• Korean Journal of Head & Neck Oncology
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• v.39 no.1
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• pp.1-9
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• 2023

Technological advancement in human genome analysis and ICT (information & communication technologies) brought 'precision medicine' into our clinical practice. Precision medicine is a novel medical approach that provides personalized treatments tailored to each individual by precisely segmenting patient populations, based on robust data including a person's genetic information, disease information, lifestyle information, etc. Precision medicine has a potential to be applied to treating a range of tumors, in addition to non-small cell lung cancer, in which precision oncology has been actively practiced. In this article, we are reviewing precision medicine in head and neck cancer (HNC) with focus on tumor agnostic biomarkers and treatments such as NTRK, MSI-H/dMMR, TMB-H and BRAF V600E, all of which were recently approved by U.S. Food and Drug Administration (FDA).

• Korean Journal of Poultry Science
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• v.50 no.3
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• pp.187-191
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• 2023

Korean native ducks (KNDs) continue to have a high preference from consumers due to their excellent meat quality and taste characteristics. However, due to low productivity and fixed plumage color phenotype, it could not secure a large share in the domestic market compared to imported species. In order to improve the market share of KNDs, the genetic characteristics of the breed should be identified and used for improvement and selection. Therefore, this study was conducted to identify the genetic information of colored and white KNDs using next-generation resequencing data and screening for differences between the two groups. As a result of the analysis, the genetic variants that showed significant differences between the colored and white KND groups were mainly identified as mutations related to tyrosine activity. The variants were located in the genes that affect melanin synthesis and regulation, such as EGFR, PDGFRA, and DDR2, and these were reported as the candidate genes related to plumage pigmentation in poultry. Therefore, the results of this study are expected to be useful as a basis for understanding and utilizing the genetic characteristics of KNDs for genetic improvement and selection of white broiler KNDs.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1050-1056
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• 2023

Weizmannia coagulans (formerly Bacillus coagulans) is Gram-positive, and spore-forming bacteria causing food spoilage, especially in acidic canned food products. To control W. coagulans, we isolated a bacteriophage Youna2 from a sewage sludge sample. Morphological analysis revealed that phage Youna2 belongs to the Siphoviridae family with a non-contractile and flexible tail. Youna2 has 52,903 bp double-stranded DNA containing 61 open reading frames. There are no lysogeny-related genes, suggesting that Youna2 is a virulent phage. plyYouna2, a putative endolysin gene was identified in the genome of Youna2 and predicted to be composed of a N-acetylmuramoyl-L-alanine amidase domain (PF01520) at the N-terminus and unknown function DUF5776 domain (PF19087) at the C-terminus. While phage Youna2 has a narrow host range, infecting only certain strains of W. coagulans, PlyYouna2 exhibited a broad antimicrobial spectrum beyond the Bacillus genus. Interestingly, PlyYouna2 can lyse Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica, Pseudomonas putida and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. To the best of our knowledge, Youna2 is the first W. coagulans-infecting phage and we speculate its endolysin PlyYouna2 can provide the basis for the development of a novel biocontrol agent against various foodborne pathogens.

• Genomics & Informatics
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• v.21 no.4
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• pp.49.1-49.11
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• 2023

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.

• Clinical Nutrition Research
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• v.12 no.1
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• pp.40-53
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• 2023

Differential bitterness perception associated with genetic polymorphism in the bitter taste receptor gene taste 2 receptor member 38 (TAS2R38) may influence an individual's food preferences, nutrition consumption, and eventually chronic nutrition-related disorders including cardiovascular disease. Therefore, the effect of genetic variations on nutritional intake and clinical markers needs to be elaborated for health and disease prevention. In this study, we conducted sex-stratified analysis to examine the association between genetic variant TAS2R38 rs10246939 A > G with daily nutritional intake, blood pressure, and lipid parameters in Korean adults (males = 1,311 and females = 2,191). We used the data from the Multi Rural Communities Cohort, Korean Genome and Epidemiology Study. Findings suggested that the genetic variant TAS2R38 rs10246939 was associated with dietary intake of micronutrients including calcium (adjusted p = 0.007), phosphorous (adjusted p = 0.016), potassium (adjusted p = 0.022), vitamin C (adjusted p = 0.009), and vitamin E (adjusted p = 0.005) in females. However, this genetic variant did not influence blood glucose, lipid profile parameters, and other blood pressure markers. These may suggest that this genetic variation is associated with nutritional intake, but its clinical effect was not found. More studies are needed to explore whether TAS2R38 genotype may be a potential predictive marker for the risk of metabolic diseases via modulation of dietary intake.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.374-389
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• 2023

Organophosphorus (OP) pesticides, particularly malathion, parathion, diazinon, and chlorpyrifos, are widely used in both agricultural and residential contexts. This refractory quality is shared by certain organ phosphorus insecticides, and it may have unintended consequences for certain non-target soil species. Bioremediation cleans organic and inorganic contaminants using microbes and plants. Organophosphate-hydrolyzing enzymes can transform pesticide residues into non-hazardous byproducts and are increasingly being considered viable solutions to the problem of decontamination. When coupled with system analysis, the multi-omics technique produces important data for functional validation and genetic manipulation, both of which may be used to boost the efficiency of bioremediation systems. RNA-guided nucleases and RNA-guided base editors include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR), which are used to alter genes and edit genomes. The review sheds light on key knowledge gaps and suggests approaches to pesticide cleanup using a variety of microbe-assisted methods. Researches, ecologists, and decision-makers can all benefit from having a better understanding of the usefulness and application of systems biology and gene editing in bioremediation evaluations.

