• Journal of Plant Biotechnology
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• 제45권1호
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• pp.45-54
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• 2018

This research was conducted to study the gene expression of coffee (Coffea arabica L.) seedlings under salt stress condition. A solution of five percent ($2.3dS\;m^{-1}$) deep sea water was used for the salt treatment, and it was thereby compared to normal irrigation water ($0.2dS\;m^{-1}$) used for the control treatment. The mRNA was extracted from the leaves of the coffee seedlings for a comprehensive analysis. In this study, a total of 19,581 genes were identified and aligned to the reference sequences available in the coffee genome database. The gene ontology analysis was performed to estimate the number of genes associated with the identified biological processes, cellular components and molecular functions. Among the 19,581 genes, 7369 (37.64%) were associated with biological processes, 5909 (30.18%) with cellular components, and 5325 (27.19%) with molecular functions. The remaining 978 (4.99%) genes were therefore grouped as unclassified. A differential gene expression analysis was performed using the DESeq2 package to identify the genes that were differentially expressed between the treatments based on fold changes and p-values. Namely, a total of 611 differentially expressed genes were identified (treatment/control) in that case. Among these, 336 genes were up-regulated while 275 of the genes were down-regulated. Of the differentially expressed genes, 60 genes showed statistically significant (p < 0.05) expression, 44 of which were up-regulated and 16 which were down-regulated. We also identified 11 differentially expressed transcription factor genes, 6 of which were up-regulated and rest 5 genes were down-regulated. The data generated from this study will help in the continued interest and understanding of the responses of coffee seedlings genes associated with salinity stress, in particular. This study will also provide important resources for further functional genomics studies.

• Journal of Microbiology and Biotechnology
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• 제19권10호
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• pp.1109-1121
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• 2009

In an attempt to discover novel biomarker proteins in type 2 diabetes prognosis, we investigated the influence of hypoglycemic extracellular polysaccharides (EPS) obtained from the macrofungus Tremella fuciformis on the differential levels of plasma proteins in ob/ob mice using two-dimensional gel electrophoresis (2-DE). The 2-DE analysis demonstrated that 92 spots from about 900 visualized spots were differentially regulated, of which 40 spots were identified as principal diabetes-associated proteins. By comparing control with EPS-fed mice, we found that at least six proteins were significantly altered in ob/ob mice, including Apo A-I, IV, C-III, E, retinol-binding protein 4, and transferrin, and their levels were interestingly normalized after EPS treatment. Western blot analysis revealed that the altered levels of the two regulatory molecules highlighted in diabetes and obesity (e.g., resistin and adiponectin) were also normalized in response to EPS. The Mouse Diabetes PCR Array profiles showed that the expression of 84 genes related to the onset, development, and progression of diabetes were significantly downregulated in liver, adipocyte, and muscle of ob/ob mice. EPS might act as a potent regulator of gene expression for a wide variety of genes in ob/ob mice, particularly in obesity, insulin resistance, and complications from diabetes mellitus.

• Journal of Microbiology and Biotechnology
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• 제23권8호
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• pp.1055-1059
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• 2013

The ectomycorrhizal fungus Tricholoma matsutake grows symbiotically with Pinus densiflora. Phenylalanine ammonia-lyase (E.C. 4.3.1.24) catalyzes the conversion of L-phenylalanine to trans-cinnamic acid. The role of fungal phenylalanine ammonia-lyase, however, has not been clear until now. In this study, the gene encoding phenylalanine ammonia-lyase (PAL), which was isolated from T. matsutake, was cloned and characterized. The PAL gene (tmpal) consists of 2,160 nucleotides, coding for a polypeptide containing 719 amino acid residues. The deduced amino acid sequence of tmpal from T. matsutake shows high identity (70%) with that from Laccaria bicolor. Comparative analysis of the PAL genes among T. matsutake and other species of the class Agaricomycetes showed that both active sites and binding sites were significantly conserved among these genes. The transcriptional analysis of the PAL gene revealed a differential gene expression pattern depending on the developmental stages (mycelium, primordium, stipe, pileus, and gills) of T. matsutake. These results suggest that the PAL gene in T. matsutake plays an important role in multiple physiological functions.

