• Microbiology and Biotechnology Letters
• /
• v.49 no.4
• /
• pp.510-518
• /
• 2021

Bacteriophages are considered excellent sensing elements for platforms detecting bacteria. However, their lytic cycle has restricted their efficacy. Here, we used the minor coat protein pIII domain (N1N2) of phage CTXφ to construct a novel surface plasmon resonance (SPR) biosensor that could detect Vibrio cholerae. N1N2 harboring the domains required for phage adsorption and entry was obtained from Escherichia coli using recombinant protein expression and purification. SDS-PAGE revealed an approximate size of 30 kDa for N1N2. Dot blot and transmission electron microscopy analyses revealed that the protein bound to the host V. cholerae but not to non-host E. coli K-12 cells. Next, we used amine-coupling to develop a novel recombinant N1N2 (rN1N2)-functionalized SPR biosensor by immobilizing rN1N2 proteins on gold substrates and using SPR to monitor the binding kinetics of the proteins with target bacteria. We observed rapid detection of V. cholerae in the range of approximately 10³ to 10⁹ CFU/ml but not of E. coli at any tested concentration, thereby confirming that the biosensor exhibited differential recognition and binding. The results indicate that the novel biosensor can rapidly monitor a target pathogenic microorganism in the environment and is very useful for monitoring food safety and facilitating early disease prevention.

• Korean Journal of Food Science and Technology
• /
• v.26 no.1
• /
• pp.74-80
• /
• 1994

As a preliminary study about the reduction of the antigenicity of whey protein isolate(WPI) by treatment of chymotrypsin, trypsin, pancreatin, and protease from Aspergillus oryzae, the properties and antigenicities of whey protein hydrolysates(WPH) were investigated. When degrees of hydrolysis (DH) were measured by use of trinitrobenzensulfonic acid(TNBS), the DH of the WPH treated by pancreatin or protease from Aspergillus oryzae$(5.05{\sim}11.47)$ were much higher than those of the tryptic or chymotryptic WPH$(15.67{\sim}20.20)$. And the pretreatments of heat$(75^{\circ}C)$, 20 min and/or pepsin resulted in higher DH of WPH, generally. When the molecular distributions of the WPH were determined by high performance size exclusion chromatography(HPSEC), the ratios of polypeptides with molecular weight more than 10kDa ranged from 12% to 36%, and the average molecular weights and the average peptide lengths of the WPH were $4,252{\sim}9,132$ dalton and $38{\sim}83$ amino acids, respectively. And there was no bitter taste in all of the WPH. Results of SDS-PAGE showed that most of intact native proteins were eliminated by the enzymatic hydrolysis but there were a few bands of peptides larger than 14.2 kDa in some WPH. When antigenicity was assayed by competitive inhibition enzyme-linked immunosorbent assay(cELISA), monovalent antigenicity of WPH to rabbit anti-WPI antiserum were lowered to $10^{-1.7}-10^{-4.9}$ times and less by the enzymatic hydrolysis. And the pretreatments of heat and pepsin resulted in the lowest antigenicicy within a group of enzymatic hydrolysis, especially in case of the pancreatic hydrolysate(PDP) whose antigenicity was found almost to be removed.

