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Biomedical subjects

Herbert Levine

Publications and source records attributed to Herbert Levine.

31 records · Page 2Linked to original sources

Bacterial linguistic communication and social intelligence.

Bacteria have developed intricate communication capabilities (e.g. quorum-sensing, chemotactic signaling and plasmid exchange) to cooperatively self-organize into highly structured colonies with elevated environmental adaptability. We propose that bacteria use their intracellular flexibility, involving signal transduction networks and genomic plasticity, to collectively maintain linguistic communication: self and shared interpretations of chemical cues, exchange of chemical messages (semantic) and dialogues (pragmatic). Meaning-based communication permits colonial identity, intentional behavior (e.g. pheromone-based courtship for mating), purposeful alteration of colony structure (e.g. formation of fruiting bodies), decision-making (e.g. to sporulate) and the recognition and identification of other colonies - features we might begin to associate with a bacterial social intelligence. Such a social intelligence, should it exist, would require going beyond communication to encompass unknown additional intracellular processes to generate inheritable colonial memory and commonly shared genomic context.

Adaptation, Physiological↗

Cooperativity can reduce stochasticity in intracellular calcium dynamics.

The opening of inositol (1,4,5)-triphosphate (IP(3)) receptors, clustered at discrete sites on the endoplasmic reticulum, can lead to large-scale intracellular calcium waves. Recent experiments in Xenopus oocytes have shown that the inter-wave intervals for these waves have a standard deviation that is much smaller than their mean and that the background calcium concentration exhibits a slow rise during the interwave interval. Using a simple mathematical model, we examine the possibility that this slow rise increases the cooperativity between the openings of the clusters. We find that our model, coupled to the usual assumption that the pumps on the endoplasmic reticulum are activated instantaneously, is unable to explain the observed data: the clusters are found to fire independently and the inter-wave interval distribution is a Poisson distribution with a standard deviation that is approximately equal to its mean. On the other hand, we find that incorporating pumps that slowly activate leads to a slow increase in the background calcium concentration which makes global events progressively more likely to occur. We show that this cooperativity results in much smaller standard deviations and inter-wave interval distributions that are clearly not Poisson distributions.

Animals↗

Physical schemata underlying biological pattern formation-examples, issues and strategies.

Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the harnessing of pattern-forming processes of non-equilibrium physics and chemistry. For these systems, the study of biological pattern formation starts with placing a biological phenomenon of interest within the context of the proper pattern-formation schema and then focusing on the ways in which control is exerted to adapt the pattern to the needs of the organism. This approach is illustrated by several examples, notably bacterial colonies (diffusive-growth schema) and intracellular calcium waves (excitable-media schema).

Animals↗

Wave nucleation rate in excitable systems in the low noise limit.

Motivated by recent experiments on intracellular calcium dynamics, we study the general issue of fluctuation-induced nucleation of waves in excitable media. We utilize a stochastic Fitzhugh-Nagumo model for this study, a spatially extended nonpotential pair of equations driven by thermal (i.e., white) noise. The nucleation rate is determined by finding the most probable escape path via minimization of an action related to the deviation of the fields from their deterministic trajectories. Our results pave the way both for studies of more realistic models of calcium dynamics as well as of nucleation phenomena in other nonequilibrium pattern-forming processes.

Journal Article↗

Computational approach for modeling intra- and extracellular dynamics.

We introduce a phase-field approach for diffusion inside and outside a closed cell with damping and with source terms at the stationary interface. The method is compared to exact solutions (where possible) and the more traditional finite element method. It is shown to be very accurate, easy to implement, and computationally inexpensive. We apply our method to a recently introduced model for chemotaxis by Rappel et al. [Biophys. J. 83, 1361 (2002)].

Journal Article↗

Does the continuum theory of dynamic fracture work?

We investigate the validity of the linear elastic fracture mechanics approach to dynamic fracture. We first test the predictions in a lattice simulation, using a formula of Eshelby for the time-dependent stress intensity factor. Excellent agreement with the theory is found. We then use the same method to analyze the experiment of Sharon and Fineberg. The data here are not consistent with the theoretical expectation.

Journal Article↗

Dynamics of competitive evolution on a smooth landscape.

We study competitive DNA sequence evolution directed by in vitro protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain this dynamical behavior within a continuum mean-field framework. Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant.

Binding, Competitive↗

Spectral mixing of rhythmic neuronal signals in sensory cortex.

