on Earth’s component chemistry, with implications for guiding our search for missing biochemical diversity on Earth or for biochemistries that might deviate from the exact chemical makeup of life as we know it, such as at the origins of life, in alien environments, or in the design of synthetic life.

Organismal and cellular interactions in vertebrate-alga symbioses

Photosymbioses, intimate interactions between photosynthetic algal symbionts and heterotrophic hosts, are well known in invertebrate and protist systems. Vertebrate animals are an exception where photosynthetic microorganisms are not often considered part of the normal vertebrate microbiome, with a few exceptions in amphibian eggs. Here, we review the breadth of vertebrate diversity and explore where algae have taken hold in vertebrate fur, on vertebrate surfaces, in vertebrate tissues, and within vertebrate cells. We find that algae have myriad partnerships with vertebrate animals, from fishes to mammals, and that those symbioses range from apparent mutualisms to commensalisms to parasitisms. The exception in vertebrates, compared with other groups of eukaryotes, is that intracellular mutualisms and commensalisms with algae or other microbes are notably rare. We currently have no clear cell-in-cell (endosymbiotic) examples of a trophic mutualism in any vertebrate, while there is a broad diversity of such interactions in invertebrate animals and protists. This functional divergence in vertebrate symbioses may be related to vertebrate physiology or a byproduct of our adaptive immune system. Overall, we see that diverse algae are part of the vertebrate microbiome, broadly, with numerous symbiotic interactions occurring across all vertebrate and many algal clades. These interactions are being studied for their ecological, organismal, and cellular implications. This synthesis of vertebrate-algal associations may prove useful for the development of novel therapeutics: pairing algae with medical devices, tissue cultures, and artificial ecto- and endosymbioses.

The global ocean size spectrum from bacteria to whales

It has long been hypothesized that aquatic biomass is evenly distributed among logarithmic body mass size classes. Although this community structure has been observed regionally, mostly among plankton groups, its generality has never been formally tested across all marine life over the global ocean, nor have the impacts of humans on it been globally assessed. Here, we bring together data at the global scale to test the hypothesis from bacteria to whales. We find that biomass within most order of magnitude size classes is indeed remarkably constant, near 1 gigatonne (Gt) wet weight (10¹⁵ g), but bacteria and large marine mammals are markedly above and below this value, respectively. Furthermore, human impacts appear to have significantly truncated the upper one-third of the spectrum. This dramatic alteration to what is possibly life’s largest-scale regularity underscores the global extent of human activities.

Phage strategies facilitate bacterial coexistence under environmental variability

Bacterial communities are often exposed to temporal variations in resource availability, which exceed bacterial generation times and thereby affect bacterial coexistence. Bacterial population dynamics are also shaped by bacteriophages, which are a main cause of bacterial mortality. Several strategies are proposed in the literature to describe infections by phages, such as "Killing the Winner", "Piggyback the loser" (PtL) or "Piggyback the Winner" (PtW). The two temperate phage strategies PtL and PtW are defined by a change from lytic to lysogenic infection when the host density changes, from high to low or from low to high, respectively. To date, the occurrence of different phage strategies and their response to environmental variability is poorly understood. In our study, we developed a microbial trophic network model using ordinary differential equations (ODEs) and performed 'in silico' experiments. To model the switch from the lysogenic to the lytic cycle, we modified the lysis rate of infected bacteria and their growth was turned on or off using a density-dependent switching point. We addressed whether and how the different phage strategies facilitate bacteria coexistence competing for limiting resources. We also studied the impact of a fluctuating resource inflow to evaluate the response of the different phage strategies to environmental variability. Our results show that the viral shunt (i.e. nutrient release after bacterial lysis) leads to an enrichment of the system. This enrichment enables bacterial coexistence at lower resource concentrations. We were able to show that an established, purely lytic model leads to stable bacterial coexistence despite fluctuating resources. Both temperate phage models differ in their coexistence patterns. The model of PtW yields stable bacterial coexistence at a limited range of resource supply and is most sensitive to resource fluctuations. Interestingly, the purely lytic phage strategy and PtW both result in stable bacteria coexistence at oligotrophic conditions. The PtL model facilitates stable bacterial coexistence over a large range of stable and fluctuating resource inflow. An increase in bacterial growth rate results in a higher resilience to resource variability for the PtL and the lytic infection model. We propose that both temperate phage strategies represent different mechanisms of phages coping with environmental variability. Our study demonstrates how phage strategies can maintain bacterial coexistence in constant and fluctuating environments.

