• Genomics & Informatics
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• 제19권3호
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• pp.33.1-33.10
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• 2021

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. In this study, two individuals of Eucalyptus tereticornis (ET217 and ET86), one individual each from E. camaldulensis (EC17) and E. grandis (EG9) were subjected to whole genome resequencing. Low coverage (10×) genome sequencing was used to find polymorphic SSRs between the individuals. Average number of SSR loci identified was 95,513 and the density of SSRs per Mb was from 157.39 in EG9 to 155.08 in EC17. Among all the SSRs detected, the most abundant repeat motifs were di-nucleotide (59.6%-62.5%), followed by tri- (23.7%-27.2%), tetra- (5.2%-5.6%), penta- (5.0%-5.3%), and hexa-nucleotide (2.7%-2.9%). The predominant SSR motif units were AG/CT and AAG/TTC. Computational genome analysis predicted the SSR length variations between the individuals and identified the gene functions of SSR containing sequences. Selected subset of polymorphic markers was validated in a full-sib family of eucalypts. Additionally, genome-wide characterization of single nucleotide polymorphisms, InDels and transcriptional regulators were carried out. These variations will find their utility in genome-wide association studies as well as understanding of molecular mechanisms involved in key economic traits. The genomic resources generated in this study would provide an impetus to integrate genomics in marker-trait associations and breeding of tropical eucalypts.

• 한국균학회지
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• 제23권3호통권74호
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• pp.202-208
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• 1995

본 실험결과 느타리버섯속에서의 재현성 있는 최적 RAPD 조건은 $50\;{\mu}l$ 반응액에서 80 ng template DNA, 30 pmole primer, $200\;{\mu}M$ dNTP, 2 mM $MgCl_2$, 50 mM KCl, 10 mM Tris-HCI(pH 9.0), 0.1% Triton X-100, 1.5 unit Taq polymerase(promega)였다. 여섯 개의 primer가 Pleurotus속 8종의 균주에서 RAPD polymorphism을 보임을 알 수 있었으며, 이들의 염기배열은 PR2(GGG GGG AAG C), PR3(GCG GTT GAG G), PR4(CGC ACC GCA C), PR10(CAA TCG CCG T), PR11(CAG CAC CCA C), PR17(TAG GCG TAT CAG GAG GCC CT)이었다.

• The Korean Journal of Ecology
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• 제17권4호
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• pp.523-531
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• 1994

Optimal conditions for the seed germination and growth of Hedyotis diffusa were studied. As photoperiod was increased from 12 hr to 24hr, the germination rate of Hedyotis diffusa was gradually increased. The photoperiod and temperature inflenced on the fermination synergistically. After the growth of 20 weeks under the natural condition (June~Oct.), the length of H. diffusa was $38.9{\pm}4.2cm$ (15.5~52.5cm), and total dry weight per $3.3m^2$ was $316.7{\pm}10.3g$. It is considered that H. diffusa could be cultivated in a part of inland. The anticancer effect of H. diffusa extract was examined. F-344 rats aged 6 weeks were divided into 3 groups and were given an I.P. of diethylnitrosamine at 200mg/kg body weight as a promoter, initially. And in two weeks after the beginnign of the experiment, group 1 was supplied iwth feed containing 0.02% 2-AAG as a promoter for 6 weeks. Group 2 was supplied with feed containing extracts of H.diffusa (0.02%) for two weeks. Group3 was supplied with only basal diet. All rats were sacrificed for partial hepatectomu, and the antipromoting effect was examined by the number 문 area per $cm^2$ of foci in river. In group 1, the number of hyperplastic nodule was $18.5{\pm}7.7$, but in group2, it was drastically reduced to $10.3{\pm}1.8$ rather thn those of group1. The total area of nodules $(mm^2)$ /whole liver $(cm^2)$ of group 1 and group2 were $19.2{\pm}7.7$ and $5.0{\pm}3.2$, respectively. These results indicate that extract of H.diffusa act as an anticancer agent at statistically significant level (p<0.001).

