• Journal of Microbiology and Biotechnology
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• 제34권8호
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• pp.1727-1737
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• 2024

The quality of tobacco is directly affected by macromolecular content, fermentation is an effective method to improve biochemical properties. In this study, we utilized CBHA (cellobiohydrolase A) glycosylase, which was expressed by Pichia pastoris, as an additive for fermentation. The contents of main chemical components of tobacco leaves after fermentation were determined, and the changes of microbial community structure and abundance in tobacco leaves during fermentation were analyzed. The relationship between chemical composition and changes in microbial composition was investigated, and the function of bacteria and fungi in fermentation was predicted to identify possible metabolic pathways. After 48 h of CBHA fermentation, the contents of starch, cellulose and total nitrogen in tobacco leaf decreased by 17.60%, 28.91% and 16.05%, respectively. The microbial community structure changed significantly, with Aspergillus abundance decreasing significantly, while Filobasidum, Cladosporium, Bullera, Komagataella, etc., increased in CBHA treated group. Soluble sugar was most affected by microbial community in tobacco leaves, which was negatively correlated with starch, cellulose and total nitrogen. During the fermentation process, the relative abundance of metabolism-related functional genes increased, and the expressions of cellulase and endopeptidase also increased. The results showed that the changes of bacterial community and dominant microbial community on tobacco leaves affected the content of chemical components in tobacco leaves, and adding CBHA for fermentation had a positive effect on improving the quality of tobacco leaves.

• Journal of Microbiology and Biotechnology
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• 제34권8호
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• pp.1599-1608
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• 2024

Yersinia enterocolitica is a globally distributed food-borne gastrointestinal pathogen. The O-antigen variation-determined serotype is an important characteristic of Y. enterocolitica, allowing intraspecies classification for diagnosis and epidemiology purposes. Among the 11 serotypes associated with human yersiniosis, O:3, O:5,27, O:8, and O:9 are the most prevalent, and their O-antigen gene clusters have been well defined. In addition to the O-antigen, several virulence factors are involved in infection and pathogenesis of Y. enterocolitica strains, and these are closely related to their biotypes, reflecting pathogenic properties. In this study, we identified the O-AGC of a Y. enterocolitica strain WL-21 of serotype O:10, and confirmed its functionality in O-antigen synthesis. Furthermore, we analyzed in silico the putative O-AGCs of uncommon serotypes, and found that the O-AGCs of Y. enterocolitica were divided into two genetic patterns: (1) O-AGC within the hemH-gsk locus, possibly synthesizing the O-antigen via the Wzx/Wzy dependent pathway, and (2) O-AGC within the dcuC-galU-galF locus, very likely assembling the O-antigen via the ABC transporter dependent pathway. By screening the virulence genes against genomes from GenBank, we discovered that strains representing different serotypes were grouped according to different virulence gene profiles, indicating strong links between serotypes and virulence markers and implying an interaction between them and the synergistic effect in pathogenicity. Our study provides a framework for further research on the origin and evolution of O-AGCs from Y. enterocolitica, as well as on differences in virulent mechanisms among distinct serotypes.

• Applied Microscopy
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• 제51권
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• pp.4.1-4.12
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• 2021

Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.

• Clinical Nutrition Research
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• 제13권3호
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• pp.214-225
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• 2024

Polymorphisms in the melanocortin 4 receptor (MC4R) gene with occurrence and progression of chronic diseases such as obesity and cardiovascular disease (CVD) have long been addressed but there is a lack of evidence for complex interrelationships, including direct and indirect effects of these variables. This review specifically focuses on studying the effects of healthy diet interaction and MC4R polymorphisms on the development of CVD. The quantity and quality of carbohydrates and proteins consumed are related to obesity susceptibility and cardiometabolic risk factors. A healthy dietary pattern such as a Mediterranean dietary can modulate the association between MC4R polymorphisms (rs17782313) and the risk of CVDs. Also, the Nordic diet can reduce lipid profiles such as low-density lipoprotein cholesterol (LDL-C) and total cholesterol levels. On the other hand, MC4R interaction with the dietary inflammatory index decreases high-density lipoprotein cholesterol levels and increases LDL-C and triglyceride (TG) levels. Additionally, the DASH diet decreases TG, atherogenic index of plasma, systolic blood pressure, diastolic blood pressure, and serum glucose. The interaction between MC4R genes and diets plays an important role in the development of CVD. Adherence to healthy diets such as the Mediterranean, Nordic, Anti-inflammatory, and Dash diets might be an efficient strategy to prevent CVD. The potential for personalized diets to be developed for the treatment and prevention of CVD and its related comorbidities is expected to expand as this field develops.

