Graded transcriptional response to different concentrations of a single transactivator

A mathematical model for cell cycle control: graded response or quantized response

Cell cycle is an important and complex biological system. A lot of efforts have been put in understanding cell cycle arrest for its vital role in clinical therapies. The cell-cycle-arrest outcomes upon stimulation are complicated. The response could be stringent or relaxed, and graded or quantized. A model fully addressing various cell-cycle-arrest outcomes is to be developed. Here, we developed a mathematical model of cell cycle control incorporating distinct characteristics of various cell-cycle-arrest outcomes. The model can simulate two typical properties of cell cycle arrest, quantized and graded. We also characterized the inheritable quiescence and refractory state, which were crucial in long-term response of the population. Then, we monitored cells respond to multiple stimulations, and the results indicated that cells responded to stimulations with small interval did not induce significantly sustained cell cycle arrest as the existence of refractory state. Our work will benefit fundamental research and make efforts to predicting outcomes of clinical therapeutics.

Fractional response analysis reveals logarithmic cytokine responses in cellular populations

Although we can now measure single-cell signaling responses with multivariate, high-throughput techniques our ability to interpret such measurements is still limited. Even interpretation of dose–response based on single-cell data is not straightforward: signaling responses can differ significantly between cells, encompass multiple signaling effectors, and have dynamic character. Here, we use probabilistic modeling and information-theory to introduce fractional response analysis (FRA), which quantifies changes in fractions of cells with given response levels. FRA can be universally performed for heterogeneous, multivariate, and dynamic measurements and, as we demonstrate, quantifies otherwise hidden patterns in single-cell data. In particular, we show that fractional responses to type I interferon in human peripheral blood mononuclear cells are very similar across different cell types, despite significant differences in mean or median responses and degrees of cell-to-cell heterogeneity. Further, we demonstrate that fractional responses to cytokines scale linearly with the log of the cytokine dose, which uncovers that heterogeneous cellular populations are sensitive to fold-changes in the dose, as opposed to additive changes.

Our ability to interpret single-cell multivariate signaling responses is still limited. Here the authors introduce fractional response analysis (FRA), involving fractional cell counting, capable of deconvoluting heterogeneous multivariate responses of cellular populations.

An Improved CRISPR Interference Tool to Engineer Rhodococcus opacus

Rhodococcus opacus is a nonmodel bacterium that is well suited for valorizing lignin. Despite recent advances in our systems-level understanding of its versatile metabolism, studies of its gene functions at a single gene level are still lagging. Elucidating gene functions in nonmodel organisms is challenging due to limited genetic engineering tools that are convenient to use. To address this issue, we developed a simple gene repression system based on CRISPR interference (CRISPRi). This gene repression system uses a T7 RNA polymerase system to express a small guide RNA, demonstrating improved repression compared to the previously demonstrated CRISPRi system (i.e., the maximum repression efficiency improved from 58% to 85%). Additionally, our cloning strategy allows for building multiple CRISPRi plasmids in parallel without any PCR step, facilitating the engineering of this GC-rich organism. Using the improved CRISPRi system, we confirmed the annotated roles of four metabolic pathway genes, which had been identified by our previous transcriptomic analysis to be related to the consumption of benzoate, vanillate, catechol, and acetate. Furthermore, we showed our tool's utility by demonstrating the inducible accumulation of muconate that is a precursor of adipic acid, an important monomer for nylon production. While the maximum muconate yield obtained using our tool was 30% of the yield obtained using gene knockout, our tool showed its inducibility and partial repressibility. Our CRISPRi tool will be useful to facilitate functional studies of this nonmodel organism and engineer this promising microbial chassis for lignin valorization.

Is the cell really a machine?

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

Modulated expression of the HIV-1 2LTR zinc finger efficiently interferes with the HIV integration process

Lentiviral vectors have emerged as the most efficient system to stably transfer and insert genes into cells. By adding a tetracycline (Tet)-inducible promoter, transgene expression delivered by a lentiviral vector can be expressed whenever needed and halted when necessary. Here we have constructed a doxycycline (Dox)-inducible lentiviral vector which efficiently introduces a designed zinc finger protein, 2-long terminal repeat zinc-finger protein (2LTRZFP), into hematopoietic cell lines and evaluated its expression in pluripotent stem cells. As a result this lentiviral inducible system can regulate 2LTRZFP expression in the SupT1 T-cell line and in pluripotent stem cells. Using this vector, no basal expression was detected in the T-cell line and its induction was achieved with low Dox concentrations. Remarkably, the intracellular regulatory expression of 2LTRZFP significantly inhibited HIV-1 integration and replication in HIV-inoculated SupT1 cells. This approach could provide a potential tool for gene therapy applications, which efficiently control and reduce the side effect of therapeutic genes expression.

Review of stochastic hybrid systems with applications in biological systems modeling and analysis

Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models. With the advancement of SHS theory, it is expected that insights can be obtained about biological processes such as drug effects on gene regulation. Furthermore, combining with advanced experimental methods, in silico simulations using SHS modeling techniques can be carried out for massive and rapid verification or falsification of biological hypotheses. The hope is to substitute costly and time-consuming in vitro or in vivo experiments or provide guidance for those experiments and generate better hypotheses.

Morphogene adsorption as a Turing instability regulator: Theoretical analysis and possible applications in multicellular embryonic systems

The Turing instability in the reaction-diffusion system is a widely recognized mechanism of the morphogen gradient self-organization during the embryonic development. One of the essential conditions for such self-organization is sharp difference in the diffusion rates of the reacting substances (morphogens). In classical models this condition is satisfied only for significantly different values of diffusion coefficients which cannot hold for morphogens of similar molecular size. One of the most realistic explanations of the difference in diffusion rate is the difference between adsorption of morphogens to the extracellular matrix (ECM). Basing on this assumption we develop a novel mathematical model and demonstrate its effectiveness in describing several well-known examples of biological patterning. Our model consisting of three reaction-diffusion equations has the Turing-type instability and includes two elements with equal diffusivity and immobile binding sites as the third reaction substance. The model is an extension of the classical Gierer-Meinhardt two-components model and can be reduced to it under certain conditions. Incorporation of ECM in the model system allows us to validate the model for available experimental parameters. According to our model introduction of binding sites gradient, which is frequently observed in embryonic tissues, allows one to generate more types of different spatial patterns than can be obtained with two-components models. Thus, besides providing an essential condition for the Turing instability for the system of morphogen with close values of the diffusion coefficients, the morphogen adsorption on ECM may be important as a factor that increases the variability of self-organizing structures.

