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Morimoto, J.

Publications and source records attributed to Morimoto, J..

At least 19 recordsLinked to original sources

`Q-niche': topology-preserving niche hypervolumes built using a quantum mechanics modelling analogue.

Hutchinson's n-dimensional niche hypervolume underlies many ecological analyses, yet estimating hypervolumes from finite occurrence data remains challenging, particularly when niches contain non-convex structure such as separated regions or internal holes. Here, we introduce Q-niche, a quantum-mechanics-inspired algorithm for ecological hypervolume estimation. Using an inverse Schrodinger formulation, Q-niche transforms an occurrence-derived Gaussian field into a potential surface whose low-potential regions define a hypervolume represented by a stochastic point cloud. We evaluated Q-niche against Gaussian kernel density estimation and one-class support vector machine hypervolume estimators using synthetic niches, virtual species and empirical Acacia occurrence data. Across controlled synthetic benchmarks, Q-niche preserved imposed topological features more consistently than either alternative and showed closer overall topological agreement with occurrence clouds. This preservation remained robust across the tested parameter settings. Virtual-species analyses showed that stronger preservation of environmental topology did not necessarily produce greater overlap with the known geographical distribution, showing that topology and geographical range are not necessarily coupled. The empirical Acacia dataset revealed that the inferred size and topology of a niche hypervolume is estimator-dependent, favouring the use of Q-niche when hypervolume topology is the focus of research due to its topology preservation performance. Overall, Q-niche provides a practical tool for reconstructing complex niche hypervolumes and investigating how their geometry and topology relate to potential geographical distributions.

ecology↗

Nutritional responses of bumblebees to thermal stress

Extreme climatic events impose considerable stress on organisms with consequences for key ecological interactions such as pollination. Because temperature directly affects metabolic processes, heat variations may also importantly influence the nutritional needs and feeding choices of animals. Here, we studied the effects of thermal stress on the nutritional choices and performances of bumblebees, using a 3D nutritional geometry design. At optimal temperature for colony development (30{degrees}C), bees successfully balanced carbohydrate, protein, and lipid collection, at levels beneficial for body weight and survival. Under cold stress (20{degrees}C), bees reduced their overall nutrient collection while selecting proportionally more carbohydrates, thereby prioritizing survival over weight gain. Under heat stress (35{degrees}C), nutrient balancing was disrupted and survival dropped. Notably however, across all temperatures, bees maintained stable lipid collection while flexibly adjusting the amount of carbohydrates and proteins, suggesting strong constraints on lipid regulation. Given the pivotal role of bees for pollination, identifying how their nutritional needs change in response to climatic conditions is of prior importance for food safety and the conservation of terrestrial ecosystems.

animal behavior and cognition↗

Identification and Validation of Small Molecules with Mucin-Selective Regiospecific Binding in the Gastrointestinal Tract

Oral drug delivery is a widely used method of drug administration; however, achieving localized drug release at specific regions of the gastrointestinal (GI) tract is generally accomplished by using broad environmental differences. The GI tract is a complex system with regional differences in composition, such as selective expression of mucin glycoproteins in different organs. Here, we identify small molecule ligands that can selectively bind to the different mucins to localize drug delivery to the small intestine and stomach. We demonstrate up to a 10-fold increase in particle binding to these organs and up to a 4-fold increase in selectivity compared to chitosan. Additionally, we observe up to a 9-fold increase in budesonide concentration in the small intestine and a 25-fold increase in tetracycline concentration in the stomach. These results show that we have developed a versatile platform capable of sequestering a variety of drugs in certain GI tract organs.

