RESUMEN

Neonatal herpes simplex virus (HSV) infection is a devastating disease with substantial morbidity and mortality. The genetic basis of susceptibility to HSV in neonates remains undefined. We evaluated a male infant with neonatal skin/eye/mouth (SEM) HSV-1 disease, who had complete recovery after acyclovir but developed HSV-1 encephalitis at 1 year of age. An immune workup showed an anergic PBMC cytokine response to TLR3 stimulation but no other TLRs. Exome sequencing identified rare missense variants in IFN-regulatory factor 7 (IRF7) and UNC-93 homolog B1 (UNC93B1). PBMC single-cell RNA-Seq done during childhood revealed decreased expression of several innate immune genes and a repressed TLR3 pathway signature at baseline in several immune cell populations, including CD14 monocytes. Functional studies in fibroblasts and human leukemia monocytic THP1 cells showed that both variants individually suppressed TLR3-driven IRF3 transcriptional activity and the type I IFN response in vitro. Furthermore, fibroblasts expressing the IRF7 and UNC93B1 variants had higher intracellular viral titers with blunting of the type I IFN response upon HSV-1 challenge. This study reports an infant with recurrent HSV-1 disease complicated by encephalitis associated with deleterious variants in the IRF7 and UNC93B1 genes. Our results suggest that TLR3 pathway mutations may predispose neonates to recurrent, severe HSV.

Asunto(s)

RESUMEN

Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population's range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria-Delbrück fluctuation tests, lineage tracing in a novel microfluidic incubator, cell-based simulations, and theoretical modeling, we find that the majority of mutations arise behind the expanding frontier, giving rise to clones that are mechanically "pushed out" of the growing region by the proliferating cells in front. These excluded-volume interactions result in a clone-size distribution that solely depends on where the mutation first arose relative to the front and is characterized by a simple power law for low-frequency clones. Our model predicts that the distribution depends on a single parameter-the characteristic growth layer thickness-and hence allows estimation of the mutation rate in a variety of crowded cellular populations. Combined with previous studies on high-frequency mutations, our finding provides a unified picture of the genetic diversity in expanding populations over the whole frequency range and suggests a practical method to assess growth dynamics by sequencing populations across spatial scales.

Asunto(s)

RESUMEN

Growth in confined spaces can drive cellular populations through a jamming transition from a fluidlike state to a solidlike state. Experiments have found that jammed budding yeast populations can build up extreme compressive pressures (over 1 MPa), which in turn feed back onto cellular physiology by slowing or even stalling cell growth. Using numerical simulations, we investigate how this feedback impacts the mechanical properties of model jammed cell populations. We find that feedback directs growth toward poorly coordinated regions, resulting in an excess number of cell-cell contacts that rigidify cell packings. Cell packings possess anomalously large shear and bulk moduli that depend sensitively on the strength of feedback. These results demonstrate that mechanical feedback on the single-cell level is a simple mechanism by which living systems may tune their population-level mechanical properties.

Asunto(s)

RESUMEN

Many cellular populations are tightly packed, such as microbial colonies and biofilms, or tissues and tumours in multicellular organisms. The movement of one cell in these crowded assemblages requires motion of others, so that cell displacements are correlated over many cell diameters. Whenever movement is important for survival or growth, these correlated rearrangements could couple the evolutionary fate of different lineages. However, little is known about the interplay between mechanical forces and evolution in dense cellular populations. Here, by tracking slower-growing clones at the expanding edge of yeast colonies, we show that the collective motion of cells prevents costly mutations from being weeded out rapidly. Joint pushing by neighbouring cells generates correlated movements that suppress the differential displacements required for selection to act. This mechanical screening of fitness differences allows slower-growing mutants to leave more descendants than expected under non-mechanical models, thereby increasing their chance for evolutionary rescue. Our work suggests that, in crowded populations, cells cooperate with surrounding neighbours through inevitable mechanical interactions. This effect has to be considered when predicting evolutionary outcomes, such as the emergence of drug resistance or cancer evolution.

