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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)
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)
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)
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)
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)
Porcine circovirus type 2 (PCV2) is the primary causative agent of postweaning multisystemic wasting syndrome, which leads to serious economic losses in the pig industry worldwide. While the molecular basis of PCV2 replication and pathogenicity remains elusive, it is increasingly apparent that the microRNA (miRNA) pathway plays a key role in controlling(More)
Although passively administered antibodies are known to suppress the humoral immune response, the mechanism is not fully understood. Here, we developed a mathematical model to better understand the suppression phenomena in mice. Using this model, we tested the generally accepted but difficult to prove "epitope masking hypothesis." To simulate the hypothesis(More)
Neurodegenerative diseases (NDs) are characterized by the progressive loss of neurons in the human brain. Although the majority of NDs are sporadic, evidence is accumulating that they have a strong genetic component. Therefore, significant efforts have been made in recent years to not only identify disease-causing genes but also genes that modify the(More)
The emergence of co-infections and the evolution of drug-resistant pathogens limit the utility of current therapies against infections, and developing countries in particular are facing a great challenge in combating infectious disease. Moreover, any failure to control the spread of infectious diseases would also represent a threat to developed countries.(More)