bioengineering↗

The evolution of Hutchinsonian climatic niche hypervolumes in gymnosperms

AimThe niche is a fundamental concept in theoretical and experimental ecology and is used to describe a wide range of ecological processes from species interaction with the environment to community assemblies. A common way to represent the niche is through a multidimensional geometry known as the Hutchinsonian niche hypervolume. Ecological theory predicts that niche hypervolumes have properties such as holes with broader eco-evolutionary significance, but we lack a comprehensive empirical study of niche hypervolume properties and their evolutionary significance. LocationGlobal Time periodHolocene Major taxa studiedGymnosperms MethodsWe conducted for the first time a systematic and comprehensive test of the evolution of Hutchinsonian niche hypervolume properties (volume and holes) across 65 genera and 12 families of gymnosperms, which includes many species that are endangered or threatened. Using cutting-edge computational algorithms, we measured the evolution of geometric (i.e. volume) and topological (i.e. holes) properties of gymnosperm hypervolumes across a comprehensive calibrated phylogeny. ResultsOur comparative analysis revealed weak evidence of the non-independent evolution of niche hypervolume volume and no evidence of the non-independent evolution of hypervolume holes. We also found that genera and families with low hypervolume volume such as monotypic groups like Gingko, likely experienced shifts in hypervolume evolutionary rates. Main conclusionsOur results show that geometric and topological properties of gymnosperm climatic niche hypervolumes evolve independently. This agrees with competitive exclusion hypothesis in ecological theory where extant groups are likely to be the ones which minimise niche overlap and competition.

ecology↗

The developmental environment mediates adult seminal proteome allocation in male Drosophila melanogaster

Early life conditions can have long-lasting fitness effects on organisms. In insects, crowding during larval stages impose a significant constraint on adult phenotypes due to increased intraspecific competition for resources, which can modulate males success in pre- and post-mating competition in adulthood. Evidence for larval crowding effects on male seminal fluid allocation exists but is limited to a small subset of well-known seminal fluid proteins (Sfps), and often overlooks the interactions between male and female phenotypes. We currently lack a comprehensive understanding of how male and female larval crowding interact to affect production, composition, and transfer of the wider seminal proteome. Here, we manipulated Drosophila melanogaster larval crowding (low versus high) of males and females to generate individuals with large and small body size, respectively. We mated individuals in a fully factorial design, and measured the abundance, composition, and transfer of Sfps. Large males produced Sfps in significantly higher abundances, yet this difference was marginal and not detected when Sfps were analysed individually. Conversely, small males transferred greater quantities of much of their seminal proteome to females than did large males. When analysing proteins individually, 10 Sfps were transferred in significantly higher abundances by small males than large males. Our results suggest that small males invest more on each mating opportunity, potentially as a response of overall fewer mating opportunities due to their reduced size, or due to the larval cues of high population density. This work provides an insight into early life effects on ejaculate allocation in D. melanogaster and sheds light on the physiological and behavioural responses to developmental conditions in insects.

evolutionary biology↗

No evidence that proteome composition is associated with realised thermal limit and dietary niche breadth in butterflies

Amino acids are the building blocks of proteins that perform essential physiological functions. Theory suggests that the proteome composition, the amino acid frequencies across all proteins in a genome, is associated with an organisms optimal growth temperature, offering insights into species temperature limits. However, this hypothesis, based on prokaryotes, has not been tested in complex multicellular eukaryotes where many amino acids are strictly acquired through diet. Here, we analysed amino acid frequencies in the proteomes of orthologous and non-orthologous genes from 35 butterfly species to test for correlations with maximum observed temperatures and diet breadth. Using a comparative approach, we found no evidence that proteome composition correlates with temperature or diet breadth. Our findings suggest that animal proteome composition is likely shaped more strongly by energetic and biophysical constraints rather than by ecological factors.

zoology↗

Differential amino acid usage leads to ubiquitous edge effect in proteomes across domains of life that can be explained by amino acid secondary structure propensities

