• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2030-2035
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• 2016

Bacillus cereus causes food-borne illness through contaminated foods; therefore, its pathogenicity and genome sequences have been analyzed in several studies. We sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents, 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico DNA-DNA hybridization values, B. cereus ATCC $14579^T$ was closest to FORC_021 among the complete genome-sequenced strains. Three major enterotoxins were detected in FORC_021. Comparative genomic analysis of FORC_021 with ATCC $14579^T$ revealed that FORC_021 harbored an additional genomic region encoding virulence factors, such as putative ADP-ribosylating toxin, spore germination protein, internalin, and sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021 exhibited a high level of cytotoxicity toward INT-407 human epithelial cells. This genomic information of FORC_021 will help us to understand its pathogenesis and assist in managing food contamination.

• Journal of Applied Biological Chemistry
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• v.63 no.3
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• pp.189-195
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• 2020

The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1403-1414
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• 2010

Aspergillus awamori BTMFW032, isolated from sea water, produced tannase as an extracellular enzyme under submerged culture conditions. Enzymes with a specific activity of 2,761.89 IU/mg protein, a final yield of 0.51%, and a purification fold of 6.32 were obtained after purification through to homogeneity, by ultrafiltration and gel filtration. SDS-PAGE analyses, under nonreducing and reducing conditions, yielded a single band of 230 kDa and 37.8 kDa, respectively, indicating the presence of six identical monomers. A pI of 4.4 and a carbohydrate content of 8.02% were observed in the enzyme. The optimal temperature was found to be $30^{\circ}C$, although the enzyme was active in the range of $5-80^{\circ}C$. Two pH optima, pH 2 and pH 8, were recorded, although the enzyme was instable at a pH of 8, but stable at a pH of 2.0 for 24 h. Methylgallate recorded maximal affinity, and $K_m$ and $V_{max}$ were recorded at $1.9{\times}10^{-3}$M and 830 ${\mu}Mol$/min, respectively. The impacts of a number of metal salts, solvents, surfactants, and other typical enzyme inhibitors on tannase activity were determined in order to establish the novel characteristics of the enzyme. The gene encoding tannase, isolated from A. awamori, was found to be 1.232 kb, and nucleic acid sequence analysis revealed an open reading frame consisting of 1,122 bp (374 amino acids) of one stretch in the -1 strand. In silico analyses of gene sequences, and a comparison with reported sequences of other species of Aspergillus, indicate that the acidophilic tannase from marine A. awamori differs from that of other reported species.

• BMB Reports
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• v.40 no.1
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• pp.95-99
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• 2007

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

• The Journal of Internal Korean Medicine
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• v.41 no.6
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• pp.1078-1088
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• 2020

Objective: The purpose of this study was to investigate the effect of amorfrutin of licorice for Type2 diabetes mellitus. Method: The PubMed, CNKI, Wanfang, OASIS, NDSL, J-STAGE, and CiNii databases were searched from the beginning of the search to September 20, 2020, with no limits on language. Extractions and selections from the literature were made by two authors. The study included in vivo experiments with amorfrutins in high-fat diet-induced obesity C57BL/6 mice and leptin receptor-deficient db/db mice and in silico studies. Results & Conclusion: Four studies were finally selected. We confirmed that amorfrutin treatment considerably improved insulin sensitivity and glucose tolerance and reduced plasma insulin and glucose. Amorfrutins bind to and selectively activate Peroxisome Proliferator-Activated Receptor Gamma (PPARγ), which plays an important role in glucose metabolism. Amorfrutins also strongly bind to the glucagon receptor (GCGR) and work as antagonist. Using the amorfrutins from licorice could therefore be helpful in treating type2 diabetes mellitus.

• Journal of Veterinary Science
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• v.19 no.6
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• pp.771-781
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• 2018

Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.

