The metabolomic physics of complex diseases.

Human diseases involve metabolic alterations. Metabolomic profiles have served as a vital biomarker for the early identification of high-risk individuals and disease prevention. However, current approaches can only characterize individual key metabolites, without taking into account the reality that complex diseases are multifactorial, dynamic, heterogeneous, and interdependent. Here, we leverage a statistical physics model to combine all metabolites into bidirectional, signed, and weighted interaction networks and trace how the flow of information from one metabolite to the next causes changes in health state. Viewing a disease outcome as the consequence of complex interactions among its interconnected components (metabolites), we integrate concepts from ecosystem theory and evolutionary game theory to model how the health state-dependent alteration of a metabolite is shaped by its intrinsic properties and through extrinsic influences from its conspecifics. We code intrinsic contributions as nodes and extrinsic contributions as edges into quantitative networks and implement GLMY homology theory to analyze and interpret the topological change of health state from symbiosis to dysbiosis and vice versa. The application of this model to real data allows us to identify several hub metabolites and their interaction webs, which play a part in the formation of inflammatory bowel diseases. The findings by our model could provide important information on drug design to treat these diseases and beyond.

Growth, filtration and respiration characteristics of small single-osculum demosponge Halichondria panicea explants.

Filter-feeding demosponges are modular organisms that consist of modules each with one water-exit osculum. Once a mature module has been formed, the weight-specific filtration and respiration rates do not change. Sponge modules only grow to a certain size and for a sponge to increase in size, new modules must be formed. However, the growth characteristics of a small single-osculum module sponge are fundamentally different from those of multi-modular sponges, and a theoretically derived volume-specific filtration rate scales as F/V=V-1/3, indicating a decrease with increasing total module volume (V, cm3). Here, we studied filtration rate (F, l h-1), respiration rate (R, ml O2 h-1), volume-specific (F/V) and weight-specific (F/W) filtration rates, and the ratios F/R and F/W along with growth rates of small single-osculum demosponge Halichondria panicea explants of various sizes exposed to various concentrations of algal cells. The following relationships were found: F/V=7.08V-0.24, F=a1W1.05, and R=a2W0.68 where W is the dry weight (mg). The F/R and F/W ratios were constant and essentially independent of W, and other data indicate exponential growth. It is concluded that the experimental data support the theoretical F/V∝V-1/3.

Holy grail of tissue regeneration: Size.

Cells and tissue within injured organs undergo a complicated healing process that still remains poorly understood. Interestingly, smaller organisms respond to injury with tissue regeneration and restoration of function, while humans and other large organisms respond to injury by forming dysfunctional, fibrotic scar tissue. Over the past few decades, allometric scaling principles have been well established to show that larger organisms experience exponentially higher tissue forces during movement and locomotion and throughout the organism's lifespan. How these evolutionary adaptations may affect tissue injury has not been thoroughly investigated in humans. We discuss how these adapations may affect healing and demonstrate that blocking the most evolutionary conserved biologic force sensor enables large organisms to heal after injury with true tissue regeneration. Future strategies to disrupt tissue force sensors may unlock the key to regenerating after injury in a wide range of organ systems.

A systematic review of allometric scaling exponents for IgG mAbs.

Increasing complexity of mAbs in development creates challenges in predicting human pharmacokinetic (PK) parameters from preclinical data. The aim of this analysis was to identify optimal allometric scaling exponents.Data were extracted from literature to create a central database (currently the largest available published database) of two-compartment model parameters for mAbs (n = 59) in cynomolgus monkey (CM) and human.Global allometric exponents were calculated and drug-dependent factors were investigated as potential variables in determining the optimal scaling factor.The global exponents for scaling CM mAb PK data were 0.74 (CL), 0.80 (CL with Fc-modified mAbs excluded), 0.44 (CL with Fc-modified mAbs only), 0.71 (Q), 1.12 (V1), and 0.99 (V2). These values are in line with previously published literature values.

In vitro and in vivo preclinical pharmacokinetic characterization of aficamten, a small molecule cardiac myosin inhibitor.

