• IMMUNE NETWORK
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• v.15 no.2
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• pp.66-72
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• 2015

Currently, detecting biochemical differences before and after allogeneic stem cell transplantation (SCT) for improved prediction of acute graft-versus-host disease (aGVHD) is a major clinical challenge. In this pilot study, we analyzed the kinetics of circulating adipokine levels in patients with or without aGVHD before and after allogeneic SCT. Serum samples were obtained and stored at $-80^{\circ}C$ within 3 hours after collection, prior to conditioning and at engraftment after transplantation. A protein array system was used to measure the levels of 7 adipokines of patients with aGVHD (n=20) and without aGVHD (n=20). The resistin level at engraftment was significantly increased (p<0.001) after transplantation, regardless of aGVHD occurrence. In the non-aGVHD group, the concentrations of the hepatocyte growth factor (HGF) (mean values${\pm}$SD; $206.6{\pm}34.3$ vs. $432.3{\pm}108.9pg/ml$, p=0.040) and angiopoietin-2 (ANG-2) (mean values${\pm}$SD; $3,197.2{\pm}328.3$ vs. $4,471.8{\pm}568.4pg/ml$, p=0.037) at engraftment were significantly higher than those of the pre-transplant period, whereas in the aGVHD group, the levels of adipokines did not change after transplantation. Our study suggests that changes in serum HGF and ANG-2 levels could be considered helpful markers for the subsequent occurrence of aGVHD.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3503-3507
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• 2013

Background: Although the majority of investigations concerned with TP53 and its protein have focused on coding regions, recently a set of studies highlighted significant roles of regulatory elements located in p53 mRNA, especially 5'UTR. The wrap53${\alpha}$ transcript is one of those that acts as a natural antisense agent, forming RNA-RNA hybrids with p53 mRNA and protecting it from degradation. Materials and Methods: In this study, we focused on the mutation status of exon $1{\alpha}$ of the WRAP53 gene (according to exon 1 of p53) in 160 breast tumor tissue samples and conducted a bioinformatics search for probable miRNA binding site in the p53/wrap53 overlapping region. Mutations were detected, using single stranded conformation polymorphism (SSCP) and sequencing. We applied the miRBase database for prediction of miRNAs which target overlapping region of p53/wrap53 transcripts. Results: Our results showed all samples to have wild type alleles in exon 1 of TP53 gene. We could detect a novel and unreported intronic mutation (IVS1+56, G>C) outside overlapping regions of p53/wrap53 genes in breast cancer tissues and also predict the presence of a binding site for miR-4732-5p in the 5'UTR of Wrap53 mRNA. Conclusions: From our findings we propose designing further studies focused on overexpression of miRNA-4732-5p and introducing different mutations in the overlapping region of wrap53 and p53 genes in order to study their effects on p53 and its ${\Delta}N$ isoform (${\Delta}$40p53) expression. The results may provide new pieces in the p53 targeting puzzle for cancer therapy.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.317-327
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• 2008

Phytocystatins, which are inhibitors of plant cysteine peptidases, are involved in the regulation of protein turnover and in the defense against insect pests and pathogens. Extensive searches in the Brassica rapa genome allowed the prediction of at least eight different phytocystatin genes on seven chromosomes in the B. rapa genome. Structure comparisons based on alignments of the all BrCYS ($\underline{B}$. $\underline{r}apa$ $phyto{\underline{cys}}tatin$) proteins using the CLUSTALW program revealed conservation of the three consensus motifs known to interact with the active site of cysteine peptidases. According to the phylogenetic analysis based on the deduced amino acid sequences, the eight BrCYS proteins were divided into several clusters related to the orthologous phytocystatin. The predicted three-dimensional structure models of the eight BrCYS proteins demonstrate that all of these proteins are similar to the reported crystal structure of oryzacystatin-I (OC-I). Digital northern and RT-PCR analyses indicated that the eight BrCYS genes exhibit different expression patterns in B. rapa tissues and respond differently to abiotic stimuli. The differences in gene structure and expression between the eight BrCYS genes suggest that these proteins may play diverse physiological roles in B. rapa and may interact with cysteine peptidases through different mechanisms.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1620-1620
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• 2001

