• Mass Spectrometry Letters
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• v.9 no.2
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• pp.51-55
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• 2018

Capture of non-glycoproteins during lectin affinity chromatography is frequently observed, although it would seem to be anomalous. In actuality, lectin affinity chromatography works at post-translational modification (PTM) sites on a glycoprotein which is not involved in protein-protein interactions (PPIs). In this study, serial affinity column set (SACS) using lectins followed by proteomics methods was used to identify PPI mechanisms of captured proteins in human plasma. MetaCore, STRING, Ingenuity Pathway Analysis (IPA), and IntAct were individually used to elucidate the interactions of the identified abundant proteins and to obtain the corresponding interaction maps. The abundant non-glycoproteins were captured with the binding to the selected glycoproteins. Therefore, depletion process in sample pretreatment for abundant protein removal should be considered with more caution because it may lose precious disease-related low abundant proteins through PPIs of the removed abundant proteins in human plasma during the depletion process in biomarker discovery. Glycoproteins bearing specific glycans are frequently associated with cancer and can be specifically isolated by lectin affinity chromatography. Therefore, SACS using Lycopersicon esculentum lectin (LEL) can also be used to study disease interactomes.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.spc1
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• pp.92-102
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• 2006

Abundant proteins often cause problems in proteome study. Glutelin family proteins (hereafter referred to glutelin) are present in rice proteome sample as over-whelming constituents with very high abundance. In order to increase the number of identified proteins in rice proteome study, we developed a newly improved method for sample preparation through the removal of glutelin. When the protein samples from rice seed were extracted by the conventional trichloroacetic acid (TCA) extraction method, glutelin accounts for about 60% of total rice seed proteins in SDS gels. Using our new water extraction method, glutelin consists of only about 10% of total proteins. After analyzing on a two-dimensional gel electrophoresis (2-DE), 937 protein spots were detected using the conventional TCA extraction method. On the other hand, 1240 proteins could be seen using the new water extraction method. The selectivity for non-glutelin and less abundant protein by the water extraction method was also confirmed by ESI-Q/TOF mass spectrometry analysis. Thus, the new water extraction method developed here can be efficiently used to study the proteome analysis of rice storage seed.

• Reproductive and Developmental Biology
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• v.37 no.4
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• pp.255-261
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• 2013

To profile the proteome in porcine plasma, blood samples were collected from adult male barrows and those plasma were retrieved. For the depletion or pre-fractionation of high-abundance proteins, plasma samples were treated with commercial kits. Then, protein profiling was initiated using one and two-dimensional electrophoresis. Proteins were spotted and then identified by MALDI-TOF-TOF and LC-MS-MS. In the results, more than forty six proteins were identified and the reference map was constructed. The pre-treatment for the removal of high-abundance proteins caused the changes in 2-DE images and some of the proteins were newly uncovered after the most of high abundant proteins were removed. However, it is expected for further steps necessary to identify more low-abundance proteins that may contain potential bio-markers.

• Journal of Microbiology and Biotechnology
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• v.18 no.8
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• pp.1459-1469
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• 2008