BackgroundAmino acids are the building blocks of proteins and enzymes, which are pivotal for life on Earth. Amino acid usage provides critical insights into the functional constraints acting on proteins and illuminates molecular mechanisms underpinning traits. Despite this, we have limited knowledge of the genome-wide signatures of amino acid usage across domains of life, precluding new genome and proteome patterns to being discovered. ResultsHere, we analysed the proteomes of 5,590 species across four domains of life and found that only a small subset of amino acids is most and least frequently used across proteomes. This creates a ubiquitous edge effect on amino acid usage diversity by rank that arises from protein secondary structural constrains. This edge effect was not driven by the evolutionary chronology of amino acids, showing that functional rather than evolutionary constrains shape amino acid usage in the proteome. We also tested contemporary hypotheses about similarities in amino acid usage profiles and the relationship between amino acid usage and growth temperature, and found that, contrary to previous beliefs, amino acid usage varies across domains of life and temperature only weakly contributes to variance in amino acid usage. ConclusionWe have described a novel and ubiquitous pattern of amino acid usage signature across genomes, which reveals how structural constrains shape amino acid usage at the proteome level. This can ultimately influence the way in which we probe deep evolutionary relationships of protein families across the tree of life and engineer biology in synthetic biology.

molecular biology↗

Turmeric shortens lifespan in houseflies

Climate change poses a significant threat to food security and global public health with the increasing likelihood of insect pest outbreaks. Alternative ways to control insect populations, preferably using environmental-friendly compounds, are needed. Turmeric has been suggested as a natural insecticide with toxicity properties in some insect groups. However, empirical evidence of the effects turmeric - and their interaction with other ecological factors such as diet - on insect survival has been limited. Here, we tested the effects of turmeric and its interactions with diets differing in protein source in the common housefly, Musca domestica. We found that turmeric shortened lifespan independent of diet and sex. Females in turmeric diets were heavier at death, which was likely driven by a combination of relatively lower rates of body mass loss during their lifetime and a higher percentage of water content at death. Each sex responded differently to the protein source in the diet, and the magnitude of the difference in lifespan between sexes were greatest in diets in which protein source was hydrolysed yeast; individuals from both sexes lived longest in sucrose-milk diets and shortest in diets with hydrolysed yeast. There was no evidence of an interaction between turmeric and diet, suggesting that the toxicity effects are independent of protein source in the diet. Given the seemingly opposing effects of turmeric in insects and mammals being uncovered in the literature, our findings provide further evidence in support of turmeric as a potential natural insecticide.

zoology↗

Fluctuating temperatures exacerbate nutritional stress during development in Drosophila melanogaster

Recent studies suggest that elevated temperatures interact with nutrition to exacerbate the negative effects of poor nutrition. Furthermore, populations adapted to distinct environments differ in their sensitivity to combined thermal and nutritional stress. However, most studies have tested these effects using constant temperatures, even though animals in the wild experience daily and seasonal thermal fluctuations. Here, we used two locally-adapted populations of D. melanogaster from the east coast of Australia (a tropical and a temperate population) to ask whether temperature fluctuations interact with nutrition in the same manner as constant temperature conditions to shape life history traits, and how this differs across populations. We found that fluctuating temperatures exacerbate the negative effects of a poor diet when compared to constant temperatures. Moreover, the negative effects of nutritional stress were significantly greater in the tropical population. In contrast, we found that the temperate population was able to utilize nutrition in unique ways to maintain optimal viability under warmer temperatures. Our findings reveal the ways in which temperature and nutrition interact to impact key life history traits in geographically distinct populations, while also highlighting the importance of using temperature assays representative of natural diel cycles when examining insect responses to climate change.

evolutionary biology↗

Super food or super toxic? Turmeric and spirulina as culprits for the toxic effects of food dyes in Drosophila

