• Title/Summary/Keyword: Gene Expression Patterns

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Isolation and Characterization of Cinnamoyl-CoA Reductase Gene from Panax ginseng C. A. Meyer

  • Parvin, Shohana;Pulla, Rama Krishna;Shim, Ju-Sun;Kim, Yu-Jin;Jung, Dea-Yeoung;Kim, Se-Hwa;Yang, Deok-Chun
    • Journal of Ginseng Research
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    • v.32 no.3
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    • pp.232-237
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    • 2008
  • Cinnamoyl-CoA reductase (CCR, EC 1.2.1.44) catalyses the reduction of cinnamic acid CoA esters into their corresponding aldehydes, the first step of the phenylpropanoid pathway specially dedicated to monolignol biosynthesis. A cDNA clones encoding CCR have been isolated from Panax ginseng C.A. Meyer and its expression was investigated in response to abiotic stresses. The cDNA, designated PgCCR which is 865 nucleotides long and has an open reading frame of 590 bp with a deduced amino acid sequence of 176 residues. The PgCCR encoded protein possesses substantial homology with CCRs isolated and cloned from other sources; the highest identity (51.8%) was observed with CCR from Tomato (Lycopersicon esculentum). Under various stress conditions, expression patterns of the PgCCR were highly induced in adventitious and hairy roots by several abiotic stresses. These results indicated that PgCCR plays protective role against diverse environmental stresses.

Reliability of microarray analysis for studying periodontitis: low consistency in 2 periodontitis cohort data sets from different platforms and an integrative meta-analysis

  • Jeon, Yoon-Seon;Shivakumar, Manu;Kim, Dokyoon;Kim, Chang-Sung;Lee, Jung-Seok
    • Journal of Periodontal and Implant Science
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    • v.51 no.1
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    • pp.18-29
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    • 2021
  • Purpose: The aim of this study was to compare the characteristic expression patterns of advanced periodontitis in 2 cohort data sets analyzed using different microarray platforms, and to identify differentially expressed genes (DEGs) through a meta-analysis of both data sets. Methods: Twenty-two patients for cohort 1 and 40 patients for cohort 2 were recruited with the same inclusion criteria. The 2 cohort groups were analyzed using different platforms: Illumina and Agilent. A meta-analysis was performed to increase reliability by removing statistical differences between platforms. An integrative meta-analysis based on an empirical Bayesian methodology (ComBat) was conducted. DEGs for the integrated data sets were identified using the limma package to adjust for age, sex, and platform and compared with the results for cohorts 1 and 2. Clustering and pathway analyses were also performed. Results: This study detected 557 and 246 DEGs in cohorts 1 and 2, respectively, with 146 and 42 significantly enriched gene ontology (GO) terms. Overlapping between cohorts 1 and 2 was present in 59 DEGs and 18 GO terms. However, only 6 genes from the top 30 enriched DEGs overlapped, and there were no overlapping GO terms in the top 30 enriched pathways. The integrative meta-analysis detected 34 DEGs, of which 10 overlapped in all the integrated data sets of cohorts 1 and 2. Conclusions: The characteristic expression pattern differed between periodontitis and the healthy periodontium, but the consistency between the data sets from different cohorts and metadata was too low to suggest specific biomarkers for identifying periodontitis.

Suppression of the Toll-like receptors 3 mediated pro-inflammatory gene expressions by progenitor cell differentiation and proliferation factor in chicken DF-1 cells

  • Hwang, Eunmi;Kim, Hyungkuen;Truong, Anh Duc;Kim, Sung-Jo;Song, Ki-Duk
    • Journal of Animal Science and Technology
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    • v.64 no.1
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    • pp.123-134
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    • 2022
  • Toll-like receptors (TLRs), as a part of innate immunity, plays an important role in detecting pathogenic molecular patterns (PAMPs) which are structural components or product of pathogens and initiate host defense systems or innate immunity. Precise negative feedback regulations of TLR signaling are important in maintaining homeostasis to prevent tissue damage by uncontrolled inflammation during innate immune responses. In this study, we identified and characterized the function of the pancreatic progenitor cell differentiation and proliferation factor (PPDPF) as a negative regulator for TLR signal-mediated inflammation in chicken. Bioinformatics analysis showed that the structure of chicken PPDPF evolutionarily conserved amino acid sequences with domains, i.e., SH3 binding sites and CDC-like kinase 2 (CLK2) binding sites, suggesting that relevant signaling pathways might contribute to suppression of inflammation. Our results showed that stimulation with polyinosinic:polycytidylic acids (Poly [I:C]), a synthetic agonist for TLR3 signaling, increased the mRNA expression of PPDPF in chicken fibroblasts DF-1 but not in chicken macrophage-like cells HD11. In addition, the expression of pro-inflammatory genes stimulated by Poly(I:C) were reduced in DF-1 cells which overexpress PPDPF. Future studies warrant to reveal the molecular mechanisms responsible for the anti-inflammatory capacity of PPDPF in chicken as well as a potential target for controlling viral resistance.