Using a rotating biological contactor modified with a sequencing bath reactor system (SBRBC) designed and operated to remove phosphate and nitrogen [58], the microbial community structure of the biofilm from the SBRBC system was characterized based on the extracellular polymeric substance (EPS) constituents, electron microscopy, and molecular techniques. Protein and carbohydrate were identified as the major EPS constituents at three different biofilm thicknesses, where the amount of EPS and bacterial cell number were highest in the initial thickness of 0-100${\mu}m$. However, the percent of carbohydrate in the total amount of EPS decreased by about 11.23%, whereas the percent of protein increased by about 11.15% as the biofilm grew. Thus, an abundant quantity of EPS and cell mass, as well as a specific quality of EPS were apparently needed to attach to the substratum in the first step of the biofilm growth. A FISH analysis revealed that the dominant phylogenetic group was $\beta$- and $\gamma$-Proteobacteria, where a significant subclass of Proteobacteria for removing phosphate and/or nitrate was found within a biofilm thickness of 0-250${\mu}m$. In addition, 16S rDNA clone libraries revealed that Klebsiella sp. and Citrobacter sp. were most dominant within the initial biofilm thickness of 0-250${\mu}m$, whereas sulfur-oxidizing bacteria, such as Beggiatoa sp. and Thiothrix sp., were detected in a biofilm thickness over 250${\mu}m$. The results of the bacterial community structure analysis using molecular techniques agreed with the results of the morphological structure based on scanning electron microscopy. Therefore, the overall results indicated that coliform bacteria participated in the nitrate and phosphorus removal when using the SBRBC system. Moreover, the structure of the biofilm was also found to be related to the EPS constituents, as well as the nitrogen and phosphate removal efficiency. Consequently, since this is the first identification of the bacterial community and structure of the biofilm from an RBC simultaneously removing nitrogen and phosphate from domestic wastewater, and it is hoped that the present results may provide a foundation for understanding nitrate and phosphate removal by an RBC system.

• Fisheries and Aquatic Sciences
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• v.19 no.3
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• pp.14.1-14.10
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• 2016

Isoelectric solubilization/precipitation (ISP) processing allows selective, pH-induced water solubility of proteins with concurrent separation of lipids and removal of materials not intended for human consumption such as bone, scales, skin, etc. Recovered proteins retain functional properties and nutritional value. Four roe protein isolates (RPIs) from yellowfin tuna roe were prepared under different solubilization and precipitation condition (pH 11/4.5, pH 11/5.5, pH 12/4.5 and pH 12/5.5). RPIs contained 2.3-5.0 % moisture, 79.1-87.8 % protein, 5.6-7. 4 % lipid and 3.0-3.8 % ash. Protein content of RPI-1 and RPI-2 precipitated at pH 4.5 and 5.5 after alkaline solubilization at pH 11, was higher than those of RPI-3 and RPI-4 after alkaline solubilization at pH 12 (P < 0.05). Lipid content (5.6-7.4 %) of RPIs was lower than that of freeze-dried concentrate (10.6 %). And leucine and lysine of RPIs were the most abundant amino acids (8.8-9.4 and 8.5-8.9 g/100 g protein, respectively). S, Na, P, K as minerals were the major elements in RPIs. SDS-PAGE of RPIs showed bands at 100, 45, 25 and 15 K. Moisture and protein contents of process water as a 2'nd byproduct were 98.9-99.0 and 1.3-1.8 %, respectively. Therefore, yellowfin tuna roe isolate could be a promising source of valuable nutrients for human food and animal feeds.

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.11-16
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• 2011

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Pinus and provided for the useful tools as a genetic resource.

• Journal of the Korean Society of Food Science and Nutrition
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• v.45 no.4
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• pp.542-550
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• 2016

This study was carried out to investigate the optimal processing conditions for odor removal and maximal antioxidant effects of oyster (Crassostrea gigas) hydrolysate. The optimal hydrolysis conditions were 3.3% neutrase as the protease, $50^{\circ}C$ as the hydrolysis temperature, and 8.3 h as the hydrolysis time. Fish odor of enzymatic oyster hydrolysate was greatly reduced during Saccharomyces cerevisiae fermentation at $24^{\circ}C$ with 0.5% glucose. The protein content of the fermentation product from oyster hydrolysate powder was 25.7%, which contained the major amino acids Glu, Asp, Lys, Arg, Gly, and Ala, whereas Leu, Ala, Phe, Val, and Tau were abundant free amino acids. The important minor minerals were Zn and Fe. Toxicity against Chang cells was not observed in the fermentation product from the oyster hydrolysate up to $200{\mu}g/mL$. The results suggest that fermentation with S. cerevisiae could reduce the fish odor of enzymatic oyster hydrolysate. The hydrolysate has potential application as a food ingredients and nutraceutical.