Dynamics of epigenetic regulation at the single-cell level

Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory.

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment

Cell differentiation is the foundation for tissue development and regeneration, disease modeling, and cell-based therapies. Although the differentiation of cell populations has been extensively studied in many systems, much less is known about the distribution of decision making of single cells within these populations. To characterize the differentiation of single skeletal muscle cells, we used single-molecule mRNA fluorescence in situ hybridization (smFISH) to precisely quantify the expression levels of the master myogenic regulatory factors MyoD and myogenin in individual myoblasts. We identified distinct cell states characterized by the number of myogenin transcripts expressed by a cell, with myoblasts stochastically transitioning to a myogenin-high state during differentiation. We also used MyoD overexpression to force the transdifferentiation of C3H10T1/2 cells into an induced myoblast phenotype. These reprogrammed cells revealed the presence of a critical threshold of MyoD expression required to initiate myogenin expression. These results provide quantitative single-molecule data to support the model of switch-like cell decision making and lineage specification.

Topoisomerase II plays a role in dosage compensation in Drosophila

In Drosophila, dosage compensation is mediated by the MSL complex, which binds numerous sites on the X chromosome in males and enhances the transcriptional rate of a substantial number of X-linked genes. We have determined that topoisomerase II (Topo II) is enriched on dosage compensated genes, to which it is recruited by association with the MSL complex, in excess of the amount that is present on autosomal genes with similar transcription levels. Using a plasmid model, we show that Topo II is required for proper dosage compensation and that compensated chromatin is topologically different from non-compensated chromatin. This difference, which is not the result of the enhanced transcription level due of X-linked genes and which represents a structural modification intrinsic to the DNA of compensated chromatin, requires the function of Topo II. Our results suggest that Topo II is an integral part of the mechanistic basis of dosage compensation.

Transcriptional leakage versus noise: a simple mechanism of conversion between binary and graded response in autoregulated genes

We study the response of an autoregulated gene to a range of concentrations of signal molecules. We show that transcriptional leakage and noise due to translational bursting have the opposite effects. In a positively autoregulated gene, increasing the noise converts the response from graded to binary, while increasing the leakage converts the response from binary to graded. Our findings support the hypothesis that, being a common phenomenon, leaky expression may be a relatively easy way for evolutionary tuning of the type of gene response without changing the type of regulation from positive to negative.

Construction of a single lentiviral vector containing tetracycline-inducible Alb-uPA for transduction of uPA expression in murine hepatocytes

The SCID-beige/Alb-uPA mouse model is currently the best small animal model available for viral hepatitis infection studies [1]. But the construction procedure is often costly and time-consuming due to logistic and technical difficulties. Thus, the widespread application of these chimeric mice has been hampered [2]. In order to optimize the procedure, we constructed a single lentiviral vector containing modified tetracycline-regulated system to control Alb-uPA gene expression in the cultured hepatocytes. The modified albumin promoter controlled by tetracycline (Tet)-dependent transactivator rtTA2S-M2 was integrated into a lentiviral vector. The full-length uPA cDNA was inserted into another lentiviral vector containing PTight, a modified Tet-responsive promoter. Two vectors were then digested by specific enzymes and ligated by DNA ligase 4. The ligated DNA fragment was inserted into a modified pLKO.1 cloning vector and the final lentiviral vector was then successfully constructed. H2.35 cell, Lewis lung carcinoma, primary kidney, primary hepatic interstitial and CT26 cells were infected with recombinant lentivirus at selected MOI. The expression of uPA induced by DOX was detectable only in the infected H2.35 cells, which was confirmed by real-time PCR and Western blot analysis. Moreover, DOX induced uPA expression on the infected H2.35 cells in a dose-dependent manner. The constructed single lentiviral vector has many biological advantages, including that the interested gene expression under "Tet-on/off" system is controlled by DOX in a dose-depending fashion only in murine liver cells, which provides an advantage for simplifying generation of conditional transgenic animals.

Graded or threshold response of the tet-controlled gene expression: all depends on the concentration of the transactivator

BACKGROUND

Currently, the step-wise integration of tet-dependent transactivator and tet-responsive expression unit is considered to be the most promising tool to achieve stable tet-controlled gene expression in cell populations. However, disadvantages of this strategy for integration into primary cells led us to develop an "All-In-One" vector system, enabling simultaneous integration of both components. The effect on tet-controlled gene expression was analyzed for retroviral "All-In-One" vectors expressing the M2-transactivator either under control of a constitutive or a new type of autoregulated promoter.

RESULTS

Determination of luciferase activity in transduced cell populations indicated improvement of the dynamic range of gene expression for the autoregulated system. Further differences were observed regarding induction kinetics and dose-response. Most notably, introduction of the autoregulated system resulted in a threshold mode of induction, whereas the constitutive system exhibited pronounced effector-dose dependence.

CONCLUSION

Tet-regulated gene expression in the applied autoregulated system resembles a threshold mode, whereby full induction of the tet-unit can be achieved at otherwise limiting doxycycline concentrations.

