Biology subjects

Matsuzawa, T.

Publications and source records attributed to Matsuzawa, T..

9 recordsLinked to original sources

bioRxiv2026

Partition Coefficients Reveal Changes in Properties of Low-Contrast Biomolecular Condensates

Biomolecular condensates are domains within cells with distinct compositions, held together by intermolecular cohesion. They are implicated in a variety of cellular processes, and in vitro studies have revealed the molecular driving forces that underly their condensation. However, in vitro condensates do not capture essential features of cellular condensates. In particular, enrichment of proteins, quantified by partition coefficients, is often exaggerated in these simplified systems. We show that the addition of free amino acids and other small molecules to model condensates can bring their partition coefficients within physiological range. In this limit, where there is low biochemical contrast between condensates and their surroundings, we observe striking changes to condensate behavior. Such low-contrast condensates exhibit large fluctuations in shape and composition and show enhanced sensitivity to changes in their environment. These behaviors reflect dramatic shifts to their material properties, including interfacial tension, rheology, and chemical susceptibilities. We note remarkable similarities in these effects across seemingly unrelated two-phase fluid systems. To explain these trends, we reformulate classic models of critical phenomena in terms of partition coefficients. This framework simplifies application of theory to experiments with near-critical fluids and suggests new experimental approaches for assessing condensate physiology in live cells.

biophysics↗

bioRxiv2026

Metabolites Shift Equilibria of Biomolecular Condensates

Biomolecular condensates compartmentalize biochemistry in living cells. While in vitro models of condensates involve only a few components, the cytoplasm is a complex mixture with thousands of components, including many small molecules. While many macromolecular drivers of phase separation have been revealed, the contributions from small molecules have received little attention. To quantify the impact of solutes on biomolecular condensates, we introduce susceptibility, a dimensionless descriptor of condensate response to solute perturbations. We measured how three model condensates, assembled by distinct cohesive mechanisms, respond to diverse solutes including amino acids and nucleotides. Generically, solutes shift condensate phase equilibria, with susceptibilities spanning over four orders of magnitude. These values reflect underlying molecular interactions, consistent with theoretical descriptions including Flory-Huggins and polyphasic linkages. As one example of the predictive power of susceptibility, we exploit enzymatic activity to induce condensation and modulate material properties. Our work establishes susceptibility as an indicator of the sensitivity of biomolecular condensates to solutes, with implications for cell physiology and therapeutic design. SIGNIFICANCE STATEMENTCells compartmentalize biochemistry using biomolecular condensates formed through phase separation. Although cells contain thousands of small molecules, little is known about their influence on condensation. In such complex mixtures, mapping full phase diagrams is infeasible. Alternatively, we introduce susceptibility to characterize system response around a working composition. Using three distinct model condensates and over a dozen solutes, we observe susceptibilities varying over four orders of magnitude. We provide a general thermodynamic framework that clarifies the driving forces behind these responses, rationalizing their magnitude and their dependence on location in the phase diagram. Our work provides a framework for understanding and harnessing solutes to regulate biomolecular condensation, with implications for cell physiology and therapeutic design.

biophysics↗

bioRxiv2024

Old age variably impacts chimpanzee engagement and efficiency in stone tool use

We know vanishingly little about how long-lived apes experience senescence in the wild, particularly with respect to their foraging behaviors, which are essential for survival. Some wild apes use tools during foraging and, given the additional cognitive and physical challenges presented by tool use, we predict that such behaviors are at a heightened risk of senescence. However, until the present, longitudinal analysis of the effects of progressive aging on wild ape tool-use behaviors has not been possible due to a lack of available data. In response to this research gap, we sampled data from a longitudinal video archive that contained footage of wild chimpanzees engaging in one of their most complex forms of tool use - the cracking of hard-shelled nuts with hammers and anvil stones, termed nut cracking - at an outdoor laboratory at Bossou, Guinea. By sampling data over a 17-year period, we describe how the extent to which wild chimpanzees engage in - and efficiently perform - nut cracking changes between the ages of approximately 39-44 to 56-61 years of age. Over this extended sampling period, chimpanzees began attending experimental nut cracking sites less frequently than younger individuals. Several elderly chimpanzees exhibited reductions in efficiency across multiple components of nut cracking, including taking more time to select stone tools prior to use, and taking longer to crack open nuts and consume the associated pieces of kernel. Two chimpanzees also began using less streamlined behavioral sequences to crack nuts, including a greater number of actions (such as more numerous strikes of the hammer stone). Most notably, we report interindividual variability in the extent to which elderly chimpanzees tool-use behaviors changed during our sample period - ranging from small to profound reductions in tool engagement and efficiency - as well as differences in the specific aspects of nut cracking behaviors that changed for each individual as they aged. We discuss the possible causes of these changes with reference to research into senescence in captive primates, and provide future directions for research of primate aging in both captive and wild settings.