Asunto(s)

RESUMEN

Evolutionary dynamics are controlled by a number of driving forces, such as natural selection, random genetic drift and dispersal. In this perspective article, we aim to emphasize that these forces act at the population level, and that it is a challenge to understand how they emerge from the stochastic and deterministic behaviour of individual cells. Even the most basic steric interactions between neighbouring cells can couple evolutionary outcomes of otherwise unrelated individuals, thereby weakening natural selection and enhancing random genetic drift. Using microbial examples of varying degrees of complexity, we demonstrate how strongly cell-cell interactions influence evolutionary dynamics, especially in pattern-forming systems. As pattern formation itself is subject to evolution, we propose to study the feedback between pattern formation and evolutionary dynamics, which could be key to predicting and potentially steering evolutionary processes. Such an effort requires extending the systems biology approach from the cellular to the population scale.This article is part of the theme issue 'Self-organization in cell biology'.

Asunto(s)

RESUMEN

We propose a "phase diagram" for particulate systems with purely repulsive contact forces, such as granular media and colloids. We characterize two classes of behavior as a function of the input kinetic energy per degree of freedom T_{0} and packing fraction deviation from jamming onset Δϕ=ϕ-ϕ_{J} using simulations of frictionless disks. Isocoordinated solids (ICS) exist above jamming; they possess an average contact number equal to the isostatic value z_{iso}. ICS display "strict" harmonic response, where the density of vibrational modes from the Fourier transform of the velocity autocorrelation function is a set of sharp peaks at eigenfrequencies ω_{k}{d} of the dynamical matrix. In contrast, hypocoordinated solids (HCS) occur above and below jamming and possess fluctuating networks of interparticle contacts but do not undergo cage-breaking particle rearrangements. The density of vibrational frequencies for the HCS is not a collection of sharp peaks at ω_{k}{d}, but it does possess a common form over a range of Δϕ and T_{0}.

Asunto(s)

RESUMEN

We perform numerical simulations of repulsive, frictionless athermal disks in two and three spatial dimensions undergoing cyclic quasistatic simple shear to investigate particle-scale reversible motion. We identify three classes of steady-state dynamics as a function of packing fraction φ and maximum strain amplitude per cycle γ(max). Point-reversible states, where particles do not collide and exactly retrace their intracycle trajectories, occur at low φ and γ(max). Particles in loop-reversible states undergo numerous collisions and execute complex trajectories but return to their initial positions at the end of each cycle. For sufficiently large φ and γ(max), systems display irreversible dynamics with nonzero self-diffusion. Loop-reversible dynamics enables the reliable preparation of configurations with specified structural and mechanical properties over a broad range of φ.

RESUMEN

Recently, a new class of materials emerged with the assembly of DNA-coated phospholipid nanodiscs into columnar BioNanoStacks. Within these stacks, lipid discs are periodically incorporated, resulting into quasi-one-dimensional superstructures. With each disc surrounded by two recombinant scaffolding proteins, we decided to examine whether the polyhistidine tags of these proteins could be utilized to bind additional molecules or particles to these BioNanoStacks. Here we demonstrate that patterning of gold nanoparticles onto these BioNanoStacks is indeed possible. Binding occurs via a nickel-mediated interaction between the nanogolds nitrilotriacetic acid and the histidine tags of the scaffold proteins surrounding the nanodiscs. Using Monte Carlo simulations, we determine that the binding of the nanogold particles to the stacks is not a random event. By comparing the simulation and experimental results, we find that there are preferred binding sites, which affects the binding statistics.

Asunto(s)

RESUMEN

Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP α-synuclein that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent single-molecule fluorescence energy transfer (smFRET) experiments. We find that α-synuclein is disordered, with conformational statistics that are intermediate between random walk and collapsed globule behavior. An advantage of calibrated molecular simulations over constraint methods is that physical forces act on all residues, not only on residue pairs that are monitored experimentally, and these simulations can be used to study oligomerization and aggregation of multiple α-synuclein proteins that may precede amyloid formation.

