• Journal of Periodontal and Implant Science
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• v.35 no.2
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• pp.271-275
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• 2005

본 연구는 치주낭에 biofilm형태로 부착되어 질환을 유발시키고 항생제 빚 항균제에 저항을 일으키는 세균 독성요소를 규명하기 위해 시행된 기초연구이다. 치주질환의 주 병원균의 하나인 Porphyromonas gingivalis 381 biofilm의 세포외막에 특이하게 발현되는 단백질을 규명하기 위한 기초적인 자료를 얻기 위해 시행하였다. Porphyromonas gingivalis 381을 통상적인 세균 배양용 broth를 사용하여 혐기성 세균 배양기로 24시간 배양한 것을 대조군으로 하고, tissue culture plate를 이용하여 혐기성 배양조건 하에서24시간동안 biofilm을 형성하여 실험군으로 설정하였다. 세균을 수획하여 세포외막을 분리하고 isotonic isoelectric focusing을 시행한 결과 주로 약 20-30 kilodaltons에 해당하는 수종의 세균세포막 단백질이biofilm으로 배양한 세균에서 더 상승적으로 발현됨이 관찰되었고, 상이한 수종의 단백질도 planktonic culture broth로 배양한 세균에서 다 상승적으로 발현됨을 관찰할 수 있었다. 이것은 세균의 배양조건과 환경에 따라 그 외막 단백질이 서로 다르게 발현됨을 입증하는 기초적인 자료로서 향후 단백질의 동정과 성격을 규명하는 근간 실험으로 추진할 계획이다.

• Genomics & Informatics
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• v.4 no.2
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• pp.57-64
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• 2006

We identified differentially expressed genes in RAW264.7 cells in response to single and double ligand treatments (LPS, $IFN{\gamma}$, 2MA, LPS plus $IFN{\gamma}$, and LPS plus 2MA). The majority of the regulated transcripts responded additively to dual ligand treatment. However, a significant fraction responded in a non-additive fashion. Several cytokines showing non-additive transcriptional responses to dual ligand treatment also showed non-additive protein production/secretion responses in separately performed experiments. Many of the genes with non-additive responses to LPS plus 2MA showed enhanced responses and encoded pro-inflammatory proteins. LPS plus $IFN{\gamma}$ appeared to induce both non-additive enhancement and non-additive attenuation of gene expression. The affected genes were associated with a variety of biological functions. These experiments reveal both dependent and independent regulatory pathways and point out the specific nature of the regulatory interactions.

• The Korean Journal of Physiology and Pharmacology
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• v.13 no.6
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• pp.409-416
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• 2009

Acute pancreatitis is a multifactorial disease associated with the premature activation of digestive enzymes. The genes expressed in pancreatic acinar cells determine the severity of the disease. The present study determined the differentially expressed genes in pancreatic acinar cells treated with cerulein as an in vitro model of acute pancreatitis. Pancreatic acinar AR42J cells were stimulated with $10^{-8}$ M cerulein for 4 h, and genes with altered expression were identified using a cDNA microarray for 4,000 rat genes and validated by real-time PCR. These genes showed a 2.5-fold or higher increase with cerulein: lithostatin, guanylate cyclase, myosin light chain kinase 2, cathepsin C, progestin-induced protein, and pancreatic trypsin 2. Stathin 1 and ribosomal protein S13 showed a 2.5-fold or higher decreases in expression. Real-time PCR analysis showed time-dependent alterations of these genes. Using commercially available antibodies specific for guanylate cyclase, myosin light chain kinase 2, and cathepsin C, a time-dependent increase in these proteins were observed by Western blotting. Thus, disturbances in proliferation, differentiation, cytoskeleton arrangement, enzyme activity, and secretion may be underlying mechanisms of acute pancreatitis.

