• Clinical and Experimental Pediatrics
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• v.46 no.2
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• pp.128-136
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• 2003

Purpose : Hyper IgM syndrome(HIGM) is characterized by severe recurrent bacterial infections with decreased serum levels of IgG, IgA, and IgE but elevated IgM levels. Recently, it has been classified into three groups; HIGM1, HIGM2 and a rare form of HIGM. HIGM1 is a X-linked form of HIGM and has now been identified as a T-cell deficiency in which mutations occur in the gene that encodes the CD40 ligand molecule. HIGM2 is an autosomal recessive form of HIGM. Molecular studies have shown that the mutation of HIGM2 is in the gene that encodes activation-induced cytidine deaminase(AID). Recently, another rare form of X-linked HIGM syndrome associated with hypohydrotic ectodermal dysplasia has been identified. We encountered a patient with a varient form of HIGM2. To clarify the cause of this form of HIGM, we evaluated the peripheral B cells of this patient. Methods : The lymphocytes of the patient were prepared from peripheral blood. B cells were immortalized with the infection of EBV. Cell cycle analysis was done with the immortalized B cells of the patient. Peripheral mononuclear cells were stained with monoclonal anti-CD40L antibody. Total RNA was extracted from the peripheral mononuclear cells. After RT-PCR, direct sequencing for CD40L gene and HuAID gene were done. Immunostainings of a lymph node for CD3, CD23, CD40, Fas-L, bcl-2, BAX were done. Results : The peripheral B cells of this patient showed normal expression of CD40L molecule and normal sequencing of CD40L gene, and also normal sequencing of AID gene. Interestingly, the peripheral B cells of this patient showed a decreased population of G2/mitosis phase in cell cycles which recovered to normal with the stimulation of IL-4. Conclusion : We suspect that the cause of increased serum IgM in this patient may be from a decrease of G2/mitosis phase of the peripheral B cells, which may be from the decreased production or secretion of IL-4. Therefore, this may be a new form of HIGM.

• Journal of the korean academy of Pediatric Dentistry
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• v.30 no.2
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• pp.217-228
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• 2003

Co-ordinate growth of the brain and skull is achieved through a series of tissue interactions between the developing brain, the growing bones of the skull and the sutures that unite the bones. Craniosynostosis, the premature fusion of cranial sutures, presumably involves disturbance of these interactions. Bmp2, one of bone morphogenetic proteins (Bmps), is involved in the regulation of the shapes of individual bones and the relative proportions of the skeleton. Mutations in the homeobox gene Msx2, known as a downstream gene of Bmp, cause Boston-type human craniosynostosis. The phenotype of Dlx5 homozygote mutant mouse presents craniofacial abnormalities including a delayed ossification of calvarial bone. These facts suggest important roles of Bmp2, Msx2 and Dlx5 genes in the cranial bone growth and suture morphogenesis. To elucidate the function of these molecules in the early morphogenesis of mouse cranial sutures, we first analyzed by in situ hybridization the expression of Bmp2(E15-18), Msx2 and Dlx5 genes in the developing sagittal suture of calvaria during the embryonic stage. Bmp2 mRNA was intensely expressed in the osteogenic fronts and also at the low level in the periosteum of parietal bones during embryonic stage, Msx2 mRNA was intensely expressed in the sutural mesenchyme and mildly expressed in the dura mater during the embryonic stage. Dlx5 mRNA was intensely expressed osteogenic fronts and parietal bones. To further examine the role of Bmp signaling in cranial suture, we did in vitro experiments in E15.5 mouse calvarial explants. Interestingly, implantation of Bmp2-soaked beads onto the osteogenic fronts after 48 hours organ culture resulted in the increase of the tissue thickness and cell number around Bmp2 beads, compared to BSA control beads. In addition Bmp2 induced etopic expressions of Msx2 and Dlx5 genes. On the other hand, overexpression of FGF2 did not induce the expression of Msx2 and Dlx5. Taken together, these data indicate that Bmp2 signaling molecule has a important role in regulating the cranial bone growth and early morphogenesis of cranial suture. We also suggest that Bmp signaling is involved in all the stages of osteogenesis of cranial bones and the maintenance of cranial suture by regulating Msx2 and Dlx5 genes, and that Msx2 and Dlx5 genes are specific transcription factors of Bmp signaling pathway.