• Korean Journal of Microbiology
• /
• v.52 no.1
• /
• pp.10-17
• /
• 2016

Enzyme immunoassay to analyze specific binding activity of antibody to antigen uses horseradish peroxidase (HRP) or alkaline phosphatase (AP). Chemical methods are usually used for coupling of these enzymes to antibody, which is complicated and random cross-linking process. As results, it causes decreases or loss of functional activity of either antibody or enzyme. In addition, most enzyme assays use secondary antibody to detect antigen binding activity of primary antibody. Enzymes coupled to secondary antibody provide a binding signal by substrate-based color development, suggesting secondary antibody is required in enzyme immunoassay. Additional incubation time for binding of secondary antibody should also be necessary. More importantly, non-specific binding activity caused by secondary antibody should also be eliminated. In this study, we cloned AP isolated from Escherichia coli (E. coli) chromosome by PCR and fused to) hAY4 single-chain variable domain fragment (ScFv) specific to death receptor (DR4) which is a receptor for tumor necrosis factor ${\alpha}$ related apoptosis induced ligand (TRAIL). hAY4 ScFv-AP expressed in E. coli showed 73.8 kDa as a monomer in SDS-PAGE. However, this fusion protein shown in size-exclusion chromatography (SEC) exhibited 147.6 kDa as a dimer confirming that natural dimerization of AP by non-covalent association induced ScFv-AP dimerization. In several immunoassay such as ELISA, Western blot and immunocytochemistry, it showed antigen binding activity by color development of substrates catalyzed by AP directly fused to primary hAY4 ScFv without secondary antibody. In summary, hAY4 ScFv-AP fusion protein was successfully purified as a soluble dimeric form in E. coli and showed antigen binding activity in several immunoassays without addition of secondary antibody which sometimes causes time-consuming, expensive and non-specific false binding.

• Microbiology and Biotechnology Letters
• /
• v.26 no.6
• /
• pp.483-489
• /
• 1998

We carried out the expression and characterization of yeast thioredoxin system including thioredexin 1 (Trx1), Trx2, thioredoxin reductase (TR), and a novel thioredoxin (Trx3), which was reported in the data base of Saccharomyces genome. The Trx1, 2 and TR were expressed as soluble proteins in E. coli and the sizes of purified proteins were equal to the reported their molecular weights. The expressed Trx3 was found in both soluble fraction and precipitate. The size of Trx3 purified from soluble fraction of E. coli crude extracts was estimated as 14 kDa on SDS-PAGE instead of 18 kDa for Trx3 in precipitate. N-terminal amino acid sequence of the small size of purified Trx3 from soluble fraction was analyzed as FQSSYTS which is correspond to the sequence from 20 to 26 for Trx3. Trx3 together with thioredoxin reductase and NADPH was able to reduce the disulfide bridge of insulin and 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB). Trx3 stimulated the antioxidant effect of thioredoxin peroxidase 1 (TPx1) which inhibited inactivation of glutamine synthetase (GS) in dithiothreitol (DTT) containing metal catalyzed oxidation system. The stimulation effect of Trx3 was 10% of the effect of either Trx1 or Trx2. In addition, Trx3 could reduce the disulfide of TPx to thiol, so that the TPx had thioredoxin dependant peroxidase activity. In western blotting analysis, antibodies against purified Trx3 did not cross-react with crude extracts of yeast, purified Trx1, and Trx2 proteins. But, in PCR reaction using the cDNA library of yeast as a template, gene encoding of trx3 was amplified.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.8
• /
• pp.1386-1392
• /
• 2008

A gene (sll0158) putatively encoding a glycogen branching enzyme (GBE, E.C. 2.4.1.18) was cloned from Synechocystis sp. PCC6803, and the recombinant protein expressed and characterized. The PCR-amplified putative GBE gene was ligated into a pET-21a plasmid vector harboring a T7 promoter, and the recombinant DNA transformed into a host cell, E. coli BL21(DE3). The IPTG-induced enzymes were then extracted and purified using Ni-NTA affinity chromatography. The putative GBE gene was found to be composed of 2,310 nucleotides and encoded 770 amino acids, corresponding to approx. 90.7 kDa, as confirmed by SDS-PAGE and MALDI-TOF-MS analyses. The optimal conditions for GBE activity were investigated by measuring the absorbance change in iodine affinity, and shown to be pH 8.0 and $30^{\circ}C$ in a 50 mM glycine-NaOH buffer. The action pattern of the GBE on amylose, an $\alpha$-(1,4)-linked linear glucan, was analyzed using high-performance anion-exchange chromatography (HPAEC) after isoamylolysis. As a result, the GBE displayed $\alpha$-glucosyl transferring activity by cleaving the $\alpha$-(1,4)-linkages and transferring the cleaved maltoglycosyl moiety to form new $\alpha$-(1,6)-branch linkages. A time-course study of the GBE reaction was carried out with biosynthetic amylose (BSAM; $M_p{\cong}$8,000), and the changes in the branch-chain length distribution were evaluated. When increasing the reaction time up to 48 h, the weight- and number-average DP ($DP_w$ and $DP_n$) decreased from 19.6 to 8.7 and from 17.6 to 7.8, respectively. The molecular size ($M_p$, peak $M_w{\cong}2.45-2.75{\times}10^5$) of the GBE-reacted product from BSAM reached the size of amylose (AM) in botanical starch, yet the product was highly soluble and stable in water, unlike AM molecules. Thus, GBE-generated products can provide new food and non-food applications, owing to their unique physical properties.