• BMB Reports
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• 제44권8호
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• pp.535-540
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• 2011

Reprogramming errors, which appear frequently in cloned animals, are reflected by aberrant gene expression. We previously reported the aberrant expression of TIMP-2 and PBEF in cloned placenta and differential expression of PBEF genes during pregnancy. To examine the epigenetic modifications that regulate dynamic gene expression in developing placentae, we herein analyzed the mRNA and protein expression levels of PBEF and TIMP-2 in the placentae of normal mice during pregnancy and then examined potential correlations with epigenetic modifications. DNA methylation pattern analysis revealed no difference, but ChIP assays using antibodies against H3-K9/K14 and H4-K5 histone acetylation revealed that the H3-K9/K14 acetylation levels, but not the H4-K5 acetylation levels, of the TIMP-2 and PBEF loci were significantly correlated with their gene expression levels during placentation in normal mice. These results suggest that epigenetic changes may regulate gene expression level in the developing placentae of normal mice and that inappropriate epigenetic reprogramming might be one cause of the abnormal placentae seen in cloned animals.

• Journal of Animal Science and Technology
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• 제53권3호
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• pp.195-202
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• 2011

Maintenance of adequate telomere length in developing cells is the most important concern to preserve the integrity of the genome. The length of telomere is strictly regulated by numerous telomere-binding proteins and/or interacting factors. Even though the expression of telomerase in the male reproductive tract has been characterized, developmental expressional profiling of telomerase and other telomere-associated proteins has not been determined in detail. The present study was attempted to examine expression patterns of catalytic subunit (Tert) and RNA component (Terc) of telomerase and two telomerase associated factors, telomerase associated protein 1 (Tep1) and TERF1 (TRF1) interacting nuclear factor 2 (Tinf2) in the testis and seminal vesicle of male rat during postnatal development. The real-time PCR analysis was utilized to quantify mRNA expression of molecules. The abundance of Tep1 mRNA in the testis and seminal vesicle was the highest at 5 months of age. Expressional fluctuation of Tinf2 during postnatal development was found in the testis, while expression of Tinf2 in the seminal vesicle was gradually increased until 5 months of age and then significantly decreased later. mRNA level of Tert gene in the testis was significantly increased at the adult and the elder, while the highest expression of Tert gene in the seminal vesicle was found at 5 months of age. Expression of Terc transcript in the testis and seminal vesicle was the highest at 5 months of age, followed by significant reduction at 1 and 2 years of ages. Such differential gene expression of telomere-associated factors and telomerase components in different male reproductive tissues during postnatal development indicates that maintenance of telomere length would be regulated in tissue- and/or age-specific manners.

• Asian-Australasian Journal of Animal Sciences
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• 제25권7호
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• pp.903-912
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• 2012

In Erhualian and Yorkshire reciprocal cross $F_1$ pig populations, we examined the mRNA expression characteristic of liver-derived IGF-1, IGF-1R, IGF-2, IGF-2R and IGFBP-3 during the embryonic and postnatal developmental periods (E50, E70, E90, D1, D20, D70, D120 and D180). Our results demonstrated that the IGF-system genes mRNA levels exhibited an ontogenetic expression pattern, which was potentially associated with the porcine embryonic development, postnatal growth, organogenesis and even the initiation and acceleration of puberty. The expression pattern of IGF-system genes showed variation in the reciprocal cross ($F_1$ YE and EY pigs). This study also involved the expression features of imprinted genes IGF-2 and IGF-2R. The parent-of-origin effect of imprinted genes was reflected by their differential expression between the reciprocal crosses populations. The correlation analysis also indicated that the regulatory network and mechanisms involved in the IGF system were a complex issue that needs to be more fully explored. A better understanding of IGF system components and their interactive mechanisms will enable researchers to gain insights not only into animal organogenesis but also into somatic growth development and even reproduction.

• Asian-Australasian Journal of Animal Sciences
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• 제25권8호
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• pp.1102-1116
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• 2012

During embryo implantation in pigs, the uterine endometrium undergoes dramatic morphological and functional changes accompanied with dynamic gene expression. Since the greatest amount of embryonic losses occur during this period, it is essential to understand the expression and function of genes in the uterine endometrium. Although many reports have studied gene expression in the uterine endometrium during the estrous cycle and pregnancy, the pattern of global gene expression in the uterine endometrium in response to the presence of a conceptus (embryo/fetus and associated extraembryonic membranes) has not been completely determined. To better understand the expression of pregnancy-specific genes in the endometrium during the implantation period, we analyzed global gene expression in the endometrium on day (D) 12 and D15 of pregnancy and the estrous cycle using a microarray technique in order to identify differentially expressed endometrial genes between D12 of pregnancy and D12 of the estrous cycle and between D15 of pregnancy and D15 of the estrous cycle. Results showed that the global pattern of gene expression varied with pregnancy status. Among 23,937 genes analyzed, 99 and 213 up-regulated genes and 92 and 231 down-regulated genes were identified as differentially expressed genes (DEGs) in the uterine endometrium on D12 and D15 of pregnancy compared to D12 and D15 of the estrous cycle, respectively. Functional annotation clustering analysis showed that those DEGs included genes involved in immunity, steroidogenesis, cell-to-cell interaction, and tissue remodeling. These findings suggest that the implantation process regulates differential endometrial gene expression to support the establishment of pregnancy in pigs. Further analysis of the genes identified in this study will provide insight into the cellular and molecular bases of the implantation process in pigs.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.122-122
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• 2017

