• Interdisciplinary Bio Central
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• v.1 no.2
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• pp.8.1-8.6
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• 2009

Introduction: It is a challenge to design a protein score function which stabilizes the native structures of many proteins simultaneously. The coarse-grained description of proteins to construct the pairwise-contact score function usually ignores the backbone directionality of protein structures. We propose a new two-body score function which stabilizes all native states of 1,006 proteins simultaneously. This two-body score function differs from the usual pairwise-contact functions in that it considers two adjacent amino acids at two ends of each peptide bond with the backbone directionality from the N-terminal to the C-terminal. The score is a corresponding propensity for a directional alignment of two adjacent amino acids with their local environments. Results and Discussion: We show that the construction of a directional adjacency-score function was achieved using 1,006 training proteins with the sequence homology less than 30%, which include all representatives of different protein classes. After parameterizing the local environments of amino acids into 9 categories depending on three secondary structures and three kinds of hydrophobicity of amino acids, the 32,400 adjacency-scores of amino acids could be determined by the perceptron learning and the protein threading. These could stabilize simultaneously all native folds of 1,006 training proteins. When these parameters are tested on the new distinct 382 proteins with the sequence homology less than 90%, 371 (97.1%) proteins could recognize their native folds. We also showed using these parameters that the retro sequence of the SH3 domain, the B domain of Staphylococcal protein A, and the B1 domain of Streptococcal protein G could not be stabilized to fold, which agrees with the experimental evidence.

• Nuclear Medicine and Molecular Imaging
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• v.41 no.3
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• pp.226-233
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• 2007

Purpose: Dual reporter gene imaging has several advantages for more sophisticated molecular imaging studies such as gene therapy monitoring. Herein, we have constructed hepatoma cell line expressing dual reporter genes of sodium iodide symporter (NIS) and enhanced green fluorescence protein (EGFP), and the functionalities of the genes were evaluated in vivo by nuclear and optical imaging. Materials and Methods: A pRetro-PN vector was constructed after separating NIS gene from pcDNA-NIS. RSV-EGFP-WPRE fragment separated from pLNRGW was cloned into pRetro-PN vector. The final vector expressing dual reporter genes was named pRetro-PNRGW. A human hepatoma (HepG2) cells were transfected by the retrovirus containing NIS and EGFP gene (HepG2-NE). Expression of NIS gene was confirmed by RT-PCR, radioiodine uptake and efflux studies. Expression of EGFP was confirmed by RT-PCR and fluorescence microscope. The HepG2 and HepG2-NE cells were implanted in shoulder and hindlimb of nude mice, then fluorescence image, gamma camera image and I-124 microPET image were undertaken. Results: The HepG2-NE cell was successfully constructed. RT-PCR showed NIS and EGFP mRNA expression. About 50% of cells showed fluorescence. The iodine uptake of NIS-expressed cells was about 9 times higher than control. In efflux study, $T_{1/2}$ of HepG2-NE cells was 9 min. HepG2-NE xenograft showed high signal-to-background fluorescent spots and higher iodine-uptake compared to those of HepG2 xenograft. Conclusion: A hepatoma cell line expressing NIS and EGFP dual reporter genes was successfully constructed and could be used as a potential either by therapeutic gene or imaging reporter gene.

• Fisheries and Aquatic Sciences
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• v.17 no.1
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• pp.47-57
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• 2014

Thai Jasmine rice (Oryza sativa, long grain Indica var.) is popular in southeastern Asia and China due to its non-glutinous, fluffy texture and fragrant smell. However it has a high starch digestibility, which leads to an increased glycemic index (GI). Therefore it may require modified cooking methods for diabetes patients. The objectives of this study were to optimize the ratio of Thai Jasmine rice, sea tangle, and olive oil (CLTR) based on consumers' acceptance. The GI of plain cooked Thai Jasmine rice (CLR) was measured as a control. Sensory evaluation and response surface methodology were used to determine the optimal ratio. Texture analysis and nutritional evaluation were also performed on the optimal recipe of cooked Jasmine rice with sea tangle. A multiple regression equation was developed in quadratic canonical polynomial models. We used 26 trained Chinese panelists in their forties to rate color, flavor, adhesiveness, and glossiness, which we determined were highly correlated with overall acceptability. The optimal CLTR formula was 34.8% rice, 2.8% sea tangle, 61.9% water, and 0.5% olive oil. Compared to CLR, CLTR had a lower hardness, but a higher springiness and cohesiveness. However, CLR and CLTR had the same adhesiveness and chewiness. The addition of sea tangle and olive oil delayed retro-gradation of starch in CLTR and increased total dietary fiber, and protein and ash contents. The degree of gelatinization, and in vitro protein and starch digestibility of CLTR were lower than those of CLR. Based on Wolver' method, the GI of CLTR (52.9, incremental area under the glycemic-response curve, ignoring the area below fasting, as used for calculating the GI [Inc]) was lower compared with that of CLR (70.94, Inc), which indicates that CLTR is effective in decreasing and stabilizing blood glucose level, owing to its lower degree of gelatinization and starch digestibility. Our results show that CLTR can contribute to the development of a healthier meal for families and the fast food industry.

