Biology subjects

Kameda, T.

Publications and source records attributed to Kameda, T..

3 recordsLinked to original sources

bioRxiv2018

Nearest-neighbor parameter for inosine-cytosine pairs through a combined experimental and computational approach

In RNA secondary structure prediction, nearest-neighbor parameters are used to determine the stability of a given structure. We derived the nearest-neighbor parameters for RNAs containing inosine-cytosine pairs. For parameter derivation, we developed a method that combines UV adsorption measurement experiments with free-energy calculations using molecular dynamics simulations. The method provides fast drop-in parameters for modified bases. Derived parameters were compared and found to be consistent with existing parameters for canonical RNAs. A duplex with an internal inosine-cytosine pair is 0.9 kcal/mol more unstable than the same duplex with an internal guanine-cytosine pair, and is as stable as the one with an internal adenine-uracil pair (only 0.1 kcal/mol more stable) on average.

bioinformatics↗

bioRxiv2018

Antibacterial effects of nanoimprinted moth-eye film in practical settings

Recent studies report that surfaces displaying micrometer-or nanometer-sized undulating structures exhibit antibacterial effects. In previous work, we described the use of an advanced nanofabrication technique to generate an artificial biomimetic moth-eye film by coating a polyethylene terephthalate (PET) film with nanoscale moth-eye protrusions made from a hydrophilic resin. This moth-eye film exhibited enhanced antibacterial effects in in vitro experiments. The aim of the present study was to verify the antibacterial efficacy of the Moth-eye film in practical environments. Three types of films (Moth-eye film, Flat film, and PET film) were used to compare antibacterial effects. Sample films were pasted onto hand-wash sinks at the testing locations. After several hours of elapsed time, bacteria from the surface of sample films were collected using one of three kinds of culture media stampers (to permit identification of bacterial species). The stampers were incubated for 48 hours at 35 {degrees}C, and the numbers of colonies were counted.\n\nThe number of common bacteria including E. coli and S. aureus from the Moth-eye film was significantly lower than that from the PET film (p<0.05) and that from the Flat film at 1 hour (p<0.05). This study found that the Moth-eye film had durability of antibacterial effect and the Moth-eye structure (PET coated with nanoscale cone-shaped pillars) had a physical antibacterial effect from the earlier time points. Therefore, the Moth-eye film might be useful for general-purpose applications in practical environments.

microbiology↗

bioRxiv2018

A machine-learning-guided mutagenesis platform for accelerated discovery of novel functional proteins

Molecular evolution based on mutagenesis is widely used in protein engineering. However, optimal proteins are often difficult to obtain due to a large sequence space that requires high costs for screening experiments. Here, we propose a novel approach that combines molecular evolution with machine learning. In this approach, we conduct two rounds of mutagenesis where an initial library of protein variants is used to train a machine-learning model to guide mutagenesis for the second-round library. This enables to prepare a small library suited for screening experiments with high enrichment of functional proteins. We demonstrated a proof-of-concept of our approach by altering the reference green fluorescent protein (GFP) so that its fluorescence is changed to yellow while improving its fluorescence intensity. Using 155 and 78 variants for the initial and the second-round libraries, respectively, we successfully obtained a number of proteins showing yellow fluorescence, 12 of which had better fluorescence performance than the reference yellow fluorescent protein (YFP). These results show the potential of our approach as a powerful platform for accelerated discovery of functional proteins.

bioengineering↗