Biology subjects

Tamayo, J.

Publications and source records attributed to Tamayo, J..

6 recordsLinked to original sources

bioRxiv2024

Repeated LPS induces training and tolerance of microglial responses across brain regions

BackgroundNeuroinflammation is involved in the pathogenesis of almost every central nervous system disorder. As the brains innate immune cells, microglia fine tune their activity to a dynamic brain environment. Previous studies have shown that repeated bouts of peripheral inflammation can trigger long-term changes in microglial gene expression and function, a form of innate immune memory. Methods and ResultsIn this study, we used multiple low-dose lipopolysaccharide (LPS) injections in adult mice to study the acute cytokine, transcriptomic, and microglia morphological changes that contribute to the formation of immune memory in the frontal cortex, hippocampus, and striatum, as well as the long-term effects of these changes on behavior. Training and tolerance of gene expression was shared across regions, and we identified 3 unique clusters of DEGs (2xLPS-sensitive, 4xLPS-sensitive, LPS-decreased) with different biological functions. 2xLPS-sensitive DEG promoters were enriched for binding sites for IRF and NFkB family transcription factors, two key regulators of innate immune memory. We quantified shifts in microglia morphological populations and found that while the proportion of ramified and rod-like microglia mostly remained consistent within brain regions and sexes with LPS treatment, there was a shift from ameboid towards hypertrophic morphological states across immune memory states and a dynamic emergence and resolution of trains of rod-like microglia with repeated LPS. ConclusionsTogether, findings support the dynamic regulation of microglia during the formation of immune memories in the brain and support future work to exploit this model in brain disease contexts.

neuroscience↗

bioRxiv2023

Multi-population dissolution in confined active fluids

Autonomous out-of-equilibrium agents or cells in suspension are ubiquitous in biology and engineering. Turning chemical energy into mechanical stress, they generate activity in their environment, which may trigger spontaneous large-scale dynamics. Often, these systems are composed of multiple populations that may reflect the coexistence of multiple species, differing phenotypes, or chemically varying agents in engineered settings. Here, we present a new method for modeling such multi-population active fluids subject to confinement. We use a continuum multi-scale mean-field approach to represent each phase by its first three orientational moments and couple their evolution with those of the suspending fluid. The resulting coupled system is solved using a parallel adaptive level-set-based solver for high computational efficiency and maximal flexibility in the confinement geometry. Motivated by recent experimental work, we employ our method to study the spatiotemporal dynamics of confined bacterial suspensions and swarms dominated by fluid hydrodynamic effects. Our computational explorations reproduce observed emergent collective patterns, including features of active dissolution in two-population active-passive swarms, with results clearly suggesting that hydrodynamic effects dominate dissolution dynamics. Our work lays the foundation for a systematic characterization of natural and synthetic multi-population systems such as bacterial colonies, bird flocks, fish schools, colloidal swimmers, or programmable active matter.

biophysics↗

bioRxiv2023

Size dependent diffusion and dispersion of particles in mucin

Mucus, composed significantly of glycosylated mucins, is a soft rheologically complex vis-coelastic material lining respiratory, reproductive, and gastrointestinal tracts in mammals. Mucus may present as a gel or as a fluid, and serves as a barrier to the transport of microbes including, harmful particles, and inhaled atmospheric pollutants. Studies on mucin gels have provided insight into swelling kinetics, and the diffusion and permeability of molecular constituents such as water. The transport and dispersion of micron and sub-micron tracer particles in mucin gels and solutions differs from the motion of molecular water since the much larger tracers may interact with microstructure and larger features of the mucin network. Here, using brightfield and florescence microscopy, high speed particle-tracking, and passive microrheology, we study the thermally driven stochastic movement of 0.5 - 5.0 {micro}m tracer particles in 10% mucin solutions at neutral pH, and in 10% mucin mixed with unmodified limestone rock dust, modified limestone, and crystalline silica. Particle trajectories, mean square displacements, and the displacement probability distributions, are used to assess tracer diffusion and transport. Complex moduli are concomitantly extracted using microrheology techniques. We find that under the conditions analyzed in our experiments the mucin solution present as a highly viscous, weakly viscoelastic fluid rather than as a viscoelastic gel. For small to moderately sized tracers with diameter than 2 {micro}m, effective diffusion coefficients follow predictions of classical Stokes-Einstein relationship. Diffusivity in rock-dust laden mucin is surprisingly larger than in bare mucin. Probability distributions of squared particle displacements indicate that heterogeneity, transient trapping, and electrostatic interactions impact tracer transport, especially for larger tracers. Our results prompt further exploration of physiochemical and rheological mechanisms mediating particle transport in soft, viscoelastic biopolymer networks and materials.