Prolonged exposure to food dyes, even for those considered safe for consumption, are known to have toxic effects. However, we lack a proper understanding of the underlying compounds that are responsible for the observed toxicity. In this study, we tested the toxic physiological effects of three common commercially available natural food dyes (red, green, blue), and their main ingredients (turmeric and spirulina), on Drosophila melanogaster oviposition, larval development, and larval foraging behaviour. Larval development and egg-to-adult survival was significantly impacted by blue and green dyes. These effects were recapitulated when flies were fed with increasing concentrations of turmeric and spirulina, suggesting that turmeric is a toxic component of the food dye. Red dye, which contains neither turmeric or spirulina, had little impact on fly health and behaviour. Green and blue food dyes decreased egg laying, an effect similar to that observed in increasing concentrations of turmeric and, to a lesser extent, spirulina. When given a choice, larvae preferred to feed as follows: control > red > blue > green diet patches, a pattern inversely correlating with the previously observed toxicity. Our results show that, despite turmeric being often considered a super food, it can have toxic effects that the impact organismal physiology and health.

physiology↗

Drinkable, liquid in situ-forming and tough hydrogels for gastrointestinal therapeutics

Tablets and capsules are a cornerstone of medicine, but these solid dosage forms can be challenging to swallow for geriatric and pediatric patients. While liquid formulations are easier to ingest, these formulations lack the capacity to localize therapeutics and excipients nor act as controlled release devices. To bridge the advantages of solid and liquid dosage forms, here we describe drug formulations based on liquid in situ-forming and tough (LIFT) hydrogels. Drug-loaded LIFT hydrogels are formed directly in the stomach through the sequential ingestion of a crosslinker solution of calcium and dithiol crosslinkers, followed by the ingestion of a drug-containing polymer solution of alginate and 4-arm poly(ethylene glycol)-maleimide. We show that LIFT hydrogels are mechanically tough and able to robustly form in the presence of complex gastric fluid and in vivo in rat and porcine stomachs. LIFT hydrogels are retained within the porcine stomach for up to 24 h, biocompatible, and safely cleared. These hydrogels deliver a total dose comparable to unencapsulated drug but with delayed and lower maximum drug plasma concentrations, providing a method for controlled release that may mitigate drug toxicity. Co-encapsulation of lactase as a model biologic drug and calcium carbonate mitigated gastric-mediated deactivation of encapsulated enzyme in rat and porcine models. We also demonstrate the potential of these hydrogels to encapsulate and protect a model therapeutic bacterium, E. coli Nissle 1917, against acid. LIFT hydrogels present a biocompatible means of tough, double-network hydrogel formation in situ in the gastric cavity, and may expand medication access for patients with difficulty swallowing.

bioengineering↗

Long-term recoveries of forest ecosystem components after shallow landslides were asynchronized among slope positions

Landslides are a common disturbance in mountainous areas of the world. Transporting and accumulating landslide debris, i.e., disturbance legacies, such as coarse woody debris (CWD), vegetation patches, and surface soils, generate a heterogeneous environment along slopes (zones), which are suggested to affect forest recovery. However, the long-term changes in forest ecosystems after landslides remain unknown, particularly zone-dependent change patterns. We aimed to reveal the differences in the changes in live trees, understory vegetation, CWD, and soils among zones by surveying forests with landslide ages (years since the landslide) ranging from 3 to 74 years and reference stands. The increase in live tree aboveground biomass occurred at a faster rate at the lower part of the slopes where the disturbance legacies were rich and surface soils were stabilized due to the smaller slope angle. Chronological patterns of understory vegetation amounts were determined by the differences in disturbance legacy richness and the timing of subsequent canopy closure. The amounts and decay-class diversity of CWD were determined by the differences in legacy richness and mortality through stand development. These zone-dependent chronological changes influenced litter production and determined the recovery rates of surface soil carbon stocks and nitrogen contents. The increase in the dominance rates of forest herbaceous species was faster in the lower part of the slopes due to the faster surface soil development and canopy closure. Our results illustrate that long-term forest ecosystem succession and recovery after landslides occurs more rapidly at the lower parts than at the upper parts of slopes. HighlightsO_LIRich landslide legacies and low slope angles promoted vegetation and soil recovery C_LIO_LILegacy richness and timing of canopy closure determined changes in the understory C_LIO_LILandslide mortality and stand development mortality determined changes in dead wood C_LI

