Related papers: Heterogeneous diversity of spacers within CRISPR
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
A definition of structural diversity, adapted from the biodiversity literature, is introduced to provide a general characterization of structures of condensed matter. Using the Favored Local Structure (FLS) lattice model as a testbed, the…
Protein tagging with CRISPR-Cas9 enables the investigation of protein function in its native environment but is limited by low homology-directed repair (HDR) efficiency causing low knock-in rates. We present a detailed pipeline using HDR…
Entropic repulsion between DNA ring polymers under confinement is the key mechanism governing the spatial segregation of bacterial chromosomes, although it remains incompletely understood how proteins aid the process of entropic…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key…
The article seeks to formulate a synergetic law that is posited to be of common physicochemical and biological nature: an evolving system, possessing free energy and elements with chiral asymmetry may change the type of symmetry inside one…
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and…
The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e.…
Although modeling studies are focused on the control of SIR-based systems describing epidemic data sets (particularly the COVID-19), few of them present a formal dynamic characterization in terms of equilibrium sets and stability. Such…
The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are sensitive to antibiotics. These bacteria are in a state called persistence and each bacterium can…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…
Biomimetic design principles, inspired by the structure of alligator osteoderms, are employed to provide innovative solutions for enhancing membrane distillation system performance. A novel spacer design for membrane distillation (MD)…
We investigate a stochastic individual-based model for the population dynamics of host-virus systems where the microbial hosts may transition into a dormant state upon contact with virions, thus evading infection. Such a contact-mediated…
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is…