Spatially extended population dynamics models that incorporate intrinsic noise serve as case studies for the role of fluctuations and correlations in biological systems. Including spatial structure stochastic predator-prey competition invalidates deterministic Lotka-Volterra picture neutral cycles. Stochastic yield long-lived erratic oscillations stemming from a resonant amplification mechanism. In spatially systems, one observes noise-stabilized activity persistent correlations....

Abstract For the protozoan parasite Leishmania , completion of its life cycle requires sequential adaptation cellular physiology and nutrient scavenging mechanisms to different environments a sand fly alimentary tract acidic mammalian host cell phagolysosome. Transmembrane transporters are gatekeepers intracellular environments, controlling flux solutes ions across membranes. To discover which vital for survival as amastigote forms, we carried out systematic loss-of-function screen L....

Assemblies of actin and its regulators underlie the dynamic morphology all eukaryotic cells. To understand how regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed localization diverse within filopodia in Drosophila embryos a complementary vitro system filopodia-like (FLSs). We found that composition protein complex where is incorporated (the filopodial tip complex) remarkably heterogeneous both vivo vitro. Our data reveal different pairs...

LeishGEM is a genome-wide functional annotation community resource for Leishmania mexicana, where deletion mutant growth in vitro and vivo measured protein localisation determined by endogenous tagging LOPIT-DC (localisation of organelle proteins isotope with differential centrifugation) spatial proteomics. Data are being made available pre-publication via http://leishgem.org which allows data-driven identification the mechanisms parasitism.

We investigate the competing effects and relative importance of intrinsic demographic environmental variability on evolutionary dynamics a stochastic two-species Lotka-Volterra model by means Monte Carlo simulations two-dimensional lattice. Individuals are assigned inheritable predation efficiencies; quenched randomness in spatially varying reaction rates serves as noise. find that enhances population densities both predators prey while leads to essentially neutral optimization.

Sorting nexin 9 (SNX9) is a membrane-binding scaffold protein that contributes to viral uptake and inflammation associated with worse outcomes in several cancers. It involved endocytosis of epidermal growth factor receptors, β1-integrin membrane type 1 matrix metalloprotease, formation mitochondrial-derived vesicles. The SNX9 Bin-Amphiphysin-Rvs (BAR) - Phox homology (PX) domains bind phosphoinositide lipids the Src 3 (SH3) domain interacts dynamin N-Wiskott Aldrich syndrome (N-WASP)...

Intracellular calcium is regulated in part by the release of Ca$^{2+}$ ions from endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP$_3$R) channels (among other possibilities such as RyR and L-type channels). The resulting dynamics are highly diverse, lead to local "puffs" well global waves propagating through cells, observed {\it Xenopus} oocytes, neurons, cell types. Local fluctuations number play a crucial role onset these features. Previous modeling studies puff stemming...

We study the influence of spatially varying reaction rates on a spatial stochastic two-species Lotka-Volterra lattice model for predator-prey interactions using two-dimensional Monte Carlo simulations. The effects this quenched randomness population densities, transient oscillations, correlations, and invasion fronts are investigated. find that variability in predation rate results more localized activity patches, which turn causes remarkable increase asymptotic densities both predators prey...

Filopodia are ubiquitous fingerlike protrusions, spawned by many eukaryotic cells, to probe and interact with their environments. Polymerization dynamics of actin filaments, comprising the structural core filopodia, largely determine instantaneous lengths overall lifetimes. The polymerization reactions at filopodial tip require transport G-actin, which enter tube from base diffuse toward filament barbed ends near tip. Actin filaments mechanically coupled into a tight bundle cross-linker...

Is it possible to recover the position of a source from steady-state fluxes Brownian particles small absorbing windows located on boundary domain? To address this question, we develop numerical procedure avoid tracking trajectories in entire infinite space. Instead, generate near windows, computed analytical expression exit probability. When are generated by gradient at single point, compute asymptotically holes distributed half-space and disk two dimensions, which agree with stochastic...

ABSTRACT Cells need to sense their environment ensure accurate targeting specific destinations. This occurs in developing muscles, which attach tendon cells before muscle contractions can begin. Elongating myotube tips form filopodia, are presumed have sensory roles, and later suppressed upon building the attachment site. Here, we use live imaging quantitative image analysis of lateral transverse (LT) myotubes Drosophila show that filopodia suppression as a result integrin signaling. Loss...