ecology↗

"Holey" niche! Finding holes in niche hypervolumesusing persistence homology

O_LIHutchinsons niche hypervolume concept has enabled significant progress in our understanding of species ecological needs and distributions across environmental gradients. Nevertheless, the properties of Hutchinsons n-dimensional hypervolumes can be challenging to calculate and several methods have been proposed to extract meaningful measurements of hypervolumes properties (e.g., volume). C_LIO_LIOne key property of hypervolumes are holes, which provide important information about the ecological occupancy of species. However, to date, current methods rely on volume estimates and set operations to identify holes in hypervolumes. Yet, this approach can be problematic because in high-dimensions, the volume of region enclosing a hole tends to zero. C_LIO_LIHere, we propose the use of the topological concept of persistence homology (PH) to identify holes in hypervolumes and in ecological datasets more generally. PH allows for the estimates of topological properties in n-dimensional niche hyper-volumes and is independent of the volume estimates of the hypervolume. We demonstrate the application of PH to canonical datasets and to the identification of holes in the hypervolumes of five vertebrate species with diverse niches, highlighting the potential benefits of this approach to gain further insights into animal ecology. C_LIO_LIOverall, our approach enables the study of an yet unexplored property of Hutchinsons hypervolumes (i.e., holes), and thus, have important implications to our understanding of animal ecology. C_LI

ecology↗

The transcriptomic signature of physiological trade-offs caused by larval overcrowding in Drosophila melanogaster

Intraspecific competition at the larval stage is an important ecological factor affecting life-history, adaptation and evolutionary trajectory in holometabolous insects. However, the molecular pathways and physiological trade-offs underpinning these ecological processes are poorly characterised. We reared Drosophila melanogaster at three egg densities (5, 60 and 300 eggs/ml) and sequenced the transcriptomes of pooled third-instar larvae. We also examined emergence time, egg-to-adult viability, adult mass and adult sex-ratio at each density. Medium crowding had minor detrimental effects on adult phenotypes compared to low density and yielded 24 differentially expressed genes (DEGs) including several chitinase enzymes. In contrast, high crowding had substantial detrimental effects on adult phenotypes and yielded 2107 DEGs. Among these, upregulated gene sets were enriched in sugar, steroid and amino acid metabolism as well as DNA replication pathways, whereas downregulated gene sets were enriched in ABC transporters, Taurine, Toll/Imd signalling and P450 xenobiotics metabolism pathways. Overall, our findings show that larval overcrowding has a large consistent effect on several molecular pathways (i.e., core responses) with few pathways displaying density-specific regulation (i.e., idiosyncratic responses). This provides important insights into how holometabolous insects respond to intraspecific competition during development.

ecology↗

Sugar-rich larval diet promotes lower adult pathogen load and higher survival after infection in a polyphagous fly

Nutrition is a central factor influencing immunity and resistance to infection, but the extent to which nutrition during development affects adult responses to infections is poorly understood. Our study investigated how the nutritional composition of the larval diet affects the survival, pathogen load, and food intake of adult fruit flies, Bactrocera tryoni, after bacterial septic infection. We found a sex-specific effect of larval diet composition on survival post-infection: survival rate was higher and bacterial load was lower for infected females fed sugar-rich larval diet compared with females fed protein-rich larval diet, an effect that was absent in males. Both males and females were heavier when fed a balanced larval diet compared to protein- or sugar-rich diet, while body lipid reserves were higher in the sugar-rich larval diet compared with other diets. Body protein reserve was lower for sugar-rich larval diets compared to other diets in males, but not females. Both females and males shifted their nutrient intake to ingest a sugar-rich diet when infected compared with sham-infected flies without any effect of the larval diet, suggesting that sugar-rich diets can be beneficial to fight off bacterial infection. Overall, our findings show that nutrition during early life can shape individual fitness in adulthood. Summary statementDevelopmental conditions influence adulthood. Here we showed that when the larval diet is rich in sugar, resistance to infection is increased in females at adulthood, in a polyphagous fly.

ecology↗

Leaders are made: Learning acquisition of consistent leader-follower relationships depends on implicit haptic interactions.

