Dataset Information

Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network.

ABSTRACT: Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications.

SUBMITTER: Meng H

PROVIDER: S-EPMC3613377 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network.

Meng Hailin H Wang Jianfeng J Xiong Zhiqiang Z Xu Feng F Zhao Guoping G Wang Yong Y

PloS one 20130401 4

Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, ...[more]

PMID: 23560087

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Project description:Radio refractivity plays a significant role in the development and design of radio systems for attaining the best level of performance. Refractivity in the troposphere is one of the features affecting electromagnetic waves, and hence the communication system interrupts. In this work, a modified artificial neural network (ANN) based model is applied to predict the refractivity. The suggested ANN model comprises three modules: the data preparation module, the feature selection module, and the forecast module. The first module applies pre-processing to make the data compatible for the feature selection module. The second module discards irrelevant and redundant data from the input set. The third module uses ANN for prediction. The ANN model applies a sigmoid activation function and a multi-variate auto regressive model to update the weights during the training process. In this work, the refractivity is predicted and estimated based on ten years (2002-2011) of meteorological data, such as the temperature, pressure, and humidity, obtained from the Pakistan Meteorological Department (PMD), Islamabad. The refractivity is estimated using the method suggested by the International Telecommunication Union (ITU). The refractivity is predicted for the year 2012 using the database of the previous ten years, with the help of ANN. The ANN model is implemented in MATLAB. Next, the estimated and predicted refractivity levels are validated against each other. The predicted and actual values (PMD data) of the atmospheric parameters agree with each other well, and demonstrate the accuracy of the proposed ANN method. It was further found that all parameters have a strong relationship with refractivity, in particular the temperature and humidity. The refractivity values are higher during the rainy season owing to a strong association with the relative humidity. Therefore, it is important to properly cater the signal communication system during hot and humid weather. Based on the results, the proposed ANN method can be used to develop a refractivity database, which is highly important in a radio communication system.

Dataset Information

Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network.

Publications

Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network.

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