Economies of scale shape energetics of solitary and group-living spiders and their webs

Metabolic scaling, whereby larger individuals use less energy per unit mass than smaller ones, may apply to the combined metabolic rate of group-living organisms as group size increases. Spiders that form groups in high disturbance environments can serve to test the hypothesis that economies of scale benefit social groups. Using solitary and group-living spiders, we tested the hypothesis that spiders exhibit negative allometry between body or colony mass and the standing mass of their webs and whether, and how, such a relationship may contribute to group-living benefits in a cooperative spider. Given the diverse architecture of spider webs-orb, tangle and sheet-and-tangle, and associated differences in silk content, we first assessed how standing web mass scales with spider mass as a function of web architecture and whether investment in silk differs among web types. As group-living spiders are predominantly found in clades that build the presumably costlier sheet-and-tangle webs, we then asked whether cost-sharing through cooperative web maintenance contributes to a positive energy budget in a social species. We found that larger spiders had a relatively smaller investment in silk per unit mass than smaller ones, but more complex sheet-and-tangle webs contained orders of magnitude more silk than simpler orb or tangle ones. In the group-living species, standing web mass per unit spider mass continued to decline as colony size increased with a similar slope as for unitary spiders. When web maintenance activities were considered, colonies also experienced reduced mass-specific energy expenditure with increasing colony size. Activity savings contributed to a net positive energy balance for medium and large colonies after inputs from the cooperative capture of large prey were accounted for. Economies of scale have been previously demonstrated in animal societies characterized by reproductive and worker castes, but not in relatively egalitarian societies as those of social spiders. Our findings illustrate the universality of scaling laws and how economies of scale may transcend hunting strategies and levels of organization.

Evolution of metabolic scaling among the tetrapod: Effect of phylogeny, the geologic time of class formation and uniformity of species within a class

The metabolic scaling in the animal has been discussed for over 90 years, but no consensus has been reached. Our analysis of 2,126 species of vertebrates reveals a significant allometric exponent heterogeneity. We show that classes of terrestrial vertebrates exhibit the evolution of metabolic scaling. Both the allometric coefficient "a" and the allometric exponent "b" change naturally, but differently depending on the geological time of group formation. The allometric coefficient "a" shows the measure of the evolutionary development of systems that forms resting metabolism in animals. Endothermic classes, such as birds and mammals, have a metabolic rate that is in an order of magnitude higher than that in ectothermic classes, including amphibians and reptiles. In the terrestrial vertebrate phylogeny, we find that the metabolic scaling is characterized by three main allometric exponent values: b = 3/4 (mammals), b > 3/4 (ectotherms, such as amphibians and reptiles), and b < 3/4 (birds). The heterogeneity of the allometric exponent is a natural phenomenon associated with the general evolution of vertebrates. The scaling factor decreases depending on both the external design and the size (birds vs mammals) of the animal. The metabolic rate and uniformity of species within a class increase as the geological start date of formation of the class approaches the present time. The higher the mass-specific standard metabolic rate in the class, the slower metabolic rate grows with increasing body size in this class. Our results lay the groundwork for further exploration of the evolutionary and ecological aspects of the development of metabolic scaling in animals. This article is protected by copyright. All rights reserved.

Hematopoiesis in numbers

Hematopoiesis is a dynamic process in which stem and progenitor cells give rise to the ~10¹³ blood and immune cells distributed throughout the human body. We argue that a quantitative description of hematopoiesis can help consolidate existing data, identify knowledge gaps, and generate new hypotheses. Here, we review known numbers in murine and, where possible, human hematopoiesis, and consolidate murine numbers into a set of reference values. We present estimates of cell numbers, division and differentiation rates, cell size, and macromolecular composition for each hematopoietic cell type. We also propose guidelines to improve the reporting of measurements and highlight areas in which quantitative data are lacking. Overall, we show how quantitative approaches can be used to understand key properties of hematopoiesis.

Sustained enzymatic activity and flow in crowded protein droplets

Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.

Linking species traits and demography to explain complex temperature responses across levels of organization

Microbial communities regulate ecosystem responses to climate change. However, predicting these responses is challenging because of complex interactions among processes at multiple levels of organization. Organismal traits that determine individual performance and ecological interactions are essential for scaling up environmental responses from individuals to ecosystems. We combine protist microcosm experiments and mathematical models to show that key traits-cell size, shape, and contents-each explain different aspects of species' demographic responses to changes in temperature. These differences in species' temperature responses have complex cascading effects across levels of organization-causing nonlinear shifts in total community respiration rates across temperatures via coordinated changes in community composition, equilibrium densities, and community-mean species mass in experimental protist communities that tightly match theoretical predictions. Our results suggest that traits explain variation in population growth, and together, these two factors scale up to influence community- and ecosystem-level processes across temperatures. Connecting the multilevel microbial processes that ultimately influence climate in this way will help refine predictions about complex ecosystem-climate feedbacks and the pace of climate change itself.

Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates

Membraneless compartments, also known as condensates, provide chemically distinct environments and thus spatially organize the cell. A well-studied example of condensates is P granules in the roundworm Caenorhabditis elegans that play an important role in the development of the germline. P granules are RNA-rich protein condensates that share the key properties of liquid droplets such as a spherical shape, the ability to fuse, and fast diffusion of their molecular components. An outstanding question is to what extent phase separation at thermodynamic equilibrium is appropriate to describe the formation of condensates in an active cellular environment. To address this question, we investigate the response of P granule condensates in living cells to temperature changes. We observe that P granules dissolve upon increasing the temperature and recondense upon lowering the temperature in a reversible manner. Strikingly, this temperature response can be captured by in vivo phase diagrams that are well described by a Flory-Huggins model at thermodynamic equilibrium. This finding is surprising due to active processes in a living cell. To address the impact of such active processes on intracellular phase separation, we discuss temperature heterogeneities. We show that, for typical estimates of the density of active processes, temperature represents a well-defined variable and that mesoscopic volume elements are at local thermodynamic equilibrium. Our findings provide strong evidence that P granule assembly and disassembly are governed by phase separation based on local thermal equilibria where the nonequilibrium nature of the cytoplasm is manifested on larger scales.

Consistent scaling of whole-shoot respiration between Moso bamboo (Phyllostachys pubescens) and trees

Both Moso bamboo (Phyllostachys pubescens) and tree forests have a large biomass; they are considered to play an important role in ecosystem carbon budgets. The scaling relationship between individual whole-shoot (i.e., aboveground parts) respiration and whole-shoot mass provides a clue for comparing the carbon budgets of Moso bamboo and tree forests. However, nobody has empirically demonstrated whether there is a difference between these forest types in the whole-shoot scaling relationship. We developed whole-shoot chambers and measured the shoot respiration of 58 individual mature bamboo shoots from the smallest to the largest in a Moso bamboo forest, and then compared them with that of 254 tree shoots previously measured. For 30 bamboo shoots, we measured the respiration rate of leaves, branches, and culms. We found that the scaling exponent of whole-shoot respiration of bamboo fitted by a simple power function on a log-log scale was 0.843 (95 % CI 0.797-0.885), which was consistent with that of trees, 0.826 (95 % CI 0.799-0.851), but higher than 3/4, the value typifying the Kleiber's rule. The respiration rates of leaves, branches, and culms at the whole-shoot level were proportional to their mass, revealing a constant mean mass-specific respiration of 1.19, 0.224, and 0.0978 µmol CO₂ kg^- 1 s^- 1, respectively. These constant values suggest common traits of organs among physiologically integrated ramets within a genet. Additionally, the larger the shoots, the smaller the allocation of organ mass to the metabolically active leaves, and the larger the allocation to the metabolically inactive culms. Therefore, these shifts in shoot-mass partitioning to leaves and culms caused a negative metabolic scaling of Moso bamboo shoots. The observed convergent metabolic scaling of Moso bamboo and trees may facilitate comparisons of the ecosystem carbon budgets of Moso bamboo and tree forests.

Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments

The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

Background

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome.

Results

To estimate the genome-wide neutral mutation rate (µ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. A range of bioinformatic filtering parameters were evaluated in order to minimize potential bias in mutation rate estimates that may result from SNP filtering. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated µ to be 2.64E−9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. Post-divergence gene flow was detected in one species pair. Failure to account for this post-split migration inflates our substitution rate estimates, emphasizing the importance of demographic methods that can accommodate gene flow.

Conclusions

Results from our study, both parameter estimates and bioinformatic explorations, have broad-ranging implications for phylogeographic studies in other non-model taxa using reduced representation datasets. Our best estimate of µ that accounts for coalescent and demographic processes is remarkably similar to experimentally derived mutation rates in model arthropod systems. These results contradicted recent suggestions that the closure of the Isthmus was completed much earlier (around 10 Ma), as mutation rates based on an early calibration resulted in uncharacteristically low genomic mutation rates. Also, stricter filtering parameters resulted in biased datasets that generated lower mutation rate estimates and influenced demographic parameters, serving as a cautionary tale for the adherence to conservative bioinformatic strategies when generating reduced-representation datasets at the species level. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01836-3.