Dynamical modeling of drug effect using hybrid systems

: Drug discovery today is a complex, expensive, and time-consuming process with high attrition rate. A more systematic approach is needed to combine innovative approaches in order to lead to more effective and efficient drug development. This article provides systematic mathematical analysis and dynamical modeling of drug effect under gene regulatory network contexts. A hybrid systems model, which merges together discrete and continuous dynamics into a single dynamical model, is proposed to study dynamics of the underlying regulatory network under drug perturbations. The major goal is to understand how the system changes when perturbed by drugs and give suggestions for better therapeutic interventions. A realistic periodic drug intake scenario is considered, drug pharmacokinetics and pharmacodynamics information being taken into account in the proposed hybrid systems model. Simulations are performed using MATLAB/SIMULINK to corroborate the analytical results.

Order-preserving principles underlying genotype-phenotype maps ensure high additive proportions of genetic variance

In quantitative genetics, the degree of resemblance between parents and offspring is described in terms of the additive variance (V(A)) relative to genetic (V(G)) and phenotypic (V(P)) variance. For populations with extreme allele frequencies, high V(A)/V(G) can be explained without considering properties of the genotype-phenotype (GP) map. We show that randomly generated GP maps in populations with intermediate allele frequencies generate far lower V(A)/V(G) values than empirically observed. The main reason is that order-breaking behaviour is ubiquitous in random GP maps. Rearrangement of genotypic values to introduce order-preservation for one or more loci causes a dramatic increase in V(A)/V(G). This suggests the existence of order-preserving design principles in the regulatory machinery underlying GP maps. We illustrate this feature by showing how the ubiquitously observed monotonicity of dose-response relationships gives much higher V(A)/V(G) values than a unimodal dose-response relationship in simple gene network models.

Conditioning-based modeling of contextual genomic regulation

A more complete understanding of the alterations in cellular regulatory and control mechanisms that occur in the various forms of cancer has been one of the central targets of the genomic and proteomic methods that allow surveys of the abundance and/or state of cellular macromolecules. This preference is driven both by the intractability of cancer to generic therapies, assumed to be due to the highly varied molecular etiologies observed in cancer, and by the opportunity to discern and dissect the regulatory and control interactions presented by the highly diverse assortment of perturbations of regulation and control that arise in cancer. Exploiting the opportunities for inference on the regulatory and control connections offered by these revealing system perturbations is fraught with the practical problems that arise from the way biological systems operate. Two classes of regulatory action in biological systems are particularly inimical to inference, convergent regulation, where a variety of regulatory actions result in a common set of control responses (crosstalk), and divergent regulation, where a single regulatory action produces entirely different sets of control responses, depending on cellular context (conditioning). We have constructed a coarse mathematical model of the propagation of regulatory influence in such distributed, context-sensitive regulatory networks that allows a quantitative estimation of the amount of crosstalk and conditioning associated with a candidate regulatory gene taken from a set of genes that have been profiled over a series of samples where the candidate's activity varies.

A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor

Many microorganisms, including bacteria of the class Streptomycetes, produce various secondary metabolites including antibiotics to gain a competitive advantage in their natural habitat. The production of these compounds is highly coordinated in a population to expedite accumulation to an effective concentration. Furthermore, as antibiotics are often toxic even to their producers, a coordinated production allows microbes to first arm themselves with a defense mechanism to resist their own antibiotics before production commences. One possible mechanism of coordination among individuals is through the production of signaling molecules. The gamma-butyrolactone system in Streptomyces coelicolor is a model of such a signaling system for secondary metabolite production. The accumulation of these signaling molecules triggers antibiotic production in the population. A pair of repressor-amplifier proteins encoded by scbA and scbR mediates the production and action of one particular gamma-butyrolactone, SCB1. Based on the proposed interactions of scbA and scbR, a mathematical model was constructed and used to explore the ability of this system to act as a robust genetic switch. Stability analysis shows that the butyrolactone system exhibits bistability and, in response to a threshold SCB1 concentration, can switch from an OFF state to an ON state corresponding to the activation of genes in the cryptic type I polyketide synthase gene cluster, which are responsible for production of the hypothetical polyketide. The switching time is inversely related to the inducer concentration above the threshold, such that short pulses of low inducer concentration cannot switch on the system, suggesting its possible role in noise filtering. In contrast, secondary metabolite production can be triggered rapidly in a population of cells producing the butyrolactone signal due to the presence of an amplification loop in the system. S. coelicolor was perturbed experimentally by varying concentrations of SCB1, and the model simulations match the experimental data well. Deciphering the complexity of this butyrolactone switch will provide valuable insights into how robust and efficient systems can be designed using "simple" two-protein networks.

Bimodal and hysteretic expression in mammalian cells from a synthetic gene circuit

In order to establish cells and organisms with predictable properties, synthetic biology makes use of controllable, synthetic genetic devices. These devices are used to replace or to interfere with natural pathways. Alternatively, they may be interlinked with endogenous pathways to create artificial networks of higher complexity. While these approaches have been already successful in prokaryotes and lower eukaryotes, the implementation of such synthetic cassettes in mammalian systems and even animals is still a major obstacle. This is mainly due to the lack of methods that reliably and efficiently transduce synthetic modules without compromising their regulation properties. To pave the way for implementation of synthetic regulation modules in mammalian systems we utilized lentiviral transduction of synthetic modules. A synthetic positive feedback loop, based on the Tetracycline regulation system was implemented in a lentiviral vector system and stably integrated in mammalian cells. This gene regulation circuit yields a bimodal expression response. Based on experimental data a mathematical model based on stochasticity was developed which matched and described the experimental findings. Modelling predicted a hysteretic expression response which was verified experimentally. Thereby supporting the idea that the system is driven by stochasticity. The results presented here highlight that the combination of three independent tools/methodologies facilitate the reliable installation of synthetic gene circuits with predictable expression characteristics in mammalian cells and organisms.