• Biomolecules & Therapeutics
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• 제29권1호
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• pp.73-82
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• 2021

Hsp90 is often overexpressed with activated form in cancer cells, and many key cellular proteins are dependent upon the Hsp90 machinery (these proteins are called "client protein"). Nowadays, more client proteins and more inhibitors of Hsp90 are being discovered. Chaetocin has been identified as an inhibitor of histone methyl transferase SUV39H1. Herein, we find that Chaetocin is an inhibitor of Hsp90 which binds to the C-terminal of Hsp90α. Chaetocin inhibited a variety of Hsp90 client proteins including AMl1-ETO and BCL-ABL, the mutant fusion-protein in the K562 and HL-60 cells. SUV39H1 mediates epigenetic events in the pathophysiology of hematopoietic disorders. We found that inhibition of Hsp90 by Chaetocin and 17-AAG had ability to induce degradation of SUV39H1 through proteasome pathway. In addition, SUV39H1 interacted with Hsp90 through co-chaperone HOP. These results suggest that SUV39H1 belongs to a client protein of Hsp90. Moreover, Chaetocin was able to induce cell differentiation in the two cells in the concentration range of Hsp90 inhibition. Altogether, our results demonstrate that SUV39H1 is a new client protein of Hsp90 degradated by Chaetocin as a novel C-terminal inhibitor of Hsp90. The study establishes a new relationship of Chaetocin and SUV39H1, and paves an avenue for exploring a new strategy to target SUV39H1 by inhibition of Hsp90 in leukemia.

• Genomics & Informatics
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• 제19권1호
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• pp.10.1-10.7
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• 2021

Although many models have been proposed to accurately predict the response of drugs in cell lines recent years, understanding the genome related to drug response is also the key for completing oncology precision medicine. In this paper, based on the cancer cell line gene expression and the drug response data, we established a reliable and accurate drug response prediction model and found predictor genes for some drugs of interest. To this end, we first performed pre-selection of genes based on the Pearson correlation coefficient and then used ElasticNet regression model for drug response prediction and fine gene selection. To find more reliable set of predictor genes, we performed regression twice for each drug, one with IC₅₀ and the other with area under the curve (AUC) (or activity area). For the 12 drugs we tested, the predictive performance in terms of Pearson correlation coefficient exceeded 0.6 and the highest one was 17-AAG for which Pearson correlation coefficient was 0.811 for IC₅₀ and 0.81 for AUC. We identify common predictor genes for IC₅₀ and AUC, with which the performance was similar to those with genes separately found for IC₅₀ and AUC, but with much smaller number of predictor genes. By using only common predictor genes, the highest performance was AZD6244 (0.8016 for IC₅₀, 0.7945 for AUC) with 321 predictor genes.

• Asian Pacific Journal of Cancer Prevention
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• 제16권15호
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• pp.6627-6632
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• 2015

Background: We conducted a study exploring the clinical safety and efficacy of decitabine in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), combined with a complex karyotype. Materials and Methods: From April 2009 to September 2013, a total of 35 patients with AML/MDS combined with a complex karyotype diagnosed in the First Affiliated Hospital of Soochow University were included for retrospective analysis. All patients were treated with decitabine alone ($20mg/m^2$ daily for 5 days) or combination AAG chemotherapy (Acla 20mg qod*4d, Ara-C $10mg/m^2$ q12h*7d, G-CSF $300{\mu}g$ qd, the dose of G-CSF adjusted to the amount in blood routinely). Results: In 35 patients, 15 exhibited a complete response (CR), and 6 a partial response (PR), the overall response rate (CR+PR) being 60% (21 of 35). Median disease-free survival was 18 months and overall survival was 14 months. In the 15 MDS patients with a complex karyotype, the CR rate was 53.3% (8 of 15); in 20 AML patients with complex karyotype, the overall response rate was 65% (13 of 20). The response rate of decitabine alone (22 cases) was 56.5% (13 of 22), while in the combination chemotherapy group (13 cases), the effective rate was 61.5% (8 of 13)(P>0.05). There are 15 patients with chromosome 7 aberration, after treatment with decitabine, 7 CR, 3 PR, overall response rate was 66.7% (10 of 15). Of 18 patients with 3 to 5 kinds of chromosomal abnormalities, 66.7% demonstrated a response; of 17 with more than 5 chromosomal abnormalities, 52.9% had a response. In the total of 35 patients, with one course (23 patients) and ${\geq}$two courses (12 patients), the overall response rate was 40.9% and 92.3% (P<0.05). Grade III to IV hematological toxicity was observed in 27 cases (75%). Grade III to IV infections were clinically documented in 7 (20%). Grades I to II non-hematological toxicity were infections (18 patients), haematuria (2 patients), and bleeding (3 patients). With follow-up until September 2013, 7 patients were surviving, 18 had died and 10 were lost to follow-up. In the 6 cases who underwent allogeneic hematopoietic stem cell transplantation (HSCT) all were still relapse-free survivors. Conclusions: Decitabine alone or combination with AAG can improve outcome of AML/MDS with a complex karyotype, there being no significant difference decitabine in inducing remission rates in patients with different karyotype. Increasing the number of courses can improve efficiency. This approach with fewer treatment side effects in patients with a better tolerance should be employed in order to create an improved subsequent chance for HSCT.