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The symbiotic community of microorganisms in the gut plays an important role in the health of the host. While many previous studies have been performed on the interactions between the gut microbiome and the host in mammals, studies in fish are still lacking. In this study, we investigated changes in the intestinal microbiome and pathogen susceptibility of zebrafish (Danio rerio) following chronic antibiotics exposure. The chronic antibiotics exposure assay was performed on zebrafish for 30 days using oxytetracycline (Otc), sulfamethoxazole/trimethoprim (Smx/Tmp), or erythromycin (Ery), which are antibiotics widely used in the aquaculture industry. The microbiome analysis indicated that Fusobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla in the gut microbiome of the zebrafish used in this study. However, in Smx/Tmp-treated zebrafish, the compositions of Fusobacteria and Proteobacteria were changed significantly, and in Ery-treated zebrafish, the compositions of Proteobacteria and Firmicutes were altered significantly. Although alpha diversity analysis showed that there was no significant difference in the richness, beta diversity analysis revealed a community imbalance in the gut microbiome of all chronically antibiotics-exposed zebrafish. Intriguingly, in zebrafish with dysbiosis in the gut microbiome, the pathogen susceptibility to Edwardsiella piscicida, a representative Gram-negative fish pathogen, was reduced. Gut microbiome imbalance resulted in a higher count of goblet cells in intestinal tissue and an upregulation of genes related to the intestinal mucosal barrier. In addition, as innate immunity was enhanced by the increased mucosal barrier, immune and stress-related gene expression in the intestinal tissue was downregulated. In this study, we provide new insight into the effect of gut microbiome dysbiosis on pathogen susceptibility.

Saeu-jeotgal, a Korean fermented shrimp food, is commonly used as an ingredient for making kimchi and other side dishes. The high salinity of the jeotgal contributes to its flavor and inhibits the growth of food spoilage microorganisms. Interestingly, Staphylococcus saprophyticus was discovered to be capable of growth even after treatment with 20% NaCl. To elucidate the tolerance mechanism, a genome-wide gene expression of S. saprophyticus against 0%, 10%, and 20% NaCl was investigated by RNA sequencing. A total of 831, 1314, and 1028 differentially expressed genes (DEGs) were identified in the 0% vs. 10%, 0% vs. 20%, and 10% vs. 20% NaCl comparisons, respectively. The Clusters of Orthologous Groups analysis revealed that the DEGs were involved in amino acid transport and metabolism, transcription, and inorganic ion transport and metabolism. The functional enrichment analysis showed that the expression of the genes encoding mechanosensitive ion channels, sodium/proton antiporters, and betaine/carnitine/choline transporter family proteins was downregulated, whereas the expression of the genes encoding universal stress proteins and enzymes for glutamate, glycine, and alanine synthesis was upregulated. Therefore, these findings suggest that the S. saprophyticus isolated from the saeu-jeotgal utilizes different molecular strategies for halotolerance, with glutamate as the key molecule.

In the past few decades, NAND flash memory has been one of the most successful nonvolatile storage technologies, and it is commonly used in electronic devices because of its high scalability and reliable switching properties. To overcome the scaling limit of planar NAND flash arrays, various three-dimensional (3D) architectures of NAND flash memory and their process integration methods have been investigated in both industry and academia and adopted in commercial mass production. In this paper, 3D NAND flash technologies are reviewed in terms of their architecture and fabrication methods, and the advantages and disadvantages of the architectures are compared.

A systematic device-model calibration (extraction) methodology has been proposed to reduce parameter calibration time of advanced compact model for modern nano-scale semiconductor devices. The adaptive pattern search algorithm is a variant of the direct search method, which explore in the parameter space with adaptive searching step and direction. It is very straightforward, but powerful, in high dimensional optimization problem since adaptive step and direction are decided by simple computation. The proposed method iterates less but shows superior accuracy over the conventional method. It is possible to be applied to a behavioral or empirical model correspond to emerging devices, such as tunneling field-effect transistor (TFET) and negative capacitance field-effect transistor (NCFET) due to its universality in parameter calibration for the model accuracy.

A hardware-based spiking neural network (SNN) has attracted many researcher’s attention due to its energy-efficiency. When implementing the hardware-based SNN, offline training is most commonly used by which trained weights by a software-based artificial neural network (ANN) are transferred to synaptic devices. However, it is time-consuming to map all the synaptic weights as the scale of the neural network increases. In this paper, we propose a method for quantized weight transfer using spike-timing-dependent plasticity (STDP) for hardware-based SNN. STDP is an online learning algorithm for SNN, but we utilize it as the weight transfer method. Firstly, we train SNN using the Modified National Institute of Standards and Technology (MNIST) dataset and perform weight quantization. Next, the quantized weights are mapped to the synaptic devices using STDP, by which all the synaptic weights connected to a neuron are transferred simultaneously, reducing the number of pulse steps. The performance of the proposed method is confirmed, and it is demonstrated that there is little reduction in the accuracy at more than a certain level of quantization, but the number of pulse steps for weight transfer substantially decreased. In addition, the effect of the device variation is verified.

NOR/AND flash memory was studied in neuromorphic systems to perform vector-by-matrix multiplication (VMM) by summing the current. Because the size of NOR/AND cells exceeds those of other memristor synaptic devices, we proposed a 3D AND-type stacked array to reduce the cell size. Through a tilted implantation method, the conformal sources and drains of each cell could be formed, with confirmation by a technology computer aided design (TCAD) simulation. In addition, the cell-to-cell variation due to the etch slope could be eliminated by controlling the deposition thickness of the cells. The suggested array can be beneficial in simple program/inhibit schemes given its use of Fowler–Nordheim (FN) tunneling because the drain lines and source lines are parallel. Therefore, the conductance of each synaptic device can be updated at low power level.

Phenol and formalin are major water pollutants that are frequently discharged into the aquatic milieu. These chemicals can affect broad domains of life, including microorganisms. Aquatic pollutants, unlike terrestrial pollutants, are easily diluted in water environments and exist at a sub-inhibitory concentration (sub-IC), thus not directly inhibiting bacterial growth. However, they can modulate gene expression profiles. The sub-IC values of phenol and formalin were measured by minimal inhibitory concentration (MIC) assay to be 0.146% (1.3 mM) and 0.0039% (0.38 mM), respectively, in Edwardsiella piscicida CK108, a Gram-negative fish pathogen. We investigated the differentially expressed genes (DEG) by RNA-seq when the cells were exposed to the sub-ICs of phenol and formalin. DEG analyses revealed that genes involved in major virulence factors (type I fimbriae, flagella, type III and type VI secretion system) and various cellular pathways (energy production, amino acid synthesis, carbohydrate metabolism and two-component regulatory systems) were up- or downregulated by both chemicals. The genome-wide gene expression data corresponded to the results of a quantitative reverse complementary-PCR and motility assay. This study not only provides insight into how a representative fish pathogen, E. piscicida CK108, responds to the sub-ICs of phenol and formalin but also shows the importance of controlling chemical pollutants in aquatic environments.