• Journal of KIISE:Databases
• /
• v.34 no.6
• /
• pp.546-553
• /
• 2007

As ontologies are used widely, interest for semantic similarity search is also increasing. In this paper, we suggest a query evaluation scheme for k-nearest neighbor query, which retrieves k most similar objects to the query object. We use the best match method to calculate the semantic similarity between objects and use the signature tree to index annotation information of objects in database. The signature tree is usually used for the set similarity search. When we use the signature tree in similarity search, we are required to predict the upper-bound of similarity for a node; the highest similarity value which can be found when we traverse into the node. So we suggest a prediction function for the best match similarity function and prove the correctness of the prediction. And we modify the original signature tree structure for same signatures not to be stored redundantly. This improved structure of signature tree not only reduces the size of signature tree but also increases the efficiency of query evaluation. We use the Gene Ontology(GO) for our experiments, which provides large ontologies and large amount of annotation data. Using GO, we show that proposed method improves query efficiency and present several experimental results varying the page size and using several node-splitting methods.

• Korean Journal of Microbiology
• /
• v.45 no.3
• /
• pp.233-238
• /
• 2009

The expression of Corynebacterium ammoniagenes purF was analyzed by utilizing a plasmid carrying a cat gene fused to the purF promoter region. Adenine and guanine repressed the expression of the purF gene by 20~30% but hypoxanthine did not exert such repressive effect. The expression purF was maximal at the late log phase and remained constant throughout the stationary phase. Promoter $P_{180}$ which was developed in C. glutamicum was also functional in C. ammoniagenes, achieving maximal activity at the late log phase. The promoter outperformed Escherichia coli $P_{tac}$ promoter by 40~50% level. DNA-affinity purification identified a protein which could bind to the promoter region of the purF gene. The protein showed high similarity to the CRP-family transcriptional regulator encoded by NCgl0120 in C. glutamicum. The size of the screened protein agreed with the expected protein size from the ORF NCgl0120. The corresponding gene in C. ammoniagenes encoded a 42 kDa polypeptide composed of 400 amino acids with expected pI of 4.9. The encoded protein showed 14.1% and 15.8% identity with E. coli and Bacillus subtilis PurR, respectively, suggesting that the isolated protein might be a novel type of regulatory protein involved in the regulation of purine metabolism.

