The emergence and spread of antimicrobial resistance in pathogenic bacteria of fish and shellfish have caused serious concerns in the aquaculture industry, owing to the potential health risks to humans and animals. Among these bacteria, Aeromonas salmonicida, which is one of the most important primary pathogens in salmonids, is responsible for significant economic losses in the global aquaculture industry, especially in salmonid farming because of its severe infectivity and acquisition of antimicrobial resistance. Therefore, interest in the use of alternative approaches to prevent and control A. salmonicida infections has increased in recent years, and several applications of bacteriophages (phages) have provided promising results. For several decades, A. salmonicida and phages infecting this fish pathogen have been thoroughly investigated in various research areas including aquaculture. The general overview of phage usage to control bacterial diseases in aquaculture, including the general advantages of this strategy, has been clearly described in previous reviews. Therefore, this review specifically focuses on providing insights into the phages infecting A. salmonicida, from basic research to biotechnological application in aquaculture, as well as recent advances in the study of A. salmonicida.

Oligomeric proanthocyanidins (OPCs), classified as condensed tannins, have significant antioxidation, anti-inflammation and anti-cancer effects. This study was performed to investigate the anti-inflammatory effects of OPCs and the mechanism underlying these effects in lipopolysaccharide (LPS)-stimulated bovine mammary epithelial cells (MAC-T). Real-time PCR and ELISA assays indicated that OPC treatment at 1, 3 and 5 ㎍/ml significantly reduced the mRNA and protein, respectively, of oxidant indicators cyclooxygenase-2 (COX-2) (p < 0.05) and inducible nitric oxide synthase (iNOS) (p < 0.01) as well as inflammation cytokines interleukin (IL)-6 (p < 0.01), IL-1β (p < 0.01) and tumor necrosis factor-α (TNF-α) (p < 0.05) in LPS-induced MAC-T cells. Moreover, OPCs downregulated LPS-induced phosphorylation of p65 and inhibitor of nuclear factor kappa B (NF-κB) (IκB) in the NF-κB signaling pathway (p < 0.01), and they inhibited p65 translocation from the cytoplasm to the nucleus as revealed by immunofluorescence test and western blot. Additionally, OPCs decreased phosphorylation of p38, extracellular signal regulated kinase and c-jun NH₂-terminal kinase in the MAPK signaling pathway (p < 0.01). In conclusion, the anti-inflammatory and antioxidant activities of OPCs involve NF-κB and MAPK signaling pathways, thus inhibiting expression of pro-inflammatory factors and oxidation indicators. These findings provide novel experimental evidence for the further practical application of OPCs in prevention and treatment of bovine mastitis.

Profiling the transcriptome changes involved in xylose metabolism by the fungus Trichoderma reesei allows for the identification of potential targets for ethanol production processing. In the present study, the transcriptome of T. reesei HJ-48 grown on xylose versus glucose was analyzed using next-generation sequencing technology. During xylose fermentation, numerous genes related to central metabolic pathways, including xylose reductase (XR) and xylitol dehydrogenase (XDH), were expressed at higher levels in T. reesei HJ-48. Notably, growth on xylose did not fully repress the genes encoding enzymes of the tricarboxylic acid and respiratory pathways. In addition, increased expression of several sugar transporters was observed during xylose fermentation. This study provides a valuable dataset for further investigation of xylose fermentation and provides a deeper insight into the various genes involved in this process.