• Genomics & Informatics
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• v.19 no.4
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• pp.47.1-47.12
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• 2021

Kaposi's sarcoma-associated herpesvirus (KSHV) is one of the few human oncogenic viruses, which causes a variety of malignancies, including Kaposi's sarcoma, multicentric Castleman disease, and primary effusion lymphoma, particularly in human immunodeficiency virus patients. The currently available treatment options cannot always prevent the invasion and dissemination of this virus. In recent times, siRNA-based therapeutics are gaining prominence over conventional medications as siRNA can be designed to target almost any gene of interest. The ORF57 is a crucial regulatory protein for lytic gene expression of KSHV. Disruption of this gene translation will inevitably inhibit the replication of the virus in the host cell. Therefore, the ORF57 of KSHV could be a potential target for designing siRNA-based therapeutics. Considering both sequence preferences and target site accessibility, several online tools (i-SCORE Designer, Sfold web server) had been utilized to predict the siRNA guide strand against the ORF57. Subsequently, off-target filtration (BLAST), conservancy test (fuzznuc), and thermodynamics analysis (RNAcofold, RNAalifold, and RNA Structure web server) were also performed to select the most suitable siRNA sequences. Finally, two siRNAs were identified that passed all of the filtration phases and fulfilled the thermodynamic criteria. We hope that the siRNAs predicted in this study would be helpful for the development of new effective therapeutics against KSHV.

• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.65-74
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• 2021

Serine proteases are the most versatile proteolytic enzymes with tremendous applications in various industrial processes. This study was designed to investigate the biochemical properties, critical residues, and the catalytic potential of alkaline serine protease using in-silico approaches. The primary sequence was analyzed using ProtParam, SignalP, and Phyre2 tools to investigate biochemical properties, signal peptide, and secondary structure, respectively. The three-dimensional structure of the enzyme was modeled using the MODELLER program present in Discovery Studio followed by Molecular Dynamics simulation using GROMACS 5.0.7 package with CHARMM36m force field. The proteolytic potential was measured by performing docking with casein- and keratin-enriched residues, while the effect of the inhibitor was studied using phenylmethylsulfonyl fluoride, (PMSF) applying GOLDv5.2.2. Molecular weight, instability index, aliphatic index, and isoelectric point for serine protease were 39.53 kDa, 27.79, 82.20 and 8.91, respectively. The best model was selected based on the lowest MOLPDF score (1382.82) and DOPE score (-29984.07). The analysis using ProSA-web revealed a Z-score of -9.7, whereas 88.86% of the residues occupied the most favored region in the Ramachandran plot. Ser327, Asp138, Asn261, and Thr326 were found as critical residues involved in ligand binding and execution of biocatalysis. Our findings suggest that bioengineering of these critical residues may enhance the catalytic potential of this enzyme.

• Journal of the Korean Chemical Society
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• v.67 no.1
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• pp.19-27
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• 2023

During the past few decades, toxicity science is shifting from observative to predictive science. New approach methodologies (NAMs), including in chemico, in silico, in vitro approach, gain attention to reduce, refine, replace the whole animal toxicity testing. However, actual acceptances of NAMs in regulatory decision-making have been limited due to low confidence. To address the current constraints, Accelerating the Pace of Chemical Risk Assessment (APCRA) initiative conducted several case studies and presented the perspectives of next generation risk assessment (NGRA). In this review, we suggested a concept and perspectives of NGRA through analysis on APCRA case studies.

• Natural Product Sciences
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• v.28 no.2
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• pp.45-52
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• 2022

The identification of Plasmodium falciparum enoyl acyl-carrier protein reductase (pfENR) is considered as a potential biological target against malaria. Trema orientalis is considered a rich source of phytochemicals useful in malaria treatment. This study evaluated the in-vitro inhibitory activity of the extract and isolated compounds of T. orientalis leaf; the isolated compounds and the analogues of the most active compound were subjected to in-silico molecular docking studies on pfENR. The methanolic extract of T. orientalis was subjected to repeated chromatographic separation which led to the isolation of some compounds. The isolated compounds from the plant were examined for their antimalarial activity using β-hematin inhibition assay. Virtual screening via molecular docking and ADMET studies were conducted to gain insight into the mechanism of binding of ligand and to identify effective pfENR inhibitors. The isolated compounds and the analogues of the most active isolates were gotten from PubChem library for use in docking study. Hexacosanol and β-sitosterol showed inhibition of the β-hematin formation. The docking results showed that hexacosanol, β-sitosterol and the analogues of β-sitosterol displayed binding energy ranging between -6.1 kcal/mol and -11.6 kcal/mol. Sitosterol glucoside has the highest docking score. Some of the ligands showed more binding affinity than known bioactive compounds used as reference. Analogues of β-sitosterol has been shown to be potential inhibitors of pfENR, therefore, the findings from this study suggest that sitosterol glucoside and ergosterol peroxide could act as antimalarial agents after further lead optimisation investigations.