Wheat wild relatives that have never been domesticated contained useful genetic resources such as the resistance to abiotic and biotic stresses. Leymus racemosus is one of the wild species. It can grow in a harsh environment like seaside and distribute by healthy rhizomes. Also, it has a useful genetic resource such as salt tolerance and different diseases resistance. Wheat (Triticum aestivum L. cv. Chinese Spring; CS) was crossed with L. racemosus. Wheat-L. racemosus disomic addition lines were produced. The purpose of this study is to identify protein expression in each disomic addition line compared to CS. We performed two-dimensional electrophoresis. Two-dimensional gels stained with coomassie brilliant blue (CBB), a total of 1566 differentially expressed proteins were identified by Progenesis Same Spots software from the cultivars. However, a total of 90 protein spots were identified to be either present or absent or showing significantly differential expression when the difference threshold was set to more than 1.5 fold. However, out of the 90 differentially protein spots, a total of 74 spots were sorted for mass spectrometry analysis. The identified proteins may provide important clues for better understanding the molecular changes in the chromosomes carrying Leymus racemosus.

• Journal of Microbiology and Biotechnology
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• 제14권4호
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• pp.836-843
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• 2004

Nontypeable H. influenzae (NTHi), a Gram-negative obligate human pathogen, causes pneumonia, chronic bronchitis, and otitis media, and the respiratory epithelium is the first line of defense that copes with the pathogen. In an effort to identify transcriptional responses of human respiratory epithelial cells to infection with NTHi, we examined its differential gene expression using high density cDNA microarrays. BEAS-2B human bronchial epithelial cells were exposed to NTHi for 3 hand 24 h, and the alteration of mRNA expression was analyzed using microarrays consisting of 8,170 human cDNA clones. The results indicated that approximately 2.6% of the genes present on the microarrays increased in expression over 2-fold and 3.8% of the genes decreased during the 24-h infection period. Upregulated genes included cytokines (granulocyte-macrophage colony stimulating factor 2, granulocyte chemotactic protein 2, IL-6, IL-10, IL-8), transcription factors (Kruppel-like factor 7, CCAAT/enhancer binding protein $\beta$, E2F-1, NF-$\kappa$B, cell surface molecules (CD74, ICAM-1, ICAM-2, HLA class I), as well as those involved in signal transduction and cellular transport. Selected genes were further confirmed by reverse-transcription-PCR. These data expand our knowledge of host cellular responses during NTHi infection and should provide a molecular basis for the study of host-NTHi interaction.

• Plant Biotechnology Reports
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• 제3권4호
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• pp.285-292
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• 2009

Zoysiagrass (Zoysia japonica) is one of the important turfgrass species. Extending green period of zoysiagrass via delaying leaf senescence will make this species have more potential in the turfgrass industry. In this study, we found that zoysiagrass seedlings treated with $GA_3$ could delay the leaf senescence induced by darkness. To study expression of genes responsive to staying green in zoysiagrass, suppression subtractive hybridization (SSH) was used to identify differentially expressed genes between non-$non-GA_3-treated$ and $GA_3-treated$ seedlings subjected to darkness. A total of 307 ESTs were generated, of which 226 ESTs clustered into 54 contigs and 81 were singlets. Differentially expressed genes selected by subtractions were classified into six categories according to their putative functions generated by BLAST analysis. Expression of five selected genes, Met, SAM, V-ATPase, Cry (Cryptochrome gene), and An (diphthine synthase gene) were examined by RT-PCR and Real-time PCR. Both RT-PCR and Real-time PCR results demonstrated that the differential expressions of these genes were attributable to delaying senescence by exogenously applied gibberellic acid. This is the first genome-wide study of senescence in a species of turfgrass.