animal behavior and cognition↗

bioRxiv2024

The ontogeny of chimpanzee technological efficiency

Primate extractive foraging requires years of dedicated learning. Throughout this period, learners peer at conspecifics engaging in the behaviour ("models"), interacting with the model and their tools, and sometimes stealing the freshly extracted resource. This also corresponds to an extended period of tolerance from the models. Yet the long-term effect of variation in experiences during this period on the technological efficiency of individuals is unknown for primate tool use, and no research has assessed the role of both the learner and the model(s) in generating individual differences. Using >680 hours of video spanning 25 years, we assessed whether experiences during the stone tool use social learning period ("early learning period"; ages 0-5) predicted the post-early learning period (ages 6+) technological efficiency in wild chimpanzees in Bossou, Guinea. We found that learners varied in how frequently they peered at the models whole nut-cracking bouts, how many learning opportunities their mothers presented, and the amount of tolerance and intolerance they experienced from all selected models. Learners who experienced more intolerance became less efficient tool users, whereas learners who were exposed to more social learning opportunities and tolerance became more efficient. Peering at the whole nut-cracking bout decreased subsequent efficiency, hinting at learners acquiring less efficient cultural components of the behaviour. Our findings highlight the role of social learning in the acquisition of stone tool use and support the view that social learning opportunities within a tolerant environment are key in explaining the emergence and maintenance of complex forms of primate technology. Significance StatementThe capacity and inclination to learn from others, along with social learning opportunities provided by tolerant groupmates, are thought to have enabled the evolution of technology in primates, including hominins. The influence of the learning period on long-term individual variation in technological efficiency remains unknown for non-human primates but has significant implications for cultural transmission and evolution. We provide longitudinal support for the hypothesis that exposure to social learning opportunities during development predicts subsequent technological efficiency. Moreover, we show that low amounts of intolerance, not just general tolerance, is key in the ontogeny of technological efficiency. Finally, we find aspects of behavioural acquisition relating to accurate transmission of cultural traits rather than to learning to use tools efficiently.

animal behavior and cognition↗

bioRxiv2024

A beta-Galactosidase acting on unique galactosides: the structure and function of a beta-1,2-galactosidase from Bacteroides xylanisolvens, an intestinal bacterium

Galactosides are major carbohydrates that are found in plant cell walls and various prebiotic oligosaccharides. Studying the detailed biochemical functions of {beta}-galactosidases in degrading these carbohydrates is important. In particular, identifying {beta}-galactosidases with new substrate specificities could help in the production of potentially beneficial oligosaccharides. In this study, we identified a {beta}-galactosidase with novel substrate specificity from Bacteroides xylanisolvens, an intestinal bacterium. The enzyme did not show hydrolytic activity toward natural {beta}-galactosides during the first screening. However, when -D-galactosyl fluoride (-GalF) as a donor substrate and galactose or D-fucose as an acceptor substrate were incubated with a nucleophile mutant, reaction products were detected. The galactobiose produced from the -GalF and galactose was identified as {beta}-1,2-galactobiose using NMR. Kinetic analysis revealed that this enzyme effectively hydrolyzed {beta}-1,2-galactobiose and {beta}-1,2-galactotriose. In the complex structure with methyl {beta}-galactopyranose as a ligand, the ligand is only located at subsite +1. The 2-hydroxy group and the anomeric methyl group of methyl {beta}-galactopyranose faces in the direction of subsite -1 and the solvent, respectively. This observation is consistent with the substrate specificity of the enzyme regarding linkage position and chain length. Overall, we concluded that the enzyme is a {beta}-galactosidase acting on {beta}-1,2-galactooligosaccharides. SynopsisThe structural and functional analysis of {beta}-galactosidase from an intestinal bacterium led to the discovery of a new {beta}-galactosidase hydrolyzing unique {beta}-1,2-galactooligosaccharides.

