• Asian-Australasian Journal of Animal Sciences
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• v.31 no.12
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• pp.1980-1990
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• 2018

Objective: The aim of this study was to discover the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) that were found in selective sweep regions of the Landrace genome Methods: Whole-genome re-sequencing data were obtained from 40 pigs, including 14 Landrace, 16 Yorkshire, and 10 wild boars, which were generated with the Illumina HiSeq 2000 platform. The nsSNPs in the selective sweep regions of the Landrace genome were identified, and the impacts of these variations on protein function were predicted to reveal their potential association with traits of the Landrace breed, such as reproductive capacity. Results: Total of 53,998 nsSNPs in the mapped regions of pigs were identified, and among them, 345 nsSNPs were found in the selective sweep regions of the Landrace genome which were reported previously. The genes featuring these nsSNPs fell into various functional categories, such as reproductive capacity or growth and development during the perinatal period. The impacts of amino acid sequence changes by nsSNPs on protein function were predicted using two in silico SNP prediction algorithms, i.e., sorting intolerant from tolerant and polymorphism phenotyping v2, to reveal their potential roles in biological processes that might be associated with the reproductive capacity of the Landrace breed. Conclusion: The findings elucidated the domestication history of the Landrace breed and illustrated how Landrace domestication led to patterns of genetic variation related to superior reproductive capacity. Our novel findings will help understand the process of Landrace domestication at the genome level and provide SNPs that are informative for breeding.

• Journal of Integrative Natural Science
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• v.3 no.3
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• pp.143-147
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• 2010

Since it is of great importance to know how a ligand binds to a receptor, there have been a lot of efforts to improve the quality of prediction of docking poses. Earlier efforts were focused on improving search algorithm and scoring function in a docking program resulting in a partial improvement with a lot of variations. Although these are basically very important and essential, more tangible improvements came from the reduction of search space. In a normal docking study, the approximate active site is assumed to be known. After defining active site, scoring functions and search algorithms are used to locate the expected binding pose within this search space. A good search algorithm will sample wisely toward the correct binding pose. By careful study of receptor structure, it was possible to prioritize sub-space in the active site using "receptor-based pharmacophores" or "hot spots". In a sense, these techniques reduce the search space from the beginning. Further improvements were made when the bound ligand structure is available, i.e., the searching could be directed by molecular similarity using ligand information. This could be very helpful to increase the accuracy of binding pose. In addition, if the biological activity data is available, docking program could be improved to the level of being useful in affinity prediction for a series of congeneric ligands. Since the number of co-crystal structures is increasing in protein databank, "Ligand-Guided Docking" to reduce the search space would be more important to improve the accuracy of docking pose prediction and the efficiency of virtual screening. Further improvements in this area would be useful to produce more reliable docking programs.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.10
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• pp.1522-1528
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• 2008

The objective of this study was to develop a model for simulating gastric digestion in the pig. The model was constructed to include the chemical and physical changes associated with gastric digestion such as enzyme release, digestion product removal and gastric emptying. Digesta was collected from the stomach cannula of pigs to establish system parameters and to document the ability of the model to simulate gastric digestion. The results showed that the average pH of gastric digesta increased significantly from 2.47 to 4.97 after feed consumption and then decreased 140 min postprandial. The model described the decrease in pH within the pigs' stomach as $pH_t=5.182e^{-0.0014t}$, where t represents the postprandial time in minutes. The cumulative distribution function of liquid digesta was $V_t=64.509e^{0.0109t}$. The average pepsin activity in the liquid digesta was 317Anson units/mL. There was significant gastric emptying 220 min after feed consumption. The cybernetic dynamic system of gastric digestion was set according to the above data in order to compare with in vivo changes. The time course of crude protein digestion predicted by the model was highly correlated with observed in vivo digestion (r = 0.97; p = 0.0001), Model prediction for protein digestion was higher than that observed for a traditional static in vitro method (r = 0.89; p = 0.0001).

• BMB Reports
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• v.39 no.5
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• pp.560-570
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• 2006

Mistletoe (Viscum album) lectins, which are classified as a type II ribosome-inactivating protein (RIP) due to their unique biological function and the potential medical and therapeutic application in cancer cells, receive a rising attention. The heterodimeric glycoproteins contain the A-chain with catalytic activity and the B-chain with sugar binding properties. In recent years, studies involving the lectins from the white berry European mistletoe (Viscum album) and the yellow berry Korean mistletoe (Viscum album coloratum) have been described. However, the detailed mechanism in exerting unique cytotoxic effect on cancer cells still remains unclear. Here, we aim to understand and define the molecular basis and biological effects of the type II RIPs, through the studies of the recombinant Korean mistletoe lectin. To this end, we expressed, purified the recombinant Korean mistletoe lectin (rKML), and investigated its molecular characteristics in vitro, its cytotoxicity and ability to induce apoptotic cell death in cancer cells. To gain structural basis for its catalytic activity and sugar binding properties, we performed homology modeling studies based on the high degree of sequence identity and conserved secondary structure prediction between Korean and European, Himalayan mistletoe lectins, and Ricin.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3805-3809
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• 2014