We study the effects of rapid temperature and magnetic field changes on nonequilibrium relaxation dynamics vortex lines in disordered type-II superconductors by employing an elastic line model performing Langevin molecular simulations. In a previously equilibrated system, either is suddenly changed or instantaneously altered which reflected adding removing flux to from system. The subsequent aging properties are investigated samples with randomly distributed pointlike extended columnar...

<ns3:p>We present the genome sequence of <ns3:italic>Leishmania mexicana</ns3:italic> MNYC/BZ/62/M379 modified to express Cas9 and T7 RNA-polymerase, revealing high similarity reference (MHOM/GT2001/U1103). Through RNAseq-based annotation coding sequences untranslated regions, we provide primer for construct sgRNA template generation CRISPR-assisted gene deletion endogenous tagging.</ns3:p>

Filopodia are finger-like actin-rich protrusions that extend from the cell surface and important for cell–cell communication pathogen internalization. The small size transient nature of filopodia combined with shared usage actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening isolate antibodies alter morphology filopodia-like structures (FLS) in vitro. We found all cause shorter FLS interact SNX9, an regulator binds...

We study the pinning dynamics of magnetic flux (vortex) lines in a disordered type-II superconductor. Using numerical simulations directed elastic line model, we extract time distributions vortex segments. compare different model implementations for disorder surrounding medium: discrete, localized potential wells that are either attractive and repulsive or purely attractive, whose strengths drawn from Gaussian distribution; as well continuous random landscapes. find both schemes yield...

<ns7:p>We present the genome sequence of <ns7:italic>Leishmania mexicana</ns7:italic> MNYC/BZ/62/M379 modified to express Cas9 and T7 RNA-polymerase, revealing high similarity reference (MHOM/GT2001/U1103). Through RNAseq-based annotation coding sequences untranslated regions, we provide primer for construct sgRNA template generation CRISPR-assisted gene deletion endogenous tagging.</ns7:p>

Recovering the position of a source from fluxes diffusing particles through small receptors allows biological cell to determine its relative position, spatial localization and guide it final target. However, how can be recovered point remains unclear. Using Narrow Escape approach for an open domain, we compute diffusion Brownian generated by steady-state gradient single holes distributed on surface in two dimensions. We find that location when there are at least 3 is positioned no further...

How does a cell locate the source of molecular guidance cues from within concentration gradient? We present computational approach to recover absorbed fluxes at narrow receptor windows located on surface cell. In limit fast binding, we solve steady-state diffusion equation using an asymptotic and hybrid stochastic-analytical simulations. show that sensitivity gradient direction decays too rapidly enable long-distance sensing. illustrate how this constraint can be alleviated when...

We discuss the use of Langevin molecular dynamics in investigation non-equilibrium properties disordered vortex matter. Our special focus is set on values system parameters that are realistic for high-$T_c$ superconductors such as YBCO. Using a discretized elastic line model, we study different aspects vortices far from thermal equilibrium. On one hand investigate steady-state driven magnetic flux lines environment, namely current-voltage characteristics, gyration radius, and pinning time...

We investigate the relaxation dynamics of magnetic vortex lines in type-II superconductors following rapid changes external driving current by means an elastic line model simulated with Langevin molecular dynamics. A system flux vortices a sample randomly distributed point-like defects is subjected to appropriate strength for sufficient period time so as be moving non-equilibrium steady state. The then instantaneously lowered value that pertains either or pinned regime. ensuing studied via...

In contrast to the neutral population cycles of deterministic mean-field Lotka--Volterra rate equations, including spatial structure and stochastic noise in models for predator-prey interactions yields complex spatio-temporal structures associated with long-lived erratic oscillations. Environmental variability form quenched randomness predation rates results more localized activity patches. Population fluctuations rare favorable regions turn cause a remarkable increase asymptotic densities...

We apply a perturbative Doi--Peliti field-theoretical analysis to the stochastic spatially extended symmetric Rock-Paper-Scissors (RPS) and May--Leonard (ML) models, in which three species compete cyclically. Compared two-species Lotka--Volterra predator-prey (LV) model, according numerical simulations, these cyclical models appear be less affected by intrinsic fluctuations. Indeed, we demonstrate that qualitative features of ML model are insensitive reaction noise. In contrast, although not...