• Journal of KIISE:Databases
• /
• v.28 no.3
• /
• pp.357-372
• /
• 2001

In this paper, we present the concept of generalization in constructing windows for subsequence matching and propose a new subsequence matching method. GeneralMatch, based on the generalization. The earlier work of Faloutsos et al.(FRM in short) causes a lot of false alarms due to lack of the point-filtering effect. DualMatch, which has been proposed by the authors, improves performance significantly over FRM by exploiting the point filtering effect, but it has the problem of having a smaller maximum window size (half that FRM) given the minimum query length. GeneralMatch, an improvement of DualMatch, offers advantages of both methods: it can use large windows like FRM and, at the same time, can exploit the point-filtering effect like DualMatch. GeneralMatch divides data sequences into J-sliding windows (generalized sliding windows) and the query sequence into J-disjoint windows (generalized disjoint windows). We formally prove that our GeneralMatch is correct, i.e., it incurs no false dismissal. We also prove that, given the minimum query length, there is a maximum bound of the window size to guarantee correctness of GeneralMatch. We then propose a method of determining the value of J that minimizes the number of page accesses, Experimental results for real stock data show that, for low selectivities ($10^{-6}~10^{-4}$), GeneralMatch improves performance by 114% over DualMatch and by 998% iver FRM on the average; for high selectivities ($10^{-6}~10^{-4}$), by 46% over DualMatch and by 65% over FRM on the average.

• Journal of Sericultural and Entomological Science
• /
• v.35 no.1
• /
• pp.60-68
• /
• 1993

It has been known that the silk degumming treated by hot alkali solution is easy to handle but is liable to yield poor-quality silk due to the degree of degumming loss, incomplete-degumming or over-degumming. Therefore, many studies have been carried out on the silk degumming by enzyme in order to improve the quality of silk. However, no attention has been paid to the physicochemical analysis of enzymatic degummed silk. In this paper, two different degumming methods, soap and enzymatic, are compared in aqueous solution state of silk fibroin. The results can be summarized as follows: There was no significant difference between two solutions on the bases of polarizing microscopy, TEM observation and SDS-PAGE. Spherulite of silk fibroin was not observed in polarizing microscopy, however the leaf-shape fibril structure was developed upon solidification. The size of spherulites of silk fibroin in TEM observation were 30~120nm with a wide range of size distribution. The intrinsic viscosity of enzymatic degummed fibroin solution was lower than that of soap degummed solution. This can be explained that the silk fibroin was more degraded by enzymatic degumming method compared with the soap degumming method. SDS-polyacrylamide gel electrophoresis showed that the fibroin molecule was composed of large component of molecule weight above 50 kd and small component of molecule weight about 20 kd. There was no difference in crystallinity between two degumming methods on the bases of results of DSC thermograms and IR spectra.

• Journal of Life Science
• /
• v.28 no.12
• /
• pp.1416-1423
• /
• 2018

With strong biotin binding affinity ($K_D=10^{-14}M$), the tetrameric feature of streptavidin could be used to increase the antigen binding activity of a camel heavy chain (VHH) antibody through their fusion, here stained with biotinylated horseradish peroxidase and subsequent immunoassays ELISA and Western blot analysis. For this application, we cloned the streptavidin gene amplified from the Streptomyces avidinii chromosome by PCR, and this was fused to the gene of the 8B9 VHH antibody which is specific to green fluorescent protein (GFP) antigens. To express a soluble fusion protein in Escherichia coli, we used the pUC119 plasmid-based expression system which uses the lacZ promoter for induction by IPTG, the pelB leader sequence at the N-terminus for secretion into the periplasmic space, and six polyhistidine tags at the C-terminus for purification of the expressed proteins using an $Ni^+$-NTA-agarose column. Although streptavidin is toxic to E. coli because of its strong biotin binding property, this soluble fusion protein was expressed successfully. In SDS-PAGE, the size of the purified fusion protein was 122.4 kDa in its native condition and 30.6 kDa once denatured by boiling, suggesting the tetramerization of the monomeric subunit by non-covalent association through the streptavidin moiety fusing to the 8B9 VHH antibody. In addition, this fusion protein showed biotin binding activity similar to streptavidin as well as GFP antigen binding activity through both ELISA and Western blot analysis. In conclusion, the protein resulting from the fusion of an 8B9 VHH antibody with streptavidin was successfully expressed and purified as a soluble tetramer in E. coli; it showed both biotin and GFP antigen binding activity suggesting the possible production of a tetrameric and bifunctional VHH antibody.