• BMB Reports
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• v.37 no.2
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• pp.159-166
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• 2004

Angiostatin is a potent anti-angiogenic protein. To examine the angiostatin-interacting proteins, we used the display-cloning method with a T7 phage library presenting human cDNAs. The specific T7 phage clone that bound to the immobilized angiostatin was isolated, and a novel gene encoding the displayed polypeptide on the isolated T7 phage was identified. The displayed angiostatin-binding sequence was expressed in E. coli as a soluble protein and purified to homogeneity. This novel angiostatin-binding region interacted specifically to angiostatin with a dissociation constant of $3.4{\times}10^{-7}\;M$. A sequence analysis showed that the identified sequence was a part of the large ORF of 1,998 amino acids, whose function has not yet been characterized. A Northern analysis indicated that the gene containing the angiostatin-binding sequence was expressed differentially in the developmental stages or cell types.

• Journal of Korean Neurosurgical Society
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• v.59 no.6
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• pp.544-550
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• 2016

Objective : Cerebral endothelial cells have unique biological features and are fascinating candidate cells for stroke therapy. Methods : In order to understand the molecular mechanisms of human cerebral endothelial cell (hCMEC/D3) transplantation in a rat stroke model, we performed proteomic analysis using 2-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Protein expression was confirmed by quantitative real-time PCR and Western blot. Results : Several protein spots were identified by gel electrophoresis in the sham, cerebral ischemia (CI), and CI with hCMEC/D3 treatment cerebral ischemia with cell transplantation (CT) groups, and we identified 14 differentially expressed proteins in the CT group. Proteins involved in mitochondrial dysfunction (paraplegin matrix AAA peptidase subunit, SPG7), neuroinflammation (peroxiredoxin 6, PRDX6), and neuronal death (zinc finger protein 90, ZFP90) were markedly reduced in the CT group compared with the CI group. The expression of chloride intracellular channel 4 proteins involved in post-ischemic vasculogenesis was significantly decreased in the CI group but comparable to sham in the CT group. Conclusion : These results contribute to our understanding of the early phase processes that follow cerebral endothelial cell treatment in CI. Moreover, some of the identified proteins may present promising new targets for stroke therapy.

• Journal of Microbiology and Biotechnology
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• v.17 no.1
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• pp.89-95
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• 2007

Improvements in the dissolution of proteins in two-dimensional gel electrophoresis have greatly advanced the ability to analyze the proteomes of microorganisms under a wide variety of physiological conditions. This study examined the effect of various combinations of chaotropic agents, a reducing agent, and a detergent on the dissolution of the Streptomyces peucetius cytosolic proteins. The use of urea alone in a rehydration buffer as a chaotropic agent gave the proteome a higher solubility than any of the urea and thiourea combinations, and produced the highest resolution and clearest background in two-dimensional gel electrophoresis. Two % CHAPS, as a detergent in a rehydration buffer, improved the protein solubility. After examining the effect of several concentrations of reducing agent, 50 mM DTT in a rehydration buffer was found to be an optimal condition for the proteome analysis of Streptomyces. Using this optimized buffer condition, more than 2,000 distinct and differentially expressed soluble proteins could be resolved using two-dimensional gel electrophoresis with a pI ranging from 4-7. Under this optimized condition, 15 novel small proteins with low-level expression, which could not be analyzed under the non-optimized conditions, were identified. Overall, the optimized condition helped produce a better reference gel for Streptomyces peucetius.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.8
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• pp.1000-1006
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• 2010

Phosducin (PDC) is a photoreceptor cell-specific protein that is phosphorylated by cyclic nucleotide-dependent protein kinase. PDC and PDC-like proteins (PDCL, PDCL2, and PDCL3) are members of a conserved family of small thioredoxin-like proteins that modulate the ${\beta}$- and ${\gamma}$-subunits of G-proteins. In mammals, Pdc, Pdcl, and Pdcl3 genes show ubiquitous expression; however, Pdcl2 gene expression is limited to the testis and ovary. The aim of the present study was to examine the expression patterns of chicken Pdcl2 (cPdcl2) during testicular and ovarian development. Protein sequence comparisons performed using the CLUSTAL X program revealed that the amino acid sequences and potential phosphorylation sites of cPDCL2 and mammalian PDCL2 proteins were highly conserved. Quantitative real-time PCR analysis revealed that cPdcl2 was differentially expressed in the testis and ovary. Specifically, cPdcl2 expression was detected at low levels in the ovary at all time points. In the testis, cPdcl2 expression was detected at low levels until 5 weeks of age. At 8 weeks of age, however, cPdcl2 showed increased expression levels in the testis. Using in situ hybridization, we detected high levels of cPdcl2 expression in the testis, particularly in the spermatocytes and round spermatids. In summary, our data describe expression patterns of germ cell-specific Pdcl2 during testicular and ovarian development in chickens.