Background: In Mexico, breast cancer (BCa) is the leading type of cancer in women. Cytochrome P450 (CYP450) is a superfamily of major oxidative enzymes that metabolize carcinogens and many antineoplastic drugs. In addition, these enzymes have influence on tumor development and tumor response to therapy. In this report, we analyzed the protein expression in patients with BCa and in healthy women. Links with some clinic-pathological characteristic were also assessed. Materials and Methods: Immunohistochemical analyses were conducted on 48 sets of human breast tumors and normal breast tissues enrolled in Hospital Militar de Especialidades de la Mujer y Neonatologia and Hospital Central Militar, respectively, during the time period from 2010 to 2011. Informed consent was obtained from all participants. Statistical analysis was performed using ${\chi}^2$ or Fisher exact tests to estimate associations and the Mann Whitney U test for comparison of group means. Results: We found a significant CYP3A4 overexpression in BCa stroma and gland regions in comparison with healthy tissue. A significant association between protein expression with smoking, alcoholism and hormonal contraceptives use was also observed. Additionally, we observed estrogen receptor (ER) and progesterone receptor (PR) positive association in BCa. Conclusions: We suggest that CYP3A4 expression promotes BCa development and can be used in the prediction of tumor response to different treatments. One therapeutic approach may thus be to block CYP3A4 function.

• Journal of Biosystems Engineering
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• v.43 no.2
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• pp.148-159
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• 2018

Purpose: Unmanned air vehicle (UAV) remote sensing was applied to test various vegetation indices and make prediction models of protein content of rice for monitoring grain quality and proper management practice. Methods: Image acquisition was carried out by using NIR (Green, Red, NIR), RGB and RE (Blue, Green, Red-edge) camera mounted on UAV. Sampling was done synchronously at the geo-referenced points and GPS locations were recorded. Paddy samples were air-dried to 15% moisture content, and then dehulled and milled to 92% milling yield and measured the protein content by near-infrared spectroscopy. Results: Artificial neural network showed the better performance with $R^2$ (coefficient of determination) of 0.740, NSE (Nash-Sutcliffe model efficiency coefficient) of 0.733 and RMSE (root mean square error) of 0.187% considering all 54 samples than the models developed by PR (polynomial regression), SLR (simple linear regression), and PLSR (partial least square regression). PLSR calibration models showed almost similar result with PR as 0.663 ($R^2$) and 0.169% (RMSE) for cloud-free samples and 0.491 ($R^2$) and 0.217% (RMSE) for cloud-shadowed samples. However, the validation models performed poorly. This study revealed that there is a highly significant correlation between NDVI (normalized difference vegetation index) and protein content in rice. For the cloud-free samples, the SLR models showed $R^2=0.553$ and RMSE = 0.210%, and for cloud-shadowed samples showed 0.479 as $R^2$ and 0.225% as RMSE respectively. Conclusion: There is a significant correlation between spectral bands and grain protein content. Artificial neural networks have the strong advantages to fit the nonlinear problem when a sigmoid activation function is used in the hidden layer. Quantitatively, the neural network model obtained a higher precision result with a mean absolute relative error (MARE) of 2.18% and root mean square error (RMSE) of 0.187%.

• Journal of Institute of Control, Robotics and Systems
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• v.12 no.10
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• pp.1044-1049
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• 2006

Multiple sequence alignment is a method to compare two or more DNA or protein sequences. Most of multiple sequence alignment tools rely on pairwise alignment and Smith-Waterman algorithm to generate an alignment hierarchy. Therefore, in the existing multiple alignment method as the number of sequences increases, the runtime increases exponentially. In order to remedy this problem, we adopted a parallel processing suffix tree algorithm that is able to search for common subsequences at one time without pairwise alignment. Also, the cross-matching subsequences triggering inexact-matching among the searched common subsequences might be produced. So, the cross-matching masking process was suggested in this paper. To identify the function of the clusters generated by suffix tree clustering, BLAST and CDD (Conserved Domain Database)search were combined with a clustering tool. Our clustering and annotating tool consists of constructing suffix tree, overlapping common subsequences, clustering gene sequences and annotating gene clusters by BLAST and CDD search. The system was successfully evaluated with 36 gene sequences in the pentose phosphate pathway, clustering 10 clusters, finding out representative common subsequences, and finally identifying functional domains by searching CDD database.

