• Proceedings of the Korean Society of Rheology Conference
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• 2006.06a
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• pp.61-64
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• 2006

Soft materials, such as polymer solutions, gels and filamentous protein materials in cells, show complicated behavior due to their complex structures and dynamics with multiple characteristic time and length scales. Several complementary techniques have been developed to measure viscoelastic of soft materials. Especially, particle tracking microrheology, using the Brownian motion of particles in a medium to get rheological properties, has recently been improved both theoretically and experimentally. Compared to other conventional methods, video particle tracking microrheology has some advantages such as small sample volume, detecting spatial variation of local rheological properties, and less damage to sample materials. With these advantages, microrheology is more suitable to measure the properties of complex materials than other mechanical rheometries.

• Proceedings of the Korea Information Processing Society Conference
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• 2006.05a
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• pp.3-6
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• 2006

Motif which is a recurrent feature shared by a significant segments from the proteins belonging to different families can be used to predict functional or structural properties of the protein, or to describe features common to biologically related proteins. Although there are many existed motif databases, they are unstandardized and built up by different methods. so it is difficult to get enough motif information when researches use motif databases for classification, prediction, etc. Using logical integration of biological based on cross-references between these databases is the common solution for information tracking through www. However, the problem such as the motif resource tracking method for making a united motif information page emerges from cross-reference. In this paper we propose the motif resource tracking method based on the existed motif databases for easy and comfortable interface better than in the case of using each motif database. The result which is given by this method is the review of necessary information about any motif in PROSITE database.

• Journal of Sericultural and Entomological Science
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• v.27 no.1
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• pp.37-41
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• 1985

The haemolymph protein, digestive fluid proteins and digestive fluid amylase activity of wild silkworm, Theophila mandarina those of the were studied by polyacrylamide gel electrophoresis. In addition, they was also compared with silkworm. 1. 6 main protein bands in female and 7 main protein bands in male were detected in the larval haemolymph of T. mandarina where as 8 and 7 main protein bands in female and male of B. mori were observed. Some differences in the haemolymph protein ands of T. mandarina and B. mori were observed. 2. 15 protein bands and 12 protein bands were found in the larval digestive fluid of T. mandarina and B. mori respectively. Some differences in the mobility of digestive fluid proteins of T. mandarina and B. mori were noticed. 3. Larval digestive fluid amylases were anionic and moved near the tracking dye in both T. mandarina and B. mori. Mobility of the digestive fluid amylases relative to bromophenol blue were 0.019 and 0.020 in T. mandarina and B. mori respectively.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1474-1478
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• 2010

An efficient method for labeling individual proteins in live cells is required for investigations into biological mechanisms and cellular processes. Here we describe the preparation of small quantum dots (QDs) that target membrane surface proteins bearing a hexahistidine-tag ($His_6$-tag) via specific binding to an nitrilotriacetic acid complex of nickel(II) ($NTA{\cdot}Ni^{2+}$) on the QD surfaces. We showed that the $NTA{\cdot}Ni^{2+}$-QDs bound to His-tag functionalized beads as a cellular mimic with high specificity and that QDs successfully targeted $His_6$-tagged vesicle-associated membrane proteins (VMAP) on cell surfaces. This strategy provides an efficient approach to monitoring synaptic protein dynamics in spatially restricted and confined biological environments.

• Horticultural Science & Technology
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• v.34 no.1
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• pp.32-45
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• 2016

Fruit bagging has been widely practiced in peach cultivation to produce high quality and unblemished fruit. Moreover, fruit bagging has been utilized to study the effect of shading on the quality of fruit. We conducted a proteomic analysis on peach fruit to elucidate the biochemical and physiological events that characterize the effect of bagging treatment. Comparative analysis of 2D electrophoresis (2-DE) gels showed that relative protein levels differed significantly at 125 DAFB (days after full bloom), as well as at 133 DAFB in fruit that had been bagged until 125 DAFB, followed by exposure to sunlight. Most of the proteins with altered expression were identified by MALDI TOF/TOF. Twenty-one proteins with differential expression among the groups were identified at 125 DAFB, while thirty proteins with differential expression among the groups were identified at 133 DAFB. The analysis revealed that expression of proteins involved in photosynthesis, stress responses, and biochemical processes influencing metabolism were altered during bagging treatment, suggesting that regulation of the synthesis of carbohydrates, amino acids, and proteins influenced fruit size, solid/acid ratio, and peel color. This work provides the first characterization of proteomic changes in peach in response to fruit bagging treatment. Identifying and tracking protein changes may allow us to better understand the mechanisms underlying the effects of bagging treatment.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.359-359
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• 2011

