• 제목/요약/키워드: BioInformatics

검색결과 580건 처리시간 0.025초

Fermentation of red ginseng extract by the probiotic Lactobacillus plantarum KCCM 11613P: ginsenoside conversion and antioxidant effects

  • Jung, Jieun;Jang, Hye Ji;Eom, Su Jin;Choi, Nam Soon;Lee, Na-Kyoung;Paik, Hyun-Dong
    • Journal of Ginseng Research
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    • 제43권1호
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    • pp.20-26
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    • 2019
  • Background: Ginsenosides, which are bioactive components in ginseng, can be converted to smaller compounds for improvement of their pharmacological activities. The conversion methods include heating; acid, alkali, and enzymatic treatment; and microbial conversion. The aim of this study was to determine the bioconversion of ginsenosides in fermented red ginseng extract (FRGE). Methods: Red ginseng extract (RGE) was fermented using Lactobacillus plantarum KCCM 11613P. This study investigated the ginsenosides and their antioxidant capacity in FRGE using diverse methods. Results: Properties of RGE were changed upon fermentation. Fermentation reduced the pH value, but increased the titratable acidity and viable cell counts of lactic acid bacteria. L. plantarum KCCM 11613P converted ginsenosides $Rb_2$ and $Rb_3$ to ginsenoside Rd in RGE. Fermentation also enhanced the antioxidant effects of RGE. FRGE reduced 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity and reducing power; however, it improved the inhibition of ${\beta}$-carotene and linoleic acid oxidation and the lipid peroxidation. This suggested that the fermentation of RGE is effective for producing ginsenoside Rd as precursor of ginsenoside compound K and inhibition of lipid oxidation. Conclusion: This study showed that RGE fermented by L. plantarum KCCM 11613P may contribute to the development of functional food materials.

A systemic study on the vulnerability and fatality of prostate cancer patients towards COVID-19 through analysis of the TMPRSS2, CXCL10 and their co-expressed genes

  • Raza, Md. Thosif;Mizan, Shagufta
    • Genomics & Informatics
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    • 제20권3호
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    • pp.31.1-31.15
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    • 2022
  • A pandemic of respiratory disease named coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is reported prostate cancer patients are susceptible to COVID-19 infection. To understand the possible causes of prostate cancer patients' increased vulnerability and mortality from COVID-19 infection, we focused on the two most important agents, transmembrane protease serine subtype 2 (TMPRSS2) and the C-X-C motif 10 (CXCL10). When SARS-CoV-2 binds to the host cell via S protein-angiotensin-converting enzyme-2 receptor interaction, TMPRSS2 contributes in the proteolytic cleavage of the S protein, allowing the viral and cellular membranes to fuse. CXCL10 is a cytokine found in elevated level in both COVID-19 and cancer-causing cytokine storm. We discovered that TMPRSS2 and CXCL10 are overexpressed in prostate cancer and COVID-19 using the UALCAN and GEPIA2 datasets. The functional importance of TMPRSS2 and CXCL10 in prostate cancer development was then determined by analyzing the frequency of genetic changes in their amino acid sequences using the cBioPortal online portal. Finally, we used the PANTHER database to examine the pathology of the targeted genes. We observed that TMPRSS2 and CXCL10, together with their often co-expressed genes, are important in the binding activity and immune responses in prostate cancer and COVID-19 infection, respectively. Finally, we found that TMPRSS2 and CXCL10 are two putative biomarkers responsible for the increased vulnerability and fatality of prostate cancer patients to COVID-19.

Can Panax ginseng help control cytokine storm in COVID-19?

  • Choi, Jong Hee;Lee, Young Hyun;Kwon, Tae Woo;Ko, Seong-Gyu;Nah, Seung-Yeol;Cho, Ik-Hyun
    • Journal of Ginseng Research
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    • 제46권3호
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    • pp.337-347
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    • 2022
  • Coronavirus disease 2019 (COVID-19) is currently a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 are directly associated with hyper-activation of innate immune response that excessively produce pro-inflammatory cytokines and induce cytokine storm, leading to multi-organ-failure and significant morbidity/mortality. Currently, several antiviral drugs such as Paxlovid (nirmatrelvir and ritonavir) and molnupiravir are authorized to treat mild to moderate COVID-19, however, there are still no drugs that can specifically fight against challenges of SARS-CoV-2 variants. Panax ginseng, a medicinal plant widely used for treating various conditions, might be appropriate for this need due to its anti-inflammatory/cytokine/viral activities, fewer side effects, and cost efficiency. To review Panax ginseng and its pharmacologically active-ingredients as potential phytopharmaceuticals for treating cytokine storm of COVID-19, articles that reporting its positive effects on the cytokine production were searched from academic databases. Experimental/clinical evidences for the effectiveness of Panax ginseng and its active-ingredients in preventing or mitigating cytokine storm, especially for the cascade of cytokine storm, suggest that they might be beneficial as an adjunct treatment for cytokine storm of COVID-19. This review may provide a new approach to discover specific medications using Panax ginseng to control cytokine storm of COVID-19.

