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Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

  • Lee, Yu-No;Bang, Woo-Young;Kim, Song-Mi;Lazar, Prettina;Bahk, Jeong-Dong;Lee, Keun-Woo
    • Interdisciplinary Bio Central
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    • v.1 no.1
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    • pp.3.1-3.6
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    • 2009
  • Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

Frequency and clinical characteristics of prenatally diagnosed congenital hydronephrosis and outcomes of ureteropelvic junction stenosis (산전 진단된 선천성 수신증의 빈도 및 임상적 특성과 신우요관 이행부 협착의 경과)

  • Kang, Hyun Soo;Sung, June Seung;Kim, Sun Hui;Back, Hee Jo;Kim, Young Ok;Kim, Chan Jong;Choi, Young Youn;Hwang, Tai Ju
    • Clinical and Experimental Pediatrics
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    • v.49 no.8
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    • pp.870-874
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    • 2006
  • Purpose : Popular use of fetal ultrasonography has increased to detect congenital hydronephrosis(CH) which is the most common anomaly prenatally detected. We'd like to determine the frequency and clinical characteristics of prenatally diagnosed CH and outcome of ureteropelvic junction stenosis(UPJS). Methods : The records of births between January 1994 and June 2003 in Chonnam National University Hospital(CNUH), and the records of children who were diagnosed with CH in the Department of Pediatrics of CNUH during the above period, were retrospectively analyzed. In the patients with UPJS, the initial anterior posterior diameters of renal pelvis(APD) were compared between the spontaneous regression (SR) and operation group(OP). In the SR group, sequential regression rates of APD were estimated. Results : Among a total 9,076 births, 231(2.54 percent) patients with 293 renal units were diagnosed as CH and 19(6.78 percent) renal units spontaneously regressed 3 days after birth. In 228 children(56 bilateral; 172 unilateral; total 284 renal units) diagnosed with CH in the department of pediatrics of CNUH, male(71.9 percent) and left kidney(69.2 percent) predilection were found and 78.1 percent of CH were caused by UPJS. The initial APD of the SR group(121 units) in UPJS was $7.8{\pm}6.28mm$, which was significantly smaller than the APD($26.8{\pm}12.14mm$) of the OP group(25 unit)(P<0.05). In the SR group, 81 percent spontaneously regressed within one year. Conclusions : In CH, male and left kidney predilection were found. UPJS was the most common cause of CH and initial APD in UPJS at 3 days of age was a good prognostic indicator. Close monitoring should be done for at least one year because most SR in UPJS regressed spontaneously within one year.

Evaluation of short-term cardiac function by tissue Doppler imaging in pre and postoperative period of congenital heart disease (조직 도플러 영상을 이용한 선천성 심장병 수술 전후의 단기 심기능 평가)

  • Lee, Jun-Hwa;Kim, Yeo-Hyang;Hyun, Myung-Chul;Lee, Sang-Bum
    • Clinical and Experimental Pediatrics
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    • v.50 no.5
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    • pp.476-483
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    • 2007
  • Purpose : The objective of this study was to assess ventricular function by tissue Doppler imaging (TDI) in children with congenital heart disease (CHD) who have been undergoing open heart surgery (OHS) using cardiopulmonary bypass. We tried to compare the parameters of tissue Doppler imaging before and after OHS in patients with congenital heart disease. Methods : This study was conducted on 32 patients with CHD after OHS from January 2005 to December 2005 at Kyungpook National University hospital. Patients who underwent 2-D echocardiography before and after their OHS. All patients were divided into three groups, left ventricular volume overloading group (group 1), and right ventricular volume overloading group (group 2), and right ventricular pressure overloading group (group 3). The TDIs were examined before and 1 to 3 months after OHS. Peak early diastolic (E), and peak late diastolic (A) velocity of transmitral flow were measured by pulsed wave Doppler examination. Peak systolic (Sm), peak early diastolic (Em), and peak late diastolic (Am) velocity in apical 4-chamber and 2-chamber views were measured by TDI. The author calculated E/Em ratio. Results : The patients were 14 boys and 18 girls and the average age of patients was 2 years and 3 months. The congenital heart diseases which have to get OHS were ventricular septal defect (13 cases), atrial septal defect (7), atrioventricular septal defect (3), isolated pulmonary stenosis (2) and tetralogy of Fallot (7). There were significant decrease of Sm, Em, Am measured on tricuspid annulus and E/Em measured on mitral annulus in apical 4 chamber view (P<0.05). Conclusion : This study showed significant decrease of Sm, Em, Am measured on tricuspid annulus and E/Em measured on mitral annulus in apical 4 chamber view after OHS. These changes might be due to the effects of cardiopulmonary bypass in OHS and/or hemodynamic changes after correction of congenital heart disease. To clarify these changes, further study on more patients is needed.