Fluorescence activated cell sorting of transiently transfected As4.1 cells shows renin enhancer directs on/off switching of renin promoter in vitro

1. The proximal promoter of the renin gene is weak and its activity is influenced by a strong, far-upstream enhancer. This and the ability of renin expression in renal afferent arteriolar cells to be 'recruited' under chronic stimulation is consistent with the on/off switching (variegation) model of gene expression. If true, this would provide an example in which variegation controls a physiologically regulable gene. 2. The present study tested the hypothesis that renin promoter activity may accord with the variegation model, at least in individual juxtaglomerular (mouse As4.1) cells in vitro. 3. As4.1 cells were transiently transfected with constructs containing the mouse renin (Ren-1c) enhancer adjacent to the Ren-1c promoter and a linked reporter gene encoding enhanced green fluorescent protein (EGFP). The EGFP signal from individual cells was monitored by fluorescence activated cell sorting. 4. In the presence of the renin enhancer there was 10-fold higher EGFP expression in transfected cells compared with cells transfected with EGFP constructs containing the promoter alone. There was, moreover, an 8-fold increase in the number of EGFP expressing cells. However, EGFP expression in individual transfected cells was similar in the presence or absence of the enhancer. 5. Results from the in vitro system used suggest that the Ren-1c enhancer does not regulate the rate of promoter activity, but rather increases the probability of achieving an active transcriptional state. Limitations of these findings are discussed.

Experimental validation for quantitative protein network models

Cellular responses are the consequence of complex reactions of protein networks. The complexity should ultimately be described by a set of formulas in a quantitative fashion, in which each formula defines the reactions in response to given types of input. However, testing these formulas has not been a simple task because of the lack of appropriate means for experimental validation. 'Reverse-phase' lysate microarrays have been proved to be powerful for such requirements and thus can be a good resource for providing an experimental reference point for the theoretical biology of protein networks.

Adeno-associated viral vector-mediated hypoxia-regulated VEGF gene transfer promotes angiogenesis following focal cerebral ischemia in mice

Uncontrolled expression of vascular endothelial growth factor (VEGF) in vivo may cause unexpected side effects, such as brain hemangioma or tumor growth. Because hypoxia-inducible factor-1 (HIF-1) is upregulated during cerebral ischemia and regulates gene expression by binding to a cis-acting hypoxia-responsive element (HRE), we therefore used a novel HRE, originating in the 3'-end of the erythropoietin (Epo) gene, to control gene expression in the ischemic brain. A concatemer of nine copies (H9) of the consensus sequence of HRE was used to mediate hypoxia induction. Three groups of adult CD-1 mice received AAVH9-VEGF, AAVH9-lacZ or saline injection, and then underwent 45 min of transient middle cerebral artery occlusion (tMCAO). Results show that HIF-1 was persistently expressed in the ischemic brain. VEGF was overexpressed in the ischemic perifocal region in AAVH9-VEGF-transduced mice. Double-labeled immunostaining showed that VEGF expressed in neurons and astrocytes but not endothelial cells, suggesting that adeno-associated virus (AAV) vectors transduced neurons and astrocytes predominantly. The total number of microvessels/enlarged microvessels was greatly increased in the AAVH9-VEGF-transduced mice (180+/-29/27+/-4) compared to the AAVH9-lacZ (118+/-19/14+/-3) or saline-treated (119+/-20/14+/-2) mice after tMCAO (P<0.05). Cell proliferation examination demonstrated that these microvessels were newly formed. Regional cerebral blood flow recovery in the AAVH9-VEGF-transduced mice was also better than in AAVH9-lacZ or saline-treated mice (P<0.05). Our data indicated that HRE is a novel trigger for the control of VEGF expression in the ischemic brain. VEGF overexpression through AAVH9-VEGF gene transfer showed stable focal angiogenic effects in post-ischemic repair process, providing an opportunity to rebuild injured brain tissue.

Quantitative assessment of the p53-Mdm2 feedback loop using protein lysate microarrays

Mathematical simulations of the p53-Mdm2 feedback loop suggest that both proteins will exhibit impulsive expression characteristics in response to high cellular stress levels. However, little quantitative experimental evaluation has been done, particularly of the phosphorylated forms. To evaluate the mathematical models experimentally, we used lysate microarrays from an isogenic pair of gamma-ray-irradiated cell lysates from HCT116 (p53(+/+) and p53(-/-)). Both p53 and Mdm2 proteins showed expected pulses in the wild type, whereas no pulses were seen in the knockout. Based on experimental observations, we determined model parameters and generated an in silico "knockout," reflecting the experimental data, including phosphorylated proteins.

Nonlinear regulation enhances the phenotypic expression of trans-acting genetic polymorphisms

BACKGROUND

Genetic variation explains a considerable part of observed phenotypic variation in gene expression networks. This variation has been shown to be located both locally (cis) and distally (trans) to the genes being measured. Here we explore to which degree the phenotypic manifestation of local and distant polymorphisms is a dynamic feature of regulatory design.

RESULTS

By combining mathematical models of gene expression networks with genetic maps and linkage analysis we find that very different network structures and regulatory motifs give similar cis/trans linkage patterns. However, when the shape of the cis-regulatory input functions is more nonlinear or threshold-like, we observe for all networks a dramatic increase in the phenotypic expression of distant compared to local polymorphisms under otherwise equal conditions.

CONCLUSION

Our findings indicate that genetic variation affecting the form of cis-regulatory input functions may reshape the genotype-phenotype map by changing the relative importance of cis and trans variation. Our approach combining nonlinear dynamic models with statistical genetics opens up for a systematic investigation of how functional genetic variation is translated into phenotypic variation under various systemic conditions.

Mammalian synthetic biology: Engineering of sophisticated gene networks

With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess "memory" so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.