• 한국환경농학회:학술대회논문집
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• 2009.07a
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• pp.273-282
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• 2009

The transmissible spongiform encephalopathies (TSEs) disease group are fatal neurodegenerative disorders affecting a wide range of hosts. The group includes kuru and Creutzfeldt-Jakob disease (CJD) in humans, scrapie in sheep and goats and Bovine spongiform encephalopathy (BSE) in cattle. The exact nature of the infectious agent involved in the transmission of these diseases remains controversial. However, a central event in their pathogenesis is the accumulation in infected tissues of an abnormal form of a host-encoded protein, the prion protein (PrP). Whereas the normal cellular protein is fully sensitive to protease ($PrP^{sen}$), the disease-associated prion protein ($PrP^d$) is only partly degraded ($PrP^{res}$), its amino-terminal end being removed. BSE was first reported in the mid-80s in the UK. Ten years later, a new form of human prion disease, variant CJD (vCJD) developed in the wake of the BSE epidemic, and there is now strong scientific evidence that vCJD was initiated by the exposure of humans to BSE-infected tissues, thus indicating a zoonotic disease. However, the ban on the feeding of animal-derived proteins to ruminants, and the apparent lack of vertical transmission of BSE, have led to a decline in the incidence of the disease within cattle herd and therefore, an assumed decreased risk for human contacting vCJD. The origin of the original case(s) of BSE still remains an enigma even though three hypotheses have been raised. Hypotheses are i) sheep- or goat-derived scrapie-infected tissues included in meat and bone meal fed to cattle, ii) a previously undetected sporadic or genetic bovine TSE contaminating cattle feed or iii) originating from a human TSE through animal feed contaminated with human remains. A host cellular membrane protein ($PrP^C$), which is abundant in central nervous system tissue, appear to be conformationally altered in the diseased host into a prion protein ($PrP^{Sc}$). This $PrP^{Sc}$ is detergent insoluble and partially protease-resistant ($PrP^{res}$). The term $PrP^{res}$ is normally used to describe the protein detected after protease treatment, in techniques such as Western immunoblotting, and enzyme-linked immunosorbant assay using fresh/frozen tissue. Immunohistochemistry may performed with formalin-fixed tissues. Also, clinical signs of the BSE are one of the major diagnostic indicators. Recently, atypical forms (known as H- and L-type) of BSE have appeared in several European countries, Japan, Canada and the United States. An unusual case was also reported in a miniature zebu. The atypical BSE fall into two groups based on the relative molecular mass (Mm) of the unglycosylated $PrP^{res}$ band relative to that of classical BSE, one of the higher Mm (H-type) and the other lower (L-type). Both types have been detected worldwide as rare cases in older animals, at a low prevalence consistent with the possibility of sporadic forms of prion diseases in cattle. This raises the unwelcome possibility that vCJD could increase in the human population. Now, active surveillance program against BSE is going on in Korea. In regional veterinary service lab, ELISA is applied to screen the BSE in slaughter and confirmatory tests by Western immunoblotting and immunohistochemisty are carried out if there are positive or suspect in the screening test. Also, the ruminant feed ban is rigorously enforced. Removal of specified risk materials such as brain and spinal cord from cattle is mandatory process at slaughter to prevent the infected material from entering the human food chain.

• Horticultural Science & Technology
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• v.29 no.2
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• pp.116-122
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• 2011

In this study, we report the generation and analysis of 1,392 expressed sequence tags (ESTs) from Korean Stewartia (Stewartia koreana Nakai). A cDNA library was generated from the young leaf tissue and a total of 1,392 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. Finally, 1,301 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 100 nucleotides. A total of 893 unigene, consisting of 150 contigs and 743 singletons, was identified after assembling. Also, we identified 95 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 65% of ESTs were homologous with known function and 11.6% of ESTs were matched with putative or unknown function. The remaining 23.2% of ESTs showed no significant similarity to any protein sequences found in the public database. Annotation based searches against multiple databases including wine grape and populus sequences helped to identify putative functions of ESTs and unigenes. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Stewartia and provided for the useful tools as a genetic resource.