• Molecules and Cells
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• 제44권3호
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• pp.136-145
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• 2021

Senescent cells that gradually accumulate during aging are one of the leading causes of aging. While senolytics can improve aging in humans as well as mice by specifically eliminating senescent cells, the effect of the senolytics varies in different cell types, suggesting variations in senescence. Various factors can induce cellular senescence, and the rate of accumulation of senescent cells differ depending on the organ. In addition, since the heterogeneity is due to the spatiotemporal context of senescent cells, in vivo studies are needed to increase the understanding of senescent cells. Since current methods are often unable to distinguish senescent cells from other cells, efforts are being made to find markers commonly expressed in senescent cells using bulk RNA-sequencing. Moreover, single-cell RNA (scRNA) sequencing, which analyzes the transcripts of each cell, has been utilized to understand the in vivo characteristics of the rare senescent cells. Recently, transcriptomic cell atlases for each organ using this technology have been published in various species. Novel senescent cells that do not express previously established marker genes have been discovered in some organs. However, there is still insufficient information on senescent cells due to the limited throughput of the scRNA sequencing technology. Therefore, it is necessary to improve the throughput of the scRNA sequencing technology or develop a way to enrich the rare senescent cells. The in vivo senescent cell atlas that is established using rapidly developing single-cell technologies will contribute to the precise rejuvenation by specifically removing senescent cells in each tissue and individual.

• 식품보건융합연구
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• 제9권2호
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• pp.1-6
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• 2023

As oil palm trees are an important economic source in many countries, particularly in Southeast Asia and Africa, the study of Ganoderma boninense is crucial for the sustainability of the oil palm industry. This study aims to understand the biology and ecology of the fungus, its pathogenesis, and the impact it has on oil palm trees. This knowledge can be used to develop management strategies to mitigate the damage caused by the fungus, such as the use of resistant varieties, chemical and biological control methods, and cultural practices. This study is to ensure the long-term productivity and sustainability of the oil palm industry. The main method of recent academic studies on this pathogen is molecular biology, with a focus on genetic analysis and functional genomics. Researchers have used techniques such as PCR, DNA sequencing, and transcriptomics to identify genes and pathways involved in pathogenesis and better understand the fungus's interactions with its host plant. Other methods used in recent studies include biochemical analysis, microscopy, and phytohormonal assays to investigate the biochemistry and physiology of the interaction between G. boninense and oil palm. This study is intended to provide implications from a new perspective by organizing and integrating studies on Ganoderma boninense.

• Tuberculosis and Respiratory Diseases
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• 제86권2호
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• pp.94-101
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• 2023

A recent understanding of the dynamic continuous spectrum of Mycobacterium tuberculosis infection has led to the recognition of incipient tuberculosis, which refers to the latent infection state that has begun to progress to active tuberculosis. The importance of early detection of these individuals with a high-risk of progression to active tuberculosis is emphasized to efficiently implement targeted tuberculosis preventive therapy. However, the tuberculin skin test or interferon-γ release assay, which is currently used for the diagnosis of latent tuberculosis infection, does not aid in the prediction of the risk of progression to active tuberculosis. Thus, a novel test is urgently needed. Recently, simultaneous and systematic analysis of differentially expressed genes using a high-throughput platform has enabled the discovery of key genes that may serve potential biomarkers for the diagnosis or prognosis of diseases. This host transcriptional investigation has been extended to the field of tuberculosis, providing promising results. The present review focuses on recent progress and challenges in the field of blood transcriptional signatures to predict progression to active tuberculosis.

• Journal of Veterinary Science
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• 제24권5호
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• pp.71.1-71.12
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• 2023

With the growing interest in companion animals and the rapidly expanding animal healthcare and pharmaceuticals market worldwide. With the advancements in RNAsequencing (RNA-seq) technology, it has become a valuable tool for understanding biological processes in companion animals and has multiple applications in animal healthcare. Historically, veterinary diagnoses and treatments relied solely on clinical symptoms and drugs used in human diseases. However, RNA-seq has emerged as an effective technology for studying companion animals, providing insights into their genetic information. The sequencing technology has revealed that not only messenger RNAs (mRNAs) but also noncoding RNAs (ncRNAs) such as long ncRNAs and microRNAs can serve as biomarkers. Based on the examination of RNA-seq applications in veterinary medicine, particularly in dogs and cats, this review concludes that RNA-seq has significant potential as a diagnostic and research tool. It has enabled the identification of potential biomarkers for cancer and other diseases in companion animals. Further research and development are required to maximize the utilization of RNA-seq for improved disease diagnosis and therapeutic targeting in companion animals.

