• Genes and Genomics
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• 제40권11호
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• pp.1181-1197
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• 2018

Tropical plant rubber tree (Hevea brasiliensis) is the sole source of commercial natural rubber and low-temperature stress is the most important limiting factor for its cultivation. To characterize the gene expression profiles of H. brasiliensis under the cold stress and discover the key cold stress-induced genes. Three cDNA libraries, CT (control), LT2 (cold treatment at $4^{\circ}C$ for 2 h) and LT24 (cold treatment at $4^{\circ}C$ for 24 h) were constructed for RNA sequencing (RNA-Seq) and gene expression profiling. Quantitative real time PCR (qRT-PCR) was conducted to validate the RNA-Seq and gene differentially expression results. A total of 1457 and 2328 differentially expressed genes (DEGs) in LT2 and LT24 compared with CT were respectively detected. Most significantly enriched KEGG pathways included flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, cutin, suberine and wax biosynthesis, Pentose and glucuronate interconversions, phenylalanine metabolism and starch and sucrose metabolism. A total of 239 transcription factors (TFs) were differentially expressed following 2 h or/and 24 h of cold treatment. Cold-response transcription factor families included ARR-B, B3, BES1, bHLH, C2H, CO-like, Dof, ERF, FAR1, G2-like, GRAS, GRF, HD-ZIP, HSF, LBD, MIKC-MADS, M-type MADS, MYB, MYB-related, NAC, RAV, SRS, TALE, TCP, Trihelix, WOX, WRKY, YABBY and ZF-HD. The genome-wide transcriptional response of rubber tree to the cold treatments were determined and a large number of DEGs were characterized including 239 transcription factors, providing important clues for further elucidation of the mechanisms of cold stress responses in rubber tree.

• 생명과학회지
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• 제33권1호
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• pp.73-81
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• 2023

본 연구에서는 어성초(Houttuynia cordata, HC) 와 야관문(Lespedeza cuneata, LC)의 열수 추출물과 메탄올 추출물의 순차적 유기용매 분획물을 제조하였다. LPS를 처리한 RAW264.7세포에서 HC와 LC의 열수 추출물과 메탄올 추출물의 유기용매 분획물의 항염증 활성을 연구하였다. 어성초와 야관문의 hexane, chloroform, ethyl acetate 분획물의 처리에 의해 농도의존적으로 nitric oxide (NO) 생산을 저해하였으며, iNOS의 발현도 감소되었다. 이전 연구에서 HC와 LC의 메탄올 추출물의 ethyl acetate 분획물의 플라보노이드 함량을 분석하였다. 분석된 플라보노이드 중 HC와 LC에 공통적으로 함유된 apigenin을 선택하여 추가실험을 진행하였다. Apigenin은 세포 생존율에 영향을 주지 않으면서 NO 생산을 저해하였으며, iNOS와 COX-2의 단백질 발현도 억제하였다. 또한, apigenin은 p38 MAPK와 JNK의 인산화를 억제함으로써 항염증 활성을 가지는 것으로 생각된다. Apigenin 처리에 의해 차별적으로 발현되는 유전자 발현을 확인하기 위하여 RNA-seq 분석을 수행하였다. 발현이 감소된 유전자 중 4개의 cytokine 유전자(IL-1α, IL-1β, IL-6, CSF2)의 발현 감소를 정량적 real-time PCR을 통해 확인하였다. 종합적으로, 본 연구결과는 어성초와 야관문은 항염증 활성을 가지고 있으며, apigenin이 두 약용 작물의 항염증 활성을 담당하는 중요한 성분 중의 하나가 될 수 있다는 것을 제시한다.

• 한국환경농학회지
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• 제41권4호
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• pp.335-343
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• 2022

