• Genomics & Informatics
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• 제17권1호
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• pp.5.1-5.9
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• 2019

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the $Ad{\acute{e}}lie$ (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins' transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.

• Journal of Applied Biological Chemistry
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• 제62권1호
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• pp.31-38
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• 2019

Scutellaria baicalensis Georgi (Scutellariae Radix)는 이뇨제, 고지혈증, 항박테리아, 항알레르기, 항염증제 및 항암제와 같은 건강보조식 및 전통 생약으로도 널리 사용되어 왔다. 본 연구에서 복잡한 S. baicalensis 추출물에서 지표 물질 또는 유효화합물들을 분리하는 것은 신원 확인 및 생리활성 평가를 위한 필수적인 단계다. 8개의 성분들로 구성된 타겟 분획물을 두개의 gradient elution를 사용하여 고성능 액체 크로마토 그래피에서 분석하였다. 중압 액체크로마토그래피 및 개방형칼럼으로 분취를 시뮬레이션함으로 예비실험에서 충분히 분리가 되도록 용리 조건을 결정할 수 있었다. 최적 분취방법으로 확보된 표준유효분획물로부터 8개의 지표성분들이 포함된 것을 확인하였다. 또한, 분획물은 UPLC-QTof-MS 비교 분석으로 MS, UV, HRESIMS 결과를 확인할 수 있었다. 따라서, 스케일 업 실험법은 S. baicalensis 추출물에 성공적으로 적용될 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제29권5호
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• pp.687-695
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• 2019

In a previous work, we performed de novo RNA sequencing of Allomyrina dichotoma using next generation sequencing and identified several antimicrobial peptide candidates based on transcriptome analysis. Among them, a cationic antimicrobial peptide, allomyrinasin, was selected bioinformatically based on its physicochemical properties. Here, we assessed the antimicrobial and anti-inflammatory activities of allomyrinasin against microorganisms and mouse macrophage Raw264.7 cells. Allomyrinasin showed antimicrobial activities against various microbes and decreased the nitric oxide production of the lipopolysaccharide-induced Raw264.7 cells. Furthermore, quantitative RT-PCR and ELISA revealed that allomyrinasin reduced cytokine expression levels in the Raw264.7 cells. We also identified inducible nitric oxide synthase, cyclooxygenase-2 expression, and $PGE_2$ production through western blot analysis and ELISA. We confirmed that allomyrinasin bound to bacterial cell membranes via a specific interaction with lipopolysaccharides. Taken together, these data indicate that allomyrinasin has antimicrobial and anti-inflammatory activities as exemplified in lipopolysaccharide-induced Raw264.7 cells. We have provided a potentially useful antimicrobial peptide candidate that has both antimicrobial and anti-inflammatory activities.

• Journal of Genetic Medicine
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• 제16권1호
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• pp.39-42
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• 2019

KBG syndrome is an autosomal dominant syndrome presenting with macrodontia, distinctive facial features, skeletal anomalies, and neurological problems caused by mutations in the ankyrin repeat domain 11 (ANKRD11) gene. The diagnosis of KBG is difficult in very young infants as the characteristic macrodontia and typical facial features are not obvious. The youngest patient diagnosed to date was almost one year of age. We here describe a 2-month-old Korean boy with distinctive craniofacial features but without any evidence of macrodontia due to his very early age. He also had a congenital megacolon without ganglion cells in the rectum. A de novo deletion of exons 5-9 of the ANKRD11 gene was identified in this patient by exome sequencing and real-time genomic polymerase chain reaction. As ANKRD11 is involved in the development of myenteric plexus, a bowel movement disorder including a congenital megacolon is not surprising in a patient with KBG syndrome and has possibly been overlooked in past cases.

• The Plant Pathology Journal
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• 제37권6호
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• pp.619-631
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• 2021

Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.

• Journal of Microbiology and Biotechnology
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• 제32권6호
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• pp.730-739
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• 2022

Methicillin-resistant Staphylococcus aureus (MRSA) causes severe infections and poses a global healthcare challenge. The utilization of novel molecules which confer synergistical effects to existing MRSA-directed antibiotics is one of the well-accepted strategies in lieu of de novo development of new antibiotics. Thymol is a key component of the essential oil of plants in the Thymus and Origanum genera. Despite the absence of antimicrobial potency, thymol is known to inhibit MRSA biofilm formation. However, the anti-MRSA activity of thymol analogs is not well characterized. Here, we assessed the antimicrobial activity of several thymol derivatives and found that 4-chloro-2-isopropyl-5-methylphenol (chlorothymol) has antimicrobial activity against MRSA and in addition it also prevents biofilm formation. Chlorothymol inhibited staphyloxanthin production, slowed MRSA motility, and altered bacterial cell density and size. This compound also showed a synergistic antimicrobial activity with oxacillin against highly resistant S. aureus clinical isolates and biofilms associated with these isolates. Our results demonstrate that chlorinated thymol derivatives should be considered as a new lead compound in anti-MRSA therapeutics.

