Meenakshisundaram Kandhavelu

In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps

BackgroundIn Escherichia coli the mean and cell-to-cell diversity in RNA numbers of different genes vary widely. This is likely due to different kinetics of transcription initiation, a complex process with multiple rate-limiting steps that affect RNA production.ResultsWe measured the in vivo kinetics of production of individual RNA molecules under the control of the lar promoter in E. coli. From the analysis of the distributions of intervals between transcription events in the regimes of weak and medium induction, we find that the process of transcription initiation of this promoter involves a sequential mechanism with two main rate-limiting steps, each lasting hundreds of seconds. Both steps become faster with increasing induction by IPTG and Arabinose.ConclusionsThe two rate-limiting steps in initiation are found to be important regulators of the dynamics of RNA production under the control of the lar promoter in the regimes of weak and medium induction. Variability in the intervals between consecutive RNA productions is much lower than if there was only one rate-limiting step with a duration following an exponential distribution. The methodology proposed here to analyze the in vivo dynamics of transcription may be applicable at a genome-wide scale and provide valuable insight into the dynamics of prokaryotic genetic networks.

Single-molecule dynamics of transcription of the lar promoter

We measured the in vivo production of RNA molecules tagged with MS2d-GFP in Escherichia coli, driven by the lar promoter, under weak and medium induction. The distributions of intervals between consecutive productions of RNAs are found to be sub-exponential, and the process of RNA production is found to be sub-Poissonian. We discuss possible models of transcription initiation and, based on our results and previous in vitro measurements, find that a sequential two-step model of transcription initiation at the promoter region explains the results well.

In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter

Using a single-RNA detection technique in live Escherichia coli cells, we measure, for each cell, the waiting time for the production of the first RNA under the control of PBAD promoter after induction by arabinose, and subsequent intervals between transcription events. We find that the kinetics of the arabinose intake system affect mean and diversity in RNA numbers, long after induction. We observed the same effect on Plac/ara-1 promoter, which is inducible by arabinose or by IPTG. Importantly, the distribution of waiting times of Plac/ara-1 is indistinguishable from that of PBAD, if and only if induced by arabinose alone. Finally, RNA production under the control of PBAD is found to be a sub-Poissonian process. We conclude that inducer-dependent waiting times affect mean and cell-to-cell diversity in RNA numbers long after induction, suggesting that intake mechanisms have non-negligible effects on the phenotypic diversity of cell populations in natural, fluctuating environments.

Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time

Escherichia coli cells employ an asymmetric strategy at division, segregating unwanted substances to older poles, which has been associated with aging in these organisms. The kinetics of this process is still poorly understood. Using the MS2 coat protein fused to green fluorescent protein (GFP) and a reporter construct with multiple MS2 binding sites, we tracked individual RNA-MS2-GFP complexes in E. coli cells from the time when they were produced. Analyses of the kinetics and brightness of the spots showed that these spots appear in the midcell region, are composed of a single RNA-MS2-GFP complex, and reach a pole before another target RNA is formed, typically remaining there thereafter. The choice of pole is probabilistic and heavily biased toward one pole, similar to what was observed by previous studies regarding protein aggregates. Additionally, this mechanism was found to act independently on each disposed molecule. Finally, while the RNA-MS2-GFP complexes were disposed of, the MS2-GFP tagging molecules alone were not. We conclude that this asymmetric mechanism to segregate damage at the expense of aging individuals acts probabilistically on individual molecules and is capable of the accurate classification of molecules for disposal.

Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter

The kinetics of transcription initiation in Escherichia coli depend on the duration of two rate‐limiting steps, the closed and the open complex formation. In a lac promoter variant, P lac/ara‐1 , the kinetics of these steps is controlled by IPTG and arabinose. From in vivo single‐RNA measurements, we find that induction affects the mean and normalized variance of the intervals between consecutive RNA productions. Transcript production is sub‐Poissonian in all conditions tested. The kinetics of each step is independently controlled by a different inducer. We conclude that the regulatory mechanism of P lac/ara‐1 allows the stochasticity of gene expression to be environment‐dependent.

Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)

BackgroundCell imaging is becoming an indispensable tool for cell and molecular biology research. However, most processes studied are stochastic in nature, and require the observation of many cells and events. Ideally, extraction of information from these images ought to rely on automatic methods. Here, we propose a novel segmentation method, MAMLE, for detecting cells within dense clusters.MethodsMAMLE executes cell segmentation in two stages. The first relies on state of the art filtering technique, edge detection in multi-resolution with morphological operator and threshold decomposition for adaptive thresholding. From this result, a correction procedure is applied that exploits maximum likelihood estimate as an objective function. Also, it acquires morphological features from the initial segmentation for constructing the likelihood parameter, after which the final segmentation is obtained.ConclusionsWe performed an empirical evaluation that includes sample images from different imaging modalities and diverse cell types. The new method attained very high (above 90%) cell segmentation accuracy in all cases. Finally, its accuracy was compared to several existing methods, and in all tests, MAMLE outperformed them in segmentation accuracy.