biochemistry↗

bioRxiv2024

Nonadjacent Dependencies and Syntactic Structure of Chimpanzee Action During a Natural Tool-Use Task

The hierarchical organization of sequential behaviour, and the ability to compensate for nonadjacent sequential dependencies, are fundamental and interrelated abilities supporting complex human behaviours, including language and tool use. To understand how the cognition underlying these structural properties of human behaviour evolved, we can gain valuable insight from studying the sequential behaviours of nonhuman animals. Among the behaviours of nonhuman apes, tool use has been hypothesised to be a domain of behaviour which likely involves hierarchical organization. However thus far, evidence supporting this hypothesis comes from methodologies which have been criticised in their objectivity. Additionally, the extent to which nonadjacent dependencies appear in primate action sequences during tool use has not been formally investigated. We used estimations of mutual information (MI) - a measure of dependency strength between sequence elements - to evaluate both the extent to which wild chimpanzees produce nonadjacent dependencies during a naturalistic tool-use task (nut cracking), as well as how sequences of actions are organized during tool use. Half of adult chimpanzees produce nonadjacent dependencies at significantly greater sequential distances than comparable, nonhierarchical Markov models, including when repeated actions had been accounted for. Additionally, for the majority of chimpanzees, MI decay with increasing sequential distance included a power-law relationship, which is a key indicator that most chimpanzees draw upon forms of hierarchical structuring when organizing behaviours during tool use. Our analysis offered the greatest support for a system of organization which involved the production of short subroutines of actions (2-8 actions), which are hierarchically arranged into sequences - a finding which is consistent with previous qualitative descriptions of ape tool-use behaviours. Interindividual variability was detected within our analysis in both the distance dependencies were detected, and the most likely structuring mechanism for sequential action organization. We discuss these results in light of possible interindividual variation, in addition to methodological considerations for applications of MI estimations to sequential behaviours. Moreover, we discuss our main findings alongside hypotheses for the coevolution of complex syntax in language and tool-action across hominin evolutionary history.

animal behavior and cognition↗

bioRxiv2023

Stable long-term individual variation in chimpanzee technological efficiency

Using tools to access hard-to-reach and high-quality resources, such as termites, honey, and nuts, initiated a fundamental adaptive shift in human and nonhuman primate cognitive and behavioural evolution. Variation in the efficiency of extracting calorie-rich and nutrient-dense resources directly impacts energy expenditure, and potentially has significant repercussions for cultural transmission where model selection biases are employed during skill acquisition. Assessing variation in efficiency is key to understanding the evolution of complex behavioural traits in primates. Yet, individual-level differences beyond age- and sex-class in primate extractive foraging efficiency have never been investigated. Here, we used 25 years (1992- 2017) of video data of the Bossou chimpanzee community (Guinea), to investigate whether individual differences in nut-cracking efficiency exist across the life span of chimpanzees aged [≥] 6 years. Data from 3,882 oil-palm nut-cracking bouts from over 800 hours of observation were collected. We found long-term stable and reliable individual differences in four (out of five) measures of efficiency. We found no sex effect, challenging previous research on a female bias in chimpanzee tool use. These life-long differences in extractive foraging impacts daily energy budgets, which potentially have significant individual fitness and life history consequences. Additionally, the establishment of long-term individual variation in chimpanzee stone tool use has implications for interpreting archaeological records of hominins. Our findings highlight the importance of longitudinal data from long-term field sites when investigating underlying cognitive and behavioural diversity across individual lifespans and between populations.