• Genomics & Informatics
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• 제19권4호
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• pp.40.1-40.11
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• 2021

Mutation signatures represent unique sequence footprints of somatic mutations resulting from specific DNA mutagenic and repair processes. However, their causal associations and the potential utility for genome research remain largely unknown. In this study, we performed PanCancer-scale correlative analyses to identify the genomic features associated with tumor mutation burdens (TMB) and individual mutation signatures. We observed that TMB was correlated with tumor purity, ploidy, and the level of aneuploidy, as well as with the expression of cell proliferation-related genes representing genomic covariates in evaluating TMB. Correlative analyses of mutation signature levels with genes belonging to specific DNA damage-repair processes revealed that deficiencies of NHEJ1 and ALKBH3 may contribute to mutations in the settings of APOBEC cytidine deaminase activation and DNA mismatch repair deficiency, respectively. We further employed a strategy to identify feature-driven, de novo mutation signatures and demonstrated that mutation signatures can be reconstructed using known causal features. Using the strategy, we further identified tumor hypoxia-related mutation signatures similar to the APOBEC-related mutation signatures, suggesting that APOBEC activity mediates hypoxia-related mutational consequences in cancer genomes. Our study advances the mechanistic insights into the TMB and signature-based DNA mutagenic and repair processes in cancer genomes. We also propose that feature-driven mutation signature analysis can further extend the categories of cancer-relevant mutation signatures and their causal relationships.

• 한국식품과학회지
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• 제54권4호
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• pp.398-402
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• 2022

본 연구에서는 폴리페놀 함유 블랙 초크베리가 콜레스테롤 대사에 미치는 영향을 HepG2 세포에서 콜레스테롤 대사 관련 유전자 발현을 측정함에 따라 조사하였다. 블랙 초크베리는 콜레스테롤 대사와 관련하여 콜레스테롤 흡수, 생합성, 유출과 관련된 유전자 발현을 조절하는 것으로 나타났다. 이는 블랙 초크베리의 혈중 콜레스테롤 저하 효과가 콜레스테롤 및 담즙 대사 관련 유전자 발현을 조절함에 의한 것으로 사료된다. 추후 블랙 초크베리 내 어떠한 생리활성물질이 콜레스테롤 대사 유전자 발현을 조절하여 이러한 효과를 나타내는 지에 대한 연구가 필요하며, 블랙 초크베리의 콜레스테롤 저하 효과를 동물 및 임상에서 기전 연구를 진행하여 천연 유래 기능성 소재로서의 블랙 초크베리의 중요성을 검증할 필요가 있을 것으로 사료된다.

• Journal of Genetic Medicine
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• 제19권2호
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• pp.105-110
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• 2022

The microdeletion syndrome of chromosome 2p15p16.1 (MIM: 612513) is an extremely rare contiguous gene deletion syndrome. Microdeletions of varying sizes in the 2p15-16.1 region are associated with developmental delay, intellectual disability, autism spectrum disorder, hypotonia, and craniofacial dysmorphism. Previous studies have identified two critical regions: the proximal 2p15 and distal 2p16.1 regions. BCL11A, PAPOLG, and REL genes play crucial roles in patients with 2p16.1 microdeletion. To our knowledge, only 39 patients have been reported as having 2p15p16.1 microdeletion syndrome. Here, we present another patient with 2p15p16.1 microdeletion syndrome. A nine-month-old boy was referred to our clinic for the psychomotor delay, facial dysmorphism, and congenital hypothyroidism. During his follow-up visits, he was diagnosed with global developmental delay, intellectual disability, abnormal behavior, hypotonia, microcephaly, and abnormal electroencephalography. Using a chromosomal microarray for genetic analysis, a novel, de novo, 622 kb microdeletion of 2p16.1 was identified as one of the critical regions of the 2p15p16.1 microdeletion syndrome. This is the first case of its kind in Korea. We have discussed our case and literature reviews to clarify the relationship between the genes involved and clinical phenotypes in 2p15p16.1 microdeletion syndrome.

• Journal of Microbiology and Biotechnology
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• 제32권12호
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• pp.1527-1536
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• 2022

Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA-ylbE-ylbF-ybcF that is located downstream of the allDCE-operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA, ylbE, ylbF, and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The V_max is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the K_M value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK.