• Laboratory Medicine Online
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• v.7 no.1
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• pp.13-19
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• 2017

Background: We evaluated a sensitive and quantitative method utilizing fragment analysis of the fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD), simultaneously measuring mutant allele burden and length, and verified the analytical performance. Methods: The number and allelic burden of FLT3-ITD mutations was determined by fragment analysis. Serial mixtures of mutant and wild-type plasmid DNA were used to calculate the limit of detection of fragment analysis, conventional PCR, and Sanger sequencing. Specificity was evaluated using DNA samples derived from 50 normal donors. Results of fragment analysis were compared to those of conventional PCR, using 481 AML specimens. Results: Defined mixtures were consistently and accurately identified by fragment analysis at a 5% relative concentration of mutant to wild-type, and at 10% and 20% ratios by conventional PCR and direct sequencing, respectively. No false positivity was identified. Among 481 AML specimens, 40.1% (193/481) had FLT3-ITD mutations. The mutant allele burden (1.7-94.1%; median, 28.2%) and repeated length of the mutation (14-153 bp; median, 49 bp) were variable. The concordance rate between fragment analysis and conventional PCR was 97.7% (470/481). Fragment analysis was more sensitive than conventional PCR and detected 11 additional cases: seven had mutations below 10%, three cases represented conventional PCR failure, and one case showed false negativity because of short ITD length (14 bp). Conclusions: The new fragment analysis method proved to be sensitive and reliable for the detection and monitoring of FLT3-ITD in patients with AML. This could be used to simultaneously assess ITD mutant allele burden and length.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.2
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• pp.166-170
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• 1999

The identification of quantitative trait loci (QTL) has the potential to enhance the efficiency of im- proving food processing traits of soybean. In this study, 92 restriction fragment length polymorphism (RFLP) loci and two morphological markers (W$_1$ and T) were used to identify QTL associated with food processing traits of soybean for sprout in 83 F$_2$-derived lines from a cross of ＇Pureun＇ x ＇Jinpum 2＇. The genetic map consisted of 76 loci which covered about 760 cM and converged into 20 linkage groups. Eighteen markers remained unlinked. Phenotypic data were collected for hypocotyl length, abnormal seedling rate, and sprout yield seven days after seed germination at 2$0^{\circ}C$. Based on the single-factor analysis of variance, eight independent markers were associated with hypocotyl length. Four of seven markers associated with abnormal seedling rate were identified as independent. Seven loci were associated with sprout yield. For three different traits, much of genetic variation was explained by the identified QTL in this population. Several RFLP markers in linkage group (LG) Bl were detected as being associated with three traits, providing a genetic explanation for the biological correlation of sprout yield with hypocotyl length (r=OA07＊＊＊) and with abnormal seedling rate (r=-406＊＊＊).

• Journal of Integrative Natural Science
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• v.10 no.4
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• pp.202-208
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• 2017

Xanthine Oxidase is an enzyme, which oxidizes hypoxanthine to xanthine, and xanthine to uric acid. It is widely distributed throughout various organs including the liver, gut, lungs, kidney, heart, brain and plasma. It is involved in gout pathogenesis. Hence, in the present study, Hologram based Quantitative Structure Activity Relationship Study was performed on a series of Xanthine Oxidase antagonist named 2-(indol-5-yl) thiazole derivatives. The best HQSAR model was obtained using Atoms, Bonds, Connection, Hydrogen, Chirality and Donor Acceptor as fragment distinction parameter using hologram length 71 and 4 components with fragment size of minimum 2 and maximum 5. Significant cross-validated correlation coefficient ($q^2$= 0.563) and non cross-validated correlation coefficients ($r^2$= 0.967) were obtained. The model was then used to evaluate the six external test compounds and its $r^2{_{pred}}$ was found to be 0.798. Contribution map show that presence of propyl ring in indole thiazole makes big contributions for improving the biological activities of the compounds. We hope that our HQSAR model and analysis will be helpful for future design of xanthine oxidase antagonists.