Forages, both grazed and conserved, provide the basis of ruminant production systems throughout the world. More than 90 per cent of the feed energy consumed by herbivorous animals world - wide were provided by forages. With such world - wide dependence on forages, the economic and nutritional necessity of been able to characterize them in a meaningful way is vital. The characterization of forages for productive animals is becoming important for several reasons. Relative to conventional laboratory procedures, Near Infrared Reflectance Spectroscopy (NIRS) offers advantages of simplicity, speed, reduced chemical waste, and more cost-effective prediction of product functionality. NIR spectroscopy represents a radical departure from conventional analytical methods, in that entire sample of forage is characterized in terms of its absorption properties in the near infrared region, rather than separate subsamples being treated with various chemicals to isolate specific components. This forces the analyst to abandon his/her traditional narrow focus on the sample (one analyte at a time) and to take a broader view of the relationship between components within the sample and between the sample and the population from which it comes. forage is usually analysed by NIRS in dry and ground presentation. Initial success of NIRS analysis of coarse forages suggest a need to better understand the potential for analysis of minimally processed samples. Preparation costs and possible compositional alterations could be reduced by samples presented to the instrument in undried and unground conditions. NIRS has gained widespread acceptance for the analysis of forage quality constituents on dry material, however little attention has been given to the use of NIRS for chemical determinations on undried and unground forages. Relatively few works reported the use of NIRS to determine quality parameters on undried materials, most of them on both grass and corn silage. Only two works have been found on the determination of quality parameters on fresh forages. The objectives of this paper were (1) to evaluate the use of NIRS for determination of nitrogen and moisture on undried and unground forage samples and (2) to explore two mathematical treatments and two NIR regions to predict chemical parameters on fresh forage. Four hundred forage samples (n: 400) were analysed in a NIRS 6500 instrument (NIR Systems, PA, USA) in reflectance mode. Two mathematical treatments were applied: 1,4,4,1 and 2,5,5,2. Predictive equations were developed using modified partial least squares (MPLS) with internal cross - validation. Coefficient of determination in calibration (${R^2}_{CAL}$) and standard error in cross-validation (SECV) for moisture were 0.92 (12.4) and 0.92 (12.4) for 1,4,4,1 and 2,5,5,2 respectively, on g $kg^{-1}$ dry weight. For crude protein NIRS calibration statistics yield a (${R^2}_{CAL}$) and (SECV) of 0.85 (19.8) and 0.85 (19.6) for 1,4,4,1 and 2,5,5,2 respectively, on a dry weight. It was concluded that NIRS is a suitable method to predict moisture and nitrogen on fresh forage without samples preparation.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1062-1062
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• 2001

The concept of “precision agriculture” or “site-specific farming” is usually confined to the fields of soil science, crop science and agronomy. However, because plants grow in soil, animals eat plants, and humans eat animal products, it could be argued (perhaps with some poetic licence) that the fields of feed quality, animal nutrition and animal production should also be considered in this context. NIR spectroscopy has proved over the last 20 years that it can provide a firm foundation for quality measurement across all of these fields, and with the continuing developments in instrumentation, computer capacity and software, is now a major cog in the wheel of precision agriculture. There have been a few giant leaps and a lot of small steps in the impact of NIR on the animal world. These have not been confined to the amazing advances in hardware and software, although would not have occurred without them. Rapid testing of forages, grains and mixed feeds by NIR for nutritional value to livestock is now commonplace in commercial laboratories world-wide. This would never have been possible without the pioneering work done by the USDA NIR Forage Research Network in the 1980's, following the landmark paper of Norris et al. in 1976. The advent of calibration transfer between instruments, algorithms which utilize huge databases for calibration and prediction, and the ability to directly scan whole grains and fresh forages can also be considered as major steps, if not leaps. More adventurous NIR applications have emerged in animal nutrition, with emphasis on estimating the functional properties of feeds, such as in vivo digestibility, voluntary intake, protein degradability and in vitro assays to simulate starch digestion. The potential to monitor the diets of grazing animals by using faecal NIR spectra is also now being realized. NIR measurements on animal carcasses and even live animals have also been attempted, with varying degrees of success, The use of discriminant analysis in these fields is proving a useful tool. The latest giant leap is likely to be the advent of relatively low-cost, portable and ultra-fast diode array NIR instruments, which can be used “on-site” and also be fitted to forage or grain harvesters. The fodder and livestock industries are no longer satisfied with what we once thought was revolutionary: a 2-3 day laboratory turnaround for fred quality testing. This means that the instrument needs to be taken to the samples rather than vice versa. Considerable research is underway in this area, but the challenge of calibration transfer and maintenance of instrument networks of this type remains. The animal world is currently facing its biggest challenges ever; animal welfare, alleged effects of animal products on human health, environmental and economic issues are difficult enough, but the current calamities of BSE and foot and mouth disease are “the last straw” NIR will not of course solve all these problems, but is already proving useful in some of these areas and will continue to do so.