Identification of a key signaling network regulating perennating bud dormancy in Panax ginseng

  • Jeoungeui Hong;Soeun Han;Kyoung Rok Geem;Wonsil Bae;Jiyong Kim;Moo-Geun Jee;Jung-Woo Lee;Jang-Uk Kim;Gisuk Lee;Youngsung Joo;Donghwan Shim;Hojin Ryu
    • Journal of Ginseng Research
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    • v.48 no.5
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    • pp.511-519
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    • 2024
  • Background: The cycle of seasonal dormancy of perennating buds is an essential adaptation of perennial plants to unfavorable winter conditions. Plant hormones are key regulators of this critical biological process, which is intricately connected with diverse internal and external factors. Recently, global warming has increased the frequency of aberrant temperature events that negatively affect the dormancy cycle of perennials. Although many studies have been conducted on the perennating organs of Panax ginseng, the molecular aspects of bud dormancy in this species remain largely unknown. Methods: In this study, the molecular physiological responses of three P. ginseng cultivars with different dormancy break phenotypes in the spring were dissected using comparative genome-wide RNA-seq and network analyses. These analyses identified a key role for abscisic acid (ABA) activity in the regulation of bud dormancy. Gene set enrichment analysis revealed that a transcriptional network comprising stress-related hormone responses made a major contribution to the maintenance of dormancy. Results: Increased expression levels of cold response and photosynthesis-related genes were associated with the transition from dormancy to active growth in perennating buds. Finally, the expression patterns of genes encoding ABA transporters, receptors (PYRs/PYLs), PROTEIN PHOSPHATASE 2Cs (PP2Cs), and DELLAs were highly correlated with different dormancy states in three P. ginseng cultivars. Conclusion: This study provides evidence that ABA and stress signaling outputs are intricately connected with a key signaling network to regulate bud dormancy under seasonal conditions in the perennial plant P. ginseng.

Analysis of Differential Expression of Cytochrome P450 Aromatase(Cyp19) in The Efferent Ductules and The Epididymis of Male Rats During Postnatal Development (생후 발달과정 동안 숫 흰쥐의 Efferent Ductules과 부정소에서 Cytochrome P450 Aromatase(Cyp19) 발현 양상 분석)

  • Kim, Ju-Young;Seo, Hee-Jung;Kim, Ok-Soon;Kim, Byung-Joon;Lee, Seong-Kyu;Baik, Haing-Woon;Lee, Ki-Ho
    • Journal of Animal Science and Technology
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    • v.50 no.6
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    • pp.783-792
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    • 2008
  • The present study was performed to determine expression of cytochrome P450 aromatase(Cyp19) in the efferent ductules(EDs) and the epididymis of male rat reproductive tract at different postnatal ages. Total RNAs isolated were reverse-transcribed, and cDNAs were utilized for real-time PCR analysis. In the EDs, the Cyp19 transcript was expressed at all prepubertal ages with the highest level at 14 days of age, but not at 90 days of age. Expression of Cyp19 mRNA in the epididymis was found at all age groups, except 7 days of age. Distinct expression patterns of Cyp19 transcript were shown in each segment of the epididymis. These results indicate that expression of Cyp19 gene in the excurrent duct of male reproductive tract is differentially regulated in age-dependent and segment-specific manners.