• Journal of Microbiology and Biotechnology
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• v.11 no.6
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• pp.940-945
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• 2001

Symbiobacterium toebii has been previously reported as a novel commensal thermophile exhibiting a commensal interaction with thermophilic Geobacillus sp. SK-1. We investigated the distribution of this commensal thermophile in various soils using molecular methods, such as quantitative PCR and terminal restriction fragment polymorphism analysis. Based on a nested competitive quantitative PCR the 16S rDNA of the commensal thermophile was only detected in compost soils at about $1.0{\times}10^4$ cpoies per gram of soil, corresponding to $0.25{\times}10^4$ cells per gram of soil. However, in an enrichment experiment at $60^{\circ}C$, about $1.0{\times}10^8$ copies of 16S rDNA molecules were detected per ml of enriched culture broth for all the soils, and more than 0.1 mM indole accumulated as the product of commensal bacterial growth. When incubated at $30^{\circ}C$, neither the 16S rDNA of the commensal bacterium nor any indole accumulation was detected. Accordingly, even though the 16S rDNA of the bacterium was only detected in the compost soils by a nested PCR, the presence of the 16S rDNA molecules of commensal thermophile and accumulation of indole in all the enriched cultures appeared to indicate that the commensal thermophile is widely distributed in various soils.

• Molecules and Cells
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• v.37 no.6
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• pp.457-466
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• 2014

Proteomic analysis is helpful in identifying cancerassociated proteins that are differentially expressed and fragmented that can be annotated as dysregulated networks and pathways during metastasis. To examine metastatic process in lung cancer, we performed a proteomics study by label-free quantitative analysis and N-terminal analysis in 2 human non-small-cell lung cancer cell lines with disparate metastatic potentials - NCI-H1703 (primary cell, stage I) and NCI-H1755 (metastatic cell, stage IV). We identified 2130 proteins, 1355 of which were common to both cell lines. In the label-free quantitative analysis, we used the NSAF normalization method, resulting in 242 differential expressed proteins. For the N-terminal proteome analysis, 325 N-terminal peptides, including 45 novel fragments, were identified in the 2 cell lines. Based on two proteomic analysis, 11 quantitatively expressed proteins and 8 N-terminal peptides were enriched for the focal adhesion pathway. Most proteins from the quantitative analysis were upregulated in metastatic cancer cells, whereas novel fragment of CRKL was detected only in primary cancer cells. This study increases our understanding of the NSCLC metastasis proteome.

• Journal of Integrative Natural Science
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• v.10 no.2
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• pp.78-84
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• 2017

CXC chemokine receptor 2 (CXCR2) is a prominent chemokine receptor on neutrophils. CXCR2 antagonist may reduce the neutrophil chemotaxis and alter the inflammatory response because the neutrophilic inflammation in the lung diseases is found to be largely regulated through CXCR2 receptor. Hence, in the present study, Hologram based Quantitative Structure Activity Relationship Study was performed on a series of CXCR2 antagonist named pyrimidine-5-carbonitrile-6-alkyl derivatives. The best HQSAR model was obtained using atoms, bonds, and chirality as fragment distinction parameter using hologram length 151 and 6 components with fragment size of minimum 4 and maximum 7. Significant cross-validated correlation coefficient ($q^2=0.774$) and non cross-validated correlation coefficients ($r^2=0.977$) were obtained. The model was then used to evaluate the six external test compounds and its $r^2_{pred}$ was found to be 0.614. Contribution map show that presence of cyclopropyl ring and its bulkier substituent's makes big contributions for improving the biological activities of the compounds. We hope that our HQSAR model and analysis will be helpful for future design of novel and structurally related CXCR2 antagonists.

• Journal of Integrative Natural Science
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• v.4 no.3
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• pp.210-215
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• 2011

Holographic quantitative structure-activity relationships (HQSAR) is a useful tool to correlates structures with their biological activities. HQSAR is a two dimensional (2D) QSAR methodology, which generates QSAR equations through 2D fingerprint and correlates it with biological activity. Here, we report a 2D-QSAR model for a series of fifty-one 3,4-dihydroxychalcones derivatives utilizing HQSAR methodology. We developed HQSAR model with 6 optimum numbers of components (ONC), which resulted in cross-validated correlation coefficient ($q^2$) of 0.855 with 0.283 standard error of estimate (SEE). The non-cross-validated correlation coefficient (r2) with 0.966 indicates the model is predictive enough for analysis. Developed HQSAR model was binned in to a hologram length of 257. Atomic contribution map revealed the importance of dihydroxy substitution on phenyl ring.

• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.305-315
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• 2021

The cotton leafworm, Spodoptera littoralis, is a major pest in Egypt and many countries worldwide, and causes heavy economic losses. As a result, management measures to control the spread of the worm are required. S. littoralis nucleopolyhedrovirus (SpliNPV) is one of the most promising bioagents for the efficient control of insect pests. In this study, a chitinase gene (chitA) of a 1.8 kb DNA fragment was cloned and fully characterized from SpliNPV-EG1, an Egyptian isolate. A sequence of 601 amino acids was deduced when the gene was completely sequenced with a predicted molecular mass of 67 kDa for the preprotein. Transcriptional analyses using reverse transcription polymerase chain reaction (RT-PCR) revealed that chitA transcripts were detected first at 12 h post infection (hpi) and remained detectable until 168 hpi, suggesting their transcriptional regulation from a putative late promoter motif. In addition, quantitative analysis using quantitative RT-PCR showed a steady increase of 7.86-fold at 12 hpi in chitA transcription levels, which increased up to 71.4-fold at 120 hpi. An approximately 50 kDa protein fragment with chitinolytic activity was purified from ChitA-induced bacterial culture and detected by western blotting with an anti-recombinant SpliNPV chitinase antibody. Moreover, purification of the expressed ChitA recombinant protein showed in vitro growth inhibition of two different fungi species, Fusarium solani and F. oxysporum, confirming that the enzyme assembly and activity was correct. The results supported the potential role and application of the SpliNPV-ChitA protein as a synergistic agent in agricultural fungal and pest control programs.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.92-102
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• 2019

Objective: To investigate changes in rumen fermentation characteristics and bacterial community by a sudden change to a high concentrate diet (HC) in Korean domestic ruminants. Methods: Major Korean domestic ruminants (each of four Hanwoo cows; $545.5{\pm}33.6kg$, Holstein cows; $516.3{\pm}42.7kg$, and Korean native goats; $19.1{\pm}1.4kg$) were used in this experiment. They were housed individually and were fed ad libitum with a same TMR (800 g/kg timothy hay and 200 g/kg concentrate mix) twice daily. After two-week feeding, only the concentrate mix was offered for one week in order to induce rapid rumen acidosis. The rumen fluid was collected from each animals twice (on week 2 and week 3) at 2 h after morning feeding using an oral stomach tube. Each collected rumen fluid was analyzed for pH, volatile fatty acid (VFA), and $NH_3-N$. In addition, differences in microbial community among ruminant species and between normal and an acidosis condition were assessed using two culture-independent 16S polymerase chain reaction (PCR)-based techniques (terminal restriction fragment length polymorphism and quantitative real-time PCR). Results: The HC decreased ruminal pH and altered relative concentrations of ruminal VFA (p<0.01). Total VFA concentration increased in Holstein cows only (p<0.01). Terminal restriction fragment length polymorphism and real-time quantitative PCR analysis using culture-independent 16S PCR-based techniques, revealed rumen bacterial diversity differed by species but not by HC (p<0.01); bacterial diversity was higher in Korean native goats than that in Holstein cows. HC changed the relative populations of rumen bacterial species. Specifically, the abundance of Fibrobacter succinogenes was decreased while Lactobacillus spp. and Megasphaera elsdenii were increased (p<0.01). Conclusion: The HC altered the relative populations, but not diversity, of the ruminal bacterial community, which differed by ruminant species.

• Journal of Integrative Natural Science
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• v.11 no.2
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• pp.93-100
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• 2018

Caspases, a family of cysteinyl aspartate-specific proteases plays a central role in the regulation and the execution of apoptotic cell death. Caspase-3 has been proven to be an effective target for reducing the amount of cellular and tissue damage because the activation of caspases-3 stimulates a signalling pathway that ultimately leads to the death of the cell. In this study, Hologram based Quantitative Structure Activity Relationship (HQSAR) models was generated on a series of Caspase-3 inhibitors named 3, 4-dihydropyrimidoindolones derivatives. The best HQSAR model was obtained using atoms, bonds, and hydrogen atoms (A/B/H) as fragment distinction parameter using hologram length 61 and 3 components with fragment size of minimum 5 and maximum 8. Significant cross-validated correlation coefficient ($q^2=0.684$) and non cross-validated correlation coefficients ($r^2=0.754$) were obtained. The model was then used to evaluate the eight external test compounds and its $r^2_{pred}$ was found to be 0.559. Contribution map show that presence of pyrrolidine sulfonamide ring and its bulkier substituent's makes big contributions for improving the biological activities of the compounds.