• Korean Journal of Head & Neck Oncology
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• v.27 no.2
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• pp.190-197
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• 2011

Background and Objective : Radiation resistance(RR) is one of main determinants of treatment outcome in oral squamous cell carcinoma(OSCC), but accurate prediction of RR is difficult. We aim to establish RR OSCC cell lines and identify genes related with RR by a measurement of altered gene expression after inducing RR. Material and Methods : OSCC cell lines, SCC15, SCC25 and QLL1, were treated with 2Gy radiation per session, and parts of them were alive in finally accumulated dosage of 60Gy through 30 times repetition of radiotherapy for inducing RR cell lines. We compared results of cDNA array and proteomics in non-radiated cell lines and RR cell lines to detect changes of gene expression. Western blot was used for the validation of results. Results : cDNA array revealed 265 commonly up-regulated genes and 268 commonly down-regulated genes in 3 RR cell lines comparing their non-radiated counterpart. Among them, 30 cancer related genes were obtained. Proteomics showed 51 commonly altered protein expressions in 3 RR cell lines and 18 cancer related proteins were obtained. Among the detected genes, we found NM23-H1 and PA2G4 were over-expressed in both cDNA array and proteomics. Western blot showed increased expression of NME1 in RR cell lines but not in PA2G4. Conclusion: We concluded that NM23-H1 may be a candidate of RR related gene and over-expression of NM23-H1 could be a biomarker to predict RR in OSCC.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.3
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• pp.390-397
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• 2020

Objective: The objective of this study was to measure the special expression pattern of lipid metabolism genes and investigate the molecular mechanisms underlying intramuscular fat (IMF) deposition in Longissimus dorsi muscle of Laiwu pigs. Methods: Thirty-six pigs (Laiwu n = 18; Duroc×Landrace×Yorkshire n = 18) were used for the measurement of the backfat thickness, marbling score, IMF content, and expression of lipid metabolism genes. Results: Significant correlations were found between IMF content and the mRNA expression of lipid metabolism genes. Of the 14 fat deposition genes measured, fatty acid synthase (FASN) showed the strongest correlation (r = 0.75, p = 0.001) with IMF content, and of the 6 fat removal genes, carnitine palmitoyl transferase 1B (CPT1B) exhibited the greatest negative correlation (r = -0.66, p = 0.003) with IMF content in Laiwu pig. Multiple regression analysis showed that CPT1B, FASN, solute carrier family 27 member 1 (SLC27A1), and fatty acid binding protein 3 (FABP3) contributed 38% of the prediction value for IMF content in Laiwu pigs. Of these four variables, CPT1B had the greatest contribution to IMF content (14%) followed by FASN (11%), SLC27A1 (9%), and FABP3 (4%). Conclusion: Our results indicate that the combined effects of an upregulation in fat deposition genes and downregulation in fat removal genes promotes IMF deposition in Laiwu pigs.

