• The KIPS Transactions:PartB
• /
• v.13B no.3 s.106
• /
• pp.323-328
• /
• 2006

Proteins in a cell appear as spots in a two dimensional gel image which is used in protein analysis. The spots from the same protein are in near position when comparing two gel images. Finding out the different proteins between a normal tissue and a cancer one is important information in drug development. Automatic matching of gel images is difficult because they are made from biological experimental processes. This matching problem is known to be NP-hard. Neural networks are usually used to solve such NP-hard problems. Hopfield neural network is selected since it is appropriate to solve the gel matching. An energy function with location and distance parameters is defined. The two spots which make the energy function minimum are matching spots and they came from the same protein. The energy function is designed to reflect the topology of spots by examining not only the given spot but also neighborhood spots.

• Biomedical Science Letters
• /
• v.21 no.4
• /
• pp.233-240
• /
• 2015

Some virulence proteins of Helicobacter pylori, such as vacuolating cytotoxic protein A (VacA) and cytotoxin-associated gene protein A (CagA) have been reported to be causative agents of various gastric diseases including chronic gastritis, gastric ulcer or gastric adenocarcinoma. The expression level of these virulence proteins can be regulated when H. pylori is exposed to the antibacterial agent, cyanidin 3-O-glucoside (C3G) as previously reported. In this study, we analyzed the quantitative change of various virulence proteins including CagA and VacA by C3G treatment. We used 2-dimensional electrophoresis (2-DE) to analyze the quantitative change of representative ten proteome components of H. pylori 60190 ($VacA^+/CagA^+$; standard strain of Eastern type). After 2-DE analysis, spot intensities were analyzed using ImageMaster$^{TM}$ 2-DE Platinum software then each spot was identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) or peptide sequencing using Finnigan LCQ ion trap mass spectrometer (LC-MS/MS). Next, we selected major virulence proteins of H. pylori among quantitatively meaningful ten spots and confirmed the 2-DE results by Western blot analysis. These results suggest that cyanidin 3-O-glucoside can modulate a variety of H. pylori pathogenic determinants.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.9 no.2
• /
• pp.255-259
• /
• 2004

Post-infectional biochemical changes due to Xanthomonas campestris pv. mori (Xcm) infection in five elite mulberry varieties viz., $S_1$, $S_{1635}$, $V_1$, RF $S_{175}$ and JRH was studied under inoculated condition. It was revealed that total soluble sugar and protein content was significantly declined in all the varieties due to X. campestris infection. Total phenol content was at par prior to inoculation in all varieties, but it was significantly increased in $S_1$, RF $S_{175}$, $S_{1635}$ and JRH 7 days after inoculation. The correlation coefficient (r) between total soluble sugar and total phenol content was found positive (r = 0.825) and statistically significant. Similarly, correlation coefficient (r) between total soluble protein and phenol content was found positive (r = 0.897) and statistically significant. The present study indicates that X. campestris infected leaves are nutritionally inferior in quality and the duration of phenol production in a mulberry variety play decisive role on disease resistance.nce.

• Childhood Kidney Diseases
• /
• v.26 no.1
• /
• pp.52-57
• /
• 2022

Purpose: To determine predictive factors for detecting renal parenchymal damages (RPDs) in infants with recurrent febrile urinary tract infection (fUTI). Methods: From January 2015 to December 2021, 102 infants with recurrent fUTI and who underwent ^99mTc-dimercaptosuccinic acid (DMSA) renal scan in our hospital were included in this study. Controls included infants with normal DMSA results performed 3 months apart from the 2nd episode of fUTI. DMSA-positive group included infants with positive DMSA results performed 3 months apart from the 2nd episode of fUTI or at the 3rd episode of fUTI. The recurrence rate, causative bacteria, renal size discrepancy of both kidneys, and laboratory findings including C-reactive protein (CRP) and spot urine sodium-to-potassium ratio (uNa/K) were compared between both groups. Results: Only 3.8% of 79 infants with a 2nd episode of fUTI showed positive DMSA results. fUTI recurred more frequently within 12 months of follow-up in the DMSA-positive group than in the control group (69% vs. 13%, P<0.001). CRP values were significantly higher in the DMSA-positive group than in the control group (7.3 mg/dL vs. 3.7 mg/dL, P<0.001). Spot uNa/K were significantly lower in the DMSA-positive group than in the control group (0.6 vs. 1.1, P<0.001). Conclusions: Congenital renal scar and RPDs on the DMSA scan were more frequently found in infants with recurrent fUTI than those in the control group. High CRP values and low spot uNa/K in acute infections were helpful in predicting the presence of RPD in infants with recurrent fUTI.

• Mass Spectrometry Letters
• /
• v.3 no.1
• /
• pp.10-14
• /
• 2012

Artificially oxidized cysteine residues in peroxiredoxin 6 (Prx6) were detected by electrospray interface capillary liquid chromatography-linear ion trap mass spectrometry after the preparation of two-dimensional gel electrophoresis (2D-GE). We used Prx6 as a model protein because it possesses only two cysteine residues at the 47th and 91st positions. The spot of Prx6 on 2D-GE undergoes a basic (isoelectric point, pI 6.6) to acidic (pI 6.2) shift by exposure to peroxide due to selective overoxidation of the active-site cysteine Cys-47 but not of Cys-91. However, we detected a tryptic peptide containing cysteine sulfonic acid at the 47th position from the basic spot and a peptide containing both oxidized Cys-47 and oxidized Cys-91 from the acidic spot of Prx6 after the separation by 2D-GE. We prepared two types of oxidized Prx6s: carrying oxidized Cys-47 (single oxidized Prx6), and other carrying both oxidized Cys-47 and Cys-91 (double oxidized Prx6). Using these oxidized Prx6s, the single oxidized Prx6 and double oxidized Prx6 migrated to pIs at 6.2 and 5.9, respectively. These results suggest that oxidized Cys-47 from the basic spot and oxidized Cys-91 from the acidic spot are generated by artificial oxidation during sample handling processes after isoelectric focusing of 2D-GE. Therefore, it is important to make sure of the origin of cysteine oxidation, if it is physiological or artificial, when an oxidized cysteine residue(s) is identified.