• ALGAE
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• 제39권3호
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• pp.207-222
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• 2024

In this study, the regulation of abscisic acid (ABA) on cell growth and lipid biosynthesis was investigated under salt-induced stress in Chlorella pyrenoidosa. It is found that as suffering from only salt stress, although the lipid content of single cell was improved, the inhibitory effects of stress on cell proliferation was visible. When the algal cells were exposed to salt stress and ABA conditions, lipid productivity was increased (45.35 mg L^-1 d^-1) by 1.17-fold compared to that of control cells (20.91 mg L^-1 d^-1), and the inhibition to cell growth was relieved. Transcriptomic analysis revealed that after adding ABA, these genes involved in antioxidant activity, jasmonic acid (JA) biosynthesis, and lipid biosynthesis were upregulated. Subsequently, we observed that the levels of glutathione, total antioxidant capacity, trehalose, and JA were elevated and the levels of reactive oxygen species were reduced. This study presents an effective approach to improve lipid production in algal cells, a new mechanism on that ABA alleviates intracellular oxidative stress through JA signaling pathway was elaborated.

• 식물병연구
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• 제30권3호
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• pp.283-287
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• 2024

임실군농업기술센터에서 전시용으로 재배 중인 국화 잎에 갈색에서 검은색의 반점이 형성되고, 시간이 지날수록 병반이 확대되며 심하면 식물체가 고사하는 증상이 나타났다. 국화의 병든 잎 부위에서 병원균을 분리하여 ITS, TUB2, ACT 유전자 염기 서열 분석을 통해 동정한 결과 Epicoccum sorghinum으로 확인되었다. 분리된 균의 균학적 특성을 확인해 본 결과, PDA 배지에서 배양한 균을 UV 광에 12시간 동안 노출 후 암실에 두었을 때 병자각이 형성되었으며, 격벽이 없는 타원형의 무색 투명한 분생포자(3.2-6.0×1.7-3.0 ㎛)가 형성되는 것을 확인할 수 있었다. PDA 배지에서 배양한 균주의 agar plug를 국화 잎에 접종하여 병원성을 검정한 결과, 접종한 국화 잎에서 담갈색에서 검은색의 불규칙한 모양의 병반이 형성되었다. 따라서 E. sorghinum에 의한 국화 점무늬병을 국내 처음으로 보고하고자 한다.

• Journal of Microbiology and Biotechnology
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• 제34권9호
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• pp.1757-1768
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• 2024

The expression of two major virulence factors of Vibrio cholerae, cholera toxin (CT) and toxin co-regulated pilus (TCP), is induced by environmental stimuli through a cascade of interactions among regulatory proteins known as the ToxR regulon when the bacteria reach the human small intestine. ToxT is produced via the ToxR regulon and acts as the direct transcriptional activator of CT (ctxAB), TCP (tcp gene cluster), and other virulence genes. Unsaturated fatty acids (UFAs) and several small-molecule inhibitors of ToxT have been developed as antivirulence agents against V. cholerae. This study reports the inhibitory effects of fatty acids and virstatin (a small-molecule inhibitor of ToxT) on the transcriptional activation functions of ToxT in isogenic derivatives of V. cholerae strains containing various toxT alleles. The fatty acids and virstatin had discrete effects depending on the ToxT allele (different by 2 amino acids), V. cholerae strain, and culture conditions, indicating that V. cholerae strains could overcome the effects of UFAs and small-molecule inhibitors by acquiring point mutations in toxT. Our results suggest that small-molecule inhibitors should be examined thoroughly against various V. cholerae strains and toxT alleles during development.

• Journal of Rhinology
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• 제59권1호
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• pp.49-58
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• 2021

Background: Nasal polyps in the nasal cavity and mucous discharge inside the maxillary sinus exhibit compressive stress on the nasal mucosal epithelium. However, there have been only a few studies on how compressive stress impacts the human nasal mucosal epithelium. Methodology: We investigated the effect of compressive stress on collective migration, junctional proteins, transepithelial electrical resistance, epithelial permeability, and gene expression in well-differentiated normal human nasal epithelial (NHNE) cells and human nasal polyp epithelial (HNPE) cells. Results: NHNE cells barely showed collective migration at compressive stress up to 150 mmH₂0. However, HNPE cells showed much greater degree of collective migration at a lower compressive stress of 100 mmH₂0. The cell migration of HNPE cells subjected to 100 mmH₂O compression was significantly decreased at day 3 and was recovered to the status prior to the compressive stress by day 7, indicating that HNPE cells are relatively more sensitive to mechanical pressure than NHNE cells. Compressive stress also increased transepithelial electrical resistance and decreased epithelial permeability, indicating that the compressive stress disturbed the structural organization rather than physical interactions between cells. In addition, we found that compressive stress induced gene expressions relevant to airway inflammation and tissue remodelling in HNPE cells. Conclusion: Taken together, these findings demonstrate that compressive stress on nasal polyp epithelium is capable of inducing collective migration and induce increased expression of genes related to airway inflammation, innate immunity, and polyp remodelling, even in the absence of inflammatory mediators.