• KIISE Transactions on Computing Practices
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• v.20 no.9
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• pp.513-518
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• 2014

It has become possible for small scale laboratories to interpret large scale genomic DNA, thanks to the reduction of the sequencing cost by the development of next generation sequencing (NGS). De novo assembly is a method which creates a putative original sequence by reconstructing reads without using a reference sequence. There have been various study results on de novo assembly, however, it is still difficult to get the desired results even by using the same assembly procedures and the analysis tools which were suggested in the studies reported. This is mainly because there are no specific guidelines for the assembly procedures or know-hows for the use of such analysis tools. In this study, to resolve these problems, we introduce steps to finding whole genome of an unknown DNA via NGS technology and de novo assembly, while providing the pros and cons of the various analysis tools used in each step. We used 350Mbp of Toxocara canis DNA as an application case for the detailed explanations of each stated step. We also extend our works for prediction of protein-coding genes and their functions from the draft genome sequence by comparing its homology with reference sequences of other nematodes.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.15
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• pp.6449-6453
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• 2014

Background: Prior studies showed a relationship between serum albumin and the albumin to globulin ratio with different types of cancer. We aimed to evaluate the predictive value of the albumin-globulin ratio (AGR) for survival of patients with lung adenocarcinoma. Materials and Methods: This retrospective study included 240 lung adenocarcinoma patients. Biochemical parameters before chemotherapy were collected and survival status was obtained from the hospital registry. The AGR was calculated using the equation AGR=albumin/(total protein-albumin) and ranked from lowest to highest, the total number of patients being divided into three equal tertiles according to the AGR values. Furthermore, AGR was divided into two groups (low and high tertiles) for ROC curve analysis. Cox model analysis was used to evaluate the prognostic value of AGR and AGR tertiles. Results: The mean survival time for each tertile was: for the $1^{st}$ 9.8 months (95%CI:7.765-11.848), $2^{nd}$ 15.4 months (95%CI:12.685-18.186), and $3^{rd}$ 19.9 months (95%CI:16.495-23.455) (p<0.001). Kaplan-Meier curves showed significantly higher survival rates with the third and high tertiles of AGR in comparison with the first and low tertiles, respectively. At multivariate analysis low levels of albumin and AGR, low tertile of AGR and high performance status remained an independent predictors of mortality. Conclusions: Low AGR was a significant predictor of long-term mortality in patients with lung adenocarcinoma. Serum albumin measurement and calculation of AGR are easily accessible and cheap to use for predicting mortality in patients with lung adenocarcinoma.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.5
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• pp.1949-1953
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• 2014

Background: CA125 and HE4 are used in calculating Risk of Malignancy Algorithm (ROMA); and Risk of Malignancy Index (RMI). However, studies showed that normal levels of CA125, and HE4 differ among ethnicities such as between Asians and Caucasians, thus affecting the accuracy of the RMI score and ROMA in predicting ovarian malignancy. This study aimed to determine whether new or modified cutoff values for Ca125, HE4, the RMI score, and ROMA resulted in a better prediction of malignancy compared with the previous or standard ones. Materials and Methods: Serum level of CA125 and HE4 from 128 patients with diagnosis of ovarian tumor that had been collected before surgery at Cipto Mangunkusumo General Hospital (CMH) in Jakarta from November 2010 until May 2011 were reviewed and analysed. The standard cutoff values of these biomarkers, RMI, and ROMA were modified by using logistic regression model. The modified cutoff values were compared to the standard cutoff values in terms of sensitivity, specificity, and accuracy. Results: The modified cutoff value of CA125, HE4, RMI score and ROMA were 165.2 U/mL, 103.4 pM, 368.7, 28/54. The sensitivity and specificity of the modified cutoff values CA125, HE 4, RMI score and ROMA in differentiating benign from malignant and borderline were 67% and 75,4%; 73.1% and 85.2%; 73.1% and 80.3%; and 77.6% and 86.9%. While the sensitivity and specificity of the standard cutoff value of CA125; HE4; RMI score; and ROMA were 91% and 24.6%; 83.6% and 65%; 80.6% and 65.6%; and 91.0% and 42.6%. The accuracy of modified cutoff values compared with standard cutoff values were: 71.2% vs 59.3%, 78.9% vs 75% vs, 76.5% vs 73.4%, and 82% vs 67.9%. Conclusions: The new or modified cutoff values of Ca125, HE4, RMI score and ROMA resulted in higher accuracy compared to the previous or standard ones, at the cost of reduced sensitivity.