Learn More
Small regulatory RNAs (sRNAs) regulate gene expression in bacteria. We designed synthetic sRNAs to identify and modulate the expression of target genes for metabolic engineering in Escherichia coli. Using synthetic sRNAs for the combinatorial knockdown of four candidate genes in 14 different strains, we isolated an engineered E. coli strain (tyrR- and(More)
BACKGROUND Within the emerging field of synthetic biology, engineering paradigms have recently been used to design biological systems with novel functionalities. One of the essential challenges hampering the construction of such systems is the need to precisely optimize protein expression levels for robust operation. However, it is difficult to design mRNA(More)
MOTIVATION RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation(More)
Phenol is an industrially versatile commodity chemical and is currently produced from fossil resources. Phenol's biological production from renewable resources has been limited due to its toxicity to microorganisms. Here, we simultaneously engineered 18 Escherichia coli strains for the production of phenol using synthetic regulatory small RNA (sRNA)(More)
Growing concerns over limited fossil resources and associated environmental problems are motivating the development of sustainable processes for the production of chemicals, fuels and materials from renewable resources. Metabolic engineering is a key enabling technology for transforming microorganisms into efficient cell factories for these compounds.(More)
Subcellular localization is one of the key functional characteristics of proteins. An automatic and efficient prediction method for the protein subcellular localization is highly required owing to the need for large-scale genome analysis. From a machine learning point of view, a dataset of protein localization has several characteristics: the dataset has(More)
Metabolic engineering has enabled us to develop strains suitable for their use as microbial factories of chemicals and materials from renewable sources. It has recently become more powerful with the advanced in synthetic biology, which is allowing us to create novel and fine-controlled metabolic and regulatory circuits maximizing metabolic fluxes to the(More)
Gene knockout experiments are often essential in functional genomics and metabolic engineering studies. However, repeated multiple gene knockout experiments are laborious, time consuming and sometimes impossible to perform for those genes that are essential for cell function. Small regulatory RNAs (sRNAs) are short noncoding RNAs in prokaryotes that can(More)
Hepatocytes have been used for in vitro hepatotoxicity assays because of their ability to sustain intact liver-specific functions. Here, we demonstrate a hepatotoxicity assay system using primary human hepatocytes trapped in microholes of a microfluidic device, providing a microscale in vivo liver-like environment. We performed microfluidic hepatotoxicity(More)