• Mass Spectrometry Letters
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• v.15 no.1
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• pp.1-25
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• 2024

Protein glycosylation, a highly significant and ubiquitous post-translational modification (PTM) in eukaryotic cells, has attracted considerable research interest due to its pivotal role in a wide array of essential biological processes. Conducting a comprehensive analysis of glycoproteins is imperative for understanding glycoprotein bio-functions and identifying glycosylated biomarkers. However, the complexity and heterogeneity of glycan structures, coupled with the low abundance and poor ionization efficiencies of glycopeptides have all contributed to making the analysis and subsequent identification of glycans and glycopeptides much more challenging than any other biopolymers. Nevertheless, the significant advancements in enrichment techniques, chromatographic separation, and mass spectrometric methodologies represent promising avenues for mitigating these challenges. Numerous substrates and multifunctional materials are being designed for glycopeptide enrichment, proving valuable in glycomics and glycoproteomics. Mass spectrometry (MS) is pivotal for probing protein glycosylation, offering sensitivity and structural insight into glycopeptides and glycans. Additionally, enhanced MS-based glycopeptide characterization employs various separation techniques like liquid chromatography, capillary electrophoresis, and ion mobility. In this review, we highlight recent advances in enrichment methods and MS-based separation techniques for analyzing different types of protein glycosylation. This review also discusses various approaches employed for glycan release that facilitate the investigation of the glycosylation sites of the identified glycoproteins. Furthermore, numerous bioinformatics tools aiding in accurately characterizing glycan and glycopeptides are covered.

• Current Research on Agriculture and Life Sciences
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• v.11
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• pp.121-132
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• 1993

This study was carried out to research the effect of the chemotaxis of Bradyrhizobium japonicum KCTC 2422 and its mutant toward soybean root exudate and to elucidate the effect of the lectin of host specificity (Host Recognition) in soybean-Bradyrhizobium symbiosis. The results obtained were as follows: The homogeneities of the purified lectins from soybean and pea seed was ascertained chromatographically and electrophoretically. Gel electrophoresis of soybean lectin in the presence of sodium dodecyl sulfate appeared a single protein band, whereas pea lectin appeared two protein bands. Soybean lectin from 2 cultivars formed immunoprecipitin arcs at same position with anti-soybean lectin rabbit IgG, but pea lectin did not form immunoprecipitin lines with anti-soybean lectin rabbit IgG. Chemotactic responses of KCTC 2422, LPN-100 and LCR-101 toward proline in capillary assays were 3.1, 1.3 and 1.0-fold above background, respectively. The chemotactic responses of KCTC 2422, LPN-100, and LCR-101 toward Paldal crude root exudate in capillary assays were 3.5, 1.4 and 1.4-fold above background, respectively. The present work shows that B. japonicum and its mutants are capable of very different responses toward root exudate fraction. The chemotactic responses of KCTC 2422 was most with neutral fraction, least with anionic fraction and intermediate with cationic fraction. The nitrogenase activity of soybean nodule was shown in 15days after inoculation with LCR-101. However, we couldn't find out the nodules when soybean was inoculated with LPN-100. From these result we can suppose that the chemotaxis of Bradyrhizobium plays inportant the role of forming the nodule (host recognition) in the soybean-B. japonicum symbiosis.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.3
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• pp.198-204
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• 2000

In order to utilize by-products which would normally be discarded in marine processing plants, cod teiset protein was hydrolyzed and antioxidative actiTity of the hydrolysate was investigated. AntioxidatiTe peptide was isolated using ultrafiltration membrane, ion-exchange chromatography on a SP-Sephadex C-25 column, gel filtration on a Sephadex G-15 column, high performance liquid chromatography on an ODS column, and capillary electrophoresis chromatography. Antioxidative activities of the cod teiset hydrolysate were compared with ${\alpha}-tocopherol$, one of the commercial antioxidant. The hydrolysate passed through a membrane with molecular weight cut-off (MWCO) 1 kDa was shown the strongest antioxidative activity, and the activity was higher $10{\%}$ as compared with ${\alpha}-tocopherol$. In addition, the peptide isolated by ion-exchange chromatography, gel filtration, and HPLC, respectively, was higher $53{\%}$ as compared with ${\alpha}-tocopherol$, and the amino acid sequence was Ser-Asn-Pro-Glu-Trp-Ser-Trp-Asn.