Aficamten, a small molecule selective inhibitor of cardiac myosin, was characterised in preclinical in vitro and in vivo studies.Protein binding in human plasma was 10.4% unbound and ranged from 1.6% to 24.9% unbound across species. Blood-to-plasma ratios ranged from 0.69 to 1.14 across species. Aficamten hepatic clearance in human was predicted to be low from observed high metabolic stability in vitro in human liver microsomes. Aficamten demonstrated high permeability in Caco-2 cell monolayers.Aficamten in vivo clearance was low across species at 8.8, 2.1, 3.3, and 11 mL/min/kg in mouse, rat, dog, and monkey, respectively. The volume of distribution was low-to-high ranging from 0.53 in rat to 11 L/kg in dog. Oral bioavailability ranged from 41% in monkey to 98% in mouse.Aficamten was metabolised in vitro to eight metabolites with hydroxylated metabolites M1a and M1b predominating. CYP phenotyping indicated multiple CYPs (2C8, 2C9, 2D6, and 3A4) contributing to the metabolism of aficamten.Human clearance (1.1 mL/min/kg) and volume of distribution (6.5 L/kg) were predicted using 4-species allometry employing 'rule-of-exponents'. A predicted 69 hour half-life is consistent with observed half-life in human Phase-1.No CYP-based drug-drug interaction liability as a precipitant was predicted for aficamten.

Is there tree senescence? The fecundity evidence.

Despite its importance for forest regeneration, food webs, and human economies, changes in tree fecundity with tree size and age remain largely unknown. The allometric increase with tree diameter assumed in ecological models would substantially overestimate seed contributions from large trees if fecundity eventually declines with size. Current estimates are dominated by overrepresentation of small trees in regression models. We combined global fecundity data, including a substantial representation of large trees. We compared size-fecundity relationships against traditional allometric scaling with diameter and two models based on crown architecture. All allometric models fail to describe the declining rate of increase in fecundity with diameter found for 80% of 597 species in our analysis. The strong evidence of declining fecundity, beyond what can be explained by crown architectural change, is consistent with physiological decline. A downward revision of projected fecundity of large trees can improve the next generation of forest dynamic models.

Inter-Species Pharmacokinetic Modeling and Scaling for Drug Repurposing of Pyronaridine and Artesunate.

Even though several new targets (mostly viral infection) for drug repurposing of pyronaridine and artesunate have recently emerged in vitro and in vivo, inter-species pharmacokinetic (PK) data that can extend nonclinical efficacy to humans has not been reported over 30 years of usage. Since extrapolation of animal PK data to those of humans is essential to predict clinical outcomes for drug repurposing, this study aimed to investigate inter-species PK differences in three animal species (hamster, rat, and dog) and to support clinical translation of a fixed-dose combination of pyronaridine and artesunate. PK parameters (e.g., steady-state volume of distribution (Vss), clearance (CL), area under the concentration-time curve (AUC), mean residence time (MRT), etc.) of pyronaridine, artesunate, and dihydroartemisinin (an active metabolite of artesunate) were determined by non-compartmental analysis. In addition, one- or two-compartment PK modeling was performed to support inter-species scaling. The PK models appropriately described the blood concentrations of pyronaridine, artesunate, and dihydroartemisinin in all animal species, and the estimated PK parameters in three species were integrated for inter-species allometric scaling to predict human PKs. The simple allometric equation (Y = a × Wb) well explained the relationship between PK parameters and the actual body weight of animal species. The results from the study could be used as a basis for drug repurposing and support determining the effective dosage regimen for new indications based on in vitro/in vivo efficacy data and predicted human PKs in initial clinical trials.

Prediction of Human Pharmacokinetics of E0703, a Novel Radioprotective Agent, Using Physiologically Based Pharmacokinetic Modeling and an Interspecies Extrapolation Approach.

