• Journal of the Korean Society of Industry Convergence
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• v.14 no.3
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• pp.105-111
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• 2011

Landmark Spots in 2D gel electrophoresis are used in many methods of 2DEG spot matching. Landmark Spots are obtained manually and it is a bottle neck in the entire protein analysis process. Automated landmark spots detection is a very crucial topic in processing a massive amount of 2DGE data. In this paper, Automated landmark spot detection is proposed using point pattern matching and graph theory. Neighbor spots are defined by a graph theory to use and only a centered spot and its neighbor spots are considered for spot matching. Normalized Hausdorff distance is introduced as a criterion for measuring degree of similarity. In the conclusion, the method proposed in this paper can get about 50% of the total spot pairs and the accuracy rate is almost 100%, which the requirements of landmark spots are fully satisfied.

• Journal of Life Science
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• v.14 no.4
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• pp.627-635
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• 2004

In order to distinguish the genetic polymorphism among the olive flounder (Paralichthys olivaceus) obtained from East sea of Jumunjin, aquaculture of Tongyoung and Geoje, and East sea of North Korea, the ND-4 and cytochrome b genes of olive flounder were divided into 5 regions. Each region was analyzed by degenerating gel electrophoresis scanning (DGES), and by subsequent DNA sequencing. The DGES disclosed characteristic DNA polymorphisms in ND-4-2 and ND-4-3 regions of olive flounder, which were also confirmed by the DNA sequencing. The olive flounders obtained from the different marine areas showed DNA mutations in ND-4-2 region (G390A, C402T, and A411G； GenBank： AB028664), and also showed frequent DNA mutations in ND-4-3 region (C515G, C537T, C538T, A567G, G714A, C736T, G756A, A759T, T817C, and T829G), white the cytochrome b gene showed no DNA mutation both in the DGES and DNA sequencing. These data suggest that the ND-4-2 and ND-4-3 regions are candidate loci to distinguish the origin of olive flounder, and that the DGES used in this study provided fast and reliable informations for the genetic polymorphism.

• Clinical and Experimental Pediatrics
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• v.64 no.7
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• pp.355-363
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• 2021

Background: Nephrotic syndrome (NS) is a common renal disorder in children attributed to podocyte injury. However, children with the same diagnosis have markedly variable treatment responses, clinical courses, and outcomes, suggesting molecular heterogeneity. Purpose: This study aimed to explore the molecular responses of podocytes to nephrotic plasma to identify specific genes and signaling pathways differentiating various clinical NS groups as well as biological processes that drive injury in normal podocytes. Methods: Transcriptome profiles from immortalized human podocyte cell line exposed to the plasma of 8 subjects (steroid-sensitive nephrotic syndrome [SSNS], n=4; steroid-resistant nephrotic syndrome [SRNS], n=2; and healthy adult individuals [control], n=2) were generated using microarray analysis. Results: Unsupervised hierarchical clustering of global gene expression data was broadly correlated with the clinical classification of NS. Differential gene expression (DGE) analysis of diseased groups (SSNS or SRNS) versus healthy controls identified 105 genes (58 up-regulated, 47 down-regulated) in SSNS and 139 genes (78 up-regulated, 61 down-regulated) in SRNS with 55 common to SSNS and SRNS, while the rest were unique (50 in SSNS, 84 genes in SRNS). Pathway analysis of the significant (P≤0.05, -1≤ log2 FC ≥1) differentially expressed genes identified the transforming growth factor-β and Janus kinase-signal transducer and activator of transcription pathways to be involved in both SSNS and SRNS. DGE analysis of SSNS versus SRNS identified 2,350 genes with values of P≤0.05, and a heatmap of corresponding expression values of these genes in each subject showed clear differences in SSNS and SRNS. Conclusion: Our study observations indicate that, although podocyte injury follows similar pathways in different clinical subgroups, the pathways are modulated differently as evidenced by the heatmap. Such transcriptome profiling with a larger cohort can stratify patients into intrinsic subtypes and provide insight into the molecular mechanisms of podocyte injury.