• 한국동물생명공학회지
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• 제39권3호
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• pp.169-178
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• 2024

Background: Typical difficulties encountered during in vitro fertilization (IVF) to produce embryos in pigs include poor pronucleus formation and poor-quality fertilized embryos because of high polysperm invasion. In this study, we evaluated the effects of supplementation with apple seed extract (ASE) and coculture systems on porcine in vitro-fertilized embryo culture. Methods: Slaughterhouse-derived ovaries were used to obtain cumulus-oocyte complexes (COCs). COCs were conventionally used to perform IVF. We examined the differences in apoptosis and metabolism during development following addition of ASE to normal culture and coculture systems. Matrix metalloproteinases (MMPs), cell development-related factors, and apoptotic proteins were compared in porcine embryos produced under different conditions. Results: The expression of genes related to insulin-like growth factor (IGF) signaling was increased in the coculture system. In the ASE group, early apoptosis and necrosis were reduced in fertilized embryos and the late survival rate increased. Supplementation of the coculture system with ASE led to increased expression of BCL-2 and decreased expression of Casp-3 in the cytoplasm, thereby lowering the apoptosis rate and inducing MMP expression. In addition, compared with the extract-supplemented group in normal culture, the activity of MMP-2 decreased in the coculture system supplemented with ASE, activity of MMP-9 increased, and the expression of dynactin p62 and BrdU in the cytoplasm was higher than that in the other groups. Conclusions: The coculture system increased the activity of the embryonic cytoplasm compared with the non-coculture system. Supplementation with ASE may induce cell activity and inhibit the expression of apoptotic factors.

• Journal of Animal Science and Technology
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• 제49권5호
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• pp.549-558
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• 2007

C4B 및 BAT2는 SLA class III 영역에 존재하며, 최근 들어 사람의 질병과의 연관성이 보고되고 있다. GenBank database로부터 수집된 사람과 마우스의 C4B 및 BAT2의 CDS를 염기정렬하여 상동성이 높은 부분에서 primer를 제작한 후 RT-PCR 및 RACE-PCR을 수행하여 돼지 C4B 및 BAT2 유전자의 CDS 서열을 결정하였다. 염기서열이 결정된 돼지 C4B와 BAT2의 CDS 길이가 각각 5226 bp와 6501 bp로 나타났다. 이들 각각의 CDS 및 아미노산 서열을 사람 및 마우스와 비교한 결과 CDS는 76~87%, 아미노산 서열은 72~90%의 상동성을 보였으며, C4B가 BAT2에 비해 다소 낮게 나타났다. 두 유전자에서 나타나는 cSNP를 분석하기 위해서 exon 영역을 증폭하기 위한 primer를 제작하였으며, 돼지 6품종을 대상으로 direct sequencing을 실시하였다. 그 결과 C4B로부터 4개, BAT2로부터 3개의 cSNP가 확인되었다. 또한 7개의 cSNP 중 C4B의 C4248T를 제외한 6개의 cSNP에 의해서 아미노산 치환이 발생하였다. 동일한 DNA를 사용하여 7개의 cSNP를 대상으로 Multiplex-ARMS 방법을 사용하여 유전자형 분석을 실시한 결과 direct sequencing 결과와 일치하였다. Multiplex-ARMS 방법의 재현성을 재확인하기 위해 무작위로 2개의 DNA 시료를 선택하여 direct sequencing과 Multiplex-ARMS 분석을 실시하여 유전자형이 일치함을 다시 확인하였다. 따라서 본 연구에서 확인된 7개의 cSNP는 SLA class III 지역의 haplotype 분석을 위한 기초 자료로 사용될 수 있으며, Multiplex- ARMS 기법은 이종장기 개발에 필수적인 SLA 전체 영역 내 유전자들의 유전자형 분석을 위한 효율적인 분석방법이라고 사료된다.