Our previous report determined that miR-144 is a key regulator of intestinal epithelial permeability in irritable bowel syndrome with diarrhea (IBS-D) rats. Recent evidence has shown that lactobacilli play an important role in the relief of IBS-D symptoms. However, few studies have addressed the mechanisms by which microRNAs and lactobacilli exert their beneficial effects on intestinal epithelial permeability. Hence, to elucidate whether miRNAs and lactobacilli play roles in intestinal epithelial barrier regulation, we compared miRNA expression levels in intestinal epithelial cells (IECs) under Lactobacillus casei (L. casei LC01) treatment. IECs and L. casei LC01 were co-cultured and then subjected to microRNA microarray assay. qRT-PCR, western blot and ELISA were used to detect the expression of occludin (OCLN) and zonula occludens 1 (ZO1/TJP1). The interaction between miRNAs and L. casei LC01 acting in IECs was investigated through transfection of RNA oligoribonucleotides and pcDNA 3.1 plasmid. The results are as follows: 1) L. casei LC01 decreased the expression of miR-144 and FD4 and promoted OCLN and ZO1 expression in IECs; 2) L. casei LC01 enhanced the barrier function of IECs via downregulation of miR-144 and upregulation of OCLN and ZO1; 3) Under L. casei LC01 treatment, OCLN and ZO1 overexpression could partially eliminate the promoting effect of miR-144 on intestinal permeability in IECs. Our results demonstrate that L. casei LC01 regulates intestinal permeability of IECs through miR-144 targeting of OCLN and ZO1. L. casei LC01 can be a possible therapeutic target for managing dysfunction of the intestinal epithelial barrier.

Rho guanine nucleotide dissociation inhibitor 1 (RhoGDI1) plays important roles in numerous cellular processes, including cell motility, adhesion, and proliferation, by regulating the activity of Rho GTPases. Its expression is altered in various human cancers and is associated with malignant progression. Here, we show that RhoGDI1 interacts with Cullin 3 (CUL3), a scaffold protein for E3 ubiquitin ligase complexes. Ectopic expression of CUL3 increases the ubiquitination of RhoGDI1. Furthermore, potassium channel tetramerization domain containing 5 (KCTD5) also binds to RhoGDI1 and increases its interaction with CUL3. Ectopic expression of KCTD5 increases the ubiquitination of RhoGDI1, whereas its knockdown by RNA interference has the opposite effect. Depletion of KCTD5 or expression of dominant-negative CUL3 (DN-CUL3) enhances the stability of RhoGDI1. Our findings reveal a previously unknown mechanism for controlling RhoGDI1 degradation that involves a CUL3/KCTD5 ubiquitin ligase complex.

The study of climate and respiratory viral infections using big data may enable the recognition and interpretation of relationships between disease occurrence and climatic variables. In this study, real-time reverse transcription quantitative PCR (qPCR) methods were used to identify Human respiratory coronaviruses (HCoV). infections in patients below 10 years of age with respiratory infections who visited Dankook University Hospital in Cheonan, South Korea, from January 1, 2012, to December 31, 2018. Out of the 9010 patients who underwent respiratory virus real-time reverse transcription qPCR test, 364 tested positive for HCoV infections. Among these 364 patients, 72.8% (n = 265) were below 10 years of age. Data regarding the frequency of infections was used to uncover the seasonal pattern of the two viral strains, which was then compared with local meteorological data for the same time period. HCoV-229E and HCoV-OC43 showed high infection rates in patients below 10 years of age. There was a negative relationship between HCoV-229E and HCoV-OC43 infections with air temperature and wind-chill temperatures. Both HCoV-229E and HCoV-OC43 rates of infection were positively related to atmospheric pressure, while HCoV-229E was also positively associated with particulate matter concentrations. Our results suggest that climatic variables affect the rate in which children below 10 years of age are infected with HCoV. These findings may help to predict when prevention strategies may be most effective.