A Discrete Mathematical Model Applied to Genetic Regulation and Metabolic Networks

  • Asenjo, J.A.;Ramirez, P.;Rapaport, I.;Aracena, J.;Goles, E.;Andrews, B.A.
    • Journal of Microbiology and Biotechnology
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    • v.17 no.3
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    • pp.496-510
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    • 2007
  • This paper describes the use of a discrete mathematical model to represent the basic mechanisms of regulation of the bacteria E. coli in batch fermentation. The specific phenomena studied were the changes in metabolism and genetic regulation when the bacteria use three different carbon substrates (glucose, glycerol, and acetate). The model correctly predicts the behavior of E. coli vis-a-vis substrate mixtures. In a mixture of glucose, glycerol, and acetate, it prefers glucose, then glycerol, and finally acetate. The model included 67 nodes; 28 were genes, 20 enzymes, and 19 regulators/biochemical compounds. The model represents both the genetic regulation and metabolic networks in an integrated form, which is how they function biologically. This is one of the first attempts to include both of these networks in one model. Previously, discrete mathematical models were used only to describe genetic regulation networks. The study of the network dynamics generated 8 $(2^3)$ fixed points, one for each nutrient configuration (substrate mixture) in the medium. The fixed points of the discrete model reflect the phenotypes described. Gene expression and the patterns of the metabolic fluxes generated are described accurately. The activation of the gene regulation network depends basically on the presence of glucose and glycerol. The model predicts the behavior when mixed carbon sources are utilized as well as when there is no carbon source present. Fictitious jokers (Joker1, Joker2, and Repressor SdhC) had to be created to control 12 genes whose regulation mechanism is unknown, since glycerol and glucose do not act directly on the genes. The approach presented in this paper is particularly useful to investigate potential unknown gene regulation mechanisms; such a novel approach can also be used to describe other gene regulation situations such as the comparison between non-recombinant and recombinant yeast strain, producing recombinant proteins, presently under investigation in our group.

Roc10, a Rice HD-Zip transcription factor gene, modulates lignin biosynthesis for drought tolerance

  • Bang, Seung Woon;Lee, Dong-Keun;Jung, Harin;Chung, Pil Joong;Kim, Youn Shic;Choi, Yang Do;Suh, Joo-Won;Kim, Ju-Kon
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.159-159
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    • 2017
  • Drought, a common environmental constraint, induces a range of physiological, biochemical and molecular changes in plants, and can cause severe reductions in crop yield. Consequently, understanding the molecular mechanisms of drought tolerance is an important step towards crop biotechnology. Here, we report that the rice (Oryza sativa) homeodomain-leucine zipper class IV transcription factor gene, ${\underline{R}ice}$ ${\underline{o}utermost}$ ${\underline{c}ell-specific}$ gene 10 (Roc10), enhances drought tolerance and grain yield by increasing lignin accumulation in ground tissues. Overexpression of Roc10 in rice significantly increased drought tolerance at the vegetative stages of growth and promoted both more effective photosynthesis and a reduction in water loss rate, compared with non-transgenic controls or RNAi transgenic plants. Importantly, Roc10 overexpressing plants had a higher drought tolerance at the reproductive stage of growth and a higher grain yield compared with the controls under field-drought conditions. Roc10 is mainly expressed in outer cell layers including the epidermis and the vasculature of the shoots, which coincides with areas of cell wall lignification. Roc10 overexpression elevated the expression levels of lignin biosynthetic genes in shoots, with a concomitant increase in the accumulation of lignin, while the overexpression and RNAi lines showed opposite patterns of lignin accumulation. We identified downstream target genes of Roc10 by performing RNA-seq and chromatin immunoprecipitation (ChIP)-seq analyses of shoot tissues. Roc10 was found to directly bind to the promoter of PEROXIDASEN/PEROXIDASE38, a key gene in lignin biosynthesis. Together, our findings suggest that Roc10 confers drought stress tolerance by promoting lignin biosynthesis in ground tissues.

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Characterization of Oszinc626, knock-out in zinc finger RING-H2 protein gene, in Ac/Ds mutant lines of rice(Oryza sativar L.) (Zinc finger RING-H2 protein관련 Ac/Ds전이인자 삽입 변이체 Oszinc626 유전자의 특성 분석)