E0703, a new steroidal compound optimized from estradiol, significantly increased cell proliferation and the survival rate of KM mice and beagles after ionizing radiation. In this study, we characterize its preclinical pharmacokinetics (PK) and predict its human PK using a physiologically based pharmacokinetic (PBPK) model. The preclinical PK of E0703 was studied in mice and Rhesus monkeys. Asian human clearance (CL) values for E0703 were predicted from various allometric methods. The human PK profiles of E0703 (30 mg) were predicted by the PBPK model in Gastro Plus software 9.8 (SimulationsPlus, Lancaster, CA, USA). Furthermore, tissue distribution and the human PK profiles of different administration dosages and forms were predicted. The 0.002 L/h of CL and 0.005 L of Vss in mice were calculated and optimized from observed PK data. The plasma exposure of E0703 was availably predicted by the CL using the simple allometry (SA) method. The plasma concentration-time profiles of other dosages (20 and 40 mg) and two oral administrations (30 mg) were well-fitted to the observed values. In addition, the PK profile of target organs for E0703 exhibited a higher peak concentration (Cmax) and AUC than plasma. The developed E0703-PBPK model, which is precisely applicable to multiple species, benefits from further clinical development to predict PK in humans.

Is the 90-day dog study necessary for pesticide toxicity testing?

When registering a new pesticide, 90-day oral toxicity studies performed with both rodent and non-rodent species, typically rats and dogs, are part of a standard battery of animal tests required in most countries for human health risk assessment (RA). This analysis set out to determine the need for the 90-day dog study in RA by reviewing data from 195 pesticides evaluated by the US Environmental Protection Agency (USEPA) from 1998 through 2021. The dog study was used in RA for only 42 pesticides, mostly to set the point of departure (POD) for shorter-term non-dietary pesticide exposures. Dog no-observed-adverse-effect-levels (NOAELs) were lower than rat NOAELs in 90-day studies for 36 of the above 42 pesticides, suggesting that the dog was the more sensitive species. However, lower NOAELs may not necessarily correspond to greater sensitivity as factors such as dose spacing and/or allometric scaling need to be considered. Normalizing doses between rats and dogs explained the lower NOAELs in 22/36 pesticides, indicating that in those cases the dog was not more sensitive, and the comparable rat study could have been used instead for RA. For five of the remaining pesticides, other studies of appropriate duration besides the 90-day rat study were available that would have offered a similar level of protection if used to set PODs. In only nine cases could no alternative be found in the pesticide's database to use in place of the 90-day dog study for setting safe exposure levels or to identify unique hazards. The present analysis demonstrates that for most pesticide risk determinations the 90-day dog study provided no benefit beyond the rat or other available data.

First-in-Patient Dose Prediction for Adeno-Associated Virus-Mediated Hemophilia Gene Therapy Using Allometric Scaling.

In this study, the author compared the performance of two allometric scaling approaches and body-weight-based dose conversion approach for first-in-patient (FIP) dose prediction for adeno-associated virus (AAV)-mediated hemophilia gene therapy using preclinical and clinical efficacy data of nine AAV vectors. In general, body-weight-based direct conversion of effective doses in monkeys or dogs was more likely to underestimate FIP dose but worked for one bioengineered vector with a high transduction efficiency specifically in humans. In contrast, allometric scaling between gene efficiency factor (log GEF) and body weight (log W) was likely to overestimate FIP dose but worked for two vectors with capsid-specific T-cell responses in patients. The third approach, allometric scaling between log GEF and W-0.25 was appropriate for FIP dose prediction in the absence of T-cell responses to AAV vectors or a dramatic difference in vector transduction efficiency between animals and humans.

Strong positive allometry of bite force in leaf-cutter ants increases the range of cuttable plant tissues.

Atta leaf-cutter ants are the prime herbivore in the Neotropics: differently sized foragers harvest plant material to grow a fungus as a crop. Efficient foraging involves complex interactions between worker size, task preferences and plant-fungus suitability; it is, however, ultimately constrained by the ability of differently sized workers to generate forces large enough to cut vegetation. In order to quantify this ability, we measured bite forces of Atta vollenweideri leaf-cutter ants spanning more than one order of magnitude in body mass. Maximum bite force scaled almost in direct proportion to mass; the largest workers generated peak bite forces 2.5 times higher than expected from isometry. This remarkable positive allometry can be explained via a biomechanical model that links bite forces with substantial size-specific changes in the morphology of the musculoskeletal bite apparatus. In addition to these morphological changes, we show that bite forces of smaller ants peak at larger mandibular opening angles, suggesting a size-dependent physiological adaptation, probably reflecting the need to cut leaves with a thickness that corresponds to a larger fraction of the maximum possible gape. Via direct comparison of maximum bite forces with leaf mechanical properties, we demonstrate (i) that bite forces in leaf-cutter ants need to be exceptionally large compared with body mass to enable them to cut leaves; and (ii), that the positive allometry enables colonies to forage on a wider range of plant species without the need for extreme investment in even larger workers. Our results thus provide strong quantitative arguments for the adaptive value of a positively allometric bite force.

Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies.

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arises across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-million-year-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. Using a combination of selection analyses on visual opsin sequences, in vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy and neural tracing, we quantify and describe physiological, anatomical and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: (i) relaxed selection on visual opsins, perhaps mediated by habitat preference, (ii) interspecific shifts in visual system physiology and anatomy, and (iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at the perceptual, processing and molecular level.

Relationships among sporophytic and gametophytic traits of 27 subtropical montane moss species.

PREMISE: Moss sporophytes differ strongly in size and biomass partitioning, potentially reflecting reproductive and dispersal strategies. Understanding how sporophyte traits are coordinated is essential for understanding moss functioning and evolution. This study aimed to answer: (1) how the size and proportions of the sporophyte differ between moss species with and without a prominent central strand in the seta, (2) how anatomical and morphological traits of the seta are related, and (3) how sporophytic biomass relates to gametophytic biomass and nutrient concentrations. METHODS: We studied the relationships between seta anatomical and morphological traits, the biomass of seta, capsule, and gametophyte, and carbon, nitrogen, and phosphorus concentrations of 27 subtropical montane moss species. RESULTS: (1) Moss species with a prominent central strand in the seta had larger setae and heavier capsules than those without a prominent strand. (2) With increasing seta length, setae became thicker and more rounded for both groups, while in species with a prominent central strand, the ratio of transport-cell area to epidermal area decreased. (3) In both groups, mosses with greater gametophytic biomass tended to have heavier sporophytes, but nitrogen and phosphorus concentrations in the gametophyte were unrelated to sporophytic traits. CONCLUSIONS: Our study highlights that the central strand in the seta may have an important functional role and affect the allometry of moss sporophytes. The coordinated variations in sporophyte morphological and anatomical traits follow basic biomechanical principles of cylinder-like structures, and these traits relate only weakly to the gametophytic nutrient concentrations. Research on moss sporophyte functional traits and their relationships to gametophytes is still in its infancy but could provide important insights into their adaptative strategies.

Lotka-Volterra model with Allee effect: equilibria, coexistence and size scaling of maximum and minimum abundance.

The Lotka-Volterra competition model (LVCM) is a fundamental tool for ecology, widely used to represent complex communities. The Allee effect (AE) is a phenomenon in which there is a positive correlation between population density and fitness, at low population densities. However, the interplay between the LVCM and AE has been seldom analyzed in multispecies models. Here, we analyze the mathematical properties of the LVCM [Formula: see text] AE, investigating the coexistence of species interacting through neutral diffuse competition, their equilibria and stable points. Minimum viable population density arises as the threshold below which species go extinct, characteristic of strong Allee effects. Then, by imposing relationships of main parameters to body size, i.e. allometric scaling, we derive a general solution to the size-scaling maximum and minimum expected density under plausible scenarios. The scaling of maximum population density is consistent with the literature, but we also provide novel predictions on the scaling of the lower limit to population density, a critical value for conservation science. The resulting framework is general and yields results that increase our current understanding of how complex demographic processes can be linked to ubiquitous ecological patterns.

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.

Predicting the response of disease vectors to global change: The importance of allometric scaling.

The distribution of disease vectors such as mosquitoes is changing. Climate change, invasions and vector control strategies all alter the distribution and abundance of mosquitoes. When disease vectors undergo a range shift, so do disease burdens. Predicting such shifts is a priority to adequately prepare for disease control. Accurate predictions of distributional changes depend on how factors such as temperature and competition affect mosquito life-history traits, particularly body size and reproduction. Direct estimates of both body size and reproduction in mosquitoes are logistically challenging and time-consuming, so the field has long relied upon linear (isometric) conversions between wing length (a convenient proxy of size) and reproductive output. These linear transformations underlie most models projecting species' distributions and competitive interactions between native and invasive disease vectors. Using a series of meta-analyses, we show that the relationship between wing length and fecundity are nonlinear (hyperallometric) for most mosquito species. We show that whilst most models ignore reproductive hyperallometry (with respect to wing length), doing so introduces systematic biases into estimates of population growth. In particular, failing to account for reproductive hyperallometry overestimates the effects of temperature and underestimates the effects of competition. Assuming isometry also increases the potential to misestimate the efficacy of vector control strategies by underestimating the contribution of larger females in population replenishment. Finally, failing to account for reproductive hyperallometry and variation in body size can lead to qualitative errors via the counter-intuitive effects of Jensen's inequality. For example, if mean sizes decrease, but variance increases, then reproductive outputs may actually increase. We suggest that future disease vector models incorporate hyperallometric relationships to more accurately predict changes in mosquito distribution in response to global change.