• Journal of Nutrition and Health
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• v.55 no.6
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• pp.684-698
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• 2022

Purpose: Recent studies have reported a significant association between skeletal muscle, muscle strength and non-alcoholic fatty liver disease (NAFLD). The effect of nutrient intake on the prediction of skeletal muscle mass and strength or its suggested correlation with metabolic diseases has been primarily reported in healthy individuals. The current study explores the association between energy intake and handgrip strength (HGS) in individuals with NAFLD. Methods: Data were obtained from the Korea National Health and Nutrition Examination Surveys 2016-2018. Data from 12,469 participants were extracted and 1,293 men and 1,401 women aged 20 years and older were included in the analyses of patients with NAFLD. The presence of NAFLD was determined using the hepatic steatosis index. To estimate relative skeletal muscle strength, HGS was measured using a digital dynamometer and calculated by adjusting the body mass index of the dominant arm. Study subjects in the NAFLD and non-NAFLD groups were separately categorized according to quartiles of the calculated HGS. Results: We found that individuals with low (EQ1) energy intake had lower odds of HGS compared to subjects with high (EQ4) energy intake, irrespective of their NAFLD status (p < 0.0001). However, the HGS did not differ based on the level of protein or fat intake ratio. Additionally, the effect of energy intake on HGS was more pronounced in men than in women. Conclusion: Energy intake was associated with the risk of weak HGS in men with NAFLD. The results indicate that energy intake may be a key factor in nutrition care for NAFLD patients with low muscle function.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1942-1949
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• 2019

Objective: Leukocyte cell-derived chemotaxin 2 (LECT2) is associated with several physiological processes including inflammation, tumorigenesis, and natural killer T cell generation. Chicken LECT2 (chLECT2) gene was originally identified as one of the differentially expressed genes in chicken kidney tissue, where the chickens were fed with different calcium doses. In this study, the molecular characteristics and gene expression of chLECT2 were analyzed under the stimulation of toll-like receptor 3 (TLR3) ligand to understand the involvement of chLECT2 expression in chicken metabolic disorders. Methods: Amino acid sequence of LECT2 proteins from various species including fowl, fish, and mammal were retrieved from the Ensembl database and subjected to Insilco analyses. In addition, the time- and dose-dependent expression of chLECT2 was examined in DF-1 cells which were stimulated with polyinosinic:polycytidylic acid (poly [I:C]), a TLR3 ligand. Further, to explore the transcription factors required for the transcription of chLECT2, DF-1 cells were treated with poly (I:C) in the presence or absence of the nuclear factor ${\kappa}B$ ($NF{\kappa}B$) and activated protein 1 (AP-1) inhibitors. Results: The amino acid sequence prediction of chLECT2 protein revealed that along with duck LECT2 (duLECT2), it has unique signal peptide different from other vertebrate orthologs, and only chLECT2 and duLECT2 have an additional 157 and 161 amino acids on their carboxyl terminus, respectively. Phylogenetic analysis suggested that chLECT2 is evolved from a common ancestor along with the actinopterygii hence, more closely related than to the mammals. Our quantitative polymerase chain reaction results showed that, the expression of chLECT2 was up-regulated significantly in DF-1 cells under the stimulation of poly (I:C) (p<0.05). However, in the presence of $NF{\kappa}B$ or AP-1 inhibitors, the expression of chLECT2 is suppressed suggesting that both $NF{\kappa}B$ and AP-1 transcription factors are required for the induction of chLECT2 expression. Conclusion: The present results suggest that chLECT2 gene might be a target gene of TLR3 signaling. For the future, the expression pattern or molecular mechanism of chLECT2 under stimulation of other innate immune receptors shall be studied. The protein function of chLECT2 will be more clearly understood if further investigation about the mechanism of LECT2 in TLR pathways is conducted.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.10
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• pp.5883-5890
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• 2013

Previously, we demonstrated overexpression of semaphorin4D (SEMA4D, CD100) to be closely related to tumor angiogenesis in epithelial ovarian cancers (EOCs). However, the function and expression of SEMA4D in the EOC microenvironment has yet to be clarified in detail. In this study, we confirmed that overexpression of SEMA4D in primary tumors and ascites was related to low differentiation, platinum resistance and a refractory status (P<0.05), while high M2 macrophage count and percentage were evident in EOC patients with advanced FIGO stage and platinum resistance (P<0.05), using immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), and fluorescence-activated cell sorting (FACS), respectively. The data showed correlations of SEMA4D expression and M2 macrophage counts in primary tumors and M2 macrophage percentage in ascites (r=0.281 and 0.355, each P<0.05). In the Cox proportional hazard mode, SEMA4D expression was an independent indicator of overall survival (OS) and progression-free survival (PFS) for EOC patients. Furthermore, higher expression of SEMA4D in ovarian cancer cell lines (SKOV3, A2780, and SW626) and their supernatants were found than that in a human primary cultured ovarian cell and its supernatant by reversed transcript PCR (RT-PCR), Western blotting and ELISA, respectively. Interestingly, peripheral blood monocytes (MOs) tended towards the M2-polarized macrophage phenotype ($CD163^{high}$) in vitro after human recombined soluble SEMA4D protein stimulation. These findings suggest that SEMA4D might possibly serve as a reliable tool for early and accurate prediction of EOC poor prognosis and could playan important role in promoting tumor dissemination and metastasis in the EOC microenvironment. Thus SEMA4D and its role in macrophage polarization in EOC warrants further study.