Drought is a major abiotic factor and has drastically reduced crop yield globally, thus damaging the agricultural industry. Drought stress decreases crop productivity by negatively affecting crop morphological, physiological, and biochemical factors. The use of drought tolerant bacteria improves agricultural productivity by counteracting the negative effects of drought stress on crops. In this study, we isolated bacteria from the rhizosphere of broccoli field located in Daehaw-myeon, Republic of Korea. Sixty bacterial isolates were screened for their growth-promoting capacity, in vitro abscisic acid (ABA), and sugar production activities. Among these, bacterial isolates YNA59 was selected based on their plant growth-promoting bacteria traits, ABA, and sugar production activities. Isolate YNA59 highly tolerated oxidative stress, including hydrogen peroxide (H₂O₂) and produces superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) activities in the culture broth. YNA59 treatment on broccoli significantly enhanced plant growth attributes, chlorophyll content, and moisture content under drought stress conditions. Under drought stress, the endogenous levels of ABA, jasmonic acid (JA), and salicylic acid (SA) increased; however, inoculation of YNA59 markedly reduced ABA (877 ± 22 ng/g) and JA (169.36 ± 20.74 ng/g) content, while it enhanced SA levels (176.55 ± 9.58 ng/g). Antioxidant analysis showed that the bacterial isolate YNA59 inoculated into broccoli plants contained significantly higher levels of SOD, CAT, and APX, with a decrease in GPX levels. The bacterial isolate YNA59 was therefore identified as Variovorax sp. YNA59. Our current findings suggest that newly isolated drought tolerant rhizospheric Variovorax sp. YNA59 is a useful stress-evading rhizobacterium that improved drought-stress tolerance of broccoli and could be used as a bio-fertilizer under drought conditions.

Trimethylamine (TMA) is a well-known off-odor compound in fish and fishery products and is a metabolic product of trimethylamine N-oxide (TMAO) generated by the enzymatic action of microorganisms. The off-odor is a factor that can debase the value of fish and fishery products. The present study aimed to remove TMA using lactic acid bacteria (LAB). A total of fifteen isolates exhibiting the TMA reduction efficacy were isolated from Korean traditional fermented foods. Among these isolates, five LAB isolates (Lactobacillus plantarum SKD 1 and 4; Lactobacillus paraplantarum SKD 15; Pediococcus stilesii SKD 11; P. pentosaceus SKD 14) were selected based on their high TMA reduction efficacy. In situ reduction of TMA efficacy by the LAB cell-free supernatant was evaluated using a spoiled fish sample. The results showed effective TMA reduction by our selected strains: SKD1 (45%), SKD4 (62%), SKD11 (60%), SKD14 (59%), and SKD15 (52%), respectively. This is the first study on TMA reduction by the metabolic activity of LAB and in situ reduction of TMA using cell-free supernatant of LAB. The present finding suggests an economically useful and ecofriendly approach to the reduction of TMA.

Climate change is expected to affect not only availability and quality of water, the valuable resource of human life on Earth, but also ultimately public health issue. A six-year monitoring (total 20 times) of Escherichia coli O157, Salmonella enterica, Legionella pneumophila, Shigella sonnei, Campylobacter jejuni, and Vibrio cholerae was conducted at five raw water sampling sites including two lakes, Hyundo region (Geum River) and two locations near Water Intake Plants of Han River (Guui region) and Nakdong River (Moolgeum region). A total 100 samples of 40 L water were tested. Most of the targeted bacteria were found in 77% of the samples and at least one of the target bacteria was detected (65%). Among all the detected bacteria, E. coli O157 were the most prevalent with a detection frequency of 22%, while S. sonnei was the least prevalent with a detection frequency of 2%. Nearly all the bacteria (except for S. sonnei) were present in samples from Lake Soyang, Lake Juam, and the Moolgeum region in Nakdong River, while C. jejuni was detected in those from the Guui region in Han River. During the six-year sampling period, individual targeted noxious bacteria in water samples exhibited seasonal patterns in their occurrence that were different from the indicator bacteria levels in the water samples. The fact that they were detected in the five Korea's representative water environments make it necessary to establish the chemical and biological analysis for noxious bacteria and sophisticated management systems in response to climate change.

Synthetic dyes are widely used in various industries and their wastage causes severe environmental problems while being hazardous to human health, leading to the need for eco-friendly degradation techniques. The split-gill fungus Schizophyllum commune, which is found worldwide, has the potential to degrade all components of the lignocellulosic biomass and is a candidate for the treatment of synthetic dyes. A systematic molecular analysis of 75 Korean and 6 foreign S. commune strains has revealed the high genetic diversity of this population and its important contribution to the total diversity of S. commune. We examined the dye decolorization ability of this population and revealed 5 excellent strains that strongly decolorized 3 dyes: Crystal Violet, Congo Red and Methylene Blue. Finally, comparison of dye decolorization ability and the phylogenetic identification of these strains generalized their genetic and physiological diversity. This study provides an initial resource for physiological and genetic research projects as well as the bioremediation of textile dyes.