The ability to compute the difference between two frequencies depends on a nonlinear operation that mixes two periodic signals. Behavioral and psychophysical evidence suggest that such mixing is likely to occur in the mammalian nervous system as a means to compare two rhythmic sensory signals, such as occurs in human audition, and as a means to lock an intrinsic rhythm to a sensory input. However, a neurological substrate for mixing has not been identified. Here we address the issue of nonlinear mixing of neuronal activity in the vibrissa primary sensory cortex of rat, a region that receives intrinsic as well as sensory-driven rhythmic input during natural whisking. In our preparation, the intrinsic signal originates from cortical oscillations that were induced by anesthetics, and the extrinsic input is introduced by periodic stimulation of vibrissae. We observed that the local extracellular current in vibrissa primary sensory cortex contained oscillatory components at the sum and difference of the intrinsic and extrinsic frequencies. In complementary experiments, we observed that the simultaneous stimulation of contralateral and ipsilateral vibrissae at different frequencies also led to current flow at the sum and difference frequencies. We show theoretically that the relative amplitudes of the observed mixture terms can be accounted for by a threshold nonlinearity in the input-output relation of the underlying neurons. In general, our results provide a neurological substrate for the modulation and demodulation of rhythmic neuronal signals for sensory coding and feedback stabilization of motor output.

Animals↗

Mode-I fracture in a nonlinear lattice with viscoelastic forces.

We study mode-I fracture in a viscoelastic lattice model with a nonlinear force law, with a focus on the velocity and linear stability of the steady-state propagating solution. This study is a continuation both of the study of the piecewise-linear model in mode I, and the study of more general nonlinear force laws in mode-III fracture. At small driving, there is a strong dependency of the velocity curve on the dissipation and a strong sensitivity to the smoothness of the force law at large dissipation. At large driving we calculate, via a linear stability analysis, the critical velocity for the onset of instability as a function of the smoothness, the dissipation and the ratio of lattice spacing to critical extension. This critical velocity is seen to be very sensitive to these parameters. We confirm our calculations via direct numerical simulations of the initial value problem.

Journal Article↗

Establishing direction during chemotaxis in eukaryotic cells.

Several recent studies have demonstrated that eukaryotic cells, including amoeboid cells of Dictyostelium discoideum and neutrophils, respond to chemoattractants by translocation of PH-domain proteins to the cell membrane, where these proteins participate in the modulation of the cytoskeleton and relay of the signal. When the chemoattractant is released from a pipette, the localization is found predominantly on the proximal side of the cell. The recruitment of PH-domain proteins, particularly for Dictyostelium cells, occurs very rapidly (<2 s). Thus, the mechanism responsible for the first step in the directional sensing process of a cell must be able to establish an asymmetry on the same time scale. Here, we propose a simple mechanism in which a second messenger, generated by local activation of the membrane, diffuses through the interior of the cell, suppresses the activation of the back of the cell, and converts the temporal gradient into an initial cellular asymmetry. Numerical simulations show that such a mechanism is plausible. Available evidence suggests that the internal inhibitor may be cGMP, which accumulates within less than a second following treatment of cells with external cAMP.

Animals↗

Modeling spatial patterns in Dictyostelium.

The life cycle of Dictyostelium discoideum provides a striking example of the transition from single cell behavior to multicellular cooperativity. In this paper the status of the attempts at making semiquantitative models of the aggregation phase of this cycle is reviewed. Specifically, it is discussed how the propagation of cAMP waves is a typical example of excitable signaling, which is then rendered unstable by coupling to cell chemotaxis. To investigate the streaming pattern that emerges from this clumping instability, we next turn to a new simulation strategy, which couples dynamical cell-like entities ("bions") to continuum chemical concentration fields. Finally, we discuss two directions for further research: One is the study of the robustness with respect to the variation of system parameters (such as the cell density) exhibited by the biological system, but not by any simple model. The other concerns going beyond the aggregation phase to tackle the three-dimensional problem of slug formation and motion.

Journal Article↗

Coupled map lattice techniques for simulating interfacial phenomena in reaction-diffusion systems.

Interfacial patterns arise due to the dynamical evolution of phase boundaries in physical, chemical and biological systems. Coupled map lattices (CML) offer a useful tool for the simulation of such systems, being able to naturally accommodate the disparate length and time scales inherent in the dynamics of these processes. We illustrate this idea by reviewing work done on applying CML methods to crystal growth and to excitable media.

Journal Article↗