• Interdisciplinary Bio Central
• /
• v.3 no.2
• /
• pp.8.1-8.6
• /
• 2011

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful genegene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steady-state results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

• Journal of Ginseng Research
• /
• v.13 no.2
• /
• pp.254-259
• /
• 1989

A radioprotective ginseng protein fraction was obtained from Korean white ginseng powder by the following isolation and purification procedures: Tris-HCI buffer extraction, 70% ammonium sulfate fractionation, CM-rellulosr column chromatography, heat inactivation and Sephadex G-75 column chromatography. This fraction was further purified by Sepharose 4B and Sephadex G-150 column chromatographies. Three fractions obtained were subjected to Native-PAGE and SDS-PAGE using gradient gels and the silver staining method. Molecular weights of the native proteins and their subunits were estimated.

• Journal of Sensor Science and Technology
• /
• v.20 no.4
• /
• pp.226-229
• /
• 2011

Label-free detection of biomolecular interactions was performed using BioFET(Biologically sensitive Field-Effect Transistor) and SPR(Surface Plasmon Resonance). Qualitative information on the immobilization of an anti-IgG and antibody-antigen interaction was gained using the SPR analysis system. The BioFET was used to explore the pI value of the protein and to monitor biomolecular interactions which caused an effective charge change at the gate surface resulting in a drain current change. The results show that the BioFET can be a useful monitoring tool for biomolecular interactions and is complimentary to the SPR system.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.3
• /
• pp.507-513
• /
• 2017

Bacillus subtilis spores can be used for protein display to engineer protein properties. This method overcomes viability and protein-folding concerns associated with traditional protein display methods. Spores remain viable under extreme conditions and the genotype/phenotype connection remains intact. In addition, the natural sporulation process eliminates protein-folding concerns that are coupled to the target protein traveling through cell membranes. Furthermore, ATP-dependent chaperones are present to assist in protein folding. CotA was optimized as a whole-cell biocatalyst immobilized in an inert matrix of the spore. In general, proteins that are immobilized have advantages in biocatalysis. For example, the protein can be easily removed from the reaction and it is more stable. The aim is to improve the pH stability using spore display. The maximum activity of CotA is between pH 4 and 5 for the substrate ABTS (ABTS = diammonium 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate). However, the activity dramatically decreases at pH 4. The activity is not significantly altered at pH 5. A library of approximately 3,000 clones was screened. A E498G variant was identified to have a half-life of inactivation ($t_{1/2}$) at pH 4 that was 24.8 times greater compared with wt-CotA. In a previous investigation, a CotA library was screened for organic solvent resistance and a T480A mutant was found. Consequently, T480A/E498G-CotA was constructed and the $t_{1/2}$ was 62.1 times greater than wt-CotA. Finally, E498G-CotA and T480A/E498G-CotA yielded 3.7- and 5.3-fold more product than did wt-CotA after recycling the biocatalyst seven times over 42 h.

• Journal of Life Science
• /
• v.27 no.10
• /
• pp.1191-1198
• /
• 2017

Vesicles and organelles are transported along microtubule and delivered to appropriate compartments in cells. The intracellular transport process is mediated by molecular motor proteins, kinesin, and dynein. Kinesin is a plus-end-directed molecular motor protein that moves the various cargoes along microtubule tracks. Kinesin 1 is first isolated from squid axoplasm is a dimer of two heavy chains (KHCs, also called KIF5s), each of which is associated with the light chain (KLC). KIF5s interact with many different binding proteins through their carboxyl (C)-terminal tail region, but their binding proteins have yet to be specified. To identify the interacting proteins for KIF5A, we performed the yeast two-hybrid screening and found a specific interaction with Ras-GTPase-activating protein (GAP) Src homology3 (SH3)-domain-binding protein 2 (G3BP2), which is involved in stress granule formation and mRNA-protein (mRNP) localization. G3BP2 bound to the C-terminal 73 amino acids of KIF5A but did not interact with the KIF5B, nor the KIF5C in the yeast two-hybrid assay. The arginine-glycine-glycine (RGG)/Gly-rich region domain of G3BP2 is a minimal binding domain for interaction with KIF5A. However, G3BP1 did not interact with KIF5A. When co-expressed in HEK-293T cells, G3BP2 co-localized with KIF5A and was co-immunoprecipitated with KIF5A. These results indicate that G3BP2, which was originally identified as a Ras-GAP SH3 domain-binding protein, is a protein that interacts with KIF5A.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.17 no.11
• /
• pp.640-647
• /
• 2016

By minimizing fluorescence interference phenomena, aequorin-based luminescence technology can provide a relatively sensitive detection platform with integration of $G{\alpha}16$ protein in order to track internal calcium mobilization by G protein-coupled receptors (GPCR). In this type of cell-based functional assay format, it is essential to optimize the transfection process of a receptor and $G{\alpha}16$ protein. For this study, corticotropin releasing factor receptor subtype 2(CRF2) was set as a model system to generate three stable cells with CRF2 and $G{\alpha}16$ in addition to transiently transfected cells under three different conditions. Agonist (sauvagine) and antagonist (K41498) responses in those cells were analyzed to develop the optimum transfection process. As a result, the effective signal ratio in the dose response experiments of sauvagine and K41498 were at least 10-fold higher (z'=0.77) in CRF2-$G{\alpha}16$ stable cells. For the transient transfection cells, stable expression of $G{\alpha}16$ prior to the CRF2 represented a two-fold higher signal (z'=0.84) than the other cases of transient transfection. In conclusion, for the utilization of transient transfection processes to develop a cell-based GPCR functional assay system, it is suggested to introduce various target receptors after stable expression of $G{\alpha}16$ protein.