• BMB Reports
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• v.39 no.6
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• pp.677-685
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• 2006

Proteins that are unfolded or misfolded in the endoplasmic reticulum (ER) must be targeted for refolding or degradation to maintain the homeostasis of the ER. Derlin-1 was reportedly implicated in the retro-translocation of misfolded proteins from the ER to the cytosol for degradation. In this report, we showed that Derlin-1 was down-regulated in the endothelial cells derived from human hepatic cavernous hemangioma (CHEC) compared with other tested cells. Electron microscopy analysis showed that ER was aberrantly enlarged in CHEC cells, but not in other tested cells. When overexpressed, Derlin-1 induced the dilated ER to return normal size. This ER dynamic was associated with the activation of unfolded protein response (UPR). In CHEC cells where Derlin-1 was down-regulated, increased expression of the immunoglobulin heavy chain-binding protein (Bip) and UPR-specific splicing of X-box DNA-binding protein 1 (XBP1) mRNA were detected, as compared with that in other tested cells, indicating that UPR was activated. After Derlin-1 overexpression, the extent of UPR activation diminished, as evidenced by decreased expression of Bip, reduced amount of the spliced form of XBP1 ($XBP1_S$), and elevated expression of the unspliced form of XBP1 ($XBP1_U$). Taken together, these findings provide another example of a single protein being able to affect ER dynamic in mammalian cells, and an insight into the possible molecular mechanism(s).

• Pediatric Infection and Vaccine
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• v.24 no.3
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• pp.141-145
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• 2017

Purpose: Clinical and laboratory features of two Kawasaki disease (KD) groups were evaluated; the patient with pyuria and those without pyuria. Methods: From January 2015 to December 2016, the medical records of 140 (86 males and 54 females) inpatients with KD were retro-spectively analyzed. Results: Forty-eight KD patients (34.3%) presented with pyuria. KD patients with pyuria showed a higher level of C-reactive protein (CRP) and a higher proportion of elevated liver enzymes than those without pyuria. There were no differences in the proportions of unresponsiveness to intravenous immunoglobulin and coronary artery lesions between the two groups. Six KD patients (12.5%) with pyuria underwent a renal imaging study to rule out the possibility of a urinary tract infections. Thirty-two KD patients (66.7%) with pyuria received treatment with antibiotics in addition to the standard treatment for KD. Conclusions: KD patients with pyuria showed a higher level of CRP and elevated levels of liver enzymes than those without pyuria. These findings suggest that KD patients with pyuria have more severe systemic inflammation than those without pyuria.

• The Journal of Korean Society of Virology
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• v.27 no.1
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• pp.39-47
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• 1997

A large number of viruses belonging to Genus Hantavirus in Family Bunyaviridae are etiologic agents for hemorrhagic fever with renal syndrome (HFRS), or hantavirus pulmonary syndrome (HPS). Hantaan (HTN), Seoul (SED), Belgrade (BEL), Puumala (PUU) serotype viruses are well known causative agents for HFRS in Eurasian continent. Among those viruses Hantaan and Seoul serotypes are well known to cause HFRS in Korea, but there are some sporadic incidence by other than Hantaan or Seoul viruses. Recently we have developed the combined Hantaan-Puumala virus vaccine to prevent world-wide occuring HFRS. This combined vaccine is formalin inactivated, suckling mouse and suckling hamster brain extracts for Hantaan and Puumala viruses, respectively. Protein contents of this purified candidate vaccine is $27\;{\mu}g/ml$, which contains 1,024 ELISA antigen units to each virus, but content of myelin basic protein which is causing experimental allergic encephalomyelitis is less than 0.1 ng/ml. Thirty hamsters were given twice at one month interval intra-muscularly and bled on 30 days after each vaccination from retro-orbital sinus vein. Antibody titers were tested against 5 major serotype viruses, Hantaan, Seoul, Belgrade, Puumala and Sin Nombre viruses by IFA and PRNT. The mean IF antibody titers on 30 days after primary shot were 78.4, 68.8, 68.8, 37.9, and 15.6; mean neutralizing antibody titers were 65.4, 12, 6.1, 65.6 and 0.5 against Hantaan, Seoul, Belgrade, Puumala and Sin Nombre viruses, respectively. The mean IF antibody titers on 30 days after booster shot were 686.9, 567.5, 550.4, 516.3, and 430.9; and neutralizing antibody titers were 710.8, 41.9, 24.3, 409.9, and 1.6 against Hantaan, Seoul, Belgrade, Puumala and Sin Nombre viruses, respectively.