Comparison and optimization of transient transfection methods at human astrocytoma cell line 1321N1

Gene delivery to eukaryotic cells is the technique to study the regulation of gene expression. Human astrocytoma cell line 1321N1 could be useful to study G-protein-coupled receptors (GPCRs). Different transient transfection methods, namely calcium phosphate, Lipofectamine, FuGENE, Arrest-In, and microporation (Microporator), were investigated. Results were analyzed by fluorescence-activated cell sorting and fluorescence microscope using green fluorescent protein (GFP) as a reporter gene. To verify the transfection efficiency of these techniques, the expression of human GPR17 gene (hgpr17) was analyzed by transcription quantitative polymerase chain reaction. Microporation resulted in the best method to promote enriched hgpr17 delivery into the human astrocytoma cell line.

An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy.

Gene expression and other cellular processes are stochastic, thus their study requires observing multiple events in multiple cells. Therefore, confocal microscopy cell imaging has recently gained much interest. In time‐lapse imaging, adjustments are needed at short intervals to compensate for focus drift. There are several automated methods for this purpose. In general, before acquiring higher resolution images, software‐based autofocus algorithms require a set of low‐resolution images along the z‐axis to determine the plane for which a predefined focusing function is maximized. These algorithms require 10–100 z‐slices each time, and there is no fixed number or upper limit of required z‐slices that ensures optimal focusing. The higher is this number, the stronger is photo bleaching, hampering the feasibility of long‐time series measurements.

Synthesis of Phenol-derivatives and Biological Screening for Anticancer Activity

BACKGROUND Phenolic compounds are known for their cytotoxic properties against cancer cells despite their still unclear general mechanism of action. Herein is reported the evaluation of the cytotoxic effects of on human osteosarcoma cells of nine phenol derivatives against osteosarcoma cells, and some insights on their mechanism. METHOD AND RESULTS The cytotoxicity was characterized by cell viability, scratch assay, cellular DNA content measurement, Annexin V apoptosis, mitochondrial calcium and caspase 3/7 assays. The study shows that out of the nine compounds used in this study, a tetrahydroquinoline derivative, 2-((1,2,3,4-tetrahydroquinolin-1-yl)(4- methoxyphenyl)methyl) phenol, was found to exhibit strong inhibitory response with IC50 of 50.5 ± 3.8 µM, and therefore can be a potential chemotherapeutic agent. Further experiments revealed that this compound induces cell death by apoptosis and also act as a migration inhibitor. Analysis of the mitochondrial calcium following treatment with the compound on U2OS cells showed a significant reduction in the level of mitochondrial calcium concentration suggesting a mitochondrial calcium-independent mechanism in triggering apoptosis. Treatment of HEK293 cells with the compound confirmed the cytotoxic effects of the compound, however, an increase in the level of mitochondrial calcium was observed. Moreover, the caspase 3/7 mediated cell death was also observed in both cell types. CONCLUSION Overall, the study suggests that the derivatives of this compound can be used for development of new therapeutics for osteosarcoma and other cancers.

Origins of Transcriptional Transition: Balance between Upstream and Downstream Regulatory Gene Sequences

ABSTRACT By measuring individual mRNA production at the single-cell level, we investigated the lac promoter’s transcriptional transition during cell growth phases. In exponential phase, variation in transition rates generates two mixed phenotypes, low and high numbers of mRNAs, by modulating their burst frequency and sizes. Independent activation of the regulatory-gene sequence does not produce bimodal populations at the mRNA level, but bimodal populations are produced when the regulatory gene is activated coordinately with the upstream and downstream region promoter sequence (URS and DRS, respectively). Time-lapse microscopy of mRNAs for lac and a variant lac promoter confirm this observation. Activation of the URS/DRS elements of the promoter reveals a counterplay behavior during cell phases. The promoter transition rate coupled with cell phases determines the mRNA and transcriptional noise. We further show that bias in partitioning of RNA does not lead to phenotypic switching. Our results demonstrate that the balance between the URS and the DRS in transcriptional regulation determines population diversity. IMPORTANCE By measuring individual mRNA production at the single-cell level, we investigated the lac promoter transcriptional transition during cell growth phases. In exponential phase, variation in transition rate generates two mixed phenotypes producing low and high numbers of mRNAs by modulating the burst frequency and size. Independent activation of the regulatory gene sequence does not produce bimodal populations at the mRNA level, while it does when activated together through the coordination of upstream/downstream promoter sequences (URS/DRS). Time-lapse microscopy of mRNAs for lac and a lac variant promoter confirm this observation. Activation of the URS/DRS elements of the promoter reveals a counterplay behavior during cell phases. The promoter transition rate coupled with cell phases determines the mRNA and transcriptional noise. We further show that bias in partitioning of RNA does not lead to phenotypic switching. Our results demonstrate that the balance between URS and DRS in transcription regulation is determining the population diversity. By measuring individual mRNA production at the single-cell level, we investigated the lac promoter transcriptional transition during cell growth phases. In exponential phase, variation in transition rate generates two mixed phenotypes producing low and high numbers of mRNAs by modulating the burst frequency and size. Independent activation of the regulatory gene sequence does not produce bimodal populations at the mRNA level, while it does when activated together through the coordination of upstream/downstream promoter sequences (URS/DRS). Time-lapse microscopy of mRNAs for lac and a lac variant promoter confirm this observation. Activation of the URS/DRS elements of the promoter reveals a counterplay behavior during cell phases. The promoter transition rate coupled with cell phases determines the mRNA and transcriptional noise. We further show that bias in partitioning of RNA does not lead to phenotypic switching. Our results demonstrate that the balance between URS and DRS in transcription regulation is determining the population diversity.