• Journal of Life Science
• /
• v.11 no.1
• /
• pp.19-23
• /
• 2001

To develop the effective microbial screening method, pyrolysis mass spectrometry (PyMS) fingerprinting was evaluated as a tool that discriminate various yeast strains. The target yeast strains were isolated from industrial wastewater. Seventeen environmental isolated yeast strains were examined by pyrolysis mass spectrometry and sequencing analysis of the large subunit rRNA gene D1/D2 region. The PyMS results were compared with those of sequencing analysis. Taxonomic correlations were observed between the PyMS data and the sequencing results. It was concluded that PyMS provides a rapid, reliable and cost-reducing method for discrimination of the yeast strains.

• Korean Journal of Clinical Laboratory Science
• /
• v.37 no.3
• /
• pp.173-177
• /
• 2005

YMDD motif mutants of the hepatitis B virus(HBV) emerge in chronic hepatitis B patients after prolonged lamivudine treatment. HBV DNA breakthrough may be accompained by the emergence of YMDD mutants. We compared the performance of the sequencing method with that of RFMP method in chronic hepatitis B patients who had suffered the HBV DNA breakthrough after lamivudine treatment. Both sequencing and RFMP methods were used to detect YMDD variants in 20 chronic hepatitis B patients. YMDD mutants were detected in 17 samples (85.0%) by both methods. Among them, no mutants were detected in two samples(10.0%), while they were detected in the other sample(5.0%) with the RFMP method. The concordance rate between both methods was 95.0%. There was inconsistency in one sample showing mutants detected by the RFMP method, but not by sequencing method. In the sequencing method, the mutants was detected in the major type virus, but not in the minor type virus. However, both sequencing and RFMP methods were highly concordant except in one sample, so it is suggested that both methods are useful to detect YMDD mutants of chronic hepatitis B patients.

• Journal of Microbiology and Biotechnology
• /
• v.15 no.5
• /
• pp.1054-1059
• /
• 2005

An extracellular protease was identified from Bacillus subtilis KCCM 10257 by N-terminal sequencing and mass spectral analysis. The molecular mass of the extracellular protease was estimated to be 28 kDa by SDS-PAGE. Sequencing of the N-terminal of the protease revealed the sequence of A(G,S,R)QXVPYG(A)V(P,L)SQ. The N-terminal sequence exhibited close similarity to the sequence of other proteases from Bacillus sp. A mass list of the monoisotopic peaks in the MALDI-TOF spectrum was searched after peptide fragmentation of the protease. Six peptide sequences exhibiting monoisotopic masses of 1,276.61, 1,513.67, 1,652.81, 1,661.83, 1,252.61, and 1,033.46 were observed from the fragmented protease. These monisotopic masses corresponded to the lytic enzyme L27 from Bacillus subtilis 168, and the Mowse score was found to be 75. A doubly charged Top product (MS) at a m/z of 517.3 exhibiting a molecular mass of 1034.6 was further analyzed by de novo sequencing using a PE Sciex QSTAR Hybrid Quadropole-TOF (MS/MS) mass spectrometer. MS/MS spectra of the Top product (MS) at a m/z of 517.3 obtained from the fragmented peptide mixture of protease with Q-star contained the b-ion series of 114.2, 171.2, 286.2, 357.2, 504.2, 667.4, 830.1, and 887.1 and y-ion series of 147.5, 204.2, 367.2, 530.3, 677.4, 748.4, 863.4, and 920.5. The sequence of analyzed peptide ion was identified as LGDAFYYG from the b- and y-ion series by de novo sequencing and corresponded to the results from the MALDI-TOF spectrum. From these results the extracellular protease from Bacillus subtilis KCCM 10257 was successfully identified with the lytic enzyme L27 from Bacillus subtilis 168.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.11
• /
• pp.2769-2772
• /
• 2009

• BMB Reports
• /
• v.29 no.2
• /
• pp.122-126
• /
• 1996

A series of oligonucleotides were synthesized by automatic DNA synthesizer. The purity of crude products was checked and their molecular weights determined by matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) with an accuracy of better than 0.05% deviation even without using an internal standard. This mass determining technology in combination with partial digestion of oligonucleotides by 5'- and 3'-exonuclease provides a straightforward and simple method to obtain sequence information of oligonucleotides. The extension of this technology to the sequencing of modified oligonucleotides and genomic DNA and RNA might become possible.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.7
• /
• pp.1112-1121
• /
• 2018

