• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.259-261
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• 2004

생물학 분야의 문헌으로부터 유전자 및 단백질 이름을 추출하는 기술은 바이오 텍스트 마이닝 분야의 기반 기술로 그 중요성이 점차 증대되고 있다. 이 연구에서는 생물학 분야 문헌의 초록으로부터 하나의 토큰으로 구성된 single gene name은 물론 여러 개의 토큰으로 이루어진 multi gene name까지 유전자나 단백질의 이름을 자동으로 추출하는 시스템 TagGeN(Tagger for Gene Name)을 제안한다. TagGeN은 기존의 태거와 달리, 문자나 숫자 이외의 기호를 포함한 유전자나 단백질 이름의 품사 처리에 있어 개선 방안을 제시하고, 여러 토큰으로 이루어진 이름의 인식에 있어 나란한 두 토큰이 갖는 태그 정보를 이용한 조건부 확률에 근거하여 Markov 모델을 도입한다. 위와 같은 개선방안을 구현한 TagGeN은 성능면에서 기존의 유사시스템에 비해 recall 20.8%, precision 4.7%의 성능향상을 보임으로써 본 연구에서 제안한 방법론의 효과를 입증한다.

• Korean Journal of Clinical Laboratory Science
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• v.51 no.1
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• pp.78-85
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• 2019

Membrane proteins are involved in many common diseases, including heart disease and cancer. In various disease states, such as cancer, abnormal signaling pathways that are related to the membrane proteins cause the cells to divide out of control and the expression of membrane proteins can be altered. Membrane proteins have the hydrophobic environment of a lipid bilayer, which makes an analysis of the membrane proteins notoriously difficult. Therefore, this study evaluated the efficacy of two different methods for optimal membrane protein extraction. High-speed centrifuge and reagent-based method with a -/+ filter aided sample preparation (FASP) were compared. As a result, the high-speed centrifuge method is quite effective in analyzing the mitochondrial inner membranes, while the reagent-based method is useful for endoplasmic reticulum membrane analysis. In addition, the function of the membrane proteins extracted from the two methods were analyzed using GeneGo software. GO processes showed that the endoplasmic reticulum-related responses had higher significance in the reagent-based method. An analysis of the process networks showed that one cluster in the high-speed centrifuge method and four clusters in the reagent-based method were visualized. In conclusion, the two methods are useful for the analysis of different subcellular membrane proteins, and are expected to assist in selecting the membrane protein extraction method by considering the target subcellular membrane proteins for study.

• The Korean Journal of Community Living Science
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• v.16 no.4
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• pp.39-45
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• 2005

The aim of this study is to investigate the effects of hot water soluble extract from green tea on the components of serum and the liver and the antioxidative effects in accordance with the different protein types. For this purpose, four experimental groups were set up. As for the protein source casein, isolated soy protein was supplemented to the rats, together with hot water soluble extract from green tea. Four experimental groups kept eight Sprague-Dawley rats respectively. The CP group was supplemented with casein only, the CG group was supplemented with casein and hot water soluble extract from green tea, the ISP group was supplemented with isolated soy protein only, and the ISG group was supplemented with the isolated soy protein with hot water soluble extract from green tea. After 4 weeks of feeding with experimental diet, the levels of serum and liver lipid and antioxidant enzyme activity and TBARS in the liver were measured. The results are; 1. Weight gain and FER were higher in the casein group than in the isolated soy protein group in general. In the casein group, the weight gain and FER were reduced significantly when hot water soluble extract from green tea was supplemented (P < 0.05). There was no significant difference in feed intake. 2. In general, total cholesterol and LDL-cholesterol in the serum were higher in the casein group than in the isolated soy protein group, however just the concentration of LDL-cholesterol in the casein group was significantly lower when the hot water soluble extract from green tea was supplemented (P < 0.05). 3. Triglycerides in the liver were higher in the casein group than in the isolated soy protein group general, however when hot water soluble extract from green teas was supplemented only in the isolated soy protein group, the content of triglyceride in liver was significantly lower (P < 0.05). 4. There was no significant difference in antioxidant enzyme activity in the liver in all the groups, however the content of TBARS was low only in the casein group when hot water soluble extract from green tea was supplemented (P < 0.05).

• Korean Journal of Fisheries and Aquatic Sciences
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• v.32 no.2
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• pp.211-216
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• 1999

Protein nutritional quality of fish extracts processed at $110^{\circ}C$ for 5 hours with spicy vegetables (garlic, onion and ginger) were evaluated using in vitro and in vivo (rat assay) parameters, Protein and total lipid contents were closely related to the degree of discarding floated lipid on fish extracts and the kinds of added spicy vegetables. Hydrocooking ($110^{\circ}C$, 5 hours) tended to result in better protein qualities than high temperature cooking ($136\~140^{\circ}C$). Spicy vegetables had not remarkable effects on improving in vitro protein quality parameters. The fish extract with $10\%$ of ginger was generally higher in vitro protein digestibility than those of the other vegetables. In spite of generally higher in vivo protein digestibility of fish extracts containing spicy vegetables processed at mild condition ($110^{\circ}C$), Protein efficiency ratios (PER) of-these extracts were not higher than those of extracts processed at severe conditions ($136\~140^{\circ}C$).

