• Fisheries and Aquatic Sciences
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• 제21권8호
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• pp.28.1-28.12
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• 2018

Intertidal macroalgae are exposed to many abiotic stress factors, and they must regularly react to changes in their environment. We used RNA-seq to describe how Porphyra umbilicalis (Rhodophyta) changes gene expression patterns to interact with different habitats. Tissue samples were taken from a typical habitat along the open-coast of the Northwest Atlantic, as well as from a rare, atypical habitat in an estuarine tidal rapid environment. Differential gene expression analyses suggest that pathogic bacteria and viruses may be a significant factor influencing the transcriptome in the human-impacted estuarine environment, but the atypical habitat does not necessarily induce more stress in Porphyra umbilicalis growing there. We found genes related to nitrogen transport are over-expressed in tissue from the open-coastal site compared to those from the estuarine site, where environmental N levels approach hypertrophic levels. Low N levels impede growth, but high levels are toxic to cells, and we use qPCR to show this species regulates expression of a putative high-affinity $NH_4{^+}$ transporter under low and high N conditions. Differences in expression of this transporter in these habitats appear to be inherited from parent to offspring and have general implications for adaptation to habitat in other species that are capable of asexual reproduction, as well as more specific implications for this species' use in aquaculture.

• 한국미생물·생명공학회지
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• 제49권3호
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• pp.440-448
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• 2021

Helicobacter pylori (H. pylori) establishes long-term infections associated with severe gastric diseases such as peptic ulceration and gastric cancer. Exposure to an antibacterial agent can help regulate the expression levels of its pathogenic genes. In this study, we analyzed the transcriptional changes in H. pylori genes induced by β-caryophyllene. We used next-generation sequencing (NGS) to analyze RNA expression changes, and reverse transcription-polymerase chain reaction (RT-PCR) was performed as required to verify the results. The NGS results showed that 30 out of 1,632 genes were expressed differentially by β-caryophyllene treatment. Eleven genes associated with DNA replication, virulence factors, and T4SS components were significantly downregulated. RT-PCR confirmed that treatment reduced the expression levels of 11 genes. RT-PCR showed the reduced expression of 11 genes (dnaE, dnaN, holB, gyrA, cagA, vacA, secA, flgE, virB2, virB4, and virB8) following β-caryophyllene treatment. These results suggest that β-caryophyllene can modulate various H. pylori pathogenic determinants and be a potential therapeutic agent for H. pylori infection.

• The Plant Pathology Journal
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• 제38권5호
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• pp.432-448
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• 2022

Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.

• Journal of Microbiology and Biotechnology
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• 제33권3호
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• pp.319-328
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• 2023

Malassezia and Staphylococcus are the most dominant genera in human skin microbiome. To explore the inter-kingdom interactions between the two genera, we examined the transcriptional changes in Malassezia and Staphylococcus species induced upon co-culturing. RNA-seq analyses revealed that genes encoding ribosomal proteins were upregulated, while those encoding aspartyl proteases were downregulated in M. restricta after co-culturing with Staphylococcus species. We identified MRET_3770 as a major secretory aspartyl protease coding gene in M. restricta through pepstatin-A affinity chromatography followed by mass spectrometry and found that the expression of MRET_3770 was significantly repressed upon co-culturing with Staphylococcus species or by incubation in media with reduced pH. Moreover, biofilm formation by Staphylococcus aureus was inhibited in the spent medium of M. restricta, suggesting that biomolecules secreted by M. restricta such as secretory aspartyl proteases may degrade the biofilm structure. We also examined the transcriptional changes in S. aureus co-cultured with M. restricta and found co-cultured S. aureus showed increased expression of genes encoding ribosomal proteins and downregulation of those involved in riboflavin metabolism. These transcriptome data of co-cultured fungal and bacterial species demonstrate a dynamic interplay between the two co-existing genera.

• 한국축산식품학회지
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• 제43권6호
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• pp.1067-1086
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• 2023

With rapid advances in meat science in recent decades, changes in meat quality during the pre-slaughter phase of muscle growth and the post-slaughter process from muscle to meat have been investigated. Commonly used techniques have evolved from early physicochemical indicators such as meat color, tenderness, water holding capacity, flavor, and pH to various omic tools such as genomics, transcriptomics, proteomics, and metabolomics to explore fundamental molecular mechanisms and screen biomarkers related to meat quality and taste characteristics. This review highlights the application of omics and integrated multi-omics in meat quality and taste characteristics studies. It also discusses challenges and future perspectives of multi-omics technology to improve meat quality and taste. Consequently, multi-omics techniques can elucidate the molecular mechanisms responsible for changes of meat quality at transcriptome, proteome, and metabolome levels. In addition, the application of multi-omics technology has great potential for exploring and identifying biomarkers for meat quality and quality control that can make it easier to optimize production processes in the meat industry.

