• BMB Reports
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• v.37 no.3
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• pp.298-303
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• 2004

In general, a SYPRO Ruby dye is well known as a sensitive fluorescence-based method for detecting proteins by one-or two-dimensional SDS-PAGE (1-DE or 2-DE). Based on the SYPRO Ruby dye system, the combined two-dimensional fibrin zymography (2-D FZ) with SYPRO Ruby staining was newly developed to identify the Bacillus sp. proteases. Namely, complex protein mixtures from Bacillus sp. DJ-4, which were screened from Doen-Jang (Korean traditional fermented food), showed activity on the zymogram gel. The gel spots on the SYPRO Ruby gel, which corresponded to the active spots showing on the 2-D FZ gel, were analyzed by a matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometric analysis. Five intracellular fibrinolytic enzymes of Bacillus sp. DJ-4 were detected through 2-D FZ. The gel spots on the SYPRO Ruby dye stained 2-D gel corresponding to 2-D FZ were then analyzed by MALID TOF MS. Three of the five gel spots proved to be quite similar to the ATP-dependent protease, extracellular neutral metalloprotease, and protease of Bacillus subtilis. Also, the extracellular proteases of Bacillus sp. DJ-4 employing this combined system were identified on three gels (e.g., casein, fibrin, and gelatin) and the proteolytic maps were established. This combined system of 2-D zymography and SYPRO Ruby dye should be useful for searching the specific protease from complex protein mixtures of many other sources (e.g., yeast and cancer cell lines).

• Preventive Nutrition and Food Science
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• v.7 no.4
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• pp.432-436
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• 2002

A proteomic map of Hanwoo loin was obtained using 2-D SDS-PAGE and mass spectrometric analysis: 27 bovine proteins plus 2 proteins having similarities to other mammal proteins out of 52 proteins analyzed. The identified proteins consisted of 50 % basic house keeping proteins involved in metabolism, 30% muscle proteins, and other miscellaneous proteins. Many proteins on the 2-D gel with different molecular weights and isoelectric points were identified as same proteins due to posttranslational modification. As many of the identified house keeping proteins showed the high sequence similarities to other mammal equivalent proteins, searching the mammal databases could confirm the annotation. The preliminary identification of the proteome in bovine loin tissue could reveal the functions of proteins at over 50 % of chance with high fidelities. Using the established loin proteome map, proteomic difference between 1 yr and 2 yr Hanwoo loin tissues were compared on 2D gel. Regardless of the difficulty normalizing protein concentrations and sample-to-sample variations, three unidentified proteins and myoglobin were selected as up-regulated proteins during the fat deposition period. This study contributes to a move thorough and holistic understanding of beef meat, helping to build the basis for future identification of new markers for good quality meat.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.427-433
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• 2005

With the completely discovery of the Drosophila genome sequence, the next great challenge is to extract its biological information by systematic expression and to perform functional analysis of the gene. Here we reported a proteome analysis of D. melanogaster with two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS). The cell extracts of D. melanogaster, $200{\mu}g$ were resolved to more than 400 silver-stained spots by 2-DE. The most abundant protein spots were ranged from 4.0-7.5 of pI and from 15-90 kDa of molecular weight. The excised spots were destained and in-gel digested by trypsin. The masses of the resulting peptide mixtures were measured by MALDI-TOF-MS. Identified proteins were compared with measured peptide mass and a dynamic peptide searching database which is accessible via the internet. The results revealed that identified proteins were produced by 59 genes derived from 65 protein spots.

• Journal of the Korean Society of Food Science and Nutrition
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• v.32 no.1
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• pp.42-46
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• 2003

This research was carried out for searching the treatment conditions of organic acid and heating to prepare oligomers from the carrageenan. The applied treatments were autoclaving, micraowaving, and ultrasonicating with acetate, citrate, lactate, malate, and succinate. Among several physical depolymerization methods, auo-claving treatment was the most effective for hydrolyzing the carrageenan to low molecular compounds such as oligosaccharides. Citrate or malate was the most effective catalyst in hydrolyzing carrageenan to some oligo-saccharides among 5~7 different organic acids. An acceptable autoclaving condition for hydrolyzing carrageenan to oligosaccharides was to treat for 120 min at 110~12$0^{\circ}C$. The maximum depolymerization ratio produced by autoclaving was about 23.0%. The depolymerized carrageenan prepared by autoclaving at 12$0^{\circ}C$ had oligo-saccharides of 5~7 species.

• Archives of Plastic Surgery
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• v.37 no.4
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• pp.317-322
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• 2010

Purpose: There is no clear evidence of the original cause of hypertrophic scar, and the effective method of treatment is not yet established. Recently the steps of searching in gene and molecular level are proceeding. we are trying to recognize the difference between keratinocytes of hypertrophic scar and normal skin. Then we do support the comprehension of the scar formation mechanism and scar management. Methods: Total RNAs were extracted from cultured keratinocytes from 4 hypertrophic scars and normal skins. The cDNA chips were prepared. A total of 3063 cDNAs from human cDNA library were arrayed. And the scanning data were analyzed. Results: On microarray, heat shock protein, pyruvate kinase, tumor rejection antigen were more than 2 fold intensity genes. Among them, heat shock 70 kd protein showed the strongest intensity difference. Conclusion: In this study, it can be concluded that heat shock proteins play an important role in the process of wound healing and scar formation. This study provides basic biologic information for scar research. The new way of the prevention and treatment of scar formation would be introduced with further investigations.