bioengineering↗

bioRxiv2022

Effect of ambient fluid rheology on oscillatory instabilities in filament-motor systems

Filaments and filament bundles such as microtubules or actin interacting with molecular motors such as dynein or myosin constitute a common motif in biology. Synthetic mimics, examples being artificial muscles and reconstituted active networks, also feature active filaments. A common feature of these filament-motor systems is the emergence of stable oscillations as a collective dynamic response. Here, using a combination of classical linear stability analysis and non-linear numerical solutions, we study the dynamics of a minimal filament-motor system immersed in model viscoelastic fluids. We identify steady states, test the linear stability of these states, derive analytical stability boundaries, and investigate emergent oscillatory solutions and their properties. We show that the interplay between motor activity, aggregate elasticity and fluid viscoelasticity allows for stable oscillations or limit cycles to bifurcate from steady states. For highly viscous Newtonian media, frequencies at onset decay with viscosity as [Formula]. In viscoelastic fluids that have the same viscosity as the Newtonian fluid but additionally allow for temporary energy storage, emergent limit cycles are associated with higher frequencies. The magnitude of the increase in the frequency depends on motor mechanochemistry and the interplay between fluid relaxation time-scales and time-scales associated with motor binding and unbinding. Our results suggest that stability and dynamical response in filamentous active systems may be controlled by tailoring the rheology of the ambient environment.

biophysics↗

bioRxiv2020

Swarming bacterial fronts: Dynamics and morphology of active swarm interfaces propagating through passive frictional domains

Swarming, a multicellular mode of flagella-based motility observed in many bacteria species, enables coordinated and rapid surface translocation, expansion and colonization. In the swarming state, bacterial films display several characteristics of active matter including intense and persistent long-ranged flocks and strong fluctuating velocity fields with significant vorticity. Swarm fronts are typically dynamically evolving interfaces. Many of these fronts separate motile active domains from passive frictional regions comprised of dead or non-motile bacteria. Here, we study the dynamics and structural features of a model active-passive interface in swarming Serratia marcescens. We expose localized regions of the swarm to high intensity wide-spectrum light thereby creating large domains of tightly packed immotile bacteria. When the light source is turned off, swarming bacteria outside this passivated region advance into this highly frictional domain and continuously reshape the interphase boundary. Combining results from Particle Image Velocimetry (PIV) and intensity based image analysis, we find that the evolving interface has quantifiable and defined roughness. Correlations between spatially separated surface fluctuations and damping of the same are influenced by the interaction of the interphase region with adjacently located and emergent collective flows. Dynamical growth exponents characterizing the spatiotemporal features of the surface are extracted and are found to differ from classically expected values for passive growth or erosion. To isolate the effects of hydrodynamic interactions generated by collective flows and that arising from steric interactions, we propose and analyze agent-based simulations with full hydrodynamics of rod-shaped, self-propelled particles. Our computations capture qualitative features of the swarm and predict correlation lengths consistent with experiments. We conclude that hydrodynamic and steric interactions enable different modes of surface dynamics, morphology and thus front invasion.

bioengineering↗

bioRxiv2018

Antimicrobial, Antioxidant and Anti-Inflammatory Activities of Proteins of Phaseoulus lunatus (Fabaceae) Baby Lima Beans Produced in Ecuador

Phaseoulus lunatus L., a variety of baby lima bean, which is produced in the coastal region of Ecuador, is a profitable crop of that country. Various cultivars of this common bean are considered a sources for nutraceutical compounds, such as bioactive peptides. To assess the potential biologic activities of protein isolates and hydrolysates of P. lunatus baby lima beans, this study evaluates the proteins antimicrobial, antioxidant and anti-inflammatory activities. Antioxidant activity was measured by the TBARS method. In-vitro anti-inflammatory activity was measured by the inhibition of denatured protein as well as a diffusion method, according with CLSI guidelines by antimicrobial activity. Both fractions (isolate and hydrolysates) showed anti-inflammatory and antioxidant activity. However, protein hydrolysates (pH 5) had a better performance than protein isolates. The same effect was observed in antimicrobial activity, when protein hydrolysates had a broad-spectrum antimicrobial activity against Gram-negative and Gram-positive bacteria. These preliminary studies suggest that P. lunatus baby lima beans could have a considerable biological activity for nutraceutical applications.

microbiology↗