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Full-Text Articles in Physics
Reconciling Molecular Regulatory Mechanisms With Noise Patterns Of Bacterial Metabolic Promoters In Induced And Repressed States, Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Ovidiu Radulescu, Nathalie Declerck, Catherine A. Royer
Reconciling Molecular Regulatory Mechanisms With Noise Patterns Of Bacterial Metabolic Promoters In Induced And Repressed States, Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Ovidiu Radulescu, Nathalie Declerck, Catherine A. Royer
Matthew L. Ferguson
Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell level and with single-molecule sensitivity, the absolute concentration of fluorescent proteins produced from the two Bacillus subtilis promoters that control the switch between glycolysis and gluconeogenesis. We quantified cell-to-cell variations in GFP concentrations in reporter strains grown on glucose or malate, including very weakly transcribed genes under strong catabolite repression. Results revealed strong transcriptional bursting, particularly for …
Absolute Quantification Of Gene Expression In Individual Bacterial Cells Using Two-Photon Fluctuation Microscopy, Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Nathalie Declerck, Catherine A. Royer
Absolute Quantification Of Gene Expression In Individual Bacterial Cells Using Two-Photon Fluctuation Microscopy, Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Nathalie Declerck, Catherine A. Royer
Matthew L. Ferguson
Quantification of promoter activity or protein expression in gene regulatory networks is generally achieved via measurement of fluorescent protein (FP) intensity, which is related to the true FP concentration by an unknown scaling factor, thereby limiting analysis and interpretation. Here, using approaches originally developed for eukaryotic cells, we show that two-photon (2p) fluorescence fluctuation microscopy, specifically scanning number and brightness (sN&B) analysis, can be applied to determine the absolute concentrations of diffusing FPs in live bacterial cells. First, we demonstrate the validity of the approach, despite the small size of the bacteria, using the central pixels and spatial averaging. We …
Physical Basis Of The Inducer-Dependent Cooperativity Of The Central Glycolytic Genes Repressor/Dna Complex, Denis Chaix, Matthew L. Ferguson, Cedric Atmanene, Alain Van Dorsselaer, Sarah Sanglier-Cianférani, Catherine A. Royer, Nathalie Declerck
Physical Basis Of The Inducer-Dependent Cooperativity Of The Central Glycolytic Genes Repressor/Dna Complex, Denis Chaix, Matthew L. Ferguson, Cedric Atmanene, Alain Van Dorsselaer, Sarah Sanglier-Cianférani, Catherine A. Royer, Nathalie Declerck
Matthew L. Ferguson
The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphosphate (FBP), reduces the binding cooperativity of the CggR/DNA complex. Here, we have determined the effect of FBP on the size, shape and stoichiometry of CggR complexes with full-length and half-site operator sequence by small-angle X-ray scattering, size-exclusion chromatography, fluorescence cross-correlation spectroscopy and noncovalent mass spectrometry (MS). Our results show that CggR forms a compact …
Clathrin Triskelia Show Evidence Of Molecular Flexibility, Matthew L. Ferguson, Kondury Prasad, Hacene Boukari, Dan L. Sackett, Susan Krueger, Eileen M. Lafer, Ralph Nossal
Clathrin Triskelia Show Evidence Of Molecular Flexibility, Matthew L. Ferguson, Kondury Prasad, Hacene Boukari, Dan L. Sackett, Susan Krueger, Eileen M. Lafer, Ralph Nossal
Matthew L. Ferguson
The clathrin triskelion, which is a three-legged pinwheel-shaped heteropolymer, is a major component in the protein coats of certain post-Golgi and endocytic vesicles. At low pH, or at physiological pH in the presence of assembly proteins, triskelia will self-assemble to form a closed clathrin cage, or “basket”. Recent static light scattering and dynamic light scattering studies of triskelia in solution showed that an individual triskelion has an intrinsic pucker similar to, but differing from, that inferred from a high resolution cryoEM structure of a triskelion in a clathrin basket. We extend the earlier solution studies by performing small-angle neutron scattering …
Dynamics Of A Gravitational Billiard With A Hyperbolic Lower Boundary, Matthew L. Ferguson, B. N. Miller, M. A. Thompson
Dynamics Of A Gravitational Billiard With A Hyperbolic Lower Boundary, Matthew L. Ferguson, B. N. Miller, M. A. Thompson
Matthew L. Ferguson
Gravitational billiards provide a simple method for the illustration of the dynamics of Hamiltonian systems. Here we examine a new billiard system with two parameters, which exhibits, in two limiting cases, the behaviors of two previously studied one-parameter systems, namely the wedge and parabolic billiard. The billiard consists of a point mass moving in two dimensions under the influence of a constant gravitational field with a hyperbolic lower boundary. An iterative mapping between successive collisions with the lower boundary is derived analytically. The behavior of the system during transformation from the wedge to the parabola is investigated for a few …