Single-step method for β-galactosidase assays in Escherichia coli using a 96-well microplate reader

AbstractHistorically, the lacZ gene is one of the most universally used reporters of gene expression in molecular biology. Its activity can be quantified using an artificial substrate, o-nitrophenyl-ß-d-galactopyranoside (ONPG). However, the traditional method for measuring LacZ activity (first described by J. H. Miller in 1972) can be challenging for a large number of samples, is prone to variability, and involves hazardous compounds for lysis (e.g., chloroform, toluene).Here we describe a single-step assay using a 96-well microplate reader with a proven alternative cell permeabilization method. This modified protocol reduces handling time by 90%

Characterization of Knots and Links Arising From Site-specific Recombination on Twist Knots

We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly prescribed. Finally, we give two simple examples to illustrate how this model can help determine previously uncharacterized experimental data.Comment: 32 pages, 7 tables, 27 figures, revised: figures re-arranged, and minor corrections. To appear in Journal of Physics

A data comparison between a traditional and the single-step β-galactosidase assay

This article describes reproducibility of a single-step automated β-galactosidase, and the equivalence of its data to the traditional assay ("Experiments in Molecular Genetics" [1]). This was done via a pairwise comparison of both methods using strains with Miller Unit [MU] values ranging from 0 to over 2000. The data presented in this article is associated with the research article entitled "A single-step method for mid to high throughput β-galactosidase assays in Escherichia coli using a microplate reader" [2]

Cellular and molecular phenotypes depending upon the RNA repair system RtcAB of Escherichia coli

Biotechnology and Biological Sciences Research Council (BBSRC) [BB/J00717X/1]; Medical Research Council (MRC) [MR/M017672/1]; Queen's Fellowship (Queen's University Belfast, UK) (to C.E.); Antimicrobial Resistance Cross Council Initiative. Funding for open access charge: BBSRC [BB/J00717X/1]; MRC [MR/M017672/1]

A Multi-signal Variant for the GPU-based Parallelization of Growing Self-Organizing Networks

Among the many possible approaches for the parallelization of self-organizing networks, and in particular of growing self-organizing networks, perhaps the most common one is producing an optimized, parallel implementation of the standard sequential algorithms reported in the literature. In this paper we explore an alternative approach, based on a new algorithm variant specifically designed to match the features of the large-scale, fine-grained parallelism of GPUs, in which multiple input signals are processed at once. Comparative tests have been performed, using both parallel and sequential implementations of the new algorithm variant, in particular for a growing self-organizing network that reconstructs surfaces from point clouds. The experimental results show that this approach allows harnessing in a more effective way the intrinsic parallelism that the self-organizing networks algorithms seem intuitively to suggest, obtaining better performances even with networks of smaller size.Comment: 17 page

The route to transcription initiation determines the mode of transcriptional bursting in E. coli

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (σ70 and σ54). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the σ70-controlled stress response is regulated via the burst size, while that of the σ54-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving σ54 differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems

Bremsstrahlung in Alpha-Decay

We present the first fully quantum mechanical calculation of photon radiation accompanying charged particle decay from a barrier resonance. The soft-photon limit agrees with the classical results, but differences appear at next-to-leading-order. Under the conditions of alpha-decay of heavy nuclei, the main contribution to the photon emission stems from Coulomb acceleration and may be computed analytically. We find only a small contribution from the tunneling wave function under the barrier.Comment: 12 pages, 2 Postscript figure

Information and Particle Physics

Information measures for relativistic quantum spinors are constructed to satisfy various postulated properties such as normalisation invariance and positivity. Those measures are then used to motivate generalised Lagrangians meant to probe shorter distance physics within the maximum uncertainty framework. The modified evolution equations that follow are necessarily nonlinear and simultaneously violate Lorentz invariance, supporting previous heuristic arguments linking quantum nonlinearity with Lorentz violation. The nonlinear equations also break discrete symmetries. We discuss the implications of our results for physics in the neutrino sector and cosmology

Baryon structure in a quark-confining non-local NJL model

We study the nucleon and diquarks in a non-local Nambu-Jona-Lasinio model. For certain parameters the model exhibits quark confinement, in the form of a propagator without real poles. After truncation of the two-body channels to the scalar and axial-vector diquarks, a relativistic Faddeev equation for nucleon bound states is solved in the covariant diquark-quark picture. The dependence of the nucleon mass on diquark masses is studied in detail. We find parameters that lead to a simultaneous reasonable description of pions and nucleons. Both the diquarks contribute attractively to the nucleon mass. Axial-vector diquark correlations are seen to be important, especially in the confining phase of the model. We study the possible implications of quark confinement for the description of the diquarks and the nucleon. In particular, we find that it leads to a more compact nucleon.Comment: 21 pages (RevTeX), 18 figures (eps

Immobilization of Polymer-Decorated Liquid Crystal Droplets on Chemically Tailored Surfaces

We demonstrate that the assembly of an amphiphilic polyamine on the interfaces of micrometer-sized droplets of a thermotropic liquid crystal (LC) dispersed in aqueous solutions can be used to facilitate the immobilization of LC droplets on chemically functionalized surfaces. Polymer 1 was designed to contain both hydrophobic (alkylfunctionalized) and hydrophilic (primary and tertiary amine-functionalized) side chain functionality. The assembly of this polymer at the interfaces of aqueous dispersions of LC droplets was achieved by the spontaneous adsorption of polymer from aqueous solution. Polymer adsorption triggered transitions in the orientational ordering of the LCs, as observed by polarized light and bright-field microscopy. We demonstrate that the presence of polymer 1 on the interfaces of these droplets can be exploited to immobilize LC droplets on planar solid surfaces through covalent bond formation (e.g., for surfaces coated with polymer multilayers containing reactive azlactone functionality) or through electrostatic interactions (e.g., for surfaces coated with multilayers containing hydrolyzed azlactone functionality). The characterization of immobilized LC droplets by polarized, fluorescence, and laser scanning confocal microscopy revealed the general spherical shape of the polymer-coated LC droplets to be maintained after immobilization, and that immobilization led to additional ordering transitions within the droplets that were dependent on the nature of the surfaces with which they were in contact. Polymer 1-functionalized LC droplets were not immobilized on polymer multilayers treated with poly(ethylene imine) (PEI). We demonstrate that the ability to design surfaces that promote or prevent the immobilization of polymer-functionalized LC droplets can be exploited to pattern the immobilization of LC droplets on surfaces. The results of this investigation provide the basis of an approach that could be used to tailor the properties of dispersed LC emulsions and to immobilize these droplets on functional surfaces of interest in a broad range of fundamental and applied contexts