• Journal of the Korean Society of Food Science and Nutrition
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• v.37 no.1
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• pp.8-15
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• 2008

Saussurea lappa (SL) has been used to reduce abdominal pain and tenesmus in traditional oriental medicine. SL and major compounds of SL, sesquiterpene lactones, have been suggested to possess various biological effects, including anti-tumor, anti-ulcer, anti-inflammatory, anti-viral and cardiotonic activities. Recently, it has been reported that ethanol extracts from roots of SL have antiproliferative effects on gastric cancer cells. To explore the possibility that SL has chemopreventive effects on prostate cancer, we examined whether the hexane extract of SL (HESL) inhibits the growth of LNCaP human prostate cancer cells. Cells were incubated with various concentrations ($0{\sim}4$ mg/L) of HESL in DMEM/F12 containing 5% charcoal stripped fetal bovine serum. HESL substantially decreased viable cell numbers and induced apoptosis of LNCaP cells in dose-dependent manners. HESL increased the levels of cleaved caspase-8, -9, -7 and -3, and poly (ADP-ribose) polymerase. HESL increased the levels of the pro-apoptotic Bak and truncated-Bid proteins whereas it had no effect on the anti-apoptotic Bcl-2, Bcl-xL, or Mcl-1. The present results indicate that HESL inhibits the growth of human prostate cancer cells by inducing apoptosis, which involves the activation of the caspase cascades.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.10 no.3
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• pp.151-162
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• 1977

Distribution of marine algae is diverse in Korea and the resource of edible algae is abundant marking 239,037 tons of yearly production in 1976. They have been known as a protein source and used as a supplement in Korean diet. It is necessary to estimate the potentiality and properties of usable algal proteins especially as food resources and studies of extraction and separation of the proteins, therefore, are basically required for this purpose. In this study, the influence of various factors including the sample treatment, extraction time and temperature, sample us extraction solvent ratio and pH upon the extractability of the water soluble protein was determined. And the effect of precipitation treatment for isolation of the algal protein from the extracts was also tested. Nine species of algae, the major ones in consumption as food namely Porphyra suborbiculata, Undaria pinnatifida, Hizikia fusiforme, Sargassum fulvellu, Enteromorpha linza, Codium fragile, Sargassum kjellmanianum and Ulva pertusa were collected as fresh from Kijang, Yangsan Gun, in the vicinity of Busan city. The content of crude protein $(N\times6.25)$ of the algae ranged from $9.46\%\;to\;24.14\% showing the highest value in Porphyra suborbiculata and the minimum in Hizikia fusiforme. In the effort of maceration of blending methods on the extractability, immersion freezing in dry ice-methanol solution appeared most effective yielding 1.5 to 2.5 times extractability than that of the mortar grinding method. The effect of the ratio of sample vs solvent on extractability differed from species. It was enhanced at the ratio of 1:20 (w/v) in Ulva pertusa and Enteromorpha linza while the ratio was 1:30 (w/v) for Cedium fragile, Undaria pinnatifida, Hizikia fusiferme, Sargassum fulvellum and Porphyra suborbiculata and 1:40 for Sargassum kjellmanianum respectively. The effect of extraction time and temperature was revealed differently from species which might be caused by differences in the constitution of algal tissues resulting in that the extraction for 1 hour at $50^{\circ}C$ gave the maximum extractabilily in Ulva pertusa and Enteromorpha linza, 2 hours in Porphyra suborbiculata, Hikikia fusiforme, Undaria pinnatifida, Sargassum kjellmanianum and 3 hours in Codium fragile. And the extractability was higher at $50^{\circ}C$ to $60^{\circ}C$ for the most of the tested samples except Hizikia fusiforme. The optimum pH for the extraction was 9 to 12. The recovery of extractable nitrogen to the total nitrogen was $63\%$ in average with the first extracts and $8.6\%$ with the second extracts respectively. Both extracts were prepared by 2 hour extraction at $50{\pm}1^{\circ}C$ with dry ice-methanol frozen and seasand macerated materials. And these conditions assumed to be an optimum for the extraction of water soluble algal proteins since the nitrogen content after the first extraction covered $90\%$ of the total water extractable nitrogen. In the precipitation of the extracted proteins, Barnstein method and methanol treatment seemed to be more efficient than other precipitation methods.

