In vitro characterization of Trypanosoma cruzi infection dynamics in skeletal and cardiac myotubes models suggests a potential cell-to-cell transmission in mediating cardiac pathology.

Chagas disease predominantly affects the heart, esophagus, and colon in its chronic phase. However, the precise infection mechanisms of the causal agent Trypanosoma cruzi in these tissue types remain incompletely understood. This study investigated T.

Exploring the mechanisms underlying stroke volume variability reduction in a murine model of heart failure with reduced ejection fraction.

Heart failure with reduced ejection fraction (HFrEF) is accompanied by disregulation of cardiovascular function. Heart rate variability (HRV) is commonly used to assess autonomic dysfunction in HFrEF. However, analysis of stroke volume variability (SVV) may provide additional insights.

Thermodynamic performance of coupled enzymatic reactions: A chemical kinetics model for analyzing cotransporters, ion pumps, and ATP synthases.

Previous research has suggested that molecular energy converters such as ATP synthases, ion pumps, and cotransporters operate via spatially separate pathways for free energy donor and acceptor reactions linked by a protein molecule. We present a chemical kinetics model based on these works, with the basic assumption that all molecular energy converters can be thought of as linked enzymatic reactions, one running downhill the chemical potential gradient and driving the other uphill. To develop the model we first look at how an enzyme process can be forced to go backwards using a basic kinetic model.

On the effects of diabetes mellitus on the mechanical properties of DRG sensory neurons and their possible relation with diabetic neuropathy.

Diabetic neuropathy (DN) is one of the principal complications of diabetes mellitus (DM). Dorsal root ganglion (DRG) neurons are the primary sensory neurons that transduce mechanical, chemical, thermal, and pain stimuli. Diabetes-caused sensitivity alterations and presence of pain are due to cellular damage originated by persistent hyperglycemia, microvascular insufficiency, and oxidative and nitrosative stress.

Hybrid reaction-diffusion and clock-and-wavefront model for the arrest of oscillations in the somitogenesis segmentation clock.

The clock and wavefront paradigm is arguably the most widely accepted model for explaining the embryonic process of somitogenesis. According to this model, somitogenesis is based upon the interaction between a genetic oscillator, known as segmentation clock, and a differentiation wavefront, which provides the positional information indicating where each pair of somites is formed. Shortly after the clock and wavefront paradigm was introduced, Meinhardt presented a conceptually different mathematical model for morphogenesis in general, and somitogenesis in particular.

Dynamics of Mammalian Cell Infection by trypomastigotes.

In a recent work we demonstrated that trypomastigotes change their motility patterns in the presence of mammalian cells, that the extent of the changes depends on the cell line, and that this extent is positively correlated with the efficiency with which parasites invade the different cell lines. These results open the question of what cellular characteristics are relevant for parasite identification and invasion. In the present work, we tackled such question.

Motility patterns of Trypanosoma cruzi trypomastigotes correlate with the efficiency of parasite invasion in vitro.

Numerous works have demonstrated that trypanosomatid motility is relevant for parasite replication and sensitivity. Nonetheless, although some findings indirectly suggest that motility also plays an important role during infection, this has not been extensively investigated. This work is aimed at partially filling this void for the case of Trypanosoma cruzi.

Crosstalk dynamics between the circadian clock and the mTORC1 pathway.

Crosstalk between the circadian clock clockwork and cellular metabolic regulatory networks is crucial to ensure an adequate response of an organism to the day/night cycle. mTOR (mammalian/mechanistic target of rapamycin) is a master growth regulator and sensor of nutrient status, which is part of the mTOR complex 1 (mTORC1). While the circadian clock confers rhythmicity to the mTOR protein by regulating its degradation rate, mTORC1 activity diminishes period and augments amplitude of circadian oscillations at the cellular level by a currently unknown mechanism.

Three-Way Interactions in an Artificial Community of Bacterial Strains Directly Isolated From the Environment and Their Effect on the System Population Dynamics.

This work is motivated by previous studies that have analyzed the population ecology of a collection of culturable thermoresistant bacteria, isolated from the Churince lagoon in Cuatro Cienegas, Mexico. In particular, it is aimed at testing a hypothesis from a modeling study, which states that antagonistic and sensitive bacteria co-exist thanks to resistant bacteria that protect sensitive ones by forming physical barriers. We selected three different bacterial strains from the referred collection: one antagonistic, one sensitive, and one resistant, and studied the population dynamics of mixed colonies.

Polymerization of sarcoplasmic-reticulum calcium-binding proteins might explain observed reticulum kinetics-on-demand behavior.

Reported experimental results, in which transient elevations of sarcoplasmic calcium levels are induced by caffeine in smooth muscle cells, apparently contradict the principle of mass conservation. The commonly accepted model assumes that the total number of Ca binding sites is fixed. A former work dealing with this problem proved that assuming the presence within the reticulum of calcium sequestering proteins whose total number of calcium binding sites increases as the existent sites get occupied, is enough to explain the above referred counter-intuitive experimental results.

Bistable behaviour and medium-dependent post-translational regulation of the tryptophanase operon regulatory pathway in Echerichia coli.

The present work is aimed at studying the dynamic behaviour of the tryptopnanase (tna) operon, which encodes the proteins necessary to uptake and metabolise tryptophan to use it as a carbon source in the absence of glucose. To this end, we designed a micro-bioreactor capable of driving a bacterial culture to a stationary state. This allowed us to explore (at the single cell level) the tna operon steady-state dynamics under multiple culture conditions.

Optimization and Stability of Heat Engines: The Role of Entropy Evolution.