Bioinformatic analyses reveal the prognostic significance and potential role of ankyrin 3 (ANK3) in kidney renal clear cell carcinoma

  • Keerakarn Somsuan;Siripat Aluksanasuwan
    • Genomics & Informatics
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    • 제21권2호
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    • pp.22.1-22.15
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    • 2023
  • Kidney renal clear cell carcinoma (KIRC) is one of the most aggressive cancer type of the urinary system. Metastatic KIRC patients have poor prognosis and limited therapeutic options. Ankyrin 3 (ANK3) is a scaffold protein that plays important roles in maintaining physiological function of the kidney and its alteration is implicated in many cancers. In this study, we investigated differential expression of ANK3 in KIRC using GEPIA2, UALCAN, and HPA databases. Survival analysis was performed by GEPIA2, Kaplan-Meier plotter, and OS-kirc databases. Genetic alterations of ANK3 in KIRC were assessed using cBioPortal database. Interaction network and functional enrichment analyses of ANK3-correlated genes in KIRC were performed using GeneMANIA and Shiny GO, respectively. Finally, the TIMER2.0 database was used to assess correlation between ANK3 expression and immune infiltration in KIRC. We found that ANK3 expression was significantly decreased in KIRC compared to normal tissues. The KIRC patients with low ANK3 expression had poorer survival outcomes than those with high ANK3 expression. ANK3 mutations were found in 2.4% of KIRC patients and were frequently co-mutated with several genes with a prognostic significance. ANK3-correlated genes were significantly enriched in various biological processes, mainly involved in peroxisome proliferator-activated receptor (PPAR) signaling pathway, in which positive correlations of ANK3 with PPARA and PPARG expressions were confirmed. Expression of ANK3 in KIRC was significantly correlated with infiltration level of B cell, CD8+ T cell, macrophage, and neutrophil. These findings suggested that ANK3 could serve as a prognostic biomarker and promising therapeutic target for KIRC.

In-silico and structure-based assessment to evaluate pathogenicity of missense mutations associated with non-small cell lung cancer identified in the Eph-ephrin class of proteins

  • Shubhashish Chakraborty;Reshita Baruah;Neha Mishra;Ashok K Varma
    • Genomics & Informatics
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    • 제21권3호
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    • pp.30.1-30.13
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    • 2023
  • Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.

A rare ginsenoside compound K (CK) induces apoptosis for breast cancer cells

  • Seun Eui Kim;Myoung-Hoon Lee;Hye-Myoung Jang;Wan-Taek Im;Joontaik Lee;Sang-Hwan Kim;Gwang Joo Jeon
    • 한국동물생명공학회지
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    • 제38권3호
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    • pp.167-176
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    • 2023
  • Background: A breast cancer is the second leading cause of cancer death in women worldwide and among different types of breast cancers, triple-negative breast cancer (TNBC) has a poor prognosis. Methods: We investigated the potential of ginsenoside compound K (CK), an active ingredient in the bio-transformed ginsenoside, to be used as a therapeutic ingredient by examining the effects of CK on cell proliferation, apoptosis, and cancer-related gene expressions in breast cancer cells. Results: From the results of treating MCF-7, an ER and PR-positive breast cancer cells, and MDA-MB-231 (TNBC) with CK at a concentration of 0-100 µM, the half maximal inhibitory concentration (IC50) values for each cell were 52.17 µM and 29.88 µM, respectively. And also, it was confirmed that cell migration was inhibited above the IC50 concentration. In addition, fluorescence analysis of Apoptosis/Necrosis showed that CK induced apoptosis rather than necrosis of breast cancer cells. Through qPCR, it was confirmed that the expression of genes related to apoptosis and cell cycle arrest was increased in CK-treated breast cancer cells, and it acted more effectively on TNBC. However, the expression of genes related to tumor invasion and metastasis is also increased, so it is necessary to consider the timing of application of CK as a potential therapeutic anticancer compound. Conclusions: CK showed a stronger inhibitory effect in TNBC with poor prognosis but considering the high tumor invasion and metastasis-related gene expression, the timing of application of CK should be considered.