Dekkera anomala YAE-1 strain separated from "airag" (Mongolian fermented mare's milk) produces β-glucosidase, which can convert ginsenoside Rb₁ from Panax ginseng. Ginseng- derived bioactive components such as ginsenoside Rb₁ have various immunological and anticancer activities. Airag was collected from five different mare milk farms located near Ulaanbaatar, Mongolia. YAE-1 strains were isolated from airag to examine the hydrolytic activities of β-glucosidase on Korean Panax ginseng using an API ZYM kit. Supernatants of selected cultures having β-glucosidase activity were examined for hydrolysis of the major ginsenoside Rb₁ at 40℃, pH 5.0. The YAE-1 strain was found to be nearly identical at 99.9% homology with Dekkera anomala DB-7B, and was thus named Dekkera anomala YAE-1. This strain exerted higher β-glucosidase activity than other enzymes. Reaction mixtures from Dekkera anomala YAE-1 showed great capacity for converting ginsenoside Rb₁ to ginsenoside Rd. The β-glucosidase produced by Dekkera anomala YAE-1 was able to hydrolyze ginsenoside Rb₁ and convert it to Rd during fermentation of the ginseng. The amount of ginsenoside Rd was highly increased from 0 to 1.404 mg/ml in fermented 20% ginseng root at 7 days.

Panax ginseng has a wide range of activities including a neuroprotective effect, skin protective effects, enhanced DNA repairing, anti-diabetic activity, and protective effects against vascular inflammation. In the present study, we sought to discover the inhibitory effects of a mixture of natural products containing Panax ginseng, Ziziphus jujube, Rubi fructus, Artemisiae asiaticae and Scutellaria baicalensis (PZRAS) on osteoclastogenesis and bone remodeling, as neither the effects of a mixture containing Panax ginseng extract, nor its molecular mechanism on bone inflammation, have been clarified yet. PZRAS upregulated the levels of catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GSH-R) and glutathione peroxidase (GSH-Px) and reduced malondialdehyde (MDA) in LPS-treated RAW264.7 cells. Moreover, treatment with PZRAS decreased the production of IL-1β and TNF-α. PZRAS also inhibited osteoclast differentiation through inhibiting osteoclastspecific genes like MMP-2, 9, cathepsin K, and TRAP in RANKL-treated RAW264.7 cells. Additionally, PZRAS has inhibitory functions on the RANKL-stimulated activation of ERK and JNK, which lead to a decrease in the expression of NFATc1 and c-Fos. In an in vivo study, bone resorption induced by LPS was recovered by treatment with PZRAS in bone volume per tissue volume (BV/TV) compared to control. Furthermore, the ratio of eroded bone surface of femurs was significantly increased in LPS-treated mice compared to vehicle group, but this ratio was significantly reversed in PZRAS-treated mice. These results suggest that PZRAS could prevent or treat disorders with abnormal bone loss.

With an increase in the consumption of non-heated fresh food, foodborne shiga toxin-producing Escherichia coli (STEC) has emerged as one of the most problematic pathogens worldwide. Endolysin, a bacteriophage-derived lysis protein, is able to lyse the target bacteria without any special resistance, and thus has been garnering interest as a powerful antimicrobial agent. In this study, rV5-like phage endolysin targeting E. coli O157:H7, named as LysECP26, was identified and purified. This endolysin had a lysozyme-like catalytic domain, but differed markedly from the sequence of lambda phage endolysin. LysECP26 exhibited strong activity with a broad lytic spectrum against various gram-negative strains (29/29) and was relatively stable at a broad temperature range (4℃-55℃). The optimum temperature and pH ranges of LysECP26 were identified at 37℃-42℃ and pH 7-8, respectively. NaCl supplementation did not affect the lytic activity. Although LysECP26 was limited in that it could not pass the outer membrane, E. coli O157: H7 could be effectively controlled by adding ethylenediaminetetraacetic acid (EDTA) and citric acid (1.44 and 1.14 log CFU/ml) within 30 min. Therefore, LysECP26 may serve as an effective biocontrol agent for gram-negative pathogens, including E. coli O157:H7.