• Molecules and Cells
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• v.22 no.1
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• pp.119-125
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• 2006

The rat is an accepted model for studying human psychiatric/neurological disorders. We provide a protocol for total soluble protein extraction using trichloroacetic acid/acetone (TCA/A) from rat (female) whole brain, 10 brain regions and the pituitary gland, and show that two-dimensional gel electrophoresis (2-DGE) using precast immobilized pH (4-7) gradient (IPG) strip gels (13 cm) in the first dimension yields clean silver nitrate stained protein profiles. Though TCA/A precipitation may not be "ideal", the important choice here is the selection of an appropriate lysis buffer (LB) for solubilizing precipitated proteins. Our results reveal enrichment of protein spots by use of individual brain regions rather than whole brain, as well as the presence of differentially expressed spots in their proteomes. Thus individual brain regions provide improved protein coverage and are better suited for differential protein detection. Moreover, using a phosphoprotein-specific dye, ingel detection of phosphoproteins was demonstrated. Representative high-resolution silver nitrate stained proteome profiles of rat whole brain total soluble protein are presented. Shortcomings apart (failure to separate membrane proteins), gel-based proteomics remains a viable option, and 2-DGE is the method of choice for generating high-resolution proteome maps of rat brain and brain regions.

• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.227-232
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• 2008

Drought stress is one of the major abiotic stresses in agriculture worldwide. We report here a proteomic approach to investigate the impact of post-fertilization drought on grain quality in rice seed endosperm (Oryza sativa cv. IR-64). Plants were stressed for 4 days at 3 days before heading. Total proteins of endosperm were extracted and separated by two-dimensional gel electrophoresis. Not many protein spots showed differential accumulation in drought-stressed samples. More than 400 protein spots were reproducibly detected, including three that were up-regulated and five down-regulated. Mass spectrometry analysis and database searching helped us to identify six spots representing different proteins. Functionally, the identified proteins were related to protein synthesis and carbohydrate metabolism, such as Granule-Bound Starch Synthase (GBSS, Wx protein), which is thought to play a very important role in starch biosynthesis and quality, a very crucial factor in determining rice grain quality.

• Parasites, Hosts and Diseases
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• v.45 no.4
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• pp.283-285
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• 2007

To examine the expressed gene profile during encystation of Acanthamoeba castellanii Castellani, we used differentially expressed gene (DGE) screening by RT-PCR with 20 sets of random primers. From this analysis, we found that approximately 16 genes showed up regulation during encystation. We chose 6 genes, which had relatively higher expression levels, for further investigation. Based on homology search in database, DEG2 showed 55% of similarity with xylose isomerase, DEG9 showed 37% of similarity with Na P-type ATPase, and DEG14 showed 77% of similarity with subtilisin-like serine proteinase. DEG3 and DEG26 were identified as hypothetical proteins and DEG25 exhibited no significant similarity to any known protein. Encystation of Acanthamoeba has been suggested to be a process to resist adverse environmental or nutritional conditions. Further characterization studies of these genes may provide us with more information on the encystation mechanism of Acanthamoeba.

• Journal of Gastric Cancer
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• v.22 no.2
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• pp.135-144
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• 2022