Adeno-associated viral vector-delivered hypoxia-inducible gene expression in ischemic hearts

This chapter describes a system using adeno-associated viral (AAV) vector to deliver hypoxia-inducible gene expression to ischemic hearts. The hypoxia induction of gene expression in this system is based on the accumulation of hypoxia-inducible factor-1 (HIF-1) in ischemic hearts and the use of hypoxia-response element (HRE) identified from the enhancers of genes, the expression of which can be induced by hypoxia. The methods of plasmid and AAV vector construction for hypoxia-inducible gene expression, viral vector production and purification, and viral titer determination are described. This chapter also illustrates the methods that can be used to test hypoxia-inducible gene expression in vitro and in vivo, including hypoxia treatment of cultured cells, generation of murine ischemic heart models, and analysis of gene expression.

A bidirectional Tet-dependent promotor construct regulating the expression of E1A for tight control of oncolytic adenovirus replication

Tight regulation of oncolytic adenoviruses (oAdV) represents an important requirement for their safe application. Here we describe a new doxycycline (Dox)-dependent oAdV with a bidirectional expression cassette, which drives the expression of the reverse tetracycline-controlled transactivator (rtTA(s)-M2) from a lung tumor-specific promoter and, in the opposite direction, the expression of the adenoviral E1A gene from a second generation TetO(7) sequence linked to an isolated TATA box. In H441 lung cancer cells, this oAdV showed a strictly Dox-dependent E1A expression, adenoviral replication, cell killing activity and a 450-fold induction of progeny virus production. The virus could be shut off again by withdrawal of Dox and, in contrast to a control oAdV expressing E1A directly from the SP-B promoter, did not replicate in non-target cells. However, the absolute values of virus production and the cell killing activity in the presence of the inducer were still reduced as compared to the control oAdV. The results demonstrate, for the first time, Dox-dependent oAdV replication from a single adenoviral vector genome. Future improvement of the Dox-dependent E1A regulation cassette should lead to the generation of an oAdV well suited to meet the demands for a highly regulated and efficient oncolytic virus for in vivo applications.

Gene-modified tissue-engineered skin: the next generation of skin substitutes

Tissue engineering combines the principles of cell biology, engineering and materials science to develop three-dimensional tissues to replace or restore tissue function. Tissue engineered skin is one of most advanced tissue constructs, yet it lacks several important functions including those provided by hair follicles, sebaceous glands, sweat glands and dendritic cells. Although the complexity of skin may be difficult to recapitulate entirely, new or improved functions can be provided by genetic modification of the cells that make up the tissues. Gene therapy can also be used in wound healing to promote tissue regeneration or prevent healing abnormalities such as formation of scars and keloids. Finally, gene-enhanced skin substitutes have great potential as cell-based devices to deliver therapeutics locally or systemically. Although significant progress has been made in the development of gene transfer technologies, several challenges have to be met before clinical application of genetically modified skin tissue. Engineering challenges include methods for improved efficiency and targeted gene delivery; efficient gene transfer to the stem cells that constantly regenerate the dynamic epidermal tissue; and development of novel biomaterials for controlled gene delivery. In addition, advances in regulatable vectors to achieve spatially and temporally controlled gene expression by physiological or exogenous signals may facilitate pharmacological administration of therapeutics through genetically engineered skin. Gene modified skin substitutes are also employed as biological models to understand tissue development or disease progression in a realistic three-dimensional context. In summary, gene therapy has the potential to generate the next generation of skin substitutes with enhanced capacity for treatment of burns, chronic wounds and even systemic diseases.

Analysis of gene regulatory network models with graded and binary transcriptional responses

The steep sigmoid framework developed by Plahte and Kjøglum [Plahte, E., Kjøglum, S., 2005. Analysis and generic properties of gene regulatory networks with graded response functions. Phys. D 201, 150-176, doi:10.1016/j.physd.2004.11.014] provides a uniform description of gene regulatory networks in which there may be both graded and binary transcriptional responses, as well as a method for analysing the models developed. Here we extend this framework. We show that there is a relation between the location of steady states and the feedback structure of a system, thus generalising existing results for Boolean type models. In addition, we justify underlying assumptions and generic features of the modelling framework in terms of biology and generalise the overall approach to take into account that each transcription factor only regulates one gene at a given threshold. By this assumption, the analysis of the models are greatly simplified.

Current status of transcriptional regulation systems

Many attempts have been undertaken to control transgene activity in mammalian cells. This is of importance for both applied biotechnology and basic research activities. State of the art regulatory systems use elements for transgene regulation which are unrelated to host regulatory networks and thus do not interfere with endogenous activities. Most of these regulation systems consist of transregulators and transregulator responding promoter elements that are derived from non mammalian origin. Apart from the tetracycline (Tet) regulated system which is most widely used for conditional gene expression at the moment, a number of new systems were created. These systems have been significantly refined and their performance makes them suitable for regulating transgenes not only in cellular systems but also in transgenic animals and for human therapeutic use.

Epigenetic silencing and tissue independent expression of a novel tetracycline inducible system in double‐transgenic pigs

The applicability of tightly regulated transgenesis in domesticated animals is severely hampered by the present lack of knowledge of regulatory mechanisms and the long generation intervals. To capitalize on the tightly controlled expression of mammalian genes made possible by using prokaryotic control elements, we have used a single-step transduction to introduce an autoregulative tetracycline-responsive bicistronic expression cassette (NTA) into transgenic pigs. Transgenic pigs carrying one NTA cassette showed a mosaic transgene expression restricted to single muscle fibers. In contrast, crossbred animals carrying two NTA cassettes with different transgenes, revealed a broad tissue-independent and tightly regulated expression of one cassette, but not of the other one. The expression pattern correlated inversely with the methylation status of the NTA transcription start sites indicating epigenetic silencing of one NTA cassette. This first approach on tetracycline regulated transgene expression in farm animals will be valuable for developing precisely controlled expression systems for transgenes in large animals relevant for biomedical and agricultural biotechnology.