• Journal of Microbiology and Biotechnology
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• v.34 no.9
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• pp.1819-1825
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• 2024

An aerobic, Gram-stain-negative, catalase-positive, rod-shaped, and motile bacteria, designated as a strain WR6^T was isolated from soil in Republic of Korea. Strain WR6^T grew at temperatures of 10-37℃, at pH of 5.0-9.0, and at NaCl concentrations of 0-3.0% (w/v). Phylogenetic and 16S rRNA gene nucleotide sequence analysis confirmed that strain WR6^T affiliated to the genus Mesorhizobium, with the nearest relative being Mesorhizobium waimense ICMP 19557^T (98.5%). The genome of strain WR6^T was 5,035,462 bp with DNA G+C content of 62.6%. In strain WR6^T, Q-10 was sole ubiquinone; summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_19:0 cyclo ω8c were predominant fatty acids; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, and phosphatidylethanolamine were major polar lipids. Based on these polyphasic taxonomic data, strain WR6^T represents a novel species in the genus Mesorhizobium. Accordingly, we propose the name Mesorhizobium koreense sp. nov., with the type strain WR6^T (=KCTC 92695^T =NBRC 116021^T).

• Journal of Life Science
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• v.20 no.4
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• pp.481-486
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• 2010

The rates of synonymous and nonsynonymous nucleotide substitutions were studied for sequences of nuclear and chloroplast genes in Sorbus aucuparia. Results suggested that DNA evolution in this species had taken place, on average, at a slower rate in the chloroplast genes than in the nuclear genes: a rate variation pattern similar to those observed in eudicot plants. Within the nucleus, the synonymous substitution rates (Ks) (2.45-2.60) were two-fold higher than nonsynonymous substitution rates (Ka) (1.15-1.30). More notably, the values of Ks (1.20-1.26) were about six-fold higher than those of Ka (0.26-0.42) within the chloroplast genome. Ka/Ks ratios for nuclear and chloroplast genes of S. aucuparia had mean values of 0.178 and 0.056, respectively. A Ka/Ks ratio < 1 indicated negative (purifying) selection. The chloroplast genes had a lower effective number of codons (ENC) values (22.4-32.2) than those of nuclear genes (35.8-38.7). The analysis of the G+C content indicated that the chloroplast genes in this investigation had a higher preference for synonymous codons ending with A and T (G+C content range, 28.4-29.1%) where there was a slight bias toward codons ending with G+C (63.2-64.2%) in the nuclear genome.

• Microbiology and Biotechnology Letters
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• v.38 no.1
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• pp.40-45
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• 2010

The gene encoding $\beta$-agarase (agaB) which hydrolyzes $\beta$-1,4 linkages of agarose from Zobellia galactanivorans was cloned and fused to Saccharomyces cerevisiae mating factor alpha-1 secretion signal ($MF{\alpha}1$), in which the transcription of $MF{\alpha}1$-AgaB was under the control of AOX1 (alcohol oxidase 1, methanol inducible) promoter. The constructed plasmid pPIC-AgaB (9 kb) was integrated into HIS4 gene locus of Pichia pastoris genome. Successful integration was confirmed by performing colony PCR. The transformed cells showed red halos around its colonies in methanol agar plate by adding iodine solution, indicating the active expression of agaB in P.pastoris. By SDS-PAGE and zymographic analysis, the molecular weight of $\beta$-agarase was estimated to be a 53 kDa and about 15% N-linked glycosylation was occurred. The activity of extracellular $\beta$-agarase reached 1.34, 1.42 and 1.53 units/mL by inducing 0.1, 0.5, and 1% methanol, respectively, at baffled flask culture of P.pastoris GS115/pPIC-AgaB for 48 hr. Most of the enzyme activity was found in the extacellular fraction and the secretion efficiency showed 98%. Thermostability of recombinant $\beta$-agarase was also increased by glycosylation.

• Journal of Life Science
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• v.30 no.3
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• pp.304-312
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• 2020

Agarase can be used in the field of basic science, as well as for production of agar-derived high-functional oligosaccharides and bioenergy production using algae. In 2012, we summarized the classification, origin, production, and applications of agar. In this paper, we briefly review the literature on the recombinant expression of agarases from 2012 to the present. Agarase genes originated from 19 genera, including Agarivorans, Flammeovirga, Pseudoalteromonas, Gayadomonas, Catenovulum, Microbulbifer, Cellulophaga, Saccharophagus, Simiduia, and Vibrio. Of the 47 recombinant agarases, there were only two α-agarases, while the rest were β-agarases. All α-agarases produced agarotetraose, while β-agarases yielded many neoagarooligosaccharides ranging from neoagarobiose to neoagarododecaose. The optimum temperature ranged between 25 and 60℃, and the optimum pH ranged from 3.0 to 8.5. There were 14 agarases with an optimum temperature of 50℃ or higher, where agar is in sol state after melting. Artificial mutations, including manipulation of carbohydrate-binding modules (CBM), increased thermostability and simultaneously raised the optimum temperature and activity. Many hosts and secretion signals or riboswitches have been used for recombinant expression. In addition to gene recombination based on the amino acid sequence after agarase purification, recombinant expression of the putative agarase genes after genome sequencing and metagenome-derived agarases have been studied. This study is expected to be actively used in the application fields of agarase and agarase itself.