arXiv subjects

Nuris Figueroa-Morales

Publications and source records attributed to Nuris Figueroa-Morales.

7 recordsLinked to original sources

arXiv2019

3D spatial exploration by E. coli echoes motor temporal variability

Unraveling bacterial strategies for spatial exploration is crucial for understanding the complexity in the organization of life. Bacterial motility determines the spatio-temporal structure of microbial communities, controls infection spreading and the microbiota organization in guts or in soils. Most theoretical approaches for modeling bacterial transport rely on their run-and-tumble motion. For Escherichia coli, the run time distribution was reported to follow a Poisson process with a single characteristic time related to the rotational switching of the flagellar motors. However, direct measurements on flagellar motors show heavy-tailed distributions of rotation times stemming from the intrinsic noise in the chemotactic mechanism. Currently, there is no direct experimental evidence that the stochasticity in the chemotactic machinery affect the macroscopic motility of bacteria. In stark contrast with the accepted vision of run-and-tumble, here we report a large behavioral variability of wild-type \emph{E. coli}, revealed in their three-dimensional trajectories. At short observation times, a large distribution of run times is measured on a population and attributed to the slow fluctuations of a signaling protein triggering the flagellar motor reversal. Over long times, individual bacteria undergo significant changes in motility. We demonstrate that such a large distribution of run times introduces measurement biases in most practical situations. Our results reconcile the notorious conundrum between run time observations and motor switching statistics. We finally propose that statistical modeling of transport properties currently undertaken in the emerging framework of active matter studies, should be reconsidered under the scope of this large variability of motility features.

physics.bio-ph↗

arXiv2019

Swimming bacteria in Poiseuille flow: the quest for active Bretherton-Jeffery trajectories

Using a 3D Lagrangian tracking technique, we determine experimentally the trajectories of non-tumbling E. coli mutants swimming in a Poiseuille flow. We identify a typology of trajectories in agreement with a kinematic "active Bretherton-Jeffery" model, featuring an axi-symmetric self-propelled ellipsoid. In particular, we recover the "swinging" and "shear tumbling" kinematics predicted theoretically by Zöttl et al. Moreover using this model, we derive analytically new features such as quasi-planar piece-wise trajectories, associated with the high aspect ratio of the bacteria, as well as the existence of a drift angle around which bacteria perform closed cyclic trajectories. However, the agreement between the model predictions and the experimental results remains local in time, due to the presence of Brownian rotational noise.

physics.flu-dyn↗

arXiv2019

E. coli "super-contaminates" narrow ducts fostered by broad run-time distribution

One striking feature of bacterial motion is their ability to swim upstream along corners and crevices, by leveraging hydrodynamic interactions. This motion through anatomic ducts or medical devices might be at the origin of serious infections. However, it remains unclear how bacteria can maintain persistent upstream motion while exhibiting run-and-tumble dynamics. Here we demonstrate that E. coli can travel upstream in microfluidic devices over distances of 15 millimeters in times as short as 15 minutes. Using a stochastic model relating the run times to the time bacteria spend on surfaces, we quantitatively reproduce the evolution of the contamination profiles when considering a broad distribution of run times. Interestingly, the experimental data cannot be reproduced using the usually accepted exponential distribution of run times. Our study demonstrates that the run-and-tumble statistics determine macroscopic bacterial transport properties. This effect, that we name "super-contamination", could explain the fast onset of some life-threatening medical emergencies.

cond-mat.soft↗

arXiv2018

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.

cond-mat.soft↗

arXiv2015

Living on the edge: transfer and traffic of E. coli in a confined flow

We quantitatively study the transport of E. coli near the walls of confined microfluidic channels, and in more detail along the edges formed by the interception of two perpendicular walls. Our experiments establish the connection between bacteria motion at the flat surface and at the edges and demonstrate the robustness of the upstream motion at the edges. Upstream migration of E. coli at the edges is possible at much larger flow rates compared to motion at the flat surfaces. Interestingly, the bacteria speed at the edges mainly results from collisions between bacteria moving along this single line. We show that upstream motion not only takes place at the edge but also in an "edge boundary layer" whose size varies with the applied flow rate. We quantify the bacteria fluxes along the bottom walls and the edges and show that they result from both the transport velocity of bacteria and the decrease of surface concentration with increasing flow rate due to erosion processes. We rationalize our findings as a function of the local variations of the shear rate in the rectangular channels and hydrodynamic attractive forces between bacteria and walls.

cond-mat.soft↗

arXiv2012

On the role of intrinsic noise on the response of the p53-Mdm2 module

The protein p53 has a well established role in protecting genomic integrity in human cells. When DNA is damaged p53 induces the cell cycle arrest to prevent the transmission of the damage to cell progeny, triggers the production of proteins for DNA repair and ultimately calls for apoptosis. In particular, the p53-Mdm2 feedback loop seems to be the key circuit in this response of cells to damage. For many years, based on measurements over populations of cells it was believed that the p53-Mdm2 feedback loop was the responsible for the existence of damped oscillations in the levels of p53 and Mdm2 after DNA damage. However, recent measurements in individual human cells have shown that p53 and its regulator Mdm2 develop sustained oscillations over long periods of time even in the absence of stress. These results have attracted a lot of interest, first because they open a new experimental framework to study the p53 and its interactions and second because they challenge years of mathematical models with new and accurate data on single cells. Inspired by these experiments standard models of the p53-Mdm2 circuit were modified introducing ad-hoc some biologically motivated noise that becomes responsible for the stability of the oscillations. Here, we follow an alternative approach proposing that the noise that stabilizes the fluctuations is the intrinsic noise due to the finite nature of the populations of p53 and Mdm2 in a single cell.

q-bio.MN↗

arXiv2011

Stochastic approximation to the specific response of the immune system

We develop a stochastic model to study the specific response of the immune system. The model is based on the dynamical interaction between Regulatory and Effector CD4+ T cells in the presence of Antigen Presenting Cells inside a lymphatic node. At a mean field level the model predicts the existence of different regimes where active, tolerant, or cyclic immune responses are possible. To study the model beyond mean field and to understand the specific responses of the immune system we use the Linear Noise Approximation and show that fluctuations due to finite size effects may strongly alter the mean field scenario. Moreover, it was found the existence of a certain characteristic frequency for the fluctuations. All the analytical predictions were compared with simulations using the Gillespie's algorithm.

q-bio.CB↗