• Proceedings of the Korea Information Processing Society Conference
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• 2012.11a
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• pp.1340-1343
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• 2012

정보의 시각화는 추상적 정보를 직관적으로 이해하기 쉽도록 시각적으로 명확하게 표현하는 방법을 말한다. 대용량의 바이오 데이터를 다루는 생물정보학(bioinformatics) 분야에서는 컴퓨터의 높은 성능을 활용하여 수많은 유전학적 데이터들을 분석하고 있다. 다양한 생물정보학 실험에서 전사체는 특정한 조건에서 발현된 RNA의 총합을 말한다. 분석된 전사체 정보는 텍스트형태로 제공이 되는데 이를 사용자가 수작업으로 비교하는 데에는 한계가 있다. 따라서 분석된 전사체 정보를 효과적으로 인지할 수 있도록 시각화하는 연구들이 진행되고 있다. 본 논문에서는 그래프 라이브러리인 yFile을 활용하여 추정된 전사체를 실시간으로 시각화하여 제공하는 방법을 제안한다. GTF파일을 입력받아서 데이터베이스에 저장하고 이 정보를 이용하여 그래프를 생성한다. 실험 결과는 전사체를 시각화 하는 방법을 통하여 다양한 전사체 정보를 알아 낼 수 있고, 최종적으로는 novel gene을 찾는 것이 가능할 것으로 기대한다.

• Horticultural Science & Technology
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• v.31 no.6
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• pp.748-755
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• 2013

This study was conducted to find a salt tolerance gene in Brassica rapa. In order to meet this objective, we analyzed data from a KBGP-24K oligo chip [BrEMD (Brassica rapa EST and microarray database)] of the B. rapa ssp. pekinensis 'Chiifu' under salt stress (250 mM NaCl). From the B. rapa KBGP-24K microarray chip analysis, 202 salt-responsive unigenes were primarily selected under salt stress. Of these, a gene with unknown function but known full-length sequence was chosen to closely investigate the gene function. The selected gene was named BrSSR (B. rapa salt stress resistance). BrSSR contains a 285 bp open reading frame encoding a putative 94-amino acid protein, and a DUF581 domain. The pSL94 vector was designed to over-express BrSSR, and was used to transform tobacco plants for salt tolerance analysis. T1 transgenic tobacco plants that over-expressed BrSSR were selected by PCR and DNA blot analyses. Quantitative real-time RT PCR revealed that the expression of BrSSR in transgenic tobacco plants increased by approximately 3.8-fold. Similar results were obtained by RNA blot analysis. Phenotypic characteristics analysis showed that transgenic tobacco plants with over-expressed BrSSR were more salt-tolerant than the wild type control under 250 mM NaCl for 5 days. Based on these results, we hypothesized that the over-expression of BrSSR may be closely related to the enhancement of salt tolerance.

• The Journal of Korean Medicine
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• v.25 no.2
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• pp.127-137
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• 2004