• Food Science of Animal Resources
• /
• v.26 no.2
• /
• pp.263-268
• /
• 2006

Probiotics including Lactobacillus acidophilus, refer to a group of nonpathogenic organisms that protect the human host against gastrointestinal(GI) infections by pathogenic bacteria such as Shiga toxin-producing E. coli(STEC). In the study, the inhibitory effects of STEC ATCC 43894 adhesion by L. acidophilus A4 was investigated on the HT-29 epithelial cells. Specific proteins regulated by cell Iysates of L. acidophilus A4 on STEC ATCC 43894 were also characterized by proteomic analysis. Both cell mass and Iysate of L. acidophilus A4 have exhibited the profound inhibitory activity on the HT-29 cells(about 1.5 log scale reduction). Two-dimensional gel electrophoresis(2-DE) revealed seven proteins that were up-regulated by cell Iysates of L. acidophilus A4 and three proteins that were down-regulated. In addition, three protein spots were only detected in the presence of cell Iysates. These results suggest that inhibitory effects of STEC adhesion by L. acidophilus may be due to the regulation of specific protein of STEC.

• 보존과학연구
• /
• s.13
• /
• pp.81-95
• /
• 1992

The old books which have been colored to brown spots were analyzed chemically to compare with white part. The original raw materials were paper mulberry (Broussonetia Kazine) and woodpulp. White part contained58.8%($\alpha$-37.2%,$\beta$-8.6%, $\gamma$-12.7%)cellulose, 21.7% hemicellulose, 19.8% lignin,4.4% pentosan and brown sopt part contained 49.1%($\alpha$-19.8%, $\beta$-14.5%,$\gamma$-14.8%) cellulose, 27.1% hemicellulose, 23.8% lignin, 4.8% pentosan. Both of brown spot and white parts contained starch without protein. The pH was 4.9 in brown and 5.0 in white part respecitively. The brown spot parts were more solidified than white parts according to SEM observation. Difference of organiccompinent in brown part came from white part were 2-hydroxy-benzaldehydeand phenol.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.2
• /
• pp.226-229
• /
• 2012

Bacterial hemoglobin from Vitreoscilla (VHb) is recognized as a good fusion protein for the soluble expression of foreign protein. In this study, we generated a monoclonal antibody (MAb) against VHb for its detection. For the rapid screening of MAb, a protein chip technology based on the Alexa-488 (A488) dye labeling method was introduced. In order to fabricate the chip, the VHb protein was chemically coupled to the chip surface and then the culture supernatants of 84 hybridoma cell lines were spotted onto the VHb chip. The bound MAbs were measured by A488-modified anti-mouse IgG. A single spot (MAb A10) exhibited significantly high signal intensity. The immunoblot analysis evidenced that the MAb A10 can detect VHb-fused proteins with high specificity.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2002.06a
• /
• pp.35-47
• /
• 2002

2D-PAGE/MALDI-TOF는 프로-테옴 연구의 중요한 실험 기법중의 하나이다. 이는 단백질의 발현 분석을 위한 방법으로, 2D-PAGE 결과로 얻어진 영상 데이터의 분석에 대한 정확도가 단백질 발현에 대한 분석 결과의 질을 결정하는 중요한 요인으로 작용한다. 2D Electrophoresis에 의한 Gel Protein Database는 현재 많은 연구자들에 의해 생산되고 있으며, 대단히 많은 데이터들이 인터넷을 통하여 접근이 가능하다. 이러한 대량 정보의 Database 활용이 가능한 상황은 2D-PAGE에 의해 생산된 Gel Image의 상호 비교에 대한 요구를 도출하였다. 본 발표에서는 영상처리 및 형태인식 기술과 2D-PAGE 연구의 결합을 주제로 하여, 2D-PAGE Gel 영상 처리 및 비교에 관련되는 전처리 (preprocessing), spot detection, feature extraction, spot matching 및 image comparison 기술을 소개한다.

• Biomedical Science Letters
• /
• v.23 no.4
• /
• pp.395-401
• /
• 2017

Various preclinical and clinical trials have been conducted the efficacy of celastrol. In data presented in the current manuscript is the first trial to inhibit Helicobacter pylori with celastrol. In this study, the quantitative change of various H. pylori proteins including CagA and VacA by the anti-bacterial effect of celastrol was determined. The anti-H. pylori effects of celastrol was investigated by performing 2-dimensional electrophoresis and additional supporting experiments. After 2-dimensional electrophoresis analysis, spot intensities were analyzed and then each spot was identified using matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) or peptide sequencing using Finnigan LCQ ion trap mass spectrometer (LC-MS/MS). The results show that celastrol has multiple effects on protein expression in H. pylori.