• 생명과학회지
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• 제33권7호
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• pp.538-548
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• 2023

식물 천연추출물에서 항균력을 갖는 활성 물질을 분리하고 이를 구강 건강 관리 제품에 사용하려는 연구가 진행되고 있다. 본 연구에서는 유기용매를 사용하여 독활과 우방자로부터 추출한 복합 화합물에 대한 구강 감염균인 Streptococcus mutans의 특정 유전자 발현 변화를 분석하여 항균 기작을 분석하고자 하였다. 전사체 분석 결과, 두 가지 천연추출물에 의해 다양한 대사 및 생리 작용과 연관된 유전자의 발현이 공통적으로 증가하거나 감소하는 것으로 나타났다. 세 가지 유전자(SMU_1584c, SMU_2133c, SMU_921)는 공통적으로 높은 수준으로 발현되었으며, 특히 이 중 SMU_921 (rcrR)은 두 가지 sugar phosphotransferase system (PTS)의 전사 활성자로써 당원의 수송과 생물막 형성에 기여하는 것으로 알려져 있다. 또한, 우방자 추출물에 비해 다수의 유전자 발현 변화에 영향을 미치는 것으로 나타난 독활 추출물의 성분 분석을 진행하였고, 활성 분획의 가스 크로마토그래피-질량분석법(GC-MS)을 통해 두 가지 활성 단일 물질을 동정하였다. 물질 분리 과정에서 여러 유기용매 분획 중 hexane층(ACEH)의 항균 활성이 가장 높게 관찰되었다. 다양종 미생물 군집을 사용한 실험결과, S. mutans에 대한 ACEH의 항균 특이성이 관찰되었으나, 상대적으로 S. sanguinis와 S. gordonii의 생균수도 크게 감소하는 것으로 나타났다. 이러한 결과는 독활 천연추출물의 광범위한 항균 활성을 시사하며, 동정한 단일 물질의 항균 기작을 분석하여 맞춤형 항균 소재 개발에 중요한 기초 자료를 제공할 수 있다.

• Journal of Korean Neurosurgical Society
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• 제67권4호
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• pp.418-430
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• 2024

Objective : Isoflurane, a widely used common inhalational anesthetic agent, can induce brain toxicity. The challenge lies in protecting neurologically compromised patients from neurotoxic anesthetics. Choline alfoscerate (L-α-Glycerophosphorylcholine, α-GPC) is recognized for its neuroprotective properties against oxidative stress and inflammation, but its optimal therapeutic window and indications are still under investigation. This study explores the impact of α-GPC on human astrocytes, the most abundant cells in the brain that protect against oxidative stress, under isoflurane exposure. Methods : This study was designed to examine changes in factors related to isoflurane-induced toxicity following α-GPC administration. Primary human astrocytes were pretreated with varying doses of α-GPC (ranging from 0.1 to 10.0 µM) for 24 hours prior to 2.5% isoflurane exposure. In vitro analysis of cell morphology, water-soluble tetrazolium salt-1 assay, quantitative real-time polymerase chain reaction, proteome profiler array, and transcriptome sequencing were conducted. Results : A significant morphological damage to human astrocytes was observed in the group that had been pretreated with 10.0 mM of α-GPC and exposed to 2.5% isoflurane. A decrease in cell viability was identified in the group pretreated with 10.0 µM of α-GPC and exposed to 2.5% isoflurane compared to the group exposed only to 2.5% isoflurane. Quantitative real-time polymerase chain reaction revealed that mRNA expression of heme-oxygenase 1 and hypoxia-inducible factor-1α, which were reduced by isoflurane, was further suppressed by 10.0 µM α-GPC pretreatment. The proteome profiler array demonstrated that α-GPC pretreatment influenced a variety of factors associated with apoptosis induced by oxidative stress. Additionally, transcriptome sequencing identified pathways significantly related to changes in isoflurane-induced toxicity caused by α-GPC pretreatment. Conclusion : The findings suggest that α-GPC pretreatment could potentially enhance the vulnerability of primary human astrocytes to isoflurane-induced toxicity by diminishing the expression of antioxidant factors, potentially leading to amplified cell damage.