• Tuberculosis and Respiratory Diseases
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• 제87권1호
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• pp.1-11
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• 2024

Acute respiratory distress syndrome (ARDS) is a common cause of severe hypoxemia defined by the acute onset of bilateral non-cardiogenic pulmonary edema. The diagnosis is made by defined consensus criteria. Supportive care, including prevention of further injury to the lungs, is the only treatment that conclusively improves outcomes. The inability to find more advanced therapies is due, in part, to the highly sensitive but relatively non-specific current syndromic consensus criteria, combining a heterogenous population of patients under the umbrella of ARDS. With few effective therapies, the morality rate remains 30% to 40%. Many subphenotypes of ARDS have been proposed to cluster patients with shared combinations of observable or measurable traits. Subphenotyping patients is a strategy to overcome heterogeneity to advance clinical research and eventually identify treatable traits. Subphenotypes of ARDS have been proposed based on radiographic patterns, protein biomarkers, transcriptomics, and/or machine-based clustering of clinical and biological variables. Some of these strategies have been reproducible across patient cohorts, but at present all have practical limitations to their implementation. Furthermore, there is no agreement on which strategy is the most appropriate. This review will discuss the current strategies for subphenotyping patients with ARDS, including the strengths and limitations, and the future directions of ARDS subphenotyping.

• Journal of Microbiology and Biotechnology
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• 제24권9호
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• pp.1170-1177
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• 2014

Mycobacterium gilvum PYR-GCK is a bacterial strain under study for its bioremediation use on heavy hydrocarbon pollutants in the environment. During the course of our study, mammalian cell entry (mce) genes, known to facilitate pathogenicity in M. tuberculosis, were highly expressed during a comparative and substrate-related cultural global transcriptomic study. RNA sequencing of the global transcriptome of the test strain in two different substrates, pyrene and glucose, showed high expression of the mce genes based on the differential results. After validating the expression of these genes with quantitative real-time PCR, we arrived at the conclusion that the genes were expressed based on the pyrene substrate (a phytosterol compound), and sterol metabolism is said to activate the expression of the mce genes in some actinomycetes bacteria, M. gilvum PYR-GCK in this case. This study is believed to be important based on the fact that some mycobacterial strains are undergoing a continuous research as a result of their use in practical bioremediation of anthropogenic exposure of toxic organic wastes in the environment.

• Journal of Microbiology and Biotechnology
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• 제28권11호
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• pp.1896-1907
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• 2018

Salmonellosis is commonly associated with meat and poultry products, but an increasing number of Salmonella outbreaks have been attributed to contaminated vegetables and fruits. Enteric pathogens including Salmonella enterica spp. can colonize diverse produce and persist for a long time. Considering that fresh vegetables and fruits are usually consumed raw without heat treatments, Salmonella contamination may subsequently lead to serious human infections. In order to understand the underlying mechanism of Salmonella adaptation to produce, we investigated the transcriptomics of Salmonella in contact with green vegetables, namely cabbage and napa cabbage. Interestingly, Salmonella pathogenicity island (SPI)-1 genes, which are required for Salmonella invasion into host cells, were up-regulated upon contact with vegetables, suggesting that SPI-1 may be implicated in Salmonella colonization of plant tissues as well as animal tissues. Furthermore, Salmonella transcriptomic profiling revealed several genetic loci that showed significant changes in their expression in response to vegetables and were associated with bacterial adaptation to unfavorable niches, including STM14_0818 and STM14_0817 (speF/potE), STM14_0880 (nadA), STM14_1894 to STM14_1892 (fdnGHI), STM14_2006 (ogt), STM14_2269, and STM14_2513 to STM14_2523 (cbi operon). Here, we show that nadA was required for bacterial growth under nutrient-restricted conditions, while the other genes were required for bacterial invasion into host cells. The transcriptomes of Salmonella in contact with cabbage and napa cabbage provided insights into the comprehensive bacterial transcriptional response to produce and also suggested diverse virulence determinants relevant to Salmonella survival and adaptation.