Transgenic tobacco culture cells expressing spike protein gene of porcine epidemic diarrhea virus (돼지 유행성 설사병 바이러스 스파크 단백질 유전자 발현 형질전환 담배 배양세포)

  • Yang, Kyoung-Sil;Kim, Hyeon-Soo;Kwon, Suk-Yoon;Kwak, Sang-Soo;Lee, Haeng-Soon
    • Journal of Plant Biotechnology
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    • v.35 no.1
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    • pp.87-94
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    • 2008
  • Porcine epidemic diarrhea virus (PEDV) is an infectious and highly contagious virus of swine. In order to develop the transgenic tobacco culture cells producing PEDV antigen protein, four vectors expressing PEDV spike protein (SP) gene under the control of a CaMV 35S promoter were constructed. Four fragments of the SP region of PEDV, SP1 (444 bp, 1487-1930 bp), SP2 (1.7 kb, 2300-3987 bp), SP3 (1.4 kb, 1559-2950 bp), and SP4 (2.6 kb, 9-2643 bp) were amplified by PCR and then C-MYC tag was fused to the end of each SP gene, respectively. These cassettes are inserted into the pCAMBIA2300 (named as 35S::SP1-M, 35S::SP2-M 35S::SP3-M, and 35S::SP4-M, respectively). Tobacco (cv. BY-2) cultured cells were transformed by co-cultivation with Agrobacterium tumefaciens harboring expression vector. We selected kanamycin-resistant calli and checked for the presence of the introduced SP gene using PCR, resulting 70% of them showed the foreign gene. We selected the lines with high-level expression of PEDV antigen protein based on dot blot analysis. Southern blot analysis confirmed that the PEDV SP gene was integrated into the genome of the tobacco cultured cells. Northern blot analysis showed that the introduced gene was highly expressed in transgenic cultured cells. Transgenic tobacco cultured cells-derived antigen induced immunogenicity in mice as determined by a plaque reduction neutralization assay. These results suggest that the vectors expressing PEDV spike protein gene in this study will be useful for the development of transgenic plants and cultured cells producing PEDV antigene protein.

Development of Korean Green Business/IT Strategies Based on Priority Analysis (한국의 그린 비즈니스/IT 실태분석을 통한 추진전략 우선순위 도출에 관한 연구)