BACKGROUND: Antibiotics used in animal husbandry for disease prevention and treatment have resulted in the rapid progression of antibiotic resistant bacteria which can be introduced into the environment through livestock feces/manure, disseminating antibiotic resistant genes (ARGs). In this study, fecal samples were collected from the livestock farms located in Jeju Island to investigate the relationship between microbial communities and ARGs. METHODS AND RESULTS: Illumina MiSeq sequencing was applied to characterize microbial communities within each fecal sample. Using quantitative PCR (qPCR), ten ARGs encoding tetracycline resistance (tetB, tetM), sulfonamide resistance (sul1, sul2), fluoroquinolone resistance (qnrD, qnrS), fluoroquinolone and aminoglycoside resistance (aac(6')-Ib), beta-lactam resistance (bla_TEM, bla_CTX-M), macrolide resistance (ermC), a class 1 integronsintegrase gene (intI1), and a class 2 integrons-integrase gene (intI2) were quantified. The results showed that Firmicutes and Bacteroidetes were dominant in human, cow, horse, and pig groups, while Firmicutes and Actinobacteria were dominant in chicken group. Among ARGs, tetM was detected with the highest number of copies, followed by sul1 and sul2. Most of the genera belonging to Firmicutes showed positive correlations with ARGs and integron genes. There were 97, 34, 31, 25, and 22 genera in chicken, cow, pig, human, and horse respectively which showed positive correlations with ARGs and integron genes. In network analysis, we identified diversity of microbial communities which correlated with ARGs and integron genes. CONCLUSION(S): In this study, antibiotic resistance patterns in human and livestock fecal samples were identified. The abundance of ARGs and integron genes detected in the samples were associated with the amount of antibiotics commonly used for human and livestocks. We found diverse microbial communities associated with antibiotics resistance genes in different hosts, suggesting that antibiotics resistance can disseminate across environments through various routes. Identifying the routes of ARG dissemination in the environment would be the first step to overcome the challenge of antibiotic resistance in the future.

• Asian-Australasian Journal of Animal Sciences
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• 제28권6호
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• pp.870-875
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• 2015

The purpose of this study was to investigate the alternative splicing in equine cordon-bleu WH2 repeat protein-like 1 (COBLL1) gene that was identified in horse muscle and blood leukocytes, and to predict functional consequences of alternative splicing by bioinformatics analysis. In a previous study, RNA-seq analysis predicted the presence of alternative spliced isoforms of equine COBLL1, namely COBLL1a as a long form and COBLL1b as a short form. In this study, we validated two isoforms of COBLL1 transcripts in horse tissues by the real-time polymerase chain reaction, and cloned them for Sanger sequencing. The sequencing results showed that the alternative splicing occurs at exon 9. Prediction of protein structure of these isoforms revealed three putative phosphorylation sites at the amino acid sequences encoded in exon 9, which is deleted in COBLL1b. In expression analysis, it was found that COBLL1b was expressed ubiquitously and equivalently in all the analyzed tissues, whereas COBLL1a showed strong expression in kidney, spinal cord and lung, moderate expression in heart and skeletal muscle, and low expression in thyroid and colon. In muscle, both COBLL1a and COBLL1b expression decreased after exercise. It is assumed that the regulation of COBLL1 expression may be important for regulating glucose level or switching of energy source, possibly through an insulin signaling pathway, in muscle after exercise. Further study is warranted to reveal the functional importance of COBLL1 on athletic performance in race horses.

• International Journal of Stem Cells
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• 제16권3호
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• pp.342-355
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• 2023

Background and Objectives: Osteoblasts are derived from bone marrow mesenchymal stem cells (BMMSCs) and play important role in bone remodeling. While our previous studies have investigated the cell subtypes and heterogeneity in osteoblasts and BMMSCs separately, cell-to-cell communications between osteoblasts and BMMSCs in vivo in humans have not been characterized. The aim of this study was to investigate the cellular communication between human primary osteoblasts and bone marrow mesenchymal stem cells. Methods and Results: To investigate the cell-to-cell communications between osteoblasts and BMMSCs and identify new cell subtypes, we performed a systematic integration analysis with our single-cell RNA sequencing (scRNA-seq) transcriptomes data from BMMSCs and osteoblasts. We successfully identified a novel preosteoblasts subtype which highly expressed ATF3, CCL2, CXCL2 and IRF1. Biological functional annotations of the transcriptomes suggested that the novel preosteoblasts subtype may inhibit osteoblasts differentiation, maintain cells to a less differentiated status and recruit osteoclasts. Ligand-receptor interaction analysis showed strong interaction between mature osteoblasts and BMMSCs. Meanwhile, we found FZD1 was highly expressed in BMMSCs of osteogenic differentiation direction. WIF1 and SFRP4, which were highly expressed in mature osteoblasts were reported to inhibit osteogenic differentiation. We speculated that WIF1 and sFRP4 expressed in mature osteoblasts inhibited the binding of FZD1 to Wnt ligand in BMMSCs, thereby further inhibiting osteogenic differentiation of BMMSCs. Conclusions: Our study provided a more systematic and comprehensive understanding of the heterogeneity of osteogenic cells. At the single cell level, this study provided insights into the cell-to-cell communications between BMMSCs and osteoblasts and mature osteoblasts may mediate negative feedback regulation of osteogenesis process.