Purpose: This study aimed to compare the surgical and oncological outcomes between totally laparoscopic pylorus-preserving gastrectomy (TLPPG) with intracorporeal anastomosis and laparoscopy-assisted pylorus-preserving gastrectomy (LAPPG) with extracorporeal anastomosis. Materials and Methods: A retrospective analysis was performed in 258 patients with cT1N0 gastric cancer who underwent laparoscopic pylorus-preserving gastrectomy using two different anastomosis methods: TLPPG with intracorporeal anastomosis (n=88) and LAPPG with extracorporeal anastomosis (n=170). The following variables were compared between the two groups to assess the postoperative surgical and oncological outcomes: proximal and distal margins, number of resected lymph nodes (LNs) in total and in LN station 6, operation time, postoperative hospital stay, and postoperative morbidity including delayed gastric emptying (DGE). Results: The average length of the proximal margin was similar between the TLPPG and LAPPG groups (2.35 vs. 2.73 cm, P=0.070). Although the distal margin was significantly shorter in the TLPPG group than in the LAPPG group (3.15 vs. 4.08 cm, P=0.001), no proximal or distal resection margin-positive cases were reported in either group. The average number of resected LN was similar in both groups (36.0 vs. 33.98, P=0.229; LN station 6, 5.72 vs. 5.33, P=0.399). The operation time was shorter in the TLPPG group than in the LAPPG (200.17 vs. 220.80 minutes, P=0.001). No significant differences were observed between the two groups in terms of postoperative hospital stay (9.38 vs. 10.10 days, P=0.426) and surgical complication rate (19.3% vs. 22.9%), including DGE (8.0% vs. 11.8%, P=0.343). Conclusions: The oncological safety and postoperative complications of TLPPG with intracorporeal anastomosis are similar to those of LAPPG with extracorporeal anastomosis.

• Korean journal of food and cookery science
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• v.9 no.4
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• pp.312-316
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• 1993

This study was carried out to develop supplementary foods for infants and monthly feeding plans of five steps. The developed supplementary foods were divided into 3 stages. First stage was designed for the babies just beginning eat pureed vegetables and fruits. Second stage was combined the nutritio-nal attributes of both vegetables and meat. Third stage was featured bite-sized pieces of tender meat and vegetables that appealed to the most mature tastes of babies. Feeding plans were divided into 5 steps according to their development. At 3 months, small amount of supplementary of smooth porri-dge can be introduced after a milk feeding each day. At 5 months, the quantity of supplementary foods can be gradually increased, and it can be given after 2 or 3 times of milk feedings. By being given different foods, infants will learn to become accustomed to new flavors at 7 months. At 9 months, the same types of additional foods are given at least 3 times a day after the milk feeds. Infants will be able to take most of the foods at 12 months, and it is important to give the infants solid foods after milk feedings at least 3 times a day.

• Journal of the Korean Society of School Health
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• v.19 no.2
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• pp.13-24
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• 2006

Purpose : The purpose of this study was to develop an obese elementary students education program available for blended learning environments, which refered to a combination of ofline and online learning. And it's also intended to verify its efect to bost the eficiency of obese schol children's learning about obesity.Methods : The subjects were 52(experimental group=21, control group=31 ) fourth, fifth and sixth graders who OVA. Results : The obese elementary students education program tailored to blended learning setting wasn't more conducive to lowering the obesity level of the obese students t han the typical obese elementary students education program. But the obese elementary students education was more efective than the typical one in improving the knowle dge of the obese students about obesity, and in enhancing the academic self-eficacy of the children. Conclusion : As the obese elementary students education program tailored to blended learning setting was effective in boosting the relevant knowledge and academic self-efficacy of the children, sustained research efforts should be put into developing obese elementary students education programs available for both online and offline to help students to access information on obesity and manage it better.

• Plant Biotechnology Reports
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• v.5 no.4
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• pp.309-315
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• 2011

Rice grown in anaerobic waterlogged soil accumulates ammonium as a major source of nitrogen (N). We have compared the physiological symptoms of rice seedlings subjected to N-starvation stress with those receiving sufficient N, based on measurements of shoot/root length and weight and an analysis of protein expression patterns. N starvation marginally increased root growth but notably decreased shoot biomass. N uptake was reduced by >50% in the roots and shoots of N-starved seedlings. To better understand the mechanism of N starvation in rice, we performed a comparative proteome analysis of proteins isolated from rice leaves. Twenty-five differentially expressed proteins were analyzed by matrixassisted laser desorption/ionization time-of-flight (TOF) mass spectrometry and electron spray ionization quadrupole TOF. Functional analysis of the N-starvation response proteins suggested their involvement in protein synthesis and fate, metabolism, and defense. These results indicate that these proteins may play important roles in regulating the plant's complex adaptation responses for N use during N starvation. The proteins may be useful for further characterization of protein function in plant N nutrition.