Atypical formations of gintonin lysophosphatidic acids as new materials and their beneficial effects on degenerative diseases

  • Ji-Hun Kim;Ra Mi Lee;Hyo-Bin Oh;Tae-Young Kim;Hyewhon Rhim;Yoon Kyung Choi;Jong-Hoon Kim;Seikwan Oh;Do-Geun Kim;Ik-Hyun Cho;Seung-Yeol Nah
    • Journal of Ginseng Research
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    • 제48권1호
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    • pp.1-11
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    • 2024
  • Fresh ginseng is prone to spoilage due to its high moisture content. For long-term storage, most fresh ginsengs are dried to white ginseng (WG) or steamed for hours at high temperature/pressure and dried to form Korean Red ginseng (KRG). They are further processed for ginseng products when subjected to hot water extraction/concentration under pressure. These WG or KRG preparation processes affect ginsenoside compositions and also other ginseng components, probably during treatments like steaming and drying, to form diverse bioactive phospholipids. It is known that ginseng contains high amounts of gintonin lysophosphatidic acids (LPAs). LPAs are simple lipid-derived growth factors in animals and humans and act as exogenous ligands of six GTP-binding-protein coupled LPA receptor subtypes. LPAs play diverse roles ranging from brain development to hair growth in animals and humans. LPA-mediated signaling pathways involve various GTP-binding proteins to regulate downstream pathways like [Ca2+]i transient induction. Recent studies have shown that gintonin exhibits anti-Alzheimer's disease and antiarthritis effects in vitro and in vivo mediated by gintonin LPAs, the active ingredients of gintonin, a ginseng-derived neurotrophin. However, little is known about how gintonin LPAs are formed in high amounts in ginseng compared to other herbs. This review introduces atypical or non-enzymatic pathways under the conversion of ginseng phospholipids into gintonin LPAs during steaming and extraction/concentration processes, which exert beneficial effects against degenerative diseases, including Alzheimer's disease and arthritis in animals and humans via LPA receptors.

Korean Red Ginseng extract ameliorates demyelination by inhibiting infiltration and activation of immune cells in cuprizone-administrated mice

  • Min Jung Lee;Jong Hee Choi;Tae Woo Kwon;Hyo-Sung Jo;Yujeong Ha;Seung-Yeol Nah;Ik-Hyun Cho
    • Journal of Ginseng Research
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    • 제47권5호
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    • pp.672-680
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    • 2023
  • Background: Korean Red Ginseng (KRG), the steamed root of Panax ginseng, has pharmacological activities for immunological and neurodegenerative disorders. But, the role of KRGE in multiple sclerosis (MS) remains unclear. Purpose: To determine whether KRG extract (KRGE) could inhibit demyelination in corpus callosum (CC) of cuprizone (CPZ)-induced murine model of MS Methods: Male adult mice were fed with a standard chow diet or a chow diet supplemented with 0.2% (w/w) CPZ ad libitum for six weeks to induce demyelination while were simultaneously administered with distilled water (DW) alone or KRGE-DW (0.004%, 0.02 and 0.1% of KRGE) by drinking. Results: Administration with KRGE-DW alleviated demyelination and oligodendrocyte degeneration associated with inhibition of infiltration and activation of resident microglia and monocyte-derived macrophages as well as downregulation of proinflammatory mediators in the CC of CPZ-fed mice. KRGE-DW also attenuated the level of infiltration of Th1 and Th17) cells, in line with inhibited Mrna expression of IFN-γ and IL-17, respectively, in the CC. These positive effects of KRGE-DW mitigated behavioral dysfunction based on elevated plus maze and the rotarod tests. Conclusion: The results strongly suggest that KRGE-DW may inhibit CPZ-induced demyelination due to its oligodendroglial protective and anti-inflammatory activities by inhibiting infiltration/activation of immune cells. Thus, KRGE might have potential in therapeutic intervention for MS.

