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The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.

Many studies have been conducted with the aim of reducing fuel consumption by the fishing industry. We examined whether drag can be reduced by changing the arrangement of gears without requiring the development of new parts for the conventional float and ground gear. Ten differently shaped floats and ground gears were measured in a water flume tank. The float and ground gear were fixed to a steel rod to measure fluid drag according to attack angle, using a multi-component load cell. To estimate the frictional drag of ground gear on the seabed, five types of large ground gear were towed on flat land while changing attack angle using the load cell to measure tension. The fluid drag of the float and ground gear was highest at an attack angle of 60°, regardless of shape, size, and flow velocity. The resistance coefficients of the float and ground gear varied depending on the attack angle and tended to be lower at small attack angles. The frictional drag of the ground gear was greater when the axis of rotation had a small attack angle in the towing direction compared to other attack angles. We then investigated a method for designing bottom-towed gear that reduces drag while maintaining the size, buoyancy, and sinking force of conventional fishing gear parts. This gear design showed 1.2% drag reduction and an estimated 0.8% improvement in fuel efficiency per haul.

The bluefin sea robin (Chelidonichthys spinosus), hereafter BSR, is one of the most important fish species in the South Sea of Korea. The production value of BSR in 2020 was USD 4,733,057. The production volume in Korea has shown an annual mean increase of 8.9% since 2010, but the efficiency of the fishing gear decreased due to excessive use. This has led to a decrease in the profitability of fishery operators, and as compensation, the use of fishing gear has further increased through competitive operations. Alternative measures for improving catch performance and reducing the use of fishing gear are needed. As one such measure, LED (Light-Emitting Diode) lights were attached to the pot, and the effects were determined. The field experiment results showed that the catch of BSR was higher for the experimental groups (n = 10–273) using fishing gear with LED lights (red, green, blue, and white) than for the control group (n = 2) (Kruskal–Wallis test, p < 0.05). Among the experimental groups, the pot with green light achieved the largest catch (n = 273). The use of LED lights was found to enhance the catch efficiency of pot fishing gear for BSR.

Although gillnet fisheries are increasingly common in Korea, few studies have conducted sea trials using tie-down gillnets. Here, we analyzed the mesh size selectivity using tie-down gillnets with four different mesh sizes (84, 90, 105, and 120 mm) to catch blackfin flounders. A total of 10 sea trials were conducted at depths of 100–140 m in the waters of Yangyang County, Gangwon Province, Korea, and the catching efficiency and mesh size selectivity were comparatively analyzed. The net with a mesh size of 84 mm showed the highest number of catches (373), followed by the 90-mm (363) and 105-mm (307) meshes. The results of the master curve estimation showed that the larger the mesh size, the higher the total length representing the same retention probability. Therefore, the catch rate of small fish decreased with the increasing mesh size. For the 84-mm net, the 50% selection length for small fish (total length ≤ 170 mm) was estimated at 186.9 mm, which was approximately 17 mm larger than the length limit. The results show that when using tie-down gillnets, the size of the fish caught changed according to the changes in the mesh size.

Mushroom ligninolytic enzymes are attractive biocatalysts that can degrade lignin through oxido-reduction. Laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase are the main enzymes that depolymerize highly complex lignin structures containing aromatic or aliphatic moieties and oxidize the subunits of monolignol associated with oxidizing agents. Among these enzymes, mushroom laccases are secreted glycoproteins, belonging to a polyphenol oxidase family, which have a powerful oxidizing capability that catalyzes the modification of lignin using synthetic or natural mediators by radical mechanisms via lignin bond cleavage. The high redox potential laccase within mediators can catalyze the oxidation of a wide range of substrates and the polymerization of lignin derivatives for value-added chemicals and materials. The chemoenzymatic process using mushroom laccases has been applied effectively for lignin utilization and the degradation of recalcitrant chemicals as an eco-friendly technology. Laccase-mediated grafting has also been employed to modify lignin and other polymers to obtain novel functional groups able to conjugate small and macro-biomolecules. In this review, the biochemical features of mushroom ligninolytic enzymes and their potential applications in catalytic reactions involving lignin and its derivatives to obtain value-added chemicals and novel materials in lignin valorization are discussed.

Genomic profiles of cancer patients such as gene expression have become a major source to predict responses to drugs in the era of personalized medicine. As large-scale drug screening data with cancer cell lines are available, a number of computational methods have been developed for drug response prediction. However, few methods incorporate both gene expression data and the biological network, which can harbor essential information about the underlying process of the drug response. We proposed an analysis framework called DrugGCN for prediction of Drug response using a Graph Convolutional Network (GCN). DrugGCN first generates a gene graph by combining a Protein-Protein Interaction (PPI) network and gene expression data with feature selection of drug-related genes, and the GCN model detects the local features such as subnetworks of genes that contribute to the drug response by localized filtering. We demonstrated the effectiveness of DrugGCN using biological data showing its high prediction accuracy among the competing methods.

Mushrooms are attractive resources for novel enzymes and bioactive compounds. Nevertheless, mushrooms spontaneously form brown pigments during food processing as well as extraction procedures for functional compounds. In this study, the dark browning pigment in the extract derived from the edible mushroom Hericium erinaceus was determined to be caused by the oxidation of endogenous polyphenol compounds by the polyphenol oxidase (PPO) enzyme family. These oxidized pigment compounds were measured quantitatively using a fluorospectrophotometer and, through chelation deactivation and heat inactivation, were confirmed to be enzymatic browning products of reactions by a metalloprotein tyrosinase in the PPO family. Furthermore, a transcript analysis of the identified putative PPO-coding genes in the different growth phases showed that tyrosinase and laccase isoenzymes were highly expressed in the mushroom fruiting body, and these could be potential PPOs involved in the enzymatic browning reaction. A metabolite profiling analysis of two different growth phases also revealed a number of potential enzymatic browning substances that were grouped into amino acids and their derivatives, phenolic compounds, and purine and pyrimidine nucleobases. In addition, these analyses also demonstrated that the mushroom contained a relatively high amount of natural antioxidant compounds that can effectively decrease the browning reaction via PPO-inhibitory mechanisms that inhibit tyrosinase and scavenge free radicals in the fruiting body. Altogether, these results contribute to an understanding of the metabolites and PPO enzymes responsible for the enzymatic browning reaction of H. erinaceus.

Time and costs are often the most critical constraints in implementing a development impact fee (DIF) for local infrastructure installation planning in South Korea. For this reason, drafting quality plan alternatives and calculating precise DIFs for improvement remain challenging. This study proposes an application of a procedural modeling method using CityEngine as an alternative to traditional methods, which rely on AutoCAD. A virtual low-density suburban development project in Jeju, South Korea was used to compare the workability of the two methods. The findings suggest that procedural modeling outperforms the other approach by significantly reducing the number of steps and commands required in the planning process. This paper also argues that procedural modeling provides real-time 2- and 3-dimensional modeling and design evaluation and allows for a more efficient assessment of plan quality and calculation of DIF. We also argue for the need to diffuse procedural modeling to better support local planning practices.