Objectives : The purpose of this investigation was to evaluate the effects of Sohaphyang-won (SH) on the alteration in gene expression in a hypoxia model using cultured rat cortical cells. Methods : E18 rat cortical cells were grown in neurobasal medium containing B27 supplement. On 12 DIV, SH was added ($20\mu\textrm{g}/ml$) to the culture media for 24 hrs. On 14 DIV, cells were given a hypoxic insult (2% O2/5% CO2, $37^{\circ}C$, 3 hrs), returned to normoxia and cultured for another 24 hrs. Total RNA was prepared from SH-untreated (control) and -treated cultures and alteration in gene expression was analyzed by microarray using rat 5K-TwinChips. Results : Effects on some of the genes whose functions are implicated in neural viability are as follows: 1) For most of the genes altered in expression, the global M values were between -05 to +0.5, Among these, 1517 genes were increased in their expression by more than global M +0.1, while 1480 genes were decreased by more than global M -0.1. 2) The expression of apoptosis-related genes such as Bad (global M =0.35), tumor protein p53 (T53) (global M =0.28) were increased, while v-akt murine thymoma viral oncogene homolog 1 (Akt1) was decreased. 3) The expression of hemoglobin alpha 1 (probably neuroglobin) was increased by about 3.2-fold (global M =1.7). 4) The expression of antioxidation-related catalase gene was increased (global M =0.26). 5) The expression of PKCzeta (prkcz), an upstream kinase of MAPK, was increased (global M =0.29). 6) The expression of retinoic acid receptor alpha (RAR), which may regulate transcription in hypoxic stress, was increased (global M =10.27). Conclusions : In summary, the microarray data suggest that SH doesn't increase the expression of oxygen capture-, anti-oxidation- and 'response to stress' -related genes but decreases some anti-apoptosis genes which would help protect the hypoxic cells from apoptosis.

• The Journal of Internal Korean Medicine
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• v.32 no.2
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• pp.301-321
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• 2011

Objectives : The purpose of this investigation was to evaluate the effects of Coptidis chinesis FRANCH. on the alteration of gene expression in a hypoxic model using cultured rat cortical cells. Methods : E18 rat cortical cells were grown in neurobasal medium containing B27 supplement. On 12 DIV, water extract from Coptidis chinesis FRANCH. was added ($20{\mu}g/ml$) to the culture media 4 hrs. On 14 DIV, cells were given hypoxic insult (2% $O_2$/5% $CO_2$, $37^{\circ}C$, 3 hrs), returned to normoxia and cultured for another 24 hrs. Total RNA was extracted from Coptidis chinesis FRANCH. treated and untreated cultures and alterations in the gene expression were analysed by microarray using rat 5K-TwinChips. Results : Effects on some of the genes whose functions were implicated in neural viability were as follows: the expression of apoptosis-related genes such as Clu (Global M = 1.3), of presynaptic inhibition's genes such as Penk-rs (Global M = 1.97), and of innate immuniti's such as Crp (Global M = 1.95), Defensin (Global M = 2.14), and Dnase1l3 (Global M = 1.57) increased. The expression of neurotrophic genes such as S100b (Global M = 1.42), and $NF{\kappa}B$ (Global M = 2.04) increased. Conclusions : Analysing the genes expressed on microarray, shows Coptidis chinesis FRANCH.protects cells by increasing viability and neural nutrition.

• Korean Journal of Microbiology
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• v.46 no.2
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• pp.134-139
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• 2010

Mycobacterium tuberculosis (Mtb) is one of the most successful pathogens to infect one third of world population. Th1-mediated immunity against Mtb infection is known as critical to express mycobacteriostatic function but it is not sufficient to resolve the infection. In this study, to verify the possibility Mtb itself change the gene expression to survive against host immune response, expression pattern of selected H37Rv genes, 16S rRNA, acr, fbpA, aceA, and ahpC, during the course of infection was measured with absolute quantitation method using real-time RT-PCR. The total number of transcripts of 16S rRNA increased during the course of infection, which was coincide with the increasing CFU. The total number of fbpA transcripts per CFU, which encode typical secreted Mtb antigen, Ag85A, increased for 10 days of infection before decreasing. The number of transcripts of acr per CFU, which encode heat shock protein, ${\alpha}$-crystallin, increased during the infection, and ahpC and aceA, they both are enzymes produced in oxidative stressful condition, increased for 20 days and then slightly decreased on day 30. These findings are one of survival strategy of pathogen evading host immune response lead to persistent infection inside host cells.