• Molecules and Cells
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• 제38권4호
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• pp.362-372
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• 2015

Setdb1, an H3-K9 specific histone methyltransferase, is associated with transcriptional silencing of euchromatic genes through chromatin modification. Functions of Setdb1 during development have been extensively studied in embryonic and mesenchymal stem cells as well as neurogenic progenitor cells. But the role of Sedtdb1 in myogenic differentiation remains unknown. In this study, we report that Setdb1 is required for myogenic potential of C2C12 myoblast cells through maintaining the expressions of MyoD and muscle-specific genes. We find that reduced Setdb1 expression in C2C12 myoblast cells severely delayed differentiation of C2C12 myoblast cells, whereas exogenous Setdb1 expression had little effect on. Gene expression profiling analysis using oligonucleotide microarray and RNA-Seq technologies demonstrated that depletion of Setdb1 results in downregulation of MyoD as well as the components of muscle fiber in proliferating C2C12 cells. In addition, exogenous expression of MyoD reversed transcriptional repression of MyoD promoter-driven luciferase reporter by Setdb1 shRNA and rescued myogenic differentiation of C2C12 myoblast cells depleted of endogenous Setdb1. Taken together, these results provide new insights into how levels of key myogenic regulators are maintained prior to induction of differentiation.

• 한국식품위생안전성학회지
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• 제34권6호
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• pp.576-582
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• 2019

Staphylococcus pseudintermedius는 개에서 기회감염을 유발하는 병원체이며, 공중보건학적으로도 주요한 인수공통 병원체이다. 개에서 분리된 S. pseudintermedius 균주들은 주로 항생제 내성 및 개에서 피부 감염을 유발하는 주요 원인균으로 연구되어 왔지만, 가축에서 분리된 S. pseudintermedius 균주들의 항생제 내성 및 장내 독소 생성에 대한 정보는 매우 제한적이다. 본 연구에서는 개, 돼지, 육우에서 분리된 S. pseudintermedius 균주들에서 18가지의 장내 독소 (staphylococcal enterotoxin; SE) 유전자와 toxic shock syndrome toxin 유전자(tst-1)의 분포양상을 조사하였다. 또한, S. pseudintermedius 균주들의 항생제 내성 양상과 더불어 mecA 유전자 및 SCCmec type 또한 확인하였다. 육우에서 분리한 하나의 균주를 제외한 모든 개와 돼지 분리주 들이 4개 이상의 항생제에 내성을 보였으며, 개에서 분리된 6개의 균주 중 4개의 S. pseudintermedius 균주들이 메티실린 내성과 더불어 SCCmec V를 가진 것으로 확인 되었다. 총 11개의 SE 유전자들 (seb, sec, see, seg, sei, sej, sel, seo, sep, seq, seu) 및 tst-1가 개, 돼지 및 육우로부터 분리된 S. pseudintermedius 균주들에서 확인 되었으며, 대부분의 분리주들 (83%)에서 2개 이상의 SE 유전자들이 확인 되었고, 그 중 sel (42%) 및 sep (42%)가 가장 빈번하게 검출 되었다. 본 연구를 통하여 반려견에서 뿐만 아니라 주요 가축에서 존재하는 S. pseudintermedius 균주들에서 높은 항생제 내성 양상을 확인 하였으며, 항생제 내성과 더불어 여러 staphylococcal enterotoxin 및 tst-1 유전자들을 전파할 가능성을 확인 하였다.