Binary gene induction and protein expression in individual cells

BACKGROUND

Eukaryotic gene transcription is believed to occur in either a binary or a graded fashion. With binary induction, a transcription activator (TA) regulates the probability with which a gene template is switched from the inactive to the active state without affecting the rate at which RNA molecules are produced from the template. With graded, also called rheostat-like, induction the gene template has continuously varying levels of transcriptional activity, and the TA regulates the rate of RNA production. Support for each of these two mechanisms arises primarily from experimental studies measuring reporter proteins in individual cells, rather than from direct measurement of induction events at the gene template.

METHODS AND RESULTS

In this paper, using a computational model of stochastic gene expression, we have studied the biological and experimental conditions under which a binary induction mode operating at the gene template can give rise to differentially expressed "phenotypes" (i.e., binary, hybrid or graded) at the protein level. We have also investigated whether the choice of reporter genes plays a significant role in determining the observed protein expression patterns in individual cells, given the diverse properties of commonly-used reporter genes. Our simulation confirmed early findings that the lifetimes of active/inactive promoters and half-lives of downstream mRNA/protein products are important determinants of various protein expression patterns, but showed that the induction time and the sensitivity with which the expressed genes are detected are also important experimental variables. Using parameter conditions representative of reporter genes including green fluorescence protein (GFP) and beta-galactosidase, we also demonstrated that graded gene expression is more likely to be observed with GFP, a longer-lived protein with low detection sensitivity.

CONCLUSION

The choice of reporter genes may determine whether protein expression is binary, graded or hybrid, even though gene induction itself operates in an all-or-none fashion.

Reproducible doxycycline-inducible transgene expression at specific loci generated by Cre-recombinase mediated cassette exchange

Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal loci, but recombination between the available recombinase targeting sites can reduce the efficiency of targeted integration. We developed a new LoxP site (designated L3), which when used with the original LoxP site (designated L2), allows highly efficient and directional replacement of chromosomal DNA with incoming DNA. A total of six independent LoxP integration sites introduced either by homologous recombination or retroviral delivery were analyzed; 70-80% of the clones analyzed in hamster and human cells were correct recombinants. We combined the RMCE strategy with a new, tightly regulated tetracycline induction system to produce a robust, highly reliable system for inducible transgene expression. We observed stable inducible expression for over 1 month, with uniform expression in the cell population and between clones derived from the same integration site. This system described should find significant applications for studies requiring high level and regulated transgene expression and for determining the effects of various stresses or oncogenic conditions in vivo and in vitro.

THY-1 induction is associated with up-regulation of fibronectin and thrombospondin-1 in human ovarian cancer

We recently identified THY-1 as a putative tumor suppressor gene for human ovarian cancer. To understand the carcinogenic role of THY-1, and its downstream effects on cancer cells, a THY-1 inducible system was established in the human ovarian cancer cell line SKOV-3 based on the tetracycline (tet) regulating system. To establish an inducible system for Thy-1 expression, two plasmids, pUHD172-1neo and pTEP4mThy-1, which are neomycin and hygromycin resistant were co-transfected into the ovarian carcinoma cell line, SKOV-3. The inducibility of Thy-1 expression in the SKOV-3 cell line by doxycycline (dox) was determined by northern blot analysis, immunocytochemistry, and flow cytometry. A time course study revealed that Thy-1 expression is induced 3 hours post dox exposure. Expression was reversible such that 12 hours post the removal of dox almost no Thy-1 could be detected. Furthermore, 2 genes, Fibronectin (FN) and Thrombospondin (TSP-1) involved in cellular differentiation and the regulation of tumor angiogenesis, respectively, were found to be up-regulated upon THY-1 induction. In contrast, the gene SPARC was found to be independent of Thy-1 expression. This study supports the hypothesis that THY-1 plays a critical role in regulating downstream genes associated with the regulation of ovarian tumor growth and cellular differentiation.

Stochastic cell

Accumulating experimental evidence of stochasticity, self-organization and abrupt non-linear transitions underlying the dynamics of cellular structure and function is increasingly more consistent with the concepts and models of phase transitions, critical phenomena and non-linear thermodynamics rather than with the conventional clockwork description of the cell. The novel emerging image of the stochastic cell suggests that familiar and convenient classico-mechanical interpretations may be limiting our ability to understand the behavior of biological systems and calls for active exploration of alternative interpretational frameworks.

Strategies of Conditional Gene Expression in Myocardium

The use of specialized reporter genes to monitor real-time, tissue-specific transgene expression in animal models offers an opportunity to circumvent current limitations associated with the establishment of transgenic mouse models. The Cre-loxP and the tetracycline (Tet)-inducible systems are useful methods of conditional gene expression that allow spatial (cell-type-specific) and temporal (inducer-dependent) control. Most often, the alpha-myosin heavy chain (alpha-MHC) promoter is used in these inducible systems to restrict expression of reporter genes and transgenes to the myocardium. An overview of each inducible system is described, along with suggested reporter genes for real-time, noninvasive imaging in the myocardium. Effective gene delivery of the inducible gene expression system is carried out by lentiviral vectors, which offer high transduction efficiency, long-term transgene expression, and low immunogenicity. This chapter outlines the packaging of myocardium-specific inducible expression systems into lentiviral vectors, in which a transgene and a reporter gene are transduced into cardiomyocytes. In doing so, transgene and reporter expression can be monitored/tracked with bioluminescence imaging (BLI) and positron emission tomography (PET).

Self-organization vs Watchmaker: stochastic gene expression and cell differentiation

Cell differentiation and organism development are traditionally described in deterministic terms of program and design, echoing a conventional clockwork perception of the cell on another scale. However, the current experimental reality of stochastic gene expression and cell plasticity is poorly consistent with the ideas of design, purpose and determinism, suggesting that the habit of classico-mechanistic interpretation of life phenomena may handicap our ability to adequately comprehend and model biological systems. An alternative conceptualization of cell differentiation and development is proposed where the developing organism is viewed as a dynamic self-organizing system of adaptive interacting agents. This alternative interpretation appears to be more consistent with the probabilistic nature of gene expression and the phenomena of cell plasticity, and is coterminous with the novel emerging image of the cell as a self-organizing molecular system. I suggest that stochasticity, as a principle of differentiation and adaptation, and self-organization, as a concept of emergence, have the potential to provide an interpretational framework that unites phenomena across different scales of biological organization, from molecules to societies.