• Molecular & Cellular Toxicology
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• v.1 no.3
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• pp.196-202
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• 2005

Nitric oxide (NO) is a small, diffusible, and highly reactive molecule, which plays dichotomous regulatory roles under physiological and pathological conditions. NO promotes apoptosis in some cells, and inhibits apoptosis in other cells. In the present study, we attempted to characterize the NO signaling pathway and cellular response in PC12 cells treated with cytokines. $IFN{\gamma}\;and\;TNF{\alpha}$ treatment resulted in a synergistic increase of nitrite accumulation, with the induction of inducible nitric oxide synthase (iNOS) in the PC12 cells. Moreover, as nitrite concentration increased, cell viability decreased. In order to explore MAP kinase involvement in nitric oxide production resultant from $IFN{\gamma}\;and\;TNF{\alpha}$ stimulation, we measured the activation of MAP kinase using specific MAP kinase inhibitors. PC12 cells pretreated with SB203580, a p38 MAP kinase-specific inhibitor, resulted in the inhibition of iNOS expression and NO production. However, PD98059, an ERK/MAP kinase-specific inhibitor, was not observed to exert such an effect. In addition, Stat1 activated by $IFN{\gamma}\;and\;TNF{\alpha}$ was interacted with p38 MAPK. These data suggest that p38 MAP kinase mediates cytokine-mediated iNOS expression in the PC12 cells, and Jak/Stat pathway interferes with p38 MAPK signaling pathway.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1156-1156
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• 2001

This work aimed to prove the feasibility of NIR spectroscopy to detect vegetable protein isolates (soy, pea and wheat) in milk powder. Two hundred and thirty-nine samples of genuine and adulterated milk powder (NIZO, Ede, NL) were analysed by NIRS using an InfraAlyzer 500 (Bran+Luebbe). NIR spectra were collected at room temperature, and data were processed by using Sesame Software (Bran+Luebbe). Separated calibrations for each non-milk protein added, in the range of 0-5%, were calculated. NIR data were processed by using Sesame Software (Bran+Luebbe). Prediction and validation were made by using a set of samples not included into the calibration set. The best calibrations were obtained by the PLSR. The type of data pre-treatment (normalisation, 1$\^$st/ derivative, etc..) was chosen to optimize the calibration parameters. NIRS technique was able to predict with good accuracy the percentage of each vegetable protein added to milk powder (soy: R$^2$ 0.994, SEE 0.193, SEcv 0.301, RMSEPall 0.148; pea: R$^2$ 0.997, SEE 0.1498, SEcv 0.207, RMSEPall 0.148, wheat: R$^2$ 0.997, SEE 0.1418, SEcv 0.335, RMSEPall 0.149). Prediction results were compared to those obtained using other two techniques: capillary electrophoresis and competitive ELISA. On the basis of the known true values of non-vegetable protein contents, the NIRS was able to determine more accurately than the other two techniques the percentage of adulteration in the analysed samples.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1158-1158
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• 2001

Fast and dynamic biochemical, enzymatic and morphological changes occur during the so-called generative development and during the vegetative processes in seeds. The most characteristic biochemical and compositional changes of this period are the formation and decline of storage components or their precursors, the change of their degree in polymerization and an extensive change in water content. The aim of the present study was to detect the maturation processes in seed nondestructively and to verify the applicability of near infrared spectroscopic methods in the measurement of physiological, chemical and biochemical changes in wheat seed. The amount and variation of different water “species” has been changed intensively during maturation. Characteristic changes of three water absorption bands (1920, 1420 and 1150 nm) during maturation were analysed. It was concluded that the free/bound transition of water molecules could be followed sensitively in different region of NIR spectra. Kinetic changes of carbohydrate reserves were characteristic during maturation. An intensive formation and decline of carbohydrate reserves were observed during early stage of maturation (0 -13 days, high energy demand). An accelerated formation of storage carbohydrates (starch) was detected in the second phase of maturation. Five characteristic absorption bands were analysed which were sensitive indicators the changes of carbohydrates occurred during maturation. Precursors of protein synthesis and the synthesis of reserve proteins and their kinetic changes during maturation were followed from NIR spectra qualitative and qualitatively. Dynamic formation of amino acids and the changes of N forms were detected by spectroscopic, chromatographic and by capillary electrophoresis methods. Calibration equations were developed and validated in order to measure the optimal maturation time protein and moisture content of developing wheat seeds. The spectroscopic methods are offering chance and measurement potential in order to detect fine details of physiological processes. The spectra have many hidden details, which can help to understand the biochemical background of processes.

• BMB Reports
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• v.34 no.3
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• pp.194-200
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• 2001

Secreted arginase from Evernia prunastri thallus has been purified 616-fold from the incubation medium. Purified arginase was resolved as only one peak in a capillary electrophoresis with a pI value of 5.35. The protein contained high amounts of acidic amino acids, such as Asx and Glx, and a relatively high quantity of Ser and Gly. The molecular mass of native, purified arginase was estimated as about 26 kDa by SE-HPLC. Substrate saturated kinetic showed a typical Michaelis-Menten relationship with a K_m value of 3.3 mM L-arginine. Atranorin behaved as a mixed activator of the enzyme (apparent $K_m$ = 0.96 mM); whereas evernic and usnic acid were revealed as non competitive inhibitors (apparent $K_m$ values were 3.16 mM and 3.05 mM, respectively). Kinetics of atranorin binding indicated that saturation was reached from 0.18 ${\mu}mol$ of the total atranorin and the occurrence of multiple sites for the ligand. This agrees with a possible aggregation of several enzyme subunits during the interaction process. A value of binding sites of about 12 was obtained. The binding of evernic acid was saturated from 23 nmol of total phenol. The number of binding sites was about 5. The loss of the binding ability of evernic acid could be interpreted as a single negative cooperatively. Usnic acid behaves in a similar way to evernic acid, although the binding saturation occurs at $0.14\;{\mu}moles$ of the ligand. This binding appears to be unspecific, and has 28 usnic acid binding sites to the protein.

