RESUMEN
Assembling high-quality microbial genomes using only cost-effective Nanopore long-read systems such as Flongle is important to accelerate research on the microbial genome and the most critical point for this is the polishing process. In this study, we performed an evaluation based on BUSCO and Prokka gene prediction in terms of microbial genome assembly for eight state-of-the-art Nanopore polishing tools and combinations available. In the evaluation of individual tools, Homopolish, PEPPER, and Medaka demonstrated better results than others. In combination polishing, the second round Homopolish, and the PEPPER × medaka combination also showed better results than others. However, individual tools and combinations have specific limitations on usage and results. Depending on the target organism and the purpose of the downstream research, it is confirmed that there remain some difficulties in perfectly replacing the hybrid polishing carried out by the addition of a short-read. Nevertheless, through continuous improvement of the protein pores, related base-calling algorithms, and polishing tools based on improved error models, a high-quality microbial genome can be achieved using only Nanopore reads without the production of additional short-read data. The polishing strategy proposed in this study is expected to provide useful information for assembling the microbial genome using only Nanopore reads depending on the target microorganism and the purpose of the research.
Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Secuenciación de Nanoporos/métodos , Análisis de Secuencia de ADN/métodos , Algoritmos , Genoma Microbiano/genética , Genómica/métodos , NanoporosRESUMEN
To utilize potentials of nitric oxide (NO) gas in anti-bacterial, anticancer, wound healing applications, numerous studies have been conducted to develop a NO delivery system in the past few decades. Even though a coating method and film types are essential to apply in biomedical device coating from previous NO delivery systems, release control from the coating system is still challenging. In this study, we introduced a multilayered polymeric coating system to overcome the uncontrollable NO release kinetics of film systems. We used biocompatible gelatin and tannic acid to construct a rough, porous structured film based on the layer-by-layer self-assembly method. The multilayered polymeric structure facilitated the controlled amount of NO release from (Gel/TA)n film and showed burst release in early period owing to their large surface area from the rough, porous structure. We synthesized the proton-responsive NO donor, N-diazeniumdiolate (NONOates), into the (Gel/TA)n film through a chemical reaction under high pressure NO gas. NO release profile was analyzed by a real-time NO analysis machine (NOA 280i). Then, the NO-releasing (Gel/TA)n film was tested its toxicity against human dermal fibroblast cells and bactericidal effects against Staphylococcus aureus.
RESUMEN
Nitric oxide (NO) gas delivery has attracted extensive interest due to its endogenous therapeutic functions and potential biomedical applications for the treatment of various diseases. The important thing about NO delivery is the emission control due to the fast diffusion rate of gas molecules. To develop NO delivery platforms using macromolecules and to comprehend the chemical NO donor generation and release mechanisms, we studied branched polyethyleneimine/alginate (BPEI/ALG) nanoblended coatings fabricated by giving structural heterogeneity to the structure through a self-assembly process for the controlled release of gas molecules. NO release could be remarkably expected via the well-organized coating structures and explained by quantification of the NO donors. Taking advantage of these polymeric coatings, this process could be applied to the treatment of various diseases based on the biocompatibility of materials and the fine control of NO release rate and its amount.