Tallo: A global tree allometry and crown architecture database.

Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research-from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non-forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC-BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology-from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.

Individual size distributions across North American streams vary with local temperature.

Parameters describing the negative relationship between abundance and body size within ecological communities provide a summary of many important biological processes. While it is considered to be one of the few consistent patterns in ecology, spatiotemporal variation of this relationship across continental scale temperature gradients is unknown. Using a database of stream communities collected across North America (18-68°N latitude, -4 to 25°C mean annual air temperature) over 3 years, we constructed 160 individual size distribution (ISD) relationships (i.e. abundance size spectra). The exponent parameter describing ISD's decreased (became steeper) with increasing mean annual temperature, with median slopes varying by ~0.2 units across the 29°C temperature gradient. In addition, total community biomass increased with increasing temperatures, contrary with theoretical predictions. Our study suggests conservation of ISD relationships in streams across broad natural environmental gradients. This supports the emerging use of size-spectra deviations as indicators of fundamental changes to the structure and function of ecological communities.

A quantitative genetics perspective on the body-mass scaling of metabolic rate.

Widely observed allometric scaling (log-log slope<1) of metabolic rate (MR) with body mass (BM) in animals has been frequently explained using functional mechanisms, but rarely studied from the perspective of multivariate quantitative genetics. This is unfortunate, given that the additive genetic slope (bA) of the MR-BM relationship represents the orientation of the 'line of least genetic resistance' along which MR and BM may most likely evolve. Here, we calculated bA in eight species. Although most bA values were within the range of metabolic scaling exponents reported in the literature, uncertainty of each bA estimate was large (only one bA was significantly lower than 3/4 and none were significantly different from 2/3). Overall, the weighted average for bA (0.667±0.098 95% CI) is consistent with the frequent observation that metabolic scaling exponents are negatively allometric in animals (b<1). Although bA was significantly positively correlated with the phenotypic scaling exponent (bP) across the sampled species, bP was usually lower than bA, as reflected in a (non-significantly) lower weighted average for bP (0.596±0.100). This apparent discrepancy between bA and bP resulted from relatively shallow MR-BM scaling of the residuals [weighted average residual scaling exponent (be)=0.503±0.128], suggesting regression dilution (owing to measurement error and within-individual variance) causing a downward bias in bP. Our study shows how the quantification of the genetic scaling exponent informs us about potential constraints on the correlated evolution of MR and BM, and by doing so has the potential to bridge the gap between micro- and macro-evolutionary studies of scaling allometry.

Complications with body-size correction in comparative biology: possible solutions and an appeal for new approaches.

The magnitude of many kinds of biological traits relates strongly to body size. Therefore, a first step in comparative studies frequently involves correcting for effects of body size on the variation of a phenotypic trait, so that the effects of other biological and ecological factors can be clearly distinguished. However, commonly used traditional methods for making these body-size adjustments ignore or do not completely separate the causal interactive effects of body size and other factors on trait variation. Various intrinsic and extrinsic factors may affect not only the variation of a trait, but also its covariation with body size, thus making it difficult to remove completely the effect of body size in comparative studies. These complications are illustrated by several examples of how body size interacts with diverse developmental, physiological, behavioral and ecological factors to affect variation in metabolic rate both within and across species. Such causal interactions are revealed by significant effects of these factors on the body-mass scaling slope of metabolic rate. I discuss five possible major kinds of methods for removing body-size effects that attempt to overcome these complications, at least in part, but I hope that my Review will encourage the development of other, hopefully better methods for doing so.