  • Kim, Jae-Kyeong;Choi, Ju-Choel;Choi, Il-Young
    • Asia pacific journal of information systems
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    • v.20 no.3
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    • pp.191-204
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    • 2010
  • Recently, the CO2 emission and energy consumption have become critical global issues to decide the future of nations. Especially, the spread of IT products and the increased use of internet and web applications result in the energy consumption and CO2 emission of IT industry though information technologies drive global economic growth. EU, the United States, Japan and other developed countries are using IT related environmental regulations such as WEEE(Waste Electrical and Electronic Equipment), RoHS(Restriction of the use of Certain Hazardous Substance), REACH(Registration, Evaluation, Authorization and Restriction of CHemicals) and EuP(Energy using Product), and have established systematic green business/IT strategies to enhance the competitiveness of IT industry. For example, the Japan government proposed the "Green IT initiative" for being compatible with economic growth and environmental protection. Not only energy saving technologies but energy saving systems have been developed for accomplishing sustainable development. Korea's CO2 emission and energy consumption continuously have grown at comparatively high rates. They are related to its industrial structure depending on high energy-consuming industries such as iron and steel Industry, automotive industry, shipbuilding industry, semiconductor industry, and so on. In particular, export proportion of IT manufacturing is quite high in Korea. For example, the global market share of the semiconductor such as DRAM was about 80% in 2008. Accordingly, Korea needs to establish a systematic strategy to respond to the global environmental regulations and to maintain competitiveness in the IT industry. However, green competitiveness of Korea ranked 11th among 15 major countries and R&D budget for green technology is not large enough to develop energy-saving technologies for infrastructure and value chain of low-carbon society though that grows at high rates. Moreover, there are no concrete action plans in Korea. This research aims to deduce the priorities of the Korean green business/IT strategies to use multi attribute weighted average method. We selected a panel of 19 experts who work at the green business related firms such as HP, IBM, Fujitsu and so on, and selected six assessment indices such as the urgency of the technology development, the technology gap between Korea and the developed countries, the effect of import substitution, the spillover effect of technology, the market growth, and the export potential of the package or stand-alone products by existing literature review. We submitted questionnaires at approximately weekly intervals to them for priorities of the green business/IT strategies. The strategies broadly classify as follows. The first strategy which consists of the green business/IT policy and standardization, process and performance management and IT industry and legislative alignment relates to government's role in the green economy. The second strategy relates to IT to support environment sustainability such as the travel and ways of working management, printer output and recycling, intelligent building, printer rationalization and collaboration and connectivity. The last strategy relates to green IT systems, services and usage such as the data center consolidation and energy management, hardware recycle decommission, server and storage virtualization, device power management, and service supplier management. All the questionnaires were assessed via a five-point Likert scale ranging from "very little" to "very large." Our findings show that the IT to support environment sustainability is prior to the other strategies. In detail, the green business /IT policy and standardization is the most important in the government's role. The strategies of intelligent building and the travel and ways of working management are prior to the others for supporting environment sustainability. Finally, the strategies for the data center consolidation and energy management and server and storage virtualization have the huge influence for green IT systems, services and usage This research results the following implications. The amount of energy consumption and CO2 emissions of IT equipment including electrical business equipment will need to be clearly indicated in order to manage the effect of green business/IT strategy. And it is necessary to develop tools that measure the performance of green business/IT by each step. Additionally, intelligent building could grow up in energy-saving, growth of low carbon and related industries together. It is necessary to expand the affect of virtualization though adjusting and controlling the relationship between the management teams.

Effects of Temperature and Fluctuation Range on Microbial Growth and Quality of Foods Stored in Domestic Refrigerator (냉장실의 온도 정온화가 냉장 식품의 품질과 미생물의 생육에 미치는 영향)

  • Jung, Dong-Sun;Kweon, Mee-Ra;Auh, Joong-Hyuck;Cho, Kwang-Yeun;Choi, Young-Hoon;Kook, Seung-Uk;Park, Kwan-Hwa
    • Korean Journal of Food Science and Technology
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    • v.28 no.4
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    • pp.632-637
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    • 1996
  • Effects of refrigeration temperature and its fluctuation range on the growth of psychrotrophic microorganisms and the quality of refrigerated foods such as apple, fish and oyster were evaluated to find optimum storage conditions for a domestic refrigerator. Refrigeration temperature was $2^{\circ}C$ or $4^{\circ}C$, and fluctuation ranges were varied: ${\pm}0.3,\;{\pm}1.0,\;{\pm}1.2,\;or\;{\pm}4.0^{\circ}C$. Changes in hardness of apples stored at $2{\pm}0.3^{\circ}C$ were much slower than those of apples stored at $4{\pm}1.2^{\circ}C$. Freshness of fish and oyster also lasted much longer at low temperature such as $2{\pm}0.3^{\circ}C$. The growth of Listeria monocytogenes inoculated on sliced ham was inhibited for 1 month at $2{\pm}0.3^{\circ}C$, but the cells at $4{\pm}1.2^{\circ}C$ began to grows as time elapsed. Therefore, it was expected that shelf-life of certain food stored in a domestic refrigerator could be extended by lowering temperature to $2^{\circ}C$ and by reducing fluctuation range of refrigerator.