Jeotgal is a Korean traditional fermented seafood with a high concentration of salt. In this study, we isolated lactic acid bacteria (LAB) from galchi (Trichiurus lepturus, hairtail) and myeolchi (Engraulis japonicas, anchovy) jeotgal on MRS agar and MRS agar containing 5% NaCl (MRS agar+5% NaCl), and identified them by using 16S rRNA gene sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as culture-dependent methods. We also performed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) as a culture-independent method to identify bacterial communities. Five samples of galchi-jeotgal and seven samples of myeolchi-jeotgal were collected from different regions in Korea. A total of 327 and 395 colonies were isolated from the galchi- and myeolchi-jeotgal samples, respectively. 16S rRNA gene sequencing and MALDI-TOF MS revealed that the genus Pediococcus was predominant on MRS agar, and Tetragenococcus halophilus on MRS agar+5% NaCl. PCR-DGGE revealed that T. halophilus, Tetragenococcus muriaticus, and Lactobacillus sakei were predominant in both types of jeotgal. T. halophilus was detected in all samples. Even though the same species were identified by both culture-dependent and -independent methods, many species identified by the culture-dependent methods were not in the bacterial list identified by the culture-independent methods. The distribution of bacteria in galchi-jeotgal was more diverse than in myeolchi-jeotgal. The diverse LAB in galchi- and myeolchi-jeotgals can be further studied as candidates for starter cultures to produce fermented foods.

• Mass Spectrometry Letters
• /
• v.4 no.4
• /
• pp.71-74
• /
• 2013

In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptide backbone fragments, were the major products in MS/MS and $MS^3$ applications of some o-TEMPO-Bz-C(O)-peptide ions, while radical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the free radical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature in their sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called "mobile-proton model". When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appear to be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.4
• /
• pp.1183-1186
• /
• 2011

The unique Br signature was utilized for C-terminal amino acid sequencing of model peptides. C-terminal carboxyl group was selectively derivatized in peptides, containing side chain carboxyl group, using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDC) and Br was introduced using 4-bromophenylhydrazine hydrochloride (BPH) in a one pot reaction. Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) tandem mass spectra were obtained carrying the Br signature in the y-series ions. The Br signature facilitated C-terminal sequencing and discrimination of C-terminal carboxyl groups in the free acid and amide forms.

• Journal of Korean Society of Water and Wastewater
• /
• v.13 no.3
• /
• pp.42-55
• /
• 1999

A mathematical model for biological nutrient removal in a sequencing batch reactor process, which is based on the IAWQ Activated Sludge Model No. 2 with a few modifications, has been developed. Twenty water quality components and twenty three kinetic equations are incorporated in the model. The model is structured in the matrix form based on the law of mass conservation using stoichiometry and kinetic equations. Stoichiometric coefficients and kinetic parameters included in the model equations are chosen from the literature. A multistep predictor-corrector algorithm of variable step-size is adopted for solving the vector nonlinear ordinary differential equations. The simulation for experimental results is conducted to evaluate the validity of the model and to calibrate coefficients and parameters. The simulation using the model well represents the experimental results from laboratory. The mathematical model developed in this study may be utilized for the design and operation of a sequencing batch reactor process under the steady and unsteady-state at various environmental conditions.

• Journal of Korean Society on Water Environment
• /
• v.23 no.5
• /
• pp.607-612
• /
• 2007

In this study, we investigated the variations of the kinetic coefficients and Chemical Oxygen Demand (COD), N and P mass used for assimilation of a sequencing batch reactor (SBR) system with the variation of SRTs; SRTs of 7.5, 10.0, 12.5, 15.0 and 20.0 days were tested in one cycle of SBR operation to determine the optimum conditions for the operation of the SBR and estimate its COD, nitrogen and phosphorus removal efficiencies. The SBR system was operated under the conditions as follows: an operation time of 6 hours per cycle, a hydraulic retention time (HRT) of 12 hours, an influent COD loading of $0.4kg/m^3/day$, and an influent nitrogen loading of $0.068kgT-N/m^3/day$. The yield coefficient (Y) and decay rate coefficient ($k_d$) were estimated to be 0.4198 kgMLVSS/kgCOD and $0.0107day^{-1}$ by calculating the removal rate of substrate according to the variation of SRT. Considering total nitrogen amount removed by sludge waste process, eliminated by denitrification, and in clarified water effluent with reference to 150 mg/cycle of influent nitrogen amount, the percentage of nitrogen mass balance from the ratio of the nitrogen amount in effluent (N output) to that in influent (N input) for Runs 1~5 were 95.5, 97.0, 95.5, 99.5, and 95.5%, respectively, which is well accounted for, with mass balances close to 100%.