animal behavior and cognition↗

bioRxiv2021

Landscaping the behavioural ecology of primate stone tool use

Ecology is fundamental to the development, transmission, and perpetuity of primate technology. Previous studies on tool site selection have addressed the relevance of targeted resources and raw materials for tools, but few have considered the broader foraging landscape. In this first landscape-scale study of the ecological contexts of wild chimpanzee (Pan troglodytes verus) tool-use, we investigate the conditions required for nut-cracking to occur and persist over time at discrete locations in Bossou (Guinea). We examine this at three levels: selection, frequency of use, and inactivity. We find that, further to the presence of a nut tree and availability of raw materials, abundance of food-providing trees as well as proximity to nest sites were significant predictors of nut-cracking occurrence. This suggests that the spatial distribution of nut-cracking sites is mediated by the broader behavioural landscape and is influenced by non-extractive foraging of predictable resources, as well as non-foraging activities. Additionally, the number of functional tools was greater at sites with higher frequency of nut-cracking and was negatively correlated with site inactivity. Our findings indicate that the technological landscape of the Bossou chimpanzees shares affinities with the favoured places model of hominin site formation and provides new insights for reconstructing ancient patterns of landscape use. ResumeLecologie est fondamentale pour le developpement, la transmission et la perennite de la technologie des primates. Des etudes anterieures ont identifie la disponibilite des ressources cibles ainsi que les matieres premieres pour les outils comme des facteurs influents dans la selection des emplacements pour les activites technologiques. Cependant, il y a peu detudes qui abordent cette recherche a lechelle du paysage et du comportement fourrager. Dans cette premiere etude paysagere sur lutilisation doutils par le chimpanze sauvage (Pan troglodytes verus), nous recherchons les conditions ecologiques qui influencent la selection, lutilisation et linactivite des emplacements utilises pour le cassage des noix en Bossou, Guinee. Nos resultats montrent quen plus de la presence dun noyer et de la disponibilite des matieres premieres, labondance darbres nourriciers ainsi que la proximite des sites de nidification etaient des predicteurs significatifs de loccurrence du cassage des noix. Cela suggere que la distribution spatiale des sites de cassage de noix est influencee par le paysage comportemental et est influencee par le fourrage non-extractive de ressources previsibles, ainsi que par des activites non-fourragers. Nos resultats indiquent que le paysage technologique des chimpanzes de Bossou partage des affinites avec le modele des << lieux favoris >> de la formation des sites hominides et fournit de nouvelles perspectives pour reconstruire les modes dutilisation du paysage anciens.

ecology↗

bioRxiv2021

Development and Validation of LAMP Primer Sets for Rapid and Correct Identification of Aspergillus fumigatus Carrying the cyp51A TR46 Azole Resistance Gene

Infections due to triazole resistant Aspergillus fumigatus are increasingly reported worldwide and are associated with treatment failure and mortality. The principal class of azole resistant isolates is characterized by the presence of tandem repeats of 34 bp or 46 bp (TR34 or TR46) within the promoter region of the cyp51A gene. Loop-mediated isothermal amplification (LAMP) is a widely used nucleic acid amplification system with high rapidity and specificity. In this paper, we report a new LAMP assay method to detect the 46 bp tandem repeat insertion in the cyp51A gene promoter region, named TR46-LAMP assay, based on the use of a newly designed specific LAMP primer sets. TR46 is a high-prevalence allele which is associated with the occurrence of multi-triazole resistance of A. fumigatus in patients as well as isolates from the environment. This newly designed TR46-LAMP assay was validated as a useful method for specific detection of azole-resistant A. fumigatus isolates bearing TR462 as well as TR463 in cyp51A gene promoter region. It could also differentiate azole-resistant isolates of TR46 tandem repeats from those with TR34 tandem repeats in cyp51A genes. These results showed this TR46-LAMP method is specific, rapid, and also provides crucial insights to enable development of novel antifungal therapeutic strategies against severe fungal infections due to A. fumigatus with TR46 tandem repeats.

molecular biology↗