• Journal of Plant Biotechnology
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• 제44권4호
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• pp.372-378
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• 2017

과육색이 다르게 발현되는 사과(Malus domestica L.) 품종의 유전자 발현을 비교하기 위해 2개의 cDNA library를 제작하였다. 붉은 색 과육 품종인 'Redfield'와 백색 과육 품종인 'Granny Smith'의 유전자 발현 차이를 보기 위해 차세대 염기서열 분석(NGS) 기술을 사용하였고 두 품종으로부터 얻은 EST의 염기서열을 결정하고 기존에 보고된 유전자와의 상동성을 분석하였다. HRM 기술은 붉은 색 과육 품종 사과와 백색 과육 품종 사과의 짧은 PCR 증폭산물에서 한 개의 서로 다른 염기서열을 구분하여 분리해낼 수 있다. 'Redfield'와 'Granny Smith'의 EST database로부터 103쌍의 단일염기다형성(SNP) 분자표지를 선발하였고, 붉은 색 과육 품종 10개와 백색 과육 품종 11개를 구분할 수 있는 SNP 분자표지를 HRM 방법으로 분석하였다. 본 연구에서는 사과 EST database를 기반으로 HRM 분석 방법을 이용하여 사과 품종의 적육계와 백육계를 구분할 수 있는 효율적인 SNP 분자표지를 개발하였다. 이러한 SNP 분자표지는 사과육종에 유용하게 사용할 수 있으며 사과 품종의 다양한 색 변화에 관한 분자 기작 연구에 좋은 참고자료가 될 수 있을 것이다.

• Journal of Applied Biological Chemistry
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• 제61권2호
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• pp.165-172
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• 2018

경제발전으로 인해 한국인의 식습관이 점차 서구화됨에 따라 웰빙(Well-being)의 문제가 야기되고 있다. 웰빙은 장내 미생물 군집과 밀접하게 연관되어 있으며, 이는 섭취한 음식에 따라 가변적이다. 이에 본 연구에서는 장내 미생물의 16S rRNA 유전자를 기반으로 하여 MiSeq을 진행하였고, 고지방 식이(HFD) 및 저식이섬유 식이(LFD)로 인한 장내의 미생물 생태 비교 및 분석하고자 수행되었다. 일반 대조군(CTL) 그룹과 비교하여 각각 LFD 그룹과 HFD 그룹은 species richness가 유의적으로 감소하였고, species evenness에서는 차이가 나타나지 않았다. phylum 수준에서는 Proteobacteria는 두 처리군에서 유의적으로 증가하였고(p<0.05), 그 중 Sutterella genus가 유의적으로 가장 많이 증가하였다. Bacteroidetes는 HFD 그룹에서 유의적으로 감소하였고, S24-7 family가 가장 큰 비율로 감소하였다. 한편 Firmicutes는 HFD:LFD 그룹에서 차이를 보였고, LFD 그룹에서 Lachnospiraceae family가 유의적으로 낮은 비율로 나타난 것이 확인되었다(p<0.05). PICUSt 기반 신진대사 분석에서 LFD 그룹은 아미노산 대사 및 탄수화물 대사에 관여하는 미생물 수가 유의적으로 감소하는 양상을 보였고(p<0.05), 에너지 대사에서는 메탄 대사에 관여하는 미생물이 유의적으로 감소하였다(p<0.01). 한편 HFD 그룹에서는 아미노산 대사에 관여하는 미생물 수가 유의적으로 증가하였다(p<0.05). 글리칸 생합성 및 대사에 관여하는 미생물은 LFD 그룹과 HFD 그룹에서 유의적으로 증가하는 것으로 나타났다(p<0.01). 이상의 결과를 통해 지속적으로 불균형한 식단을 섭취하는 것은 장내 환경을 dysbiosis시켜, 대사성 질환 및 장 기능 저하를 유발할 것으로 예상된다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권2호
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• pp.189-197
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• 2018

Objective: Hemicastration is a unilateral orchiectomy to remove an injured testis, which can induce hormonal changes and compensatory hypertrophy of the remaining testis, and may influence spermatogenesis. However, the underlying molecular mechanisms are poorly understood. Here, we investigated the impact of hemicastration on remaining testicular function. Methods: Prepubertal mice (age 24 days) were hemicastrated, and their growth was monitored until they reached physical maturity (age 72 days). Subsequently, we determined testis DNA methylation patterns using reduced representation bisulfite sequencing of normal and hemicastrated mice. Moreover, we profiled the testicular gene expression patterns by RNA sequencing (RNA-seq) to examine whether methylation changes affected gene expression in hemicastrated mice. Results: Hemicastration did not significantly affect growth or testosterone (p>0.05) compared with control. The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. Conclusion: Global profiling of DNA methylation and gene expression demonstrated that hemicastration-induced compensatory response maintained normal growth and testicular morphological structure in mice.