Local stability of maximum power and maximum compromise (Omega) operation regimes dynamic evolution for a low-dissipation heat engine is analyzed. The thermodynamic behavior of trajectories to the stationary state, after perturbing the operation regime, display a trade-off between stability, entropy production, efficiency and power output. This allows considering stability and optimization as connected pieces of a single phenomenon.

Motility of Escherichia coli in a quasi-two-dimensional porous medium.

Bacterial migration through confined spaces is critical for several phenomena, such as biofilm formation, bacterial transport in soils, and bacterial therapy against cancer. In the present work, E. coli (strain K12-MG1655 WT) motility was characterized by recording and analyzing individual bacterium trajectories in a simulated quasi-two-dimensional porous medium.

Experimental and Mathematical-Modeling Characterization of Trypanosoma cruzi Epimastigote Motility.

The present work is aimed at characterizing the motility of parasite T. cruzi in its epimastigote form. To that end, we recorded the trajectories of two strains of this parasite (a wild-type strain and a stable transfected strain, which contains an ectopic copy of LYT1 gene and whose motility is known to be affected).

Kinetics on Demand Is a Simple Mathematical Solution that Fits Recorded Caffeine-Induced Luminal SR Ca2+ Changes in Smooth Muscle Cells.

The process of Ca2+ release from sarcoplasmic reticulum (SR) comprises 4 phases in smooth muscle cells. Phase 1 is characterized by a large increase of the intracellular Ca2+ concentration ([Ca2+]i) with a minimal reduction of the free luminal SR [Ca2+] ([Ca2+]FSR). Importantly, active SR Ca2+ ATPases (SERCA pumps) are necessary for phase 1 to occur.

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach.

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities.

The utility of simple mathematical models in understanding gene regulatory dynamics.

In this review, we survey work that has been carried out in the attempts of biomathematicians to understand the dynamic behaviour of simple bacterial operons starting with the initial work of the 1960's. We concentrate on the simplest of situations, discussing both repressible and inducible systems and then turning to concrete examples related to the biology of the lactose and tryptophan operons. We conclude with a brief discussion of the role of both extrinsic noise and so-called intrinsic noise in the form of translational and/or transcriptional bursting.

Optimal performance of the tryptophan operon of E. coli: a stochastic, dynamical, mathematical-modeling approach.

In this work, we develop a detailed, stochastic, dynamical model for the tryptophan operon of E. coli, and estimate all of the model parameters from reported experimental data. We further employ the model to study the system performance, considering the amount of biochemical noise in the trp level, the system rise time after a nutritional shift, and the amount of repressor molecules necessary to maintain an adequate level of repression, as indicators of the system performance regime.

Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network.

Understanding the principles that govern community assemblages is a central goal of ecology. There is limited experimental evidence in natural settings showing that microbial assembly in communities are influenced by antagonistic interactions. We, therefore, analyzed antagonism among bacterial isolates from a taxonomically related bacterial guild obtained from five sites in sediments from a fresh water system.

Hierarchical dynamics of a transcription factors network in E. coli.

In the present work we study the transcription-factor regulatory network that controls the synthesis of flagella in E. coli. Our objective is to address how the transcription-factor dynamics (in terms of their promoter activities and associated rates) correlate with their positions in the hierarchical organization of this regulatory network.

Influence of the feedback loops in the trp operon of B. subtilis on the system dynamic response and noise amplitude.

In this paper we introduce a mathematical model for the tryptophan operon regulatory pathway in Bacillus subtilis. This model considers the transcription-attenuation, and the enzyme-inhibition regulatory mechanisms. Special attention is paid to the estimation of all the model parameters from reported experimental data.

What is the core oscillator in the speract-activated pathway of the Strongylocentrotus purpuratus sperm flagellum?

Sperm chemotaxis has an important role in fertilization. Most of our knowledge regarding this phenomenon comes from studies in organisms whose fertilization occurs externally, like sea urchins. Sea urchin spermatozoa respond to sperm-activating peptides, which diffuse from the egg jelly coat and interact with their receptor in the flagellum, triggering several physiological responses: changes in membrane potential, intracellular pH, cyclic nucleotide levels, and intracellular Ca2+ concentration ([Ca2+]).

Irreversible thermodynamics in multiscale stochastic dynamical systems.

This work extends the results of a recently developed theory of a rather complete thermodynamic formalism for discrete-state, continuous-time Markov processes with and without detailed balance. We investigate whether and in what way the thermodynamic structure is invariant in a multiscale stochastic system, that is, whether the relations between thermodynamic functions of state and process variables remain unchanged when the system is viewed at different time scales and resolutions. Our results show that the dynamics on a fast time scale contribute an entropic term to the internal energy function u(S)(x) for the slow dynamics.

Distributions for negative-feedback-regulated stochastic gene expression: dimension reduction and numerical solution of the chemical master equation.

In this work we introduce a novel approach to study biochemical noise. It comprises a simplification of the master equation of complex reaction schemes (via an adiabatic approximation) and the numerical solution of the reduced master equation. The accuracy of this procedure is tested by comparing its results with analytic solutions (when available) and with Gillespie stochastic simulations.

Bistable behavior of the lac operon in E. coli when induced with a mixture of lactose and TMG.

In this work we investigate multistability in the lac operon of Escherichia coli when it is induced by a mixture of lactose and the non-metabolizable thiomethyl galactoside (TMG). In accordance with previously published experimental results and computer simulations, our simulations predict that: (1) when the system is induced by TMG, the system shows a discernible bistable behavior while, (2) when the system is induced by lactose, bistability does not disappear but excessively high concentrations of lactose would be required to observe it. Finally, our simulation results predict that when a mixture of lactose and TMG is used, the bistability region in the extracellular glucose concentration vs.