Myoblast-mediated gene transfer for therapeutic angiogenesis and arteriogenesis

Therapeutic angiogenesis aims at generating new blood vessels by delivering growth factors such as VEGF and FGF. Clinical trials are underway in patients with peripheral vascular and coronary heart disease. However, increasing evidence indicates that the new vasculature needs to be stabilized to avoid deleterious effects such as edema and hemangioma formation. Moreover, a major challenge is to induce new vessels that persist following cessation of the angiogenic stimulus. Mature vessels may be generated by modulating timing and dosage of growth factor expression, or by combination of 'growth' factors with 'maturation' factors like PDGF-BB, angiopoietin-1 or TGF-beta. Myoblast-mediated gene transfer has unique characteristics that make it a useful tool for studying promising novel approaches to therapeutic angiogenesis. It affords robust and long-lasting expression, and can be considered as a relatively rapid form of 'adult transgenesis' in muscle. The combined insertion of different gene constructs into single myoblasts and their progeny allows the simultaneous expression of different 'growth' and 'maturation' factors within the same cell in vivo. The additional insertion of a reporter gene makes it possible to analyze the phenotype of the vessels surrounding the transgenic muscle fibers into which the myoblasts have fused. The effects of timing and duration of gene expression can be studied by using tetracycline-inducible constructs, and dosage effects by selecting subpopulations consistently expressing distinct levels of growth factors. Finally, the autologous cell-based approach using transduced myoblasts could be an alternative gene delivery system for therapeutic angiogenesis in patients, avoiding the toxicities seen with some viral vectors.

Modulation of cell cycle by graded expression of MLL-AF4 fusion oncoprotein

Acute lymphoblastic leukemia (ALLs) expressing MLL-AF4, the fusion product of t(4;11)(q21;q23), show marked leucocytosis and extramedullary disease in multiple organs, respond poorly to chemotherapy and have poor prognosis. In vitro, leukemic cells with the t(4;11) show resistance to serum deprivation-induced or interferon gamma-regulated CD95-mediated apoptosis. In addition, t(4;11) cells have prolonged doubling time and lower percentage of cells in cycle compared to non-t(4;11) B lineage cell lines. In this study, we examine the time- and level-dependent effects of MLL-AF4 conditional expression on cell cycle and differentiation of myelomonocytic leukemia cell line U937. By varying the concentration of tetracycline in growth media, we found that increasing levels of MLL-AF4 expression result in a progressive decrease in growth rate and fraction of S phase cells, paralleled by an increase in percentage of cells expressing CD11b. Our results demonstrate a dosage-dependent effect of MLL-AF4 fusion oncoprotein on cell cycle progression, with increasing expression levels resulting in the accumulation in G1, prolonged doubling time, both findings that might be responsible for the increased resistance to etoposide-mediated cytotoxicity. We propose the cell cycle control exerted by MLL-AF4 may be responsible of resistance to cell-death promoting stimuli in leukemia carrying the t(4;11) translocation.

Optimization of the Tet-on system to regulate interleukin 12 expression in the liver for the treatment of hepatic tumors

Interleukin 12 (IL-12) is a potent antitumoral cytokine, but it can be toxic at high doses. Therapy of liver tumors might benefit from the use of vectors enabling tight control of IL-12 expression in hepatic tissue for long periods of time. To this aim, we have improved the Tet-on system by modifying the minimal region of the inducible promoter and adjusting the level of the trans-activator using liver-specific promoters with graded activities. The resulting vectors allowed hepato-specific gene regulation with lower basal activity and higher inducibility compared with the original system in the absence of repressor molecules. The basal and final protein levels depend on the strength of the promoter that directs the transcripcional activator as well as the relative orientation of the two genes in the same plasmid. We have selected the construct combining minimal leakage with higher level of induced gene expression to regulate IL-12 after DNA transfer to mouse liver. Administration of doxycycline (Dox) enhanced IL-12 expression in a dose-dependent manner, whereas it was undetectable in serum in the noninduced state. Gene activation could be repeated several times, and sustained levels of IL-12 were achieved by daily administration of Dox. The antitumor effect of IL-12 was evaluated in a mouse model of metastatic colon cancer to the liver. Complete eradication of liver metastasis and prolonged survival was observed in all mice receiving Dox for 10 days. These data demonstrate the potential of a naked DNA gene therapy strategy to achieve tight control of IL-12 within the liver for the treatment of cancer.

Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression

Inducible genes are expressed in the presence of an external stimulus. Individual cells may exhibit either a binary or graded response to such signals. It has been hypothesized that the chemical kinetics of transcription factor/DNA interactions can account for both these scenarios (EMBO J. 9(9) (1990) 2835; BioEssays 14(5) (1992) 341). To explore this question, we have conducted work based on the experimental results of Fiering et al. (Genes Dev. 4 (10) (1990) 1823). In these experiments, three upstream NF-AT binding sites control transcription of the lacZ gene, which codes for the enzyme beta-Galactosidase. The experimental data show a binary response for this system. We consider the effects of fluctuations in NF-AT binding on the response of the system. Our modeling results are in good qualitative agreement with the experimental data, and illustrate how the binary and graded responses can stem from the same underlying mechanism.