• Childhood Kidney Diseases
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• v.8 no.2
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• pp.138-148
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• 2004

Purpose: Regardless of the underlying diseases, the proteinuric condition demonstrates ultrastructural changes in podocytes with retraction and effacement of the highly specialized interdigitating foot processes. We examined the molecular basis for this alteration of the podocyte phenotypes, including quantitative and distributional changes of ZO-1 protein as a candidate contributing to the pathogenic changes in the barrier to protein filtration. Methods: To investigate whether high glucose and advanced glycosylation endproduct(AGE) induce podocyte cytoskeletal changes, we cultured rat GEpC under 1) normal glucose(5 mM=control) or 2) high glucose(30 mM) or 3) AGE-added or 4) high glucose plus AGE-added conditions. The distribution of ZO-1 was observed by confocal microscope and the change of ZO-1 expression was measured by Western blotting and RT-PCR. Results: By confocal microscopy, we observed that ZO-1 moves from peripheral cytoplasm to inner actin filaments complexes in both AGE-added and high glucose condition. In Western blotting, high glucose or AGE-added condition decreased the ZO-1 protein expression by 11.1%(P>0.05) and 2.3%(P>0.05), respectively compared to the normal glucose condition. High glucose plus AGE-added condition further decreased ZO-1 protein expression to statistically significant level(12%, P<0.05). No significant change was seen in the osmotic control. In RT-PCR, high glucose plus AGE-added condition significantly decreased the expression of ZO-1 mRNA by 12% compared to normal glucose condition. Conclusion: We suggest that both high glucose and AGE-added condition induce the cytoplasmic translocation and suppresses the production of ZO-1 at transcriptional level and these changes may explain the functional changes of podocytes in diabetic conditions.

• Journal of Life Science
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• v.19 no.1
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• pp.21-33
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• 2009

In this study, we investigated the effect of Rhei Rhizoma (RR; 大黃) water extract on gene expression in a hypoxia model of cultured rat hippocampal neurons. RR water extract $(2.5{\mu}g/ml)$ was added to the culture media on day 10 in vitro (DIV10), and a hypoxic shock (2% $O_2$/5% $CO_2$, $37^{\circ}C$, 3 h) was given on DIV13. After maintaining the cultures in normoxia for 24 hr, total RNA was isolated and used for microarray analysis. The MA-plot indicated that most genes were up- or downregulated within 2-fold. There were more downregulated genes (725 ea) than upregulated ones (472 ea) when larger than Global M value 0.2 (i.e., >15% increase) or smaller than Global M value -0.2 (i.e., >15% decrease) were considered. Antiapoptosis genes such as Tegt (2.4-fold), Nfkb1 (2.4-fold) Veg (1.8-fold), Ngfr (1.6-fold) were upregulated, while pro-apoptosis genes such as Bad (-64%), Cstb (-66%) were downregulated. Genes for combating environmental stress (stress response genes) such as Defb3 (2.7-fold), Cygb (2.2-fold), Ahsg (2.18-fold), Alox5 (2-fold) were upregulated. Genes for cell proliferation (cell cycle-related genes) such as Erbb2 (1.84-fold), Mapk12 gene (1.8-fold) was upregulated. Therefore, RR water extracts upregulate many pro-survival genes while downregulating many pro-death genes. It is interpreted that these genes, in combination with other regulated genes, can promote neuronal survival in a stress such as hypoxia.

• The Korean Journal of Oral and Maxillofacial Pathology
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• v.41 no.1
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• pp.1-7
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• 2017

Lycorine, a natural alkaloid extracted from the Amaryllidaceae plant family, was reported to various physiological and pharmacological effects including anti-cancer activity. Nevertheless, there is no report of the anticancer effect of lycorine in oral cancer cells. The effects of lycorine on cell proliferation and apoptosis were examined through trypan blue exclusion assay, 4'-6-diamidino-2-phenylindole (DAPI) stain, Live/Dead assay, Western blot analysis and RT-PCR. Lycorine suppressed cell viability and induced apoptosis in MC3 and HSC-3 cell lines. Lycorine decreased survivin protein but did not affect its mRNA. It regulated survivin through accelerating protein degradation in a time-dependent manner although neither proteasome nor lysosome was not associated with lycorine-mediated protein degradation. Collectively, our results suggest that lycorine may be a potential therapeutic anti-cancer drug candidate for the treatment of human oral cancer.