Modeling E. coli Tumbles by Rotational Diffusion. Implications for Chemotaxis

The bacterium Escherichia coli in suspension in a liquid medium swims by a succession of runs and tumbles, effectively describing a random walk. The tumbles randomize incompletely, i.e. with a directional persistence, the orientation taken by the bacterium. Here, we model these tumbles by an active rotational diffusion process characterized by a diffusion coefficient and a diffusion time. In homogeneous media, this description accounts well for the experimental reorientations. In shallow gradients of nutrients, tumbles are still described by a unique rotational diffusion coefficient. Together with an increase in the run length, these tumbles significantly contribute to the net chemotactic drift via a modulation of their duration as a function of the direction of the preceding run. Finally, we discuss the limits of this model in propagating concentration waves characterized by steep gradients. In that case, the effective rotational diffusion coefficient itself varies with the direction of the preceding run. We propose that this effect is related to the number of flagella involved in the reorientation process

Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on {\em E. coli} have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with {\em E. coli}. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion

Non-local kinetic and macroscopic models for self-organised animal aggregations

The last two decades have seen a surge in kinetic and macroscopic models derived to investigate the multi-scale aspects of self-organised biological aggregations. Because the individual-level details incorporated into the kinetic models (e.g., individual speeds and turning rates) make them somewhat difficult to investigate, one is interested in transforming these models into simpler macroscopic models, by using various scaling techniques that are imposed by the biological assumptions of the models. However, not many studies investigate how the dynamics of the initial models are preserved via these scalings. Here, we consider two scaling approaches (parabolic and grazing collision limits) that can be used to reduce a class of non-local 1D and 2D models for biological aggregations to simpler models existent in the literature. Then, we investigate how some of the spatio-temporal patterns exhibited by the original kinetic models are preserved via these scalings. To this end, we focus on the parabolic scaling for non-local 1D models and apply asymptotic preserving numerical methods, which allow us to analyse changes in the patterns as the scaling coefficient ϵ is varied from ϵ=1 (for 1D transport models) to ϵ=0 (for 1D parabolic models). We show that some patterns (describing stationary aggregations) are preserved in the limit ϵ→0, while other patterns (describing moving aggregations) are lost. To understand the loss of these patterns, we construct bifurcation diagrams

Counteraction of Tetherin Antiviral Activity by Two Closely Related SIVs Differing by the Presence of a Vpu Gene

In different primate lentiviruses, three proteins (Vpu, Env and Nef) have been shown to have anti-tetherin activities. SIVden is a primate lentivirus harbored by a Cercopithecus denti (C. denti) whose genome code for a Vpu gene. We have compared the activity of HIV-1 Vpu and of SIVden Vpu on tetherin proteins from humans, from C. denti and from Cercopithecus neglectus (C. neglectus), a monkey species that is naturally infected by SIVdeb, a virus closely related to SIVden but which does not encode a Vpu protein. Here, we demonstrate that SIVden Vpu, is active against C. denti tetherin, but not against human tetherin. Interestingly, C. neglectus tetherin was more sensitive to SIVden Vpu than to HIV-1 Vpu. We also identify residues in the tetherin transmembrane domains that are responsible for the species-specific Vpu effect. Simultaneous mutation (P40L and T45I) of human tetherin conferred sensitivity to SIVden Vpu, while abolishing its sensitivity to HIV-1 Vpu. We next analyzed the anti-tetherin activity of the Nef proteins from HIV-1, SIVden and SIVdeb. All three Nef proteins were unable to rescue virus release in the presence of human or C. denti tetherin. Conversely, SIVdeb Nef enhanced virus release in the presence of C. neglectus tetherin, suggesting that SIVdeb relies on Nef in its natural host. Finally, while HIV-1 Vpu not only removed human tetherin from the cell surface but also directed it for degradation, SIVden Vpu only induced the redistribution of both C. denti and C. neglectus tetherins, resulting in a predominantly perinuclear localization

Cell morphology governs directional control in swimming bacteria

The ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology

Directional persistence of chemotactic bacteria in a traveling concentration wave

Chemotactic bacteria are known to collectively migrate towards sources of attractants. In confined convectionless geometries, concentration “waves” of swimming Escherichia coli can form and propagate through a self-organized process involving hundreds of thousands of these microorganisms. These waves are observed in particular in microcapillaries or microchannels; they result from the interaction between individual chemotactic bacteria and the macroscopic chemical gradients dynamically generated by the migrating population. By studying individual trajectories within the propagating wave, we show that, not only the mean run length is longer in the direction of propagation, but also that the directional persistence is larger compared to the opposite direction. This modulation of the reorientations significantly improves the efficiency of the collective migration. Moreover, these two quantities are spatially modulated along the concentration profile. We recover quantitatively these microscopic and macroscopic observations with a dedicated kinetic model

Functional Central Polypurine Tract Provides Downstream Protection of the Human Immunodeficiency Virus Type 1 Genome from Editing by APOBEC3G and APOBEC3B

Lentiviruses utilize two polypurine tracts for initiation of plus-strand viral DNA synthesis. We have examined to what extent human immunodeficiency virus type 1 plus-strand initiation at the central polypurine tract (cPPT) could protect the viral genome from DNA editing by APOBEC3G and APOBEC3B. The presence of a functional cPPT, but not of a mutated cPPT, extensively reduced editing by both APOBEC3G and APOBEC3B of sequences downstream, but not upstream, of the cPPT, with significant protection observed as far as 400 bp downstream. Thus, in addition to other potential functions, the cPPT could help protect lentiviruses from editing by cytidine deaminases of the APOBEC family

V3 loop sequence analysis of seven HIV type 1 group O isolates phenotyped in peripheral blood mononuclear cells and MT-2 cells

HIV-1-infected individuals from which syncytium-inducing (SI) viruses are isolated most often progress more rapidly to AIDS than individuals carrying only non-syncytium-inducing (NSI) viruses. The syncytium-inducing capacity of virus isolates is commonly determined in conjunction to replication in MT-2 cells. Comparison of HIV-1 env sequences and a site-directed mutagenesis study have indicated that the presence of a positively charged amino acid at position 11 or 25 in the V3 loop is minimally required for the SI capacity of HIV-1 subtype B viruses. Studies have also shown a similar correlation between positively charged signature amino acids in the V3 loop and syncytium formation in MT-2 cells for HIV-1 subtypes A, D, and E. In the present study virus phenotype was determined and compared to the V3 loop sequence of seven HIV-1 group O isolates. Three of the HIV-1 group O isolates showed the NSI/non-MT-2 tropic phenotype and two showed the SI/MT-2 tropic phenotype, whereas two isolates presented an uncommon NSI/MT-2 tropic phenotype. The V3 loop of the two SI/MT-2 tropic isolates had a high net positive charge and contained a positively charged amino acid at position 11 or 25. The V3 loop of the two NSI/MT-2 tropic isolates had a low net positive charge and contained a single positively charged amino acid at position 3