• 한국동물생명공학회지
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• 제39권2호
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• pp.67-80
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• 2024

Background: Post-ovulatory aging (POA) of oocytes is related to a decrease in the quality and quantity of oocytes caused by aging. Previous studies on the characteristics of POA have investigated injury to early embryonic developmental ability, but no information is available on its effects on mitochondrial fission and mitophagy-related responses. In this study, we aimed to elucidate the molecular mechanisms underlying mitochondrial fission and mitophagy in in vitro maturation (IVM) oocytes and a POA model based on RNA sequencing analysis. Methods: The POA model was obtained through an additional 24 h culture following the IVM of matured oocytes. NMN treatment was administered at a concentration of 25 μM during the oocyte culture process. We conducted MitoTracker staining and Western blot experiments to confirm changes in mitochondrial function between the IVM and POA groups. Additionally, comparative transcriptome analysis was performed to identify differentially expressed genes and associated changes in mitochondrial dynamics between porcine IVM and POA model oocytes. Results: In total, 32 common genes of apoptosis and 42 mitochondrial fission and function uniquely expressed genes were detected (≥ 1.5-fold change) in POA and porcine metaphase II oocytes, respectively. Functional analyses of mitochondrial fission, oxidative stress, mitophagy, autophagy, and cellular apoptosis were observed as the major changes in regulated biological processes for oocyte quality and maturation ability compared with the POA model. Additionally, we revealed that the activation of NAD⁺ by nicotinamide mononucleotide not only partly improved oocyte quality but also mitochondrial fission and mitophagy activation in the POA porcine model. Conclusions: In summary, our data indicate that mitochondrial fission and function play roles in controlling oxidative stress, mitophagy, and apoptosis during maturation in POA porcine oocytes. Additionally, we found that NAD⁺ biosynthesis is an important pathway that mediates the effects of DRP1-derived mitochondrial morphology, dynamic balance, and mitophagy in the POA model.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.432-443
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• 2005

Microarray technology has contributed Significantly to the understanding of bacterial genetics and transcriptional regulation. One neglected aspect of this technology has been optimization of microarray-generated signals and quality of generated information. Full genome microarrays were developed for Clostridium acetobutylicum through spotting of PCR products that were designed with minimal homology with all other genes within the genome. Using statistical analyses it is demonstrated that Signal quality is significantly improved by increasing the hybridization volume. possibly increasing the effective number of transcripts available to bind to a given spot, while changes in labeled probe amounts were found to be less sensitive to improving signal quality. In addition to Q-RT-PCR, array validation was tested by examining the transcriptional program of a mutant (M5) strain lacking the pSOL1 178-gene megaplasmid relative to the wildtype (WT) strain. Under optimal conditions, it is demonstrated that the fraction of false positive genes is 1% when considering differentially expressed genes and 7% when considering all genes with signal above background. To enhance genomic-scale understanding of organismal physiology, using data from these microarrays we estimated that $40{\sim}55%$ of the C. acetobutylicum genome is expressed at any time during batch culture, similar to estimates made for Bacillus subtilis.

• Asian Pacific Journal of Cancer Prevention
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• 제15권5호
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• pp.2309-2312
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• 2014

Esophageal squamous cell carcinoma (ESCC) is the most common histologic subtype of esophageal cancer and is characterized by a poor prognosis. Determining gene changes in ESCCs should improve understanding of putative risk factors and provide potential targets for therapy. We sequenced about 55 million pair-end reads from a pair of adjacent normal and ESCC samples to identify the gene expression level and gene fusion. Sanger sequencing was used to verify the result. About 17 thousand genes were expressed in the tissues, of which approximately 2400 demonstrated significant differences between tumor and adjacent non tumor tissue. GO and KEGG pathway analysis revealed that many of these genes were associated with cellular adherence and movement, simulation responses and immune responses. Notably we identified and validated one fusion gene, HLA-E and HLA-B, located 1 MB apart. We also identified thousands of remarkably expressed transcripts. In conclusion, a novel fusion gene HLA-E and HLA-B was identified in ESCC via whole transcriptome sequencing, which would be a biomarker for ESCC diagnosis and target for therapy, shedding new light for better understanding of ESCC tumorigenesis.