Compound K (C-K) is one of the most pharmaceutically effective ginsenosides, but it is absent in natural ginseng. However, C-K can be obtained through the hydrolysis of protopanaxadiol-type ginsenosides (PPDGs) in natural ginseng. The aim of this study was to obtain the high concentration of food-available C-K using PPDGs in Korean ginseng extract by an extracellular enzyme from Aspergillus niger KACC 46495. A. niger was cultivated in the culture medium containing the inducer carboxymethyl cellulose (CMC) for 6 days. The extracellular enzyme extracted from A. niger was prepared from the culture broth by filtration, ammonium sulfate, and dialysis. The extracellular enzyme was used for C-K production using PPDGs. The glycoside-hydrolyzing pathways for converting PPDGs into C-K by the extracellular enzyme were Rb1 → Rd → F2 → C-K, Rb2 → Rd or compound O → F2 or compound Y → C-K, and Rc → Rd or compound Mc1 → F2 or compound Mc → C-K. The extracellular enzyme from A. niger at 8.0 mg/ml, which was obtained by the induction of CMC during the cultivation, converted 6.0 mg/ml (5.6 mM) PPDGs in Korean ginseng extract into 2.8 mg/ml (4.5 mM) food-available C-K in 9 h, with a productivity of 313 mg/l/h and a molar conversion of 80%. To the best of our knowledge, the productivity and concentration of C-K of the extracellular enzyme are the highest among those by crude enzymes from wild-type microorganisms.

Ultraviolet (UV) is one of the major factors harmful to skin health. Irradiation with ultraviolet accelerates the decline of skin function, causing the skin to have deep wrinkles, dryness, decreased procollagen production, and degradation of collagen. Novel materials are needed to prevent the aging of the skin by blocking the effects of UV. Safflower seed oil (Charthamus tinctorius L., SSO) contains significantly high levels of unsaturated fatty acids and phytochemicals. SSO has been traditionally used in China, Japan, and Korea to improve skin and hair. Our objective in this study was to determine the effect of SSO and its active compound acacetin on UVB-induced skin photoaging in HaCaT cells and human dermal fibroblasts (HDF). SSO inhibited UVB-induced matrix metalloproteinase-1 (MMP-1) at both protein and mRNA levels in HaCaT cells and HDF. MMP-1 is known to play important roles in collagen degradation and wrinkle formation. Acacetin, a type of flavonoid, is present in SSO. Similar to SSO, acacetin also inhibited UVB-induced MMP-1 protein and mRNA levels in HaCaT cells and HDF. MMP-1 mRNA is primarily regulated by the mitogen-activated kinase (MAPK) signaling pathway. Acacetin regulated the phosphorylation of JNK1/2 and c-jun, but did not inhibit the phosphorylation of ERK1/2, p38 and AKT. Taken together, these results indicate that SSO and its active compound acacetin can prevent UVB-induced MMP-1 expression, which leads to skin photoaging, and may therefore have therapeutic potential as an anti-wrinkle agent to improve skin health.

Flavonoids have diverse biological functions in human health. All flavonoids contain a common 2-phenyl chromone structure (C6-C3-C6) as a scaffold. Hence, in using such a scaffold, plenty of high-value-added flavonoids can be synthesized by chemical or biological catalyzation approaches. (2S)-Naringenin is one of the most commonly used flavonoid scaffolds. However, biosynthesizing (2S)-naringenin has been restricted not only by low production but also by the expensive precursors and inducers that are used. Herein, we established an induction-free system to de novo biosynthesize (2S)-naringenin in Escherichia coli. The tyrosine synthesis pathway was enhanced by overexpressing feedback inhibition-resistant genes (aroG^fbr and tyrA^fbr) and knocking out a repressor gene (tyrR). After optimizing the fermentation medium and conditions, we found that glycerol, glucose, fatty acids, potassium acetate, temperature, and initial pH are important for producing (2S)-naringenin. Using the optimum fermentation medium and conditions, our best strain, Nar-17LM1, could produce 588 mg/l (2S)-naringenin from glucose in a 5-L bioreactor, the highest titer reported to date in E. coli.