• 대한의생명과학회지
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• 제21권4호
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• pp.181-187
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• 2015

Osteoporosis is one of the diseases caused by accumulation of effects from complex interactions between genetic and environmental factors. Aging is the major cause for osteoporosis, which normally increases skeletal fragility and bone fracture especially among the elder. "Omics" refers to a specialized research field dealing with high-throughput biological data, such as genomics, transcriptomics, proteomics or metabolomics. Integration of data from multi-omics has been approved to be a powerful strategy to colligate biological phenomenon with multiple aspects. Actually, integrative analyses of "omics" datasets were used to present pathogenesis of specific diseases or casual biomarkers including susceptible genes. In this study, we evaluated the proposed relationship of novel susceptible genes (TREML2, HTR1E, and GLO1) with osteoporosis, which genes were obtained using multi-omics integration analyses. To this end, SNPs of the susceptible genes in the Korean female cohort were analyzed. As a result, one SNP of HTR1E and five SNPs of TREML2 were identified to associate with osteoporosis. The highest significant SNP was $rs6938076^*$ of TREML2 (OR=0.63, CI: 0.45~0.89, recessive P=0.009). Consequently, the susceptible genes identified through the multi-omics analyses were confirmed to have association with osteoporosis. Therefore, multi-omics analysis might be a powerful tool to find new genes associated with a disease. We further identified that TREML2 has more associated with osteoporosis in females than did HTR1E.

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.6319-6325
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• 2012

We previously found cytotoxic effects of tomato leaf extract (TLE) on the MCF-7 breast cancer cell line. The aim of this study was to ascertain the molecular mechanisms associated with the usage of TLE as an anticancer agent by microarray analysis using mRNA from MCF-7 breast cancer cells after treatment with TLE for 1 hr and 48 hrs. Approximately 991 genes out of the 30,000 genes in the human genome were significantly (p<0.05) changed after the treatment. Within this gene set, 88 were significantly changed between the TLE treated cells and the untreated MCF-7 cells (control cells) with a cut-off fold change >2.00. In order to focus on genes that were involved in cancer cell growth, only twenty-nine genes were selected, either down-regulated or up-regulated after treatment with TLE. Microarray assay results were confirmed by analyzing 10 of the most up and down regulated genes related to cancer cells progression using real-time PCR. Treatment with TLE induced significant up-regulation in the expression of the CRYAB, PIM1, BTG1, CYR61, HIF1-${\alpha}$ and CEBP-${\beta}$ genes after 1 hr and 48 hrs, whereas the TXNIP and THBS1 genes were up-regulated after 1 hr of treatment but down-regulated after 48 hrs. In addition both the HMG1L1 and HIST2H3D genes were down-regulated after 1 hr and 48 hrs of treatment. These results demonstrate the potent activity of TLE as an anticancer agent.

• 한국식품영양과학회지
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• 제43권2호
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• pp.179-186
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• 2014

대사체학이 질병, 약물, 스트레스, 식이, 생활습관, 유전적 차이, 장내 미생물 등에 의해서 발생하는 비정상적인 대사 메커니즘을 규명하고 관련 바이오 마커 발굴에 중요한 역할이 증명됨에 따라, 식품 영양학과 대사체학이 융합된 영양 대사체학의 역할이 더욱 중요해지고 있다. 특히 잘못된 식생활에 따른 미래의 질병 예측이 가능해지고 있어 향후 적절한 질병 예방이나 치료를 위한 적절한 식생활이나 식이에 대한 정보를 제공함으로써 건강 증진은 물론 개인별 맞춤식이나 맞춤약물 처방을 통한 개인 맞춤형 건강관리(personalized health care) 시대가 멀지 않았다. 또한 복잡한 식생활 패턴, 대사 반응에 대한 개인 간 차이 그리고 방대한 대사체 데이터와의 관계들을 효과적으로 밝혀낼 수 있는 기술에 대한 지속적인 개발과 영양 대사체학(nutritional metabolomics)이 유전체학(genomics or transcriptomics)과 단백체학(proteomics) 기술과 융합적으로 연구가 이루어질 때 질병과 식사 섭취 사이의 관계가 더욱 투명하게 규명될 것이다.