ABSTRACT
Cell sorting is a widespread phenomenon pivotal to the early development of multicellular organisms. In vitro cell sorting studies have been instrumental in revealing the cellular properties driving this process. However, these studies have as yet been limited to two-dimensional analysis of three-dimensional cell sorting events. Here we describe a method to record the sorting of primary zebrafish ectoderm and mesoderm germ layer progenitor cells in three dimensions over time, and quantitatively analyze their sorting behavior using an order parameter related to heterotypic interface length. We investigate the cell population size dependence of sorted aggregates and find that the germ layer progenitor cells engulfed in the final configuration display a relationship between total interfacial length and system size according to a simple geometrical argument, subject to a finite-size effect.
Subject(s)
Cell Separation/methods , Animals , Cell Aggregation , Ectoderm/cytology , Mesoderm/cytology , Stem Cells/cytology , Zebrafish/embryologyABSTRACT
The initial stages of transcription by RNA polymerase are frequently marked by pausing and stalling events. These events have been linked to an inactive backtracked state in which the polymerase diffuses along the template DNA. We investigate theoretically the influence of RNA secondary structure in confining this diffusion. The effective confinement length peaks at transcript lengths commensurate with early stalling. This finite-size effect accounts for slow progress at the beginning of transcription, which we illustrate via stochastic hopping models for backtracking polymerases.
Subject(s)
DNA-Directed RNA Polymerases/chemistry , DNA-Directed RNA Polymerases/genetics , Models, Chemical , Models, Genetic , RNA/chemistry , RNA/genetics , Transcription, Genetic/genetics , Binding Sites , DNA-Directed RNA Polymerases/ultrastructure , Enzyme Activation , Models, Molecular , Nucleic Acid Conformation , Protein Binding , Protein Structure, Secondary , RNA/ultrastructure , Structure-Activity RelationshipABSTRACT
We investigate the behaviour of randomly cross-linked (co)polymer blends using a combination of replica theory and large-scale molecular dynamics simulations. In particular, we derive the analogue of the random phase approximation for systems with quenched disorder and show how the required correlation functions can be calculated efficiently. By post-processing simulation data for homopolymer networks we are able to describe neutron scattering measurements in heterogeneous systems without resorting to microscopic detail and otherwise unphysical assumptions. We obtain structure function data which illustrate the expected microphase separation and contain system-specific information relating to the intrinsic length scales of our networks.
