Changes in Spo0A~P pulsing frequency control biofilm matrix deactivation.

Under starvation conditions, B. subtilis survives by differentiating into one of two cell types: biofilm matrix-producing cells or sporulating cells. These two cell-differentiation pathways are activated by the same phosphorylated transcription factor - Spo0A~P.

Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters.

Bacterial gene networks have operons, each coordinating several genes under a primary promoter. Half of the operons in have been reported to also contain internal promoters. We studied their role during genome-wide stresses targeting key transcription regulators, RNA polymerase (RNAP) and gyrase.

Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starving .

Unlabelled: In starving bacteria the initiation of two survival programs-biofilm formation and sporulation-is controlled by the same phosphorylated master regulator, Spo0A~P. Its gene, is transcribed from two promoters, P and P that are, respectively, regulated by RNA polymerase (RNAP) holoenzymes bearing σ and σ. Notably, transcription is directly autoregulated by Spo0AP binding sites known as 0A1, 0A2, and 0A3 box, located in between the two promoters.

Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli.

Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms.

Sequence-dependent model of genes with dual σ factor preference.

Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ, which controls housekeeping genes, and σ, which activates genes during stationary growth and stresses.

Analytical kinetic model of native tandem promoters in E. coli.

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli.

Surface Modification of Bioresorbable Phosphate Glasses for Controlled Protein Adsorption.

The traditional silicate bioactive glasses exhibit poor thermal processability, which inhibits fiber drawing or sintering into scaffolds. The composition of the silicate glasses has been modified to enable hot processing. However, the hot forming ability is generally at the expense of bioactivity.

Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup.

Positive supercoiling buildup (PSB) is a pervasive phenomenon in the transcriptional programs of Escherichia coli. After finding a range of Gyrase concentrations where the inverse of the transcription rate of a chromosome-integrated gene changes linearly with the inverse of Gyrase concentration, we apply a LineWeaver-Burk plot to dissect the expected in vivo transcription rate in absence of PSB. We validate the estimation by time-lapse microscopy of single-RNA production kinetics of the same gene when single-copy plasmid-borne, shown to be impervious to Gyrase inhibition.

Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry.

Estimating the statistics of single-cell RNA numbers has become a key source of information on gene expression dynamics. One of the most informative methods of in vivo single-RNA detection is MS2d-GFP tagging. So far, it requires microscopy and laborious semi-manual image analysis, which hampers the amount of collectable data.

Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli.

From in vivo single-cell, single-RNA measurements of the activation times and subsequent steady-state active transcription kinetics of a single-copy Lac-ara-1 promoter in Escherichia coli, we characterize the intake kinetics of the inducer (IPTG) from the media, following temperature shifts. For this, for temperature shifts of various degrees, we obtain the distributions of transcription activation times as well as the distributions of intervals between consecutive RNA productions following activation in individual cells. We then propose a novel methodology that makes use of deconvolution techniques to extract the mean and the variability of the distribution of intake times.