축산물 유통단계의 HACCP 적용과 체계화를 위한 실시간 관제시스템에 대한 현황 (Overview of Real-time Visibility System for Food (Livestock Products) Transportation Systems on HACCP Application and Systematization)

  • 김현욱;이주연;홍완수;황선민;이봉현;임성렬;백현동
    • 한국축산식품학회지
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    • 제30권6호
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    • pp.896-904
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    • 2010
  • 축산물에 HACCP가 도입된 후 농장, 도축장, 가공장, 판매장 등 많은 업체에서 HACCP를 도입하고 있고 현재도 많은 업체들이 HACCP를 도입하기 위해 준비하고 있지만, 축산물 운반업은 타업종에 비해 HACCP 도입이 활발하게 이루어지지 않고 있다. 무선응용통신(WAP)을 이용한 HACCP 기반의 축산물 유통 실시간 관제 시스템은 GPS와 개인 휴대용 무선기기를 이용하여 축산물 운반차량 또는 보관창고의 위치정보, 온도정보, 그리고 HACCP 운반 관리점검표 등의 정보를 실시간으로 중앙의 관리시스템으로 전송하여 중앙관리자가 실시간으로 운반차량을 관제할 수 있도록 하는 시스템이다. 실시간 HACCP 관리시스템은 운반업이나, 보관업에서 HACCP을 실시하기에 어려운 점들(문서관리, 검증단계)을 시스템화하여 운반업이나 보관업의 특성 상 발생 가능한 물리적/화학적/생물학적 위해 요소를 최소화 하고, 중앙 관리자의 가시권에서 벗어날 수 있다는 단점을 실시간 관제 시스템과 접목된 정보 수신 기능을 통해 중앙 관리 및 감시를 가능하게 하여 위해 요인 제어 및 개선 조치의 기능을 강화할 수 있다. 실시간 HACCP 관리시스템은 운반업이나 보관업의 특성 상HACCP을 실시하기 어려운 유통업체의 실시간으로 HACCP 관리를 실시할 수 있게 해 주며, 특히 규모가 큰 업체의 경우 다량의 차량을 보유하여 이들의 위생상태나 안전관리가 어려운 점을 보완해 줌으로써 안전한 축산물의 유통 증대를 통해 저 품질화 제품의 유통을 감소시켜 경제적 손실을 줄일 수 있으며, 축산물의 선호도가 높아짐으로써 경제적 이익을 창출할 수 있음으로 축산물 유통에 매우 유용하다고 할 수 있다. 우리나라 축산물 운반 단계의 HACCP 적용이 자율 적용이라는 취지를 고려할 때 HACCP 적용 및 운반업의 현대화를 위한 모든 노력은 업체의 의지에 의해 이루어져야 할 것이나, 이를 위한 HACCP 교육의 확대, 시스템 개발에 대한 연구, 실행을 위한 기술적 도움 등 관련 전문가들의 관심과 협조가 동행되어야 할 것으로 여겨지며, 이를 통해 HACCP의 본 취지인 'From Farm To Table'을 실현할 수 있게 될 것이다.

양조 부산물인 주박의 주름개선 효과 (Anti-Wrinkle Effects of Korean Rice Wine Cake on Human Fibroblast)

  • 유정민;강여진;표형배;정의수;박신영;최지호;한귀정;이충환;김택중
    • 생명과학회지
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    • 제20권12호
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    • pp.1838-1843
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    • 2010
  • 피부의 노화는 유전자 돌연변이와 같은 유전적인 요소와 자외선 노출과 같은 환경적인 요소와 연관되어 있다. 이러한 요소들은 교원질과 탄력섬유와 같은 피부의 구조적인 복합체를 분해한다. 특히, 교원질은 전사인자인 AP-1에 의해 유도되는 분해효소인 MMP-1에 의해 분해되고 그 결과 피부의 주름이 발생한다. 교원질의 다른 분해 원인으로는 생체내 활성산소의 생성을 들 수 있다. 활성산소의 생성은 세포막을 공격하고 MMP-1의 활성을 유도한다. 결과적으로, 피부 탄력의 감소와 동시에 피부의 노화를 촉진시키게 된다. 본 연구에서 우리는 양조 부산물인 주박을 이용하여 항산화효과, collagen 합성촉진효과, MMP-1의 발현양상을 측정하였다. 흥미롭게도, 주박은 DPPH 라디컬의 소거활성 효과와 procollagen의 양을 증가시킴과 동시에, MMP-1의 유전자 발현을 억제시키는 효과를 나타내었다. 본 결과는 주박이 피부의 항노화 효과를 가질 수 있다는 것을 제시한다.