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An International Collaborative Program To Discover New Drugs from Tropical Biodiversity of Vietnam and Laos

  • Soejarto, Djaja D.;Pezzuto, John M.;Fong, Harry H.S.;Tan, Ghee Teng;Zhang, Hong Jie;Tamez, Pamela;Aydogmus, Zeynep;Chien, Nguyen Quyet;Franzblau, Scott G.;Gyllenhaal, Charlotte;Regalado, Jacinto C.;Hung, Nguyen Van;Hoang, Vu Dinh;Hiep, Nguyen Tien;Xuan, Le Thi;Hai, Nong Van;Cuong, Nguyen Manh;Bich, Truong Quang;Loc, Phan Ke;Vu, Bui Minh;Southavong, Boun Hoong
    • Natural Product Sciences
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    • v.8 no.1
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    • pp.1-15
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    • 2002
  • An International Cooperative Biodiversity Group (ICBG) program based at the University of Illinois at Chicago initiated its activities in 1998, with the following specific objectives: (a) inventory and conservation of of plants of Cuc Phuong National Park in Vietnam and of medicinal plants of Laos; (b) drug discovery (and development) based on plants of Vietnam and Laos; and (c) economic development of communities participating in the ICBG project both in Vietnam and Laos. Member-institutions and an industrial partner of this ICBG are bound by a Memorandum of Agreement that recognizes property and intellectual property rights, prior informed consent for access to genetic resources and to indigenous knowledge, the sharing of benefits that may arise from the drug discovery effort, and the provision of short-term and long-term benefits to host country institutions and communities. The drug discovery effort is targeted to the search for agents for therapies against malaria (antimalarial assay of plant extracts, using Plasmodium falciparum clones), AIDS (anti-HIV-l activity using HOG.R5 reporter cell line (through transactivation of the green fluorescent protein/GFP gene), cancer (screening of plant extracts in 6 human tumor cell lines - KB, Col-2, LU-l, LNCaP, HUVEC, hTert-RPEl), tuberculosis (screening of extracts in the microplate Alamar Blue assay against Mycobacterium tuberculosis $H_{37}Ra\;and\;H_{37}Rv),$ all performed at UIC, and CNS-related diseases (with special focus on Alzheimer's disease, pain and rheumatoid arthritis, and asthma), peformed at Glaxo Smith Kline (UK). Source plants were selected based on two approaches: biodiversity-based (plants of Cuc Phuong National Park) and ethnobotany-based (medicinal plants of Cuc Phuong National Park in Vietnam and medicinal plants of Laos). At mc, as of July, 2001, active leads had been identified in the anti-HIV, anticancer, antimalarial, and anti- TB assay, after the screening of more than 800 extracts. At least 25 biologically active compounds have been isolated, 13 of which are new with anti-HIV activity, and 3 also new with antimalarial activity. At GSK of 21 plant samples with a history of use to treat CNS-related diseases tested to date, a number showed activity against one or more of the CNS assay targets used, but no new compounds have been isolated. The results of the drug discovery effort to date indicate that tropical plant diversity of Vietnam and Laos unquestionably harbors biologically active chemical entities, which, through further research, may eventually yield candidates for drug development. Although the substantial monetary benefit of the drug discovery process (royalties) is a long way off, the UIC ICBG program provides direct and real-term benefits to host country institutions and communities.

Studies on Diplosis mori Yokopama (mulberry shoot Gall midge) on mulberry tree (뽕나무 순집이 혹파리에 관한 연구)