CRISPR/Cpf1 has emerged as a new CRISPR-based genome editing tool because, in comparison with CRIPSR/Cas9, it has a different T-rich PAM sequence to expand the target DNA sequence. Single-base editing in the microbial genome can be facilitated by oligonucleotide-directed mutagenesis (ODM) followed by negative selection with the CRISPR/Cpf1 system. However, single point mutations aided by Cpf1 negative selection have been rarely reported in Corynebacterium glutamicum. This study aimed to introduce an amber stop codon in crtEb encoding lycopene hydratase, through ODM and Cpf1-mediated negative selection; deficiency of this enzyme causes pink coloration due to lycopene accumulation in C. glutamicum. Consequently, on using double-, triple-, and quadruple-base-mutagenic oligonucleotides, 91.5-95.3% pink cells were obtained among the total live C. glutamicum cells. However, among the negatively selected live cells, 0.6% pink cells were obtained using single-base-mutagenic oligonucleotides, indicating that very few single-base mutations were introduced, possibly owing to mismatch tolerance. This led to the consideration of various target-mismatched crRNAs to prevent the death of single-base-edited cells. Consequently, we obtained 99.7% pink colonies after CRISPR/Cpf1-mediated negative selection using an appropriate single-mismatched crRNA. Furthermore, Sanger sequencing revealed that single-base mutations were successfully edited in the 99.7% of pink cells, while only two of nine among 0.6% of pink cells were correctly edited. The results indicate that the target-mismatched Cpf1 negative selection can assist in efficient and accurate single-base genome editing methods in C. glutamicum.

The aerobic growth and metabolic performance of Escherichia coli strains BL21 and W3110 were studied when the Vitreoscilla hemoglobin (VHb) was constitutively expressed in the chromosome. When VHb was expressed, acetate production decreased in both strains and was nearly eliminated in BL21. Transcriptional levels of the glyoxylate shunt genes decreased in both strains when VHb was expressed. However, higher transcription of the α-ketoglutarate dehydrogenase genes were observed for W3110, while for BL21 transcription levels decreased. VHb expression reduced the transcription of the cytochrome bo₃ genes only in BL21. These results are useful for better selecting a production host.

Transcription factor engineering to regulate multiple genes has shown promise in the field of microalgae genetic engineering. Here, we report the first use of transcription factor engineering in Chlorella sp. HS2, thought to have potential for producing biofuels and bioproducts. We identified seven endogenous bZIP transcription factors in Chlorella sp. HS2 and named them HSbZIP1 through HSbZIP7. We overexpressed HSbZIP1, a C-type bZIP transcription factor, in Chlorella sp. HS2 with the goal of enhancing lipid production. Phenotype screening under heterotrophic conditions showed that all transformants exhibited increased fatty acid production. In particular, HSbZIP1 37 and 58 showed fatty acid methyl ester (FAME) yields of 859 and 1,052 mg/l, respectively, at day 10 of growth under heterotrophic conditions, and these yields were 74% and 113% higher, respectively, than that of WT. To elucidate the mechanism underlying the improved phenotypes, we identified candidate HSbZIP1-regulated genes via transcription factor binding site analysis. We then selected three genes involved in fatty acid synthesis and investigated mRNA expression levels of the genes by qRT-PCR. The result revealed that the possible HSbZIP1-regulated genes involved in fatty acid synthesis were upregulated in the HSbZIP1 transformants. Taken together, our results demonstrate that HSbZIP1 can be utilized to improve lipid production in Chlorella sp. HS2 under heterotrophic conditions.