Hill Equation in Modeling Transcriptional Regulation

Bhaskaran, Silpa; Umesh, P; Nair, Achuthsankar S.

doi:10.1007/978-94-017-9514-2_5

Cited by 15 publications

(13 citation statements)

References 5 publications

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“…For example, increasing the concentration of acridine orange or of pyronin Y resulted in a relatively gradual induction. In contrast, crystal violet (CV) rapidly induced transcription, indicating a strong positive cooperativity 33 . Since CV also displayed the highest potency (EC 50 of 120 nM) and efficacy of all compounds tested (Fig.…”

Section: Resultsmentioning

confidence: 99%

Jungle Express is a versatile repressor system for tight transcriptional control

et al. 2018

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Tightly regulated promoters are essential for numerous biological applications, where strong inducibility, portability, and scalability are desirable. Current systems are often incompatible with large-scale fermentations due to high inducer costs and strict media requirements. Here, we describe the bottom-up engineering of ‘Jungle Express’, an expression system that enables efficient gene regulation in diverse proteobacteria. This system is guided by EilR, a multidrug-binding repressor with high affinity to its optimized operator and cationic dyes that act as powerful inducers at negligible costs. In E. coli, the engineered promoters exhibit minimal basal transcription and are inducible over four orders of magnitude by 1 µM crystal violet, reaching expression levels exceeding those of the strongest current bacterial systems. Further, we provide molecular insights into specific interactions of EilR with its operator and with two inducers. The versatility of Jungle Express opens the way for tightly controlled and efficient gene expression that is not restricted to host organism, substrate, or scale.

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Section: Resultsmentioning

confidence: 99%

Jungle Express is a versatile repressor system for tight transcriptional control

et al. 2018

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“…The main assumption of Boolean networks is that the activity of vertices can be classified as being active or inactive. In the context of GRNs, this assumption is justified because the rate of transcription follows as a Hill function, which approximates a Boolean classification [59]. Here, Boolean functions represent the collective regulation of a gene by several TFs.…”

Section: Box 3 Modeling Types In Stem Cell Researchmentioning

confidence: 99%

The Importance of Computational Modeling in Stem Cell Research

Sol

Jung

2021

Trends in Biotechnology

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“…The sigmoidal shape of the data may be modeled using Hill function. Hill function is traditionally used to model sigmoidal ligand-binding curves in mathematical physiology, but is used widely as a model for various other processes, including doseresponse curves in pharmacology (Bhaskaran et al, 2015;Gadagkar and Call, 2015;Keener and Sneyd, 1998). Hill function (Eqn 2) satisfies all of the biological restrictions we specified.…”

Section: Mathematical Model Formulation Of Nutritional Absorption During Zebrafish Developmentmentioning

confidence: 99%

Mathematical modeling of the interaction between yolk utilization and fish growth in zebrafish,Danio rerio

et al. 2021

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Optimal embryonic development plays a major role in the health of an individual beyond the developmental stage. Nutritional perturbation during development is associated with cardiovascular and metabolic disease later in life. With both nutritional uptake and overall growth being risk factors for eventual health, it is necessary to understand not only the behavior of the processes during development but also their interactions. In this study, we used differential equations, image analyses, curve fittings, parameter estimation and laboratory experiments to quantify the rate of yolk absorption and its effect on early development of a vertebrate model (Danio rerio). Findings from this study establish a nonlinear functional relationship between nutrient absorption and early fish growth. We found that the rate of change in fish length and yolk utilization is logistic, that is the yolk decays rapidly for a period of time before leveling out. An interesting finding from this study is that yolk utilization reaches its maximum at 84 h post-fertilization. We validated our mathematical models against experimental observations, making them powerful tools for replication and future simulations.

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Hill Equation in Modeling Transcriptional Regulation

Cited by 15 publications

References 5 publications

Jungle Express is a versatile repressor system for tight transcriptional control

Jungle Express is a versatile repressor system for tight transcriptional control

The Importance of Computational Modeling in Stem Cell Research

Mathematical modeling of the interaction between yolk utilization and fish growth in zebrafish,Danio rerio

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