• Molecules and Cells
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• v.39 no.7
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• pp.550-556
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• 2016

During meiosis, exchange of DNA segments occurs between paired homologous chromosomes in order to produce recombinant chromosomes, helping to increase genetic diversity within a species. This genetic exchange process is tightly controlled by the eukaryotic RecA homologs Rad51 and Dmc1, which are involved in strand exchange of meiotic recombination, with Rad51 participating specifically in mitotic recombination. Meiotic recombination requires an interaction between homologous chromosomes to repair programmed double-strand breaks (DSBs). In this study, we investigated the budding yeast meiosis-specific proteins Hop2 and Sae3, which function in the Dmc1-dependent pathway. This pathway mediates the homology searching and strand invasion processes. Mek1 kinase participates in switching meiotic recombination from sister bias to homolog bias after DSB formation. In the absence of Hop2 and Sae3, DSBs were produced normally, but showed defects in the DSB-to-single-end invasion transition mediated by Dmc1 and auxiliary factors, and mutant strains failed to complete proper chromosome segregation. However, in the absence of Mek1 kinase activity, Rad51-dependent recombination progressed via sister bias in the $hop2{\Delta}$ or $sae3{\Delta}$ mutants, even in the presence of Dmc1. Thus, Hop2 and Sae3 actively modulate Dmc1-dependent recombination, effectively progressing homolog bias, a process requiring Mek1 kinase activation.

• Applied Chemistry for Engineering
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• v.29 no.6
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• pp.645-651
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• 2018

Lung cancer has the highest death rate of any cancer diseases in Koreans. However, patients often feel difficult to recognize their disease before facing the terminal diagnosis due to the absence of any significant symptoms. Furthermore, the clear detection of an early cancer stage is usually obscure with existing diagnostic methods. For this reason, extensive research efforts have been made on introducing a wide range of biochemical diagnostic tools for the molecular level analysis of biological fluids for lung cancer diagnoses. A chip-based biosensor, one type of the analytical devices, can be a great potential for the diagnosis, which can be used without any further expensive analytical equipments nor skilled analysts. In this mini review, we highlight recent research trends on searching biomarker candidates and bio-chip sensors for lung cancer diagnosis in addition to discussing their future aspects.

• Journal of Animal Science and Technology
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• v.51 no.1
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• pp.1-8
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• 2009

We generated 57,598 expressed sequence tags (ESTs) from 3 cDNA libraries of Hanwooo (Korean Cattle), fat, loin, liver. Liver, intermuscular fat and longissimus dorsi tissues were obtained from a 24-month-old Hanwoo steer immediately after slaughter. cDNA library was constructed according to the oligocapped method. The EST data were clustered and assembled into unique sequences, 4,759 contigs and 7,587 singletons. To carry out functional analysis, Gene Ontology annotation and identification of significant leaf nodes were performed that were detected by searching significant p-values from $2^{nd}$ level GO terms to leaf nodes using Bonferroni correction. We found that 13, 26 and 8 significant leaf nodes are unique in the transcripts according to 3 GO categories, molecular function, biological process and cellular component. Also digital gene expression profiling using the Audic's test was performed and tissue specific genes were detected in the above 3 libraries.

• The Journal of the Korea Contents Association
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• v.16 no.6
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• pp.260-269
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• 2016

With the development of genomics, wearable device and IT/NT, a vast amount of bio-medical data are generated recently. Also, healthcare industries based on big-data are booming and big-data technology based on bio-medical data is rising rapidly as a core technology for improving the national health and aged society. Also, oriental medicine research is focused with modern research technology and validate it's various biochemical effect by combining with molecular biology technology. However there are few searching system for finding biochemical mechanism which is related to major compounds in oriental medicine. Therefore, in this paper, we collected papers related with medical herbs from PubMed and constructed a medical herbs database to store and manage chemical, gene/protein and biological interaction information extracted by a literature analysis on the papers. Also, to supporting a multidimensional analysis on the database, we developed a network analysis system based on a hierarchy structure of chemical, gene/protein and biological interaction information. Finally, we expect this system will be used the major tool to discover various biochemical effect by combining with molecular biology technology.

• Journal of Plant Biotechnology
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• v.47 no.3
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• pp.218-226
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• 2020

This report describes methods for selecting informative single nucleotide polymorphisms (SNPs), and the development of an online Solanaceae genome database, using 234 tomato resequencing data entries deposited in the NCBI SRA database. The 126 accessions of Solanum lycopersicum, 68 accessions of Solanum lycopersicum var. cerasiforme, and 33 accessions of Solanum pimpinellifolium, which are frequently used for breeding, and some wild-species tomato accessions were included in the analysis. To select tag-SNPs, we identified 29,504,960 SNPs in 234 tomatoes and then separated the SNPs in the genic and intergenic regions according to gene annotation. All tag-SNP were selected from non-synonymous SNPs among the SNPs present in the gene region and, as a result, we obtained tag-SNP from 13,845 genes. When there were no non-synonymous SNPs in the gene, the genes were selected from synonymous SNPs. The total number of tag-SNPs selected was 27,539. To increase the usefulness of the information, a Solanaceae genome database website, TGsol (http://tgsol. seeders.co.kr/), was constructed to allow users to search for detailed information on resources, SNPs, haplotype, and tag-SNPs. The user can search the tag-SNP and flanking sequences for each gene by searching for a gene name or gene position through the genome browser. This website can be used to efficiently search for genes related to traits or to develop molecular markers.