• Mass Spectrometry Letters
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• v.1 no.1
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• pp.25-28
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• 2010

The high-throughput identification and accurate quantification of proteins are essential strategies for exploring cellular functions and processes in quantitative proteomics. Stable isotope tagging is a key technique in quantitative proteomic research, accompanied by automated tandem mass spectrometry. For the differential proteome analysis of mouse neuronal cell lines, we used a multiplexed isobaric tagging method, in which a four-plex set of amine-reactive isobaric tags are available for peptide derivatization. Using the four-plex set of isobaric tag for relative and absolute quantitation (iTRAQ) reagents, we analyzed the differential proteome in several stroke time pathways (0, 4, and 8 h) after the mouse neuronal cells have been stressed using a glutamate oxidant. In order to obtain a list of the differentially expressed proteins, we selected those proteins which had apparently changed significantly during the stress test. With 95% of the peptides showing only a small variation in quantity before and after the test, we obtained a list of eight up-regulated and four down-regulated proteins for the stroke time pathways. To validate the iTRAQ approach, we studied the use of oxidant stresses for mouse neuronal cell samples that have shown differential proteome in several stroke time pathways (0, 4, and 8 h). Results suggest that histone H1 might be the key protein in the oxidative injury caused by glutamate-induced cytotoxicity in HT22 cells.

• Korean Journal of Environmental Agriculture
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• v.30 no.4
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• pp.395-401
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• 2011

BACKGROUND: Potassium (K) is one of the macronutrients which are essential for plant growth and development. Its deficiency in paddy soils is becoming one of the limiting factors for increasing rice yield in Asia. METHODS AND RESULTS: To investigate physiological symptoms under K-starvation (NP) compared with complete media (NPK) condition, we measured shoot/root length, weight, nutrients, and patterns of protein expression. The shoot growth was significantly reduced, but root growth was not affected by K-starvation. However, biomasses were decreased in both shoot and root. Uptake of K was reduced up to 85%, while total concentrations of P, Ca, Mg, Na were increased in root and shoot. To better understand the starved K mechanism of rice, comparative proteome analysis for proteins isolated from rice leaves was conducted using 2-DGE. Five spots of differentially expressed proteins were analyzed by MALDI-TOF MS. Analysis of these K-starvation response proteins suggested that they were involved in metabolism and defense. CONCLUSION(s): Physiological and 2-DGE based proteomics approach used in our study results in observation of morphology or nutrients change and identification of K-starvation responsive proteins in rice root. These results have important roles in maintaining nutrient homeostasis and would also be useful for further characterization of protein function in plant K nutrition.

• Mass Spectrometry Letters
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• v.13 no.3
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• pp.84-94
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• 2022

Neoadjuvant chemoradiotherapy (nCRT) is a standard therapy used for locally advanced rectal cancer prior to surgery, which can more effectively reduce the locoregional recurrence rate and radiation toxicity compared to postoperative chemoradiotherapy. The response of patients to nCRT varies, and thus, robust biomarkers for predicting a pathological complete response are necessary. This study aimed to identify possible biomarkers involved in the complete response/non-response of rectal cancer patients to nCRT. Comparative proteomic analysis was performed on rectal tissue samples before and after nCRT. Proteins were extracted for label-free proteomic analysis. Western blot and real-time PCR were performed using rectal cancer cell line SNU-503 and radiation-resistant rectal cancer cell line SNU-503R80Gy. A total of 135 up- and 93 down-regulated proteins were identified in the complete response group. Six possible biomarkers were selected to evaluate the expression of proteins and mRNA in SNU-503 and SNU-503R80Gy cell lines. Lyso-phosphatidylcholine acyltransferase 2, annexin A13, aldo-ketose reductase family 1 member B1, and cathelicidin antimicrobial peptide appeared to be potential biomarkers for predicting a pathological complete response to nCRT. This study identified differentially expressed proteins and some potential biomarkers in the complete response group, which would be further validated in future studies.