Vertebrate cardiac regeneration: evolutionary and developmental perspectives

Cardiac regeneration is an ancestral trait in vertebrates that is lost both as more recent vertebrate lineages evolved to adapt to new environments and selective pressures, and as members of certain species developmentally progress towards their adult forms. While higher vertebrates like humans and rodents resolve cardiac injury with permanent fibrosis and loss of cardiac output as adults, neonates of these same species can fully regenerate heart structure and function after injury - as can adult lower vertebrates like many teleost fish and urodele amphibians. Recent research has elucidated several broad factors hypothesized to contribute to this loss of cardiac regenerative potential both evolutionarily and developmentally: an oxygen-rich environment, vertebrate thermogenesis, a complex adaptive immune system, and cancer risk trade-offs. In this review, we discuss the evidence for these hypotheses as well as the cellular participators and molecular regulators by which they act to govern heart regeneration in vertebrates.

How fast do mobile organisms respond to stimuli? Response times from bacteria to elephants and whales

Quick responses to fast changes in the environment are crucial in animal behaviour and survival, for example to seize prey, escape predators, or negotiate obstacles. Here, we study the 'simple response time' that is the time elapsed between receptor stimulation and motor activation as typically shown in escape responses, for mobile organisms of various taxa ranging from bacteria to large vertebrates. We show that 95% of these simple response times lie within one order of magnitude of the overall geometric mean of about 25 ms, which is similar to that of a well-studied sensory time scale, the inverse of the critical flicker fusion frequency in vision, also lying within close bounds for all the organisms studied. We find that this time scale is a few times smaller than the minimum time to move by one body length, which is known to lie also within a relatively narrow range for all moving organisms. The remarkably small 10²-fold range of the simple response time among so disparate life forms varying over 10²⁰-fold in body mass suggests that it is determined by basic physicochemical constraints, independently on the structure and scale of the organism. We thus propose first-principle estimates of the simple response and sensory time scales in terms of physical constants and a few basic biological properties common to mobile organisms and constraining their responses.

In-vivo quantification of electron flow through photosystem I - Cyclic electron transport makes up about 35% in a cyanobacterium

Photosynthetic electron flow, driven by photosystem I and II, provides chemical energy for carbon fixation. In addition to a linear mode a second cyclic route exists, which only involves photosystem I. The exact contributions of linear and cyclic transport are still a matter of debate. Here, we describe the development of a method that allows quantification of electron flow in absolute terms through photosystem I in a photosynthetic organism for the first time. Specific in-vivo protocols allowed to discern the redox states of plastocyanin, P700 and the FeS-clusters including ferredoxin at the acceptor site of PSI in the cyanobacterium Synechocystis sp. PCC 6803 with the near-infrared spectrometer Dual-KLAS/NIR. P700 absorbance changes determined with the Dual-KLAS/NIR correlated linearly with direct determinations of PSI concentrations using EPR. Dark-interval relaxation kinetics measurements (DIRK_PSI) were applied to determine electron flow through PSI. Counting electrons from hydrogen oxidation as electron donor to photosystem I in parallel to DIRK_PSI measurements confirmed the validity of the method. Electron flow determination by classical PSI yield measurements overestimates electron flow at low light intensities and saturates earlier compared to DIRK_PSI. Combination of DIRK_PSI with oxygen evolution measurements yielded a proportion of 35% of surplus electrons passing PSI compared to PSII. We attribute these electrons to cyclic electron transport, which is twice as high as assumed for plants. Counting electrons flowing through the photosystems allowed determination of the number of quanta required for photosynthesis to 11 per oxygen produced, which is close to published values.

The conundrum of hot mitochondria

The mitochondrion is often referred as the cellular powerhouse because the organelle oxidizes organic acids and NADH derived from nutriments, converting around 40% of the Gibbs free energy change of these reactions into ATP, the major energy currency of cell metabolism. Mitochondria are thus microscopic furnaces that inevitably release heat as a by-product of these reactions, and this contributes to body warming, especially in endotherms like birds and mammals. Over the last decade, the idea has emerged that mitochondria could be warmer than the cytosol, because of their intense energy metabolism. It has even been suggested that our own mitochondria could operate under normal conditions at a temperature close to 50 °C, something difficult to reconcile with the laws of thermal physics. Here, using our combined expertise in biology and physics, we exhaustively review the reports that led to the concept of a hot mitochondrion, which is essentially based on the development and use of a variety of molecular thermosensors whose intrinsic fluorescence is modified by temperature. Then, we discuss the physical concepts of heat diffusion, including mechanisms like phonons scattering, which occur in the nanoscale range. Although most of approaches with thermosensors studies present relatively sparse data and lack absolute temperature calibration, overall, they do support the hypothesis of hot mitochondria. However, there is no convincing physical explanation that would allow the organelle to maintain a higher temperature than its surroundings. We nevertheless proposed some research directions, mainly biological, that might help throw light on this intriguing conundrum.