Many research applications in basic sciences and biology such as protein crystallography require hard x-rays in the range of 3-20 keV with high brightness. A medium energy storage ring as PLS-II with a beam energy of 3 GeV can meet such high photon energies. In-vacuum undulators (IVU) with a period length of 20 mm and a peak field of 0.97 T are used in the PLS-II ring to produce such X-rays in the fundamental or higher harmonics. Due to the many poles and high fields, insertion devices like wigglers and undulators have a significant impact on the stability of the electron beam with potential degradation of beam quality and life time. Therefore, nonlinear fields must be determined by measurement and evaluated as to their impact on beam stability. Specifically, transverse field roll-off can be a serious detriment to injection in top-up mode and must be corrected. We use magnetic field measurement data to evaluated beam stability by tracking particles using an explicit symplectic integrator in both, transverse and longitudinal planes.

• International Journal of Stem Cells
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• v.16 no.1
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• pp.93-107
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• 2023

Background and Objectives: Chronic periodontitis can lead to alveolar bone resorption and eventually tooth loss. Stem cells from exfoliated deciduous teeth (SHED) are appropriate bone regeneration seed cells. To track the survival, migration, and differentiation of the transplanted SHED, we used super paramagnetic iron oxide particles (SPIO) Molday ION Rhodamine-B (MIRB) to label and monitor the transplanted cells while repairing periodontal bone defects. Methods and Results: We determined an appropriate dose of MIRB for labeling SHED by examining the growth and osteogenic differentiation of labeled SHED. Finally, SHED was labeled with 25 ㎍ Fe/ml MIRB before being transplanted into rats. Magnetic resonance imaging was used to track SHED survival and migration in vivo due to a low-intensity signal artifact caused by MIRB. HE and immunohistochemical analyses revealed that both MIRB-labeled and unlabeled SHED could promote periodontal bone regeneration. The colocalization of hNUC and MIRB demonstrated that SHED transplanted into rats could survive in vivo. Furthermore, some MIRB-positive cells expressed the osteoblast and osteocyte markers OCN and DMP1, respectively. Enzyme-linked immunosorbent assay revealed that SHED could secrete protein factors, such as IGF-1, OCN, ALP, IL-4, VEGF, and bFGF, which promote bone regeneration. Immunofluorescence staining revealed that the transplanted SHED was surrounded by a large number of host-derived Runx2- and Col II-positive cells that played important roles in the bone healing process. Conclusions: SHED could promote periodontal bone regeneration in rats, and the survival of SHED could be tracked in vivo by labeling them with MIRB. SHED are likely to promote bone healing through both direct differentiation and paracrine mechanisms.

• Korean Journal of Veterinary Research
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• v.29 no.4
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• pp.445-455
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• 1989