• Korean Journal of Food Science and Technology
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• v.21 no.4
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• pp.542-548
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• 1989

For the selective separation of proteins, the solubilization and desolubilization of proteins in sodium-di-2-ethylhexyl sulfosuccinate (AOT)-isooctane reverse micellar system were investigated. Protein solubilization increased with increasing the concentration of AOT to 200 mM and then decreased above that concentration. Protein was solubilized into reverse micelles in the pH range below the isoelectric Point of each protein, pH 4-10 for lysozyme and pH 5-6 for trypsin and ${\alpha}-chymotrypsin$, Lysozyme, trypsin and ${\alpha}-chymotrypsin$ were efficiently extracted in the precence of KCl and NaCl while larger molecular weight proteins such as pepsin and BSA had high solubilization with $CaCl_2$. At higher ionic strength all proteins exhibited murk less tendency to solubilize and the increase of ionic strength resulted in the decrease of micelle size. Lysozyme was successfully back transfered at pH 12.2 and 1.0M KCl; trypsin at pH 12.6 and 0.5M KCl; and ${\alpha}-chymotrypsin$ at pH 6.7 and 0.5M KCl. In a test group separation experiments, complete separation of lysozyme from BSA could be obtained.

• Korean Journal of Food Science and Technology
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• v.15 no.2
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• pp.141-149
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• 1983

The purpose of the present work is to find out the optimal conditions for the production of filefish protein preparations and to define the functional properties of the protein products. Fish protein concentrate (FPC) and fish protein isolate (FPI) were prepared by extraction of whole or headed and gutted filefish with various organic solvents. The results of the present study are as follows; 1. Among the solvents tested iso-propyl alcohol appeared to be the most effective for the extraction of lipid and also for that trimethylamine from the fish muscle. 2. The optimal extraction time showed to be 20 minutes with ethyl iso-propyl alcohol at $65-70^{\circ}C$under adequate mixing. 3. The most effective solvent ratio to the weight of fish material was proved to be 5:1 at the first extraction and to be 2:1 at the second stage. 4. The lipid content of the protein preparations reduced to below 0.5% by the third stage of extraction of headed or gutted filefish. The protein concentrate from whole fish, however, showed the lipid content of 0.27-0.31% only after the fifth stage of extration. 5. The protein contents of the protein concentrate and the protein isolate from whole filefish were 81.08% and 87.41% and the lipid contents of the two protein preparations were 0.43% and 0.45% respectively. 6. Higher calcium content was found in the protein concentrate rather than in the protein isolate. No sodium and potassium in the protein isolate were detected while the fish concentrate appeared to contain a considerable amounts of both elements. 7. The functional properties, such as suspended solids, wetability, emulsion stability and foam viscosity of the filefish protein isolates were proved to be higher than those of the protein concentrate.

• Proceedings of the KAIS Fall Conference
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• 2010.05b
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• pp.1197-1200
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• 2010

Post-genomic 시대에 접어들면서 단백질의 기능의 주석이 중요한 문제로 떠오르기 시작하였다. 이런 단백질 기능을 예측하기 위해 단백질 상호작용(Protein-Protein interaction) 데이터를 이용한 방법들이 지난 10여 년간 발표되어왔다. 단백질 상호작용(Protein-Protein interaction) 데이터는 단백질들 간의 서열 등의 특징을 이용해 상호간의 연결 관련성이 있는 단백질끼리의 관계를 네트워크로 나타낸 자료이다. 현재 이러한 단백질 상호작용(Protein-Protein interaction) 데이터들은 MIPS, DIP, BioGrid등 약 5~6군데에서 제공되고 있다. 각각의 데이터는 다른 형식을 가지고 있고, 중복되는 정보도 포함하고 있다. 여러 연구 방법에서 데이터를 사용할 때 한군데에서만 추출하기 보다는 여러 데이터에서 추출하는 경우가 많기 때문에 다른 형식의 데이터를 이용하는데 불필요한 수고가 들어가게 된다. 때문에 여러군데의 데이터를 한 가지 형식으로 맞추어 통합적으로 구축하여 연구 시 데이터 사용에 용이하도록 설계 하였다. 또한 발표된 단백질 기능 예측 방법에 대한 정리를 통해 앞으로의 연구를 하는데 있어서 필요한 자료를 얻고 열람할 수 있도록 설계하였다. 이를 통해 관련 연구를 하거나 관심이 있는 사람들의 데이터를 검색하는데 많은 도움이 될 것이다.

• Applied Biological Chemistry
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• v.29 no.1
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• pp.51-56
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• 1986

Using milled barley of four varieties Olbori, Youngsan-bori, Sacheon 6, and Suwon 228, the barley proteins were fractionated by the Osborne method and the modified Osborne method. Two fractionation methods were compared. There was a steady increase in the amount of nitrogen extracted as NaCl concentration increased, reaching a maximum at 0.5M NaCl and the extraction of nitrogen by 0.5M NaCl reached a maximum at $22^{\circ}C$. Alcohol-soluble fraction was least extracted by 70% (v/v) ethanol at $4^{\circ}C$ and most by sequential extraction with 50% (v/v) propan-1-ol alone followed by 50% (v/v) propan-1-ol plus 3% (v/v) 2-mercaptoethanol. Nitrogen was least extracted between pH 4 and 6 and most extracted at higher pH than 10. The modified Osborne fractionation of the protein complex in the four barleys showed that the salt-soluble nitrogen accounted for 21,4% to 24.1%, hordein-I varied from 30.4% to 43.4%, hordein-II varied widely from 9.3% to 19.5% and borate buffer-soluble glutelin content ranged from 17.1% to 23.7%.