Are leaders made or born? Leader-follower roles have been well characterized in social science, but they remain somewhat obscure in sensory-motor coordination. Furthermore, it is unknown how and why leader-follower relationships are acquired, including innate versus acquired controversies. We developed a novel asymmetrical coordination task in which two participants (dyad) need to collaborate in transporting a simulated beam while maintaining its horizontal attitude. This experimental paradigm was implemented by twin robotic manipulanda, simulated beam dynamics, haptic interactions, and a projection screen. Clear leader-follower relationships were learned despite participants not being informed that they were interacting with each other, but only when strong haptic feedback was introduced. For the first time, we demonstrate the emergence of consistent leader-follower relationships in sensory-motor coordination, and further show that haptic interaction is essential for dyadic co-adaptation. These results provide insights into neural mechanisms responsible for the formation of leader-follower relationships in our society.

neuroscience↗

Density-by-diet interactions during larval development shape adult life-history trait expression and fitness in a polyphagous fly

Habitat quality early in life determines individual fitness, with possible long-term evolutionary effects on groups and populations. In holometabolous insects, larval ecology plays a major role in determining the expression of traits in adulthood, but how ecological conditions during larval stage interact to shape adult life-history and fitness, particularly in non-model organisms, remains subject to scrutiny. Consequently, our knowledge of the interactive effects of ecological factors on insect development is limited. Here, using the polyphagous fly Bactrocera tryoni, we conducted a fully-factorial design where we manipulated larval density and larval diet (protein-rich, standard, and sugar-rich) to gain insights into how these ecological factors interact to modulate adult fitness. As expected, a protein-rich diet resulted in faster larval development, heavier and leaner adults that were more fecund compared with standard and sugar-rich diets, irrespective of larval density. Females from the protein-rich larval diet had overall higher reproductive rate (i.e., eggs per day) than females from other diets, and reproductive rate decreased linearly with density for females from the protein-rich but non-linearly for females from the standard and sugar-rich diets over time. Surprisingly, adult lipid reserve increased with larval density for adults from the sugar-rich diet (as opposed to decreasing, as in other diets), possibly due to a stress-response to an extremely adverse condition during development (i.e., high intraspecific competition and poor nutrition). Together, our results provide insights into how ecological factors early in life interact and shape the fate of individuals through life-stages in holometabolous insects.

zoology↗

Nutrigonometry I: using right-angle triangles to quantify nutritional trade-offs in multidimensional performance landscapes

Animals regulate their diet in order to maximise the expression of fitness traits that often have different nutritional needs. These nutritional trade-offs have been experimentally uncovered using the Geometric framework for nutrition (GF). However, current analytical methods to measure such responses rely on either visual inspection or complex models applied to multidimensional performance landscapes, making these approaches subjective, or conceptually difficult, computationally expensive, and in some cases inaccurate. This limits our ability to understand how animal nutrition evolved to support life-histories within and between species. Here, we introduce a simple trigonometric model to measure nutritional trade-offs in multidimensional landscapes ( Nutrigonometry). Nutrigonometry is both conceptually and computationally easier than current approaches, as it harnesses the trigonometric relationships of right-angle triangles instead of vector calculations. Using landmark GF datasets, we first show how polynomial (Bayesian) regressions can be used for precise and accurate predictions of peaks and valleys in performance landscapes, irrespective of the underlying structure of the data (i.e., individual food intakes vs fixed diet ratios). Using trigonometric relationships, we then identified the known nutritional trade-off between lifespan and reproductive rate both in terms of nutrient balance and concentration. Nutrigonometry enables a fast, reliable and reproducible quantification of nutritional trade-offs in multidimensional performance landscapes, thereby broadening the potential for future developments in comparative research on the evolution of animal nutrition.

evolutionary biology↗