Asunto(s)

RESUMEN

We numerically investigate the mechanical properties of static packings of frictionless ellipsoidal particles in two and three dimensions over a range of aspect ratio and compression Δφ. While amorphous packings of spherical particles at jamming onset (Δφ=0) are isostatic and possess the minimum contact number z_{iso} required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming (z

Asunto(s)

RESUMEN

Many jammed particulate systems, such as granular and colloidal materials, interact via repulsive contact forces. We find that these systems possess no harmonic regime in the large system limit (N→∞) for all compressions Δϕ studied, and at jamming onset Δϕ→0 for all N. We perform fixed energy simulations following perturbations with amplitude δ along eigendirections of the dynamical matrix. The fluctuations abruptly spread to all modes for δ≈δ(c) (where a single contact breaks) in contrast to linear and weakly nonlinear behavior. For δ > δ(c), all discrete modes disappear into a continuous frequency band. <δ(c)> scales with 1/N and Δϕ, which limits harmonic behavior to only overcompressed systems. The density of vibrational modes deviates strongly from that predicted from the dynamical matrix when the system enters the nonharmonic regime, which significantly affects its mechanical and transport properties.

Asunto(s)

RESUMEN

We perform extensive computational studies of two-dimensional static bidisperse disk packings using two distinct packing-generation protocols. The first involves thermally quenching equilibrated liquid configurations to zero temperature over a range of thermal quench rates r and initial packing fractions followed by compression and decompression in small steps to reach packing fractions φ(J) at jamming onset. For the second, we seed the system with initial configurations that promote micro- and macrophase-separated packings followed by compression and decompression to φ(J). Using these protocols, we generate more than 10(4) static packings over a wide range of packing fraction, contact number, and compositional and positional order. We find that disordered, isostatic packings exist over a finite range of packing fractions in the large-system limit. In agreement with previous calculations, the most dilute mechanically stable packings with φ min ≈ 0.84 are obtained for r > r*, where r* is the rate above which φ(J) is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, several order parameters, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered (with only small changes in a number of order parameters), whereas bond-orientational and compositional order increase strongly with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies (in the harmonic approximation) of the static packings to understand the extent to which the mechanical properties of disordered, isostatic packings differ from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic.

Asunto(s)

RESUMEN

We describe the self-assembly of nonspherical particles into crystals with novel structure and optical properties combining a partial photonic band gap with birefringence that can be modulated by an external field or quenched by solvent evaporation. Specifically, we study symmetric optical-scale polymer dumbbells with an aspect ratio of 1.58. Hard particles with this geometry have been predicted to crystallize in equilibrium at high concentrations. However, unlike spherical particles, which readily crystallize in the bulk, previous experiments have shown that these dumbbells crystallize only under strong confinement. Here, we demonstrate the use of an external electric field to align and assemble the dumbbells to make a birefringent suspension with structural color. When the electric field is turned off, the dumbbells rapidly lose their orientational order and the color and birefringence quickly go away. In this way, dumbbells combine the structural color of photonic crystals with the field addressability of liquid crystals. In addition, we find that if the solvent is removed in the presence of an electric field, the particles self-assemble into a novel, dense crystalline packing hundreds of particles thick. Analysis of the crystal structure indicates that the dumbbells have a packing fraction of 0.7862, higher than the densest known packings of spheres and ellipsoids. We perform numerical experiments to more generally demonstrate the importance of controlling the orientation of anisotropic particles during a concentration quench to achieve long-range order.

Asunto(s)

Asunto(s)

RESUMEN

We study numerically frictionless ellipse packings versus the aspect ratio alpha, and find that the jamming transition is fundamentally different from that for spherical particles. The normal mode spectra possess two gaps and three distinct branches over a range of alpha. The energy from deformations along modes in the lowest-energy branch increases quartically, not quadratically. The quartic modes cause novel power-law scaling of the static shear modulus and their number matches the deviation from isostaticity. These results point to a new critical point at alpha>1 that controls jamming of aspherical particles.