  • Park, Seul-Ah;Jung, Yu-Jin;Ahn, Byung-Ohg;Yun, Doh-Won;Ji, Hyeon-So;Park, Yong-Hwan;Eun, Moo-Young;Suh, Seok-Cheol;Lee, Soon-Youl;Lee, Myung-Chul
    • Journal of Plant Biotechnology
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    • v.35 no.3
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    • pp.177-183
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    • 2008
  • Ac/Ds mutant lines of this study were transgenic rice plants, each of which harbored the maize transposable element Ds together with a GUS coding sequence under the control of a promoterless(Ds-GUS). We selected the mutants that were GUS expressed lines, because the GUS positive lines will be useful for identifying gene function in rice. One of these mutants was identified knock-out at Oszinc626(NP_001049991) gene, encoding a RING-H2 zinc-finger protein, by Ds insertion. In this mutant, while primary root development is normal, secondary root development from lateral root was very poor and seed development was incomplete compare with normal plant. RING zinc-finger proteins play important roles in the regulation of development in a variety of organisms. In the plant kingdom, a few genes encoding RING zinc-finger proteins have been documented with visible effects on plant growth and development. The consensus of the RING-H2(C3-H2-C3 type) domain for this group of protein is $Cys-X_2-Cys-X_{28}-Cys-X-His-X_2-His-X_2-Cys-X_{14}-Cys-X_2-Cys$. Oszinc626 encodes a predicted protein product of 445 amino acids residues with a molecular mass of 49 kDa, with a RING-zinc-finger motif located at the extreme end of the C-terminus. RT-PCR analysis indicated that the expression of Oszinc626 gene was induced by IAA, cold, dehydration, high-salinity and abscisic acid, but not by 2,4-D, and the transcription of Oszinc626 gene accumulated primarily in rice immature seeds, root meristem and shoots. The gene accumulation patterns were corresponded with GUS expression.

Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

  • Gim, Jeong-An;Hong, Chang Pyo;Kim, Dae-Soo;Moon, Jae-Woo;Choi, Yuri;Eo, Jungwoo;Kwon, Yun-Jeong;Lee, Ja-Rang;Jung, Yi-Deun;Bae, Jin-Han;Choi, Bong-Hwan;Ko, Junsu;Song, Sanghoon;Ahn, Kung;Ha, Hong-Seok;Yang, Young Mok;Lee, Hak-Kyo;Park, Kyung-Do;Do, Kyoung-Tag;Han, Kyudong;Yi, Joo Mi;Cha, Hee-Jae;Ayarpadikannan, Selvam;Cho, Byung-Wook;Bhak, Jong;Kim, Heui-Soo
    • Molecules and Cells
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    • v.38 no.3
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    • pp.210-220
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    • 2015
  • Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethy-lated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.

Selection and Crossbreeding in Relation to Plumage Color Inheritance in Three Chinese Egg Type Duck Breeds (Anas Platyrhynchos)

  • Lin, R.L.;Chen, H.P.;Rouvier, R.;Poivey, J.P.
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.8
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    • pp.1069-1074
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    • 2014
  • In China and South East Asia, the duck (common duck) is important in egg production for human consumption. Plumage color is a breed characteristic and of economic importance, together with egg production. Our aim in this study was to investigate the inheritance of plumage color in three Chinese indigenous egg-type duck breeds, Shan Ma (S), Putian White (F) and Putian black (P), and some of their crossbreds. These three breeds have different plumage color and are used in crossbreeding. The crossbred laying ducks $F{\times}(P{\times}S)$ and $F{\times}(S{\times}P)$ showed highly improved laying ability but heterogeneous plumage color. Genotypes at four relevant loci were investigated by studying down color and pattern in ducklings after crossbreeding. $F_1$ ducklings from the matings $F{\times}S$ and $S{\times}F$, $P{\times}S$, and $S{\times}P$ were classified into four classes of plumage color (the Shan Ma plumage color, black, white, or multicolored) over three generations. Parents were selected for the Shan Ma plumage color of their progeny. In the fourth generation, P male and P female ducks were selected according to the frequency of the desired class of plumage color (Shan Ma) of their $F_1$ progeny to obtain the so-called "Brown Putian Ma duck". The Shan Ma duck genotype was identified as having the restricted mallard color pattern ($M^RM^R$), full expression of any of the patterns or colors (CC), no extended black (ee) and no brown dilution D (D). The Putian White genotype was recessive white (cc), no extended black (ee) and no brown dilution D (D). The Putian Black genotype exhibited full expression of extended black (E gene) and no brown dilution (CCEE D [D]). It was shown that $F{\times}S$ and $S{\times}F$ tests should be implemented to eliminate the recessive white c allele in the S line and the dominant extended black E allele in the F line. It was also shown that the Brown Putian Ma obtained from Putian Black, with no extended black genotype (ee), could be used to get rid of the black plumage (E gene) in the crossbred ducks. This could provide a solution for producing 3-way crossbred ducks Putian $White{\times}$(Putian-$Ma{\times}Shan$ Ma) and Putian $White{\times}$(Shan $Ma{\times}Putian$-Ma), with the desired Shan Ma feather color.