• ALGAE
• /
• v.29 no.3
• /
• pp.227-235
• /
• 2014

The red seaweed, Gracilaria tikvahiae McLachlan, was cultivated in open water farms in urbanized estuaries of Long Island Sound (26-30 psu of salinity) and New York City (20-25 psu), USA in 2011. Plants were harvested monthly from summer (August, $24^{\circ}C$) to fall (November, $13^{\circ}C$) and analyzed for total nitrogen, protein, and amino acid content. On a dry matter (DM) basis, nitrogen and protein significantly increased over the harvest period until October and then plateaued. Nitrogen increased from $22{\pm}1g\;kg^{-1}$ DM in August to $39{\pm}3g\;kg^{-1}$ DM in October (p < 0.001). Protein increased from $107{\pm}13g\;kg^{-1}$ DM in August to $196{\pm}5g\;kg^{-1}$ DM in November (p < 0.001). With two exceptions, amino acid concentrations expressed on a crude protein (CP) basis were similar over the harvest period. Essential amino acids accounted for $48{\pm}1%$ of all amino acids present with lysine and methionine averaging $56{\pm}2g\;kg^{-1}$ CP and $18{\pm}1g\;kg^{-1}$ CP, respectively. Histidine was underrepresented among essential amino acids and averaged $13{\pm}1g\;kg^{-1}$ CP. Taurine ranged from 2.1 to $3.2g\;kg^{-1}$ DM. With its moderate levels of lysine, methionine and taurine, ocean farmed G. tikvahiae has the potential of overcoming many nutrient deficiencies currently associated with terrestrial plant ingredients in alternative feeds for fish and shrimp.

• BMB Reports
• /
• v.33 no.6
• /
• pp.483-492
• /
• 2000

The Herpes simplex virus type 1 (HSV-1) strain F glycoprotein H (gH) gene in the pHLB-4 plasmid was recombinated into a baculovirus expression vector (lacZ-HcNPV) to construct a recombinant virus GH-HcNPV expressing gH. The sequences of gH and its expression were analyzed. The gH gene was located in the 6.41 kb BglII fragment. The open reading frame (ORF) of the gH gene was 2,517 bp and codes 838 amino acid residues. Insect cells infected with this recombinant virus synthesized a high level of the matured and gX-gH fusion protein with approximately 112 kDa. The fusion gH protein was localized on the membrane of the insect cells as seen by using immunofluorescence assay and accumulated in the cultured media by the SDS-PAGE and immunoprecipitation assays. The amino acid sequence presents additional characteristics compatible with the structure of a viral glycoprotein: signal peptide, putative glycosylation sites and a long C-terminal transmembrane sequence. Antibodies raised in mice to this recombinant protein recognized viral gH and neutralized the infectivity of HSV-1 in vitro. These results demonstrate that it is possible to produce a mature protein by gene transfer in eukaryotic cells, and indicate the utility of the HcNPV-insect cell system for producing and characterizing eukaryotic proteins. Furthermore, the neutralizing antibodies would appear to protect mice against HSV; accordingly, this particular recombinant protein may be useful in the development of a subunit vaccine.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.35 no.3
• /
• pp.247-252
• /
• 2002

To prepare the edible film based on fish protein, the optimal conditions for extracting soluble protein from Alaska pollack ( Theragra chalcogramma) and mackerel (Scomber japonious) muscle were defined. The effects of protein concentration, pH and temperature of protein solution on the physical properties of films were also investigated, Contents of moisture, crude protein, crude lipid and ash in Alaska pollack muscle were 79.6, 18.2, 0.6 and $1.2\%$, respectively. Contents of moisture, crude protein, crude lipid and ash in mackerel muscle were 69,1, 20.1, 9,5 and $1.3\%$, respectively. Both soluble protein contents extracted from Alaska pollack and mackerel were the highest at pH 12.0, and then un 2.0, 11.0. But they were extracted a little at neutral range. forward the recovery yield of protein by controlling isoelectric point was the highest at pH 4.8 ($79.8\%$) for Alaska pollack and at pH 5.0 ($64.1\%$) for mackerel, For the preparation of protein films from both Alaska pollack and mackerel, the most effective conditions of film forming solution were achieved, after supplied fish protein 4 g (glycerol 1,6 g) in 100 mL of distilled water, by adjusted to pH 10.0 and then heated at $90^{\circ}C$.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.8 no.3
• /
• pp.627-631
• /
• 2007

The factors affecting on sludge sedimentation are reported as F/M ratio, ingredient, composition of influent substrate, dissolved oxygen concentration, temperature, pH, filamentous bacteria and SRT. Aeration tank applying Bacillus sp. has an important role for maintaining the dominant microorganism species to make steady progress for spore growth affecting sedimentation. This research aims to investigate the affecting factor for the sedimentation in B3 system and RABC system with aeration tank applying tapered aeration. Extracellular polymeric substances(EPS), protein and carbohydrate can be produced for the extreme condition, that is down to 0.2 mg/L of dissolved oxygen in the aeration tank. This research found out the relation between the sedimentation and the EPS production, especially the ratio of protein/carbohydrate. The spore of Bacillus sp. was formed at the low DO then microorganisms produced EPS. The results showed that the production of EPS was 109.95 mgEPS/gSS at 1.6 mg/L of DO, however it was 131.77 mgEPS/gSS at 0.5 mg/L of DO. The sedimentation was affected by protein content in EPS and the ratio of protein and carbohydrate. The settleability of sludge was not affected by the ratio of protein/carbohydrate in B3 process, meanwhile settleability was affected by the ratio of it in RABC process, respectively.