Rapid and simple determination of doxycycline in serum by high-performance liquid chromatography

A simple, rapid and sensitive reversed-phase high-performance liquid chromatographic (HPLC) method for the measurement of doxycycline concentrations in both drug delivery systems (DDS) and serum extracted from mice after intraperitoneal (free drug) and intravenous (doxycycline administered in DDS) administration, has been developed. For the analysis of doxycycline in DDS, a known amount of particles was dissolved in chloroform and, after precipitating the polymer with methanol, the drug was assessed in the supernatant. For doxycycline quantification in microsamples of serum, proteins were precipitated with acetonitrile before chromatographic analysis. After centrifugation, the supernatant was mixed with a mixture of methanol and acetic acid (1:1) for analysis. The samples were chromatographed on a narrow-bore C18 column (Alltech Alltima 150 mm x 2.1 mm) using a mobile phase with 55% acetic acid (5%), 25% acetonitrile and 20% methanol. Doxycycline was detected 347 nm and the run time was 10 min. Linearity was confirmed in the concentration range 0.4-80 microg/ml for doxycycline quantification in serum and from 1 to 800 microg/ml for doxycycline extracted from DDS samples.

Androgen regulation of SMR2 gene expression in rat submandibular gland: evidence for a graded but not a binary response

Expression of SMR2, a member of the gene family encoding salivary glutamine/glutamic acid-rich proteins, is regulated by androgens in rat submandibular gland acinar cells. To further characterize SMR2 regulation, we analyzed SMR2 expression during submandibular gland postnatal development and rat puberty at both a global and a single-cell level. Using in situ detection of mature and primary SMR2 transcripts, we show that SMR2 expression is heterogeneous among acinar cells. However, only one cell population with various amounts of mRNAs can be defined. The number of high-expressing cells increases in males during puberty and in females up to 6 weeks of age, suggesting that some factor in addition to acinar differentiation might be important for SMR2 expression in female rats. Involvement of the beta-adrenergic system in regulating SMR2 expression was tested in rats exposed daily to isoproterenol for 4 days. Under these conditions we found an increase in SMR2 expression in female rats, associated with an increase in SMR2 mRNA levels in most acinar cells. This suggests that a signaling cascade, elicited by beta-adrenergic stimuli, might act in concert with androgens to regulate SMR2 expression.

Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes

The Tet repressor protein (TetR) regulates transcription of a family of tetracycline (tc) resistance determinants in Gram-negative bacteria. The resistance protein TetA, a membrane-spanning H+-[tc.M]+ antiporter, must be sensitively regulated because its expression is harmful in the absence of tc, yet it has to be expressed before the drugs' concentration reaches cytoplasmic levels inhibitory for protein synthesis. Consequently, TetR shows highly specific tetO binding to reduce basal expression and high affinity to tc to ensure sensitive induction. Tc can cross biological membranes by diffusion enabling this inducer to penetrate the majority of cells. These regulatory and pharmacological properties are the basis for application of TetR to selectively control the expression of single genes in lower and higher eukaryotes. TetR can be used for that purpose in some organisms without further modifications. In mammals and in a large variety of other organisms, however, eukaryotic transcriptional activator or repressor domains are fused to TetR to turn it into an efficient regulator. Mechanistic understanding and the ability to engineer and screen for mutants with specific properties allow tailoring of the DNA recognition specificity, the response to inducer tc and the dimerization specificity of TetR-based eukaryotic regulators. This review provides an overview of the TetR properties as they evolved in bacteria, the functional modifications necessary to transform it into a convenient, specific and efficient regulator for use in eukaryotes and how the interplay between structure--function studies in bacteria and specific requirements of particular applications in eukaryotes have made it a versatile and highly adaptable regulatory system.

Studying gene function in eukaryotes by conditional gene inactivation

The prospect of specifically controlling gene activities in vivo has become a defining hallmark of many model organisms of biological research. Where once the aim was to gain control over gene activities using endogenous control elements, new technologies have emerged that owe their remarkable specificity to heterologous components derived from evolutionarily distant species. This review highlights inducible transcriptional systems and site-specific recombination. Their quantitative and qualitative characteristics are discussed, with examples of how recent developments have expanded the spectrum of cells and organisms that are now accessible to genetic dissection of unprecedented precision. Transgenesis has already converted the mouse into a prime model for mammalian genetics. Combined with the new approaches of conditional activation or inactivation of genes, this model has opened up new horizons for the analysis of gene function in mammals.

Communication over a large distance: enhancers and insulators

Enhancers are regulatory DNA sequences that can work over a large distance. Efficient enhancer action over a distance clearly requires special mechanisms for facilitating communication between the enhancer and its target. While the chromatin looping model can explain the majority of the observations, some recent experimental findings suggest that a chromatin scanning mechanism is used to establish the loop. These new findings help to understand the mechanism of action of the elements that can prevent enhancer-promoter communication (insulators).

Tetracycline-inducible transgene expression mediated by a single AAV vector

Regulated gene delivery systems are usually made of two elements: an inducible promoter and a transactivator. In order to optimize gene delivery and regulation, a single viral vector ensuring adequate stoichiometry of the two elements is required. However, efficient regulation is hampered by interferences between the inducible promoter and (i) the promoter used to express the transactivator and/or (ii) promoter/enhancer elements present in the viral vector backbone. We describe a single AAV vector in which transcription of both the reverse tetracycline transactivator (rtTA) and the transgene is initiated from a bidirectional tetracycline-responsive promoter and terminated at bidirectional SV40 polyadenylation sites flanking both ITRs. Up to 50-fold induction of gene expression in human tumor cell lines and 100-fold in primary cultures of rat Schwann cells was demonstrated. In addition an 80-fold induction in vivo in the rat brain has been obtained. In vitro, the autoregulatory vector exhibits an induced expression level superior to that obtained using the constitutive CMV promoter. Although extinction of the transgene after removal of tetracycline was rapid (less than 3 days), inducibility after addition of tetracycline was slow (about 14 days). This kinetics is suitable for therapeutic gene expression in slowly progressive diseases while allowing rapid switch-off in case of undesirable effects. As compared to previously described autoregulatory tet-repressible (tetOFF) AAV vectors, the tet-inducible (tetON) vector prevents chronic antibiotic administration in the uninduced state.