The proteins of the ruminant erythrocyte membranes were analysed by polyacrylamide gel electrophoresis in sodium dodecyl sulfate, and their relations to the slow erythrocyte sedimentation rate(ESR) of the ruminants were investigated by treating the erythrocytes with proteinases such as trypsin, chymotrypsin and pronase, and glycosidases such as neuraminidase and galactosidase. Protein content in the erythrocyte membrane was $2.85{\pm}0.28$ in human, $3.60{\pm}0.41$ in Korean cattle, $3.71{\pm}0.36$ in Holstein, $4.13{\pm}0.83$ in Korean native goat and $3.94{\pm}0.56mg/ml$ in sheep, showing higher in ruminant animals than in human(p<0.01). Although the general protein profiles of the ruminant erythrocyte membranes were almost similar to that of human, all the ruminant erythrocyte membranes showed one additional protein band, called band-Q in the previous report on proteins of bovine erythrocyte membrane, which migrated electrophoretically to the mid position between band-2 and band-3 in human erythrocyte membranes. The glycoprotein profiles of ruminant erythrocyte membranes revealed by periodic acid Schiff(PAS) stain showed a marked difference from that of human. The PAS-1(glycophorin) and PAS-2(sialoglycogrotein) present in human erythrocyte membranes were almost absent from the ruminant animals. Instead, a strong PAS-positive band near the origin of the electrophorograms, which was named as PAS-B in the previous report on proteins of bovine erythrocyte membranes, was shown in the ruminant animals except sheep. In addition, the erythrocyte membranes of Korean native goat and sheep showed a moderate PAS-negative band near the tracking dye of the electrophorograms, which was named as PAS-G in this study. In the erythrocyte treated with the enzymes, the migration of each protein fracture of erythrocyte membranes in response to each enzyme was diverse according to different species or breed of ruminant animals. Among others, band-Q present in ruminants was slightly or moderately decreased by trypsin-, chymotrypsin-, and pronase- treatments of the erythrocytes, but not only in sheep. It was particularly noticeable that PAS-B, a fraction of glycoprotein, present in ruminants except sheep, was better digested by proteinases than by glycosidases, showing remarkable increase(p<0.01) of the ESR in accord with complete digestion(disappearance) of the PAS-B band by pronase, trypsin or chymotrypsin treatment of erythrocytes. In sheep, there was almost no any response to the various enzymes in general protein and glycoprotein profiles of the erythrocyte membranes except PAS-G, which was markedly decreased by pronase treatment of the erythrocytes. Nevertheless, the ESRs were accelerated in erythrocytes treated with pronase, trypsin, chymotrypsin and neuraminidase. Erythrocyte osmotic fragility was increased in erythrocytes treated with only pronase among five enzymes in all the human and ruminant animals used in this study.

• Journal of Plant Biotechnology
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• v.50
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• pp.190-199
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• 2023

Date palm (Phoenix dactylifera L.: Arecaceae) is a dioecious species where only female trees bear fruits. In their natural state, date palms produce dates once a year. However, in Thailand, some trees were observed to produce dates during the off-season, despite no variations in morphology. The availability of such off-season fruits can significantly increase their market value. Interestingly, most female off-season date palms investigated in this study were obtained through micropropagation. Hence, there is an urgent need for genetic markers to distinguish female offseason flowering plantlets within tissue culture systems. In this study, we aimed to develop random amplification of polymorphic DNA-sequence characterized amplified region (RAPD-SCAR) markers for the identification of female off-season flowering date palms cultivated in Thailand. A total of 160 random decamer primers were employed to screen for specific RAPD markers in off-season flowering male and female populations. Out of these, only one primer, OPN-02, generated distinct genomic DNA patterns in female off-season flowering (FOFdp) individuals compared to female seasonal flowering genotypes. Based on the RAPD-specific sequence, specific SCAR primers denoted as FOFdpF and FOFdpR were developed. These SCAR primers amplified a single 517-bp DNA fragment, predominantly found in off-season flowering populations, with an accuracy rate of 60%. These findings underscore the potential of SCAR marker technology for tracking offseason flowering in date palms. Notably, a BLAST analysis revealed a substantial similarity between the SCAR marker sequence and the transcript variant mRNA from Phoenix dactylifera encoding the SET DOMAIN GROUP 40 protein. In Arabidopsis, this protein is involved in the epigenetic regulation of flowering time. The genetic potential of the off-season flowering traits warrants further elucidation.

• Molecules and Cells
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• v.42 no.2
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• pp.104-112
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• 2019

Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostatic tissue turnover, and stem cell function in regeneration and disease. Conventional lineage tracing involves the marking of cells either with dyes or nucleoside analogues or genetic marking with fluorescent and/or colorimetric protein reporters. Both are imaging-based approaches that have played a crucial role in the field of developmental biology as well as adult stem cell biology. However, imaging-based lineage tracing approaches are limited by their scalability and the lack of molecular information underlying fate transitions. Recently, computational biology approaches have been combined with diverse tracing methods to overcome these limitations and so provide high-order scalability and a wealth of molecular information. In this review, we will introduce such novel computational methods, starting from single-cell RNA sequencing-based lineage analysis to DNA barcoding or genetic scar analysis. These novel approaches are complementary to conventional imaging-based approaches and enable us to study the lineage relationships of numerous cell types during vertebrate, and in particular human, development and disease.