• Biomedical Science Letters
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• v.17 no.2
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• pp.151-155
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• 2011

Short tandem repeats (STRs) loci are the genetic markers used for forensic human identity test. With multiplex polymerase chain reaction (PCR) assays, STRs are examined and measured PCR product length relative to sequenced allelic ladders. In the repeat region and the flanking region of the commonly-used STR may have DNA sequence variation. A mismatch due to sequence variation in the DNA template may cause allele drop-out (i.e., a "null" or "silent" allele) when it falls within PCR primer binding sites. The STR markers were co-amplified in a single reaction by using commercial PowerPlex$^{(R)}$ 16 system and AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kits. Separation of the PCR products and fluorescence detection were performed by ABI PRISM$^{(R)}$ 3100 Genetic Analyzer with capillary electrophoresis. The GeneMapper$^{TM}$ ID software were used for size calling and analysis of STR profiles. Here, this study described a forensic human identity test in which allelic drop-out occurred in the STR system D18S51. During the course of human identity test, two samples with a homozygous (16, 16 and 21, 21) genotype at D18S51 locus were discovered using the PowerPlex$^{(R)}$ 16 system. The loss of alleles was confirmed when the samples were amplified using AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kit and resulted in a heterozygous (16, 20 and 20, 21) genotype at this locus each other. This discrepancy results suggest that appropriate measures should be taken for database comparisons and that allele should be further investigated by sequence analysis and be reported to the forensic community.

• Journal of Animal Science and Technology
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• v.55 no.2
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• pp.87-93
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• 2013

We identified four new bovine tri-nucleotide microsatellite loci and analyzed their sequence structures and genetic parameters in 105 randomly selected Korean cattle (Hanwoo). Allele numbers of the loci B17S0808, B15S6253, B8S7996, and B17S4998 were 10, 11, 12, and 29, respectively. These alleles contained a simple or compound repeat sequences with some variations. Allele distributions of all these loci were in Hardy-Weinberg equilibrium (P > 0.05). Observed heterozygosity and expected heterozygosity ranged from 0.54 (B15S6253) to 0.92 (B17S4998) and from 0.599 (B15S6253) to 0.968 (B17S4998), respectively, and two measures of heterozygosity at each locus were highly correlated. Polymorphism information content (PIC) for these 4 loci ranged from 0.551 (B15S6253) to 0.932 (B17S4998), which means that all these loci are highly informative (PIC > 0.5). Other genetic parameters, power of discrimination (PD) and probability of exclusion (PE) ranged from 0.783 (B15S6253) to 0.984 (B17S4998) and from 0.210 (B15S6253) to 0.782 (B17S4998), respectively. Their combined PD and PE values were 0.9999968 and 0.98005176, respectively. Capillary electrophoresis revealed that average peak height ratio for a stutter was 13.89% at B17S0808, 26.67% at B15S6253, 9.09% at B8S7996, and 43.75% at B17S4998. Although the degree of genetic variability of the locus B15S6253 was relatively low among these four microsatellite markers, their favorable parameters and low peak height ratios for stutters indicate that these four new tri-nucleotide microsatellite loci could be useful multiplex PCR markers for the forensic and population genetic studies in cattle including Korean native breed.

• International Journal of Oral Biology
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• v.36 no.2
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• pp.59-64
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• 2011

Anthocyanins are naturally occuring phytochemicals and the main components of the coloring of plants, flowers and fruits. They are known to elicit antioxidative, anti-inflammatory and cancer preventive activity. In this study, we investigated anthocyanins in black / yellow soybean seedcoats using different methods of detection - thin layer chromatography (TLC), capillary zone electrophoresis (CZE) and HPLC analysis. The anthocyanins in soybean seedcoats were extracted by five independent methods of extraction and the aglycons (anthocyanidins) of the corresponding anthocyanins were prepared by acid mediated hydrolysis. The anthocyanin / anthocyanidin in black soybean seedcoat showed characteristic TLC mobility, CZE electrophoretic retention and HPLC migration time while little of anthocyanins were detected from yellow soybean seedcoat. The extracted anthocyanins showed pH dependent retention time in CZE and spectral change in UV-Vis spectrum. HPLC analysis of the hydrolyzed extract of black soybean seedcoat identified the presence of four anthocyanidins. The major anthocyanin in black soybean seedcoat was cyanin (cyanidin-3-O-glucoside), with the relative order of anthocyanidin in cyanidin > delphinidin > petunidin > pelargonidin.