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Systematic Design of a Metal Ion Biosensor: A Multi-Objective Optimization Approach.

ABSTRACT: With the recent industrial expansion, heavy metals and other pollutants have increasingly contaminated our living surroundings. Heavy metals, being non-degradable, tend to accumulate in the food chain, resulting in potentially damaging toxicity to organisms. Thus, techniques to detect metal ions have gradually begun to receive attention. Recent progress in research on synthetic biology offers an alternative means for metal ion detection via the help of promoter elements derived from microorganisms. To make the design easier, it is necessary to develop a systemic design method for evaluating and selecting adequate components to achieve a desired detection performance. A multi-objective (MO) H2/H? performance criterion is derived here for design specifications of a metal ion biosensor to achieve the H2 optimal matching of a desired input/output (I/O) response and simultaneous H? optimal filtering of intrinsic parameter fluctuations and external cellular noise. According to the two design specifications, a Takagi-Sugeno (T-S) fuzzy model is employed to interpolate several local linear stochastic systems to approximate the nonlinear stochastic metal ion biosensor system so that the multi-objective H2/H? design of the metal ion biosensor can be solved by an associated linear matrix inequality (LMI)-constrained multi-objective (MO) design problem. The analysis and design of a metal ion biosensor with optimal I/O response matching and optimal noise filtering ability then can be achieved by solving the multi-objective problem under a set of LMIs. Moreover, a multi-objective evolutionary algorithm (MOEA)-based library search method is employed to find adequate components from corresponding libraries to solve LMI-constrained MO H2/H? design problems. It is a useful tool for the design of metal ion biosensors, particularly regarding the tradeoffs between the design factors under consideration.

SUBMITTER: Hsu CY

PROVIDER: S-EPMC5104392 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Systematic Design of a Metal Ion Biosensor: A Multi-Objective Optimization Approach.

Hsu Chih-Yuan CY Chen Bor-Sen BS

PloS one 20161110 11

With the recent industrial expansion, heavy metals and other pollutants have increasingly contaminated our living surroundings. Heavy metals, being non-degradable, tend to accumulate in the food chain, resulting in potentially damaging toxicity to organisms. Thus, techniques to detect metal ions have gradually begun to receive attention. Recent progress in research on synthetic biology offers an alternative means for metal ion detection via the help of promoter elements derived from microorganis ...[more]

PMID: 27832110

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Project description:BackgroundRNAs are attractive molecules as the biological parts for synthetic biology. In particular, the ability of conformational changes, which can be encoded in designer RNAs, enables us to create multistable molecular switches that function in biological circuits. Although various algorithms for designing such RNA switches have been proposed, the previous algorithms optimize the RNA sequences against the weighted sum of objective functions, where empirical weights among objective functions are used. In addition, an RNA design algorithm for multiple pseudoknot targets is currently not available.ResultsWe developed a novel computational tool for automatically designing RNA sequences which fold into multiple target secondary structures. Our algorithm designs RNA sequences based on multi-objective genetic algorithm, by which we can explore the RNA sequences having good objective function values without empirical weight parameters among the objective functions. Our algorithm has great flexibility by virtue of this weight-free nature. We benchmarked our multi-target RNA design algorithm with the datasets of two, three, and four target structures and found that our algorithm shows better or comparable design performances compared with the previous algorithms, RNAdesign and Frnakenstein. In addition to the benchmarks with pseudoknot-free datasets, we benchmarked MODENA with two-target pseudoknot datasets and found that MODENA can design the RNAs which have the target pseudoknotted secondary structures whose free energies are close to the lowest free energy. Moreover, we applied our algorithm to a ribozyme-based ON-switch which takes a ribozyme-inactive secondary structure when the theophylline aptamer structure is assumed.ConclusionsCurrently, MODENA is the only RNA design software which can be applied to multiple pseudoknot targets. Successful design results for the multiple targets and an RNA device indicate usefulness of our multi-objective RNA design algorithm.

Project description:BackgroundStatins are a class of drugs that lower cholesterol levels in the blood by inhibiting an enzyme called 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase. High cholesterol levels can lead to plaque buildup in the arteries, which can cause Atherosclerotic Cardiovascular Disease(ASCVD). Statins can reduce the risk of ASCVD events by about 25-35% but they might be associated with symptoms such as muscle pain, liver damage, or diabetes. As a result, this leads to a strong reason to discontinue statin therapy, which increases the risk of cardiovascular events and mortality and becomes a public-health problem.To solve this problem, in the previous work, we proposed a framework to produce a proactive strategy, called a personalized statin treatment plan (PSTP) to minimize the risks of statin-associated symptoms and therapy discontinuation when prescribing statin. In our previous PSTP framework, three limitations remain, and they can influence PSTP usability: (1) Not taking the counterfactual predictions and confounding bias into account. (2) The balance between multiple drug-prescribing objectives (especially trade-off objectives), such as tradeoff between benefits and risks. (3) Evaluating PSTP in retrospective data.ObjectivesThis manuscript aimed to provide solutions for the three abovementioned problems to improve PSTP robustness to produce a proactive strategy for statin prescription that can maximize the benefits (low-density lipoprotein cholesterol (LDL-C) reduction) and minimize risks (statin-associated symptoms and therapy discontinuation) at the same time.MethodsWe applied overlapping weighting counterfactual survival risk prediction (CP), multiple objective optimization (MOO), and clinical trial simulation (CTS) which consists of Random Arms, Clinical Guideline arms, PSTP Arms, and Practical Arms to improve the PSTP framework and usability.ResultsIn addition to highly balanced covariates, in the CTS, the revised PSTP showed improvements in lowering the SAS risks overall compared to other arms across all time points by at most 7.5% to at least 1.0% (Fig. 8(a)). It also has the better flexibility of identifying the optimal Statin across all time points within one year.ConclusionWe demonstrated feasibility of robust and trustworthy counterfactual survival risk prediction model. In CTS, we also demonstrated the PSTP with Pareto optimization can personalize optimal balance between Statin benefits and risks.

Dataset Information

Systematic Design of a Metal Ion Biosensor: A Multi-Objective Optimization Approach.

Publications

Systematic Design of a Metal Ion Biosensor: A Multi-Objective Optimization Approach.

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