  • 전대략;이영렬;조철호
    • Journal of Sericultural and Entomological Science
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    • v.2
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    • pp.49-61
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    • 1962
  • The insect Diplosis mori Yokoyama is causing extensive destruction of mulberry trees in Korea with a resultant loss in silk production. This study was made to determine an effective method of control. Methods and Materials Used Preliminary studies were made to determine more exactly the life cycle of the insect. Based on this information, various control measures were tested, including the use of spray methods with BHC and control of larvae by tilling. Results Obtained 1. Life cycle studies (a) In the Suwon area, this-insect has 5 generations per year. The first starts in the later part of June and the final cycle ends in the later part of September. (b) The adult insects appear about 7: 00-8: 00 P.M. and live for 2-5 days. Females live in longer periods than the male. (c) Larvae lives inside the second and third stipules (A. B.) before mulberry leaf development. They cause extensive damage to the leaves at the point where they are attached to the stem. (d) Weather conditions considerably affect the life cycle. The pupa particularly are affected and not be able to change into the moth stage when there is a long period of no rain. (e) Larvae are large......0.3 to 2.0mm......and are milky-white immediately after hatching but turn to pinkish as the worm matures. The matured worm has a jumping ability up to 15-20cm. The worm burrows into the ground 1.5 to 3.0 cm before changing into the pupal stage. (f) The pupal stage usually lasts 7-8 days, in summer weather conditions and the pupa is surrounded with a coarse cocoon. (g) These insects, as a general rule, overwinter as pupae but sometimes as larvae. 2. Control measures (a) BHC dust applied on the ground seem most effective. It should be done 4-5 days after the worm has burrowed into the ground. For this control, it is recommended that 6kg of a 2% formation Tanbo(l0ares) be used. (b) For the effective spraying against the fly, it is recommended that a formulation of liquid BHC spray terials be used at the rate of 400-600 liters per Tanbo. (c) Tillage methods which provide a cover of soil 5cm or more in depth above infested areas will effect-maively prevent the emergence of the fly from the pupal stage. 3. Conclusions Methods of control against Diplosis mori Yokoyama can be tied more closely to the life cycle of the insect with more effective results. Further studies are needed to complete information on possible controls during or after hibernation. Economic studies on the cost of these control measures are also needed.

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The Effect of Knowledge about Foods on the Foods Purchasing (식품에 대한 지식이 식품선택에 미치는 영향에 관한 조사연구)

  • 박윤정;조신호;이효지
    • Korean journal of food and cookery science
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    • v.5 no.2
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    • pp.63-73
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    • 1989
  • Family meals are very important for physical and mental health of family mebers. The purpose of this study is to contribute to change the habitual and unconscious cooking methods of housewives into more scientific moth(Ids. In order to achieve this purpose, this study tried to find out the degree to which housewives applied their knowledge of nutition and foods to actual behavior in purchasing. A special form of questionaire was prepared and distributed to 502 housewives in Seoul from Feb.8th to 22nd in 1989. The results were as follows: 1. Mean (score) of their nutritional knowledge was 14 7; if seems to be comparatively higher. 2. When they purchased food materials, their husbands' favor was the first consideration. Particularly, freshness was the first considered in purchasing meat, fishes, fruits, and vegetables. And Nutrition was so in case of seaweeds, oil, and fat. 3. For the most part, they cook three or four Subsidiary dishes for a meal. If they cooked one or two they chose to cook vegetables. If three or four they added meat and fishes. If more than four, they used various food materials.

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Quality Factors of Freshness and Palatability of Hanwoo from their Physicochemical and Sensorial Properties (한우의 이화학적, 관능적 특성을 통한 신선도와 맛의 품질 인자 설정)

  • Moon, Ji-Hye;Sung, Misun;Kim, Jong-Hun;Kim, Byeong Sam;Kim, Yoonsook
    • Food Science of Animal Resources
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    • v.33 no.6
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    • pp.796-805
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    • 2013
  • This study was conducted to investigate the relationship between quality factors and freshness or palatability of Hanwoo beef according to storage condition. The drip loss, cooking loss, volatile basic nitrogen (VBN), thiobarbituric acid reactive substance (TBARS), total viable counts (TVC) and sensorial characteristics of Hanwoo beef (raw and cooked) were investigated during storage for 36 d at 0 and $10^{\circ}C$. The drip loss, cooking loss, VBN, and TBARS were increased during storage period. The correlation between these factors and freshness was shown to be highly significant at both $10^{\circ}C$ than $0^{\circ}C$. Especially, correlation of between the cooking loss and freshness of Hanwoo beef showed high significance (p<0.01) at higher storage temperature. The correlation coefficient between factors such as VBN, cooking loss, and TVC and palatability were decreased with increased storage temperature. As a statistical analysis result, a multiple regression equation of $Y_1=10.768-0.706X_1$ (Drip loss) with $R^2=0.87$ was obtained for freshness evaluation of Hanwoo beef. Also, multiple regression with drip loss ($X_1$) and TVC ($X_5$) increased the coefficient of determination for sensorial palatability ($Y_2$) to $R^2=0.95$ with a regression equation of $Y_2=9.702-0.438X_1(Drip\;loss)-0.232X_5(TVC)$.