• Asian Pacific Journal of Cancer Prevention
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• v.17 no.3
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• pp.1023-1035
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• 2016

The purpose of this study was to investigate the role of colon cancer stem cells (CSCs) during chemically-induced rat multi-step colon carcinogenesis with or without the treatment with a specific cyclooxygenase-2 inhibitor drug (celecoxib). Two experiments were performed, the first, a short term 12 week colon carcinogenesis bioassay in which only surrogate markers for colon cancer, aberrant crypt foci (ACF) lesions, were formed. The other experiment was a medium term colon cancer rat assay in which tumors had developed after 32 weeks. Treatment with celecoxib lowered the numbers of ACF, as well as the tumor volumes and multiplicities after 32 weeks. Immunohistochemical proliferating cell nuclear antigen (PCNA) labeling indexes LI (%) were downregulated after treatment by celecoxib. Also different cell surface antigens known to associate with CSCs such as the epithelial cell adhesion molecule (EpCAM), CD44 and CD133 were compared between the two experiments and showed differential expression patterns depending on the stage of carcinogenesis and treatment with celecoxib. Flow cytometric analysis demonstrated that the numbers of CD133 cells were increased in the colonic epithelium after 12 weeks while those of CD44 but not CD133 cells were increased after 32 weeks. Moreover, aldehyde dehydrogenase-1 activity levels in the colonic epithelium (a known CSC marker) detected by ELISA assay were found down-regulated after 12 weeks, but were up-regulated after 32 weeks. The data have also shown that the protective effect of celecoxib on these specific markers and populations of CSCs and on other molecular processes such as apoptosis targeted by this drug may vary depending on the genetic and phenotypic stages of carcinogenesis. Therefore, uncovering these distinction roles of CSCs during different phases of carcinogenesis and during specific treatment could be useful for targeted therapy.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.188-188
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• 2017

Rice (Oryza sativa L.) is one of the major crops that is seriously impacted by global soil salinization. Rice is among those crops where most of the high-yielding cultivars are highly sensitive to salinity. The key to a plant survival under NaCl salt stress is by maintaining a high $K^+/Na^+$ ratio in its cells. Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay in progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) were used to find out salt tolerant rice genotypes. In the current experiment phenotyping and genotyping studies were correlated to differentiate different rice accessions for salinity tolerance. Eight rice accessions along with check plant Dongjin were screened by physiological studies using Yoshida solution with 50mM NaCl stress condition. The physiology studies identified four tolerant and four susceptible accessions based on their potassium concentration, sodium concentration, $K^+/Na^+$ ratio and biomass. 17 SSR markers were used to evaluate these rice accessions for salt tolerance out of which five molecular markers were able to discriminate tolerant accessions from the susceptible accessions. Banding pattern of the accessions was scored comparing to the banding pattern of Dongjin. The study identifies accessions based on their association of $K^+/Na^+$ ratio with molecular markers which is very reliable. These markers identified can play a significant role in screening large set of rice accessions for salt tolerance; these markers can be utilized to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.

• Genomics & Informatics
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• v.6 no.1
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• pp.8-13
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• 2008

High-density lipoprotein (HDL) whose primary role is to transport cholesterol from peripheral tissues to the liver, is associated with the incidence of coronary heart disease. We analyzed HDL cholesterol levels in a genetically isolated population of extended Mongolian families. A total of 1002 individuals (54.5% women) from 95 families were enrolled. After genotyping by use of 1000 microsatellite markers, we performed a genome-wide linkage search with variance component analysis. The estimated heritability of HDL cholesterol was 0.45, revealing that HDL cholesterol was under significant genetic influence. We found peak evidence of linkage (LOD score=1.88) for HDL cholesterol level on chromosome 6 (nearest marker D6S1660) and potential evidences for linkage on chromosomes 1, 12 and 19 with the LOD scores of 1.32, 1.44 and 1.14, respectively. These results should pave the way for the discovery of the relevant genes by fine mapping and association analysis.

• Molecules and Cells
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• v.39 no.2
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• pp.141-148
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• 2016

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

• The Plant Pathology Journal
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• v.16 no.3
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• pp.142-146
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• 2000

Ordered differential display using RT-PCR (ODD-PCR) was conducted to have a profile of the differently expressed genes between a hypovirulent strain of Cryphonectria parasitica (UEP1) and its isogenic wild type strain (EP155/2). ODD-PCR has advantages of high sensitivity, reproducibility, proportional representation, and limited number of primer combinations comparing with other differential display methods. RNAs were prepared from 1 and 5 day liquid culture of both hypovirulent and wild type strains, and were further evaluated with the marker genes of C. parasitica such as cryparin and mating factor MF2-1, which were already proven to be specifically down-regulated by the presence of mycovirus CHV1-713. ODD-PCR was conducted using those RNAs and expressed genes were categorized to five groups according to their temporal and quantitative expression patterns. Those fives groups are CPC, CPE, CPL, CPD, and CPU which represent constitutively-expressed, early-expressed, late-expressed, down-regulated, and up-regulated, respectively. Ninety two primer combinations out of a total of 192 have been tested so far. Among the twenty to fifty distinct bands per each reaction, an average of four to ten genes was identified as viral-regulated fungal genes. Those viral-specifc genes were further analyzed by DNA sequencing followed by homology search. Characterization of 30 clones including all five groups were conducted as a preliminary data and more are under investigation.

• Molecules and Cells
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• v.19 no.3
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• pp.428-435
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• 2005

This study was carried out to assess the potential of SSR markers for variety identification by comparing SSR markers and morphological traits in tests of distinctiveness, uniformity, and stability (DUS) of pepper (Capsicum annuum L.) varieties. Twenty-seven SSR markers were polymorphic in 66 pepper varieties, revealing a total of 89 alleles. Average polymorphism information content (PIC) value was 0.529, ranging from 0.03 to 0.877. Cluster analysis of the band patterns separated the varieties into three groups corresponding to varietal types. Morphological trait-based clustering showed some degree of similarity to dendrogram topologies based on the SSR index. However, no significance correlation was found between the SSR and morphological data. SSR markers could be used to complement a DUS test of a candidate variety and to select complimentary varieties by pre-screening existing varieties in the context of protecting new varieties of pepper.

• Journal of Mushroom
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• v.20 no.2
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• pp.43-49
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• 2022

Pleurotus ostreatus is a globally cultivated mushroom crop. Cap color is a quality factor in P. ostreatus. However, cap color can spontaneously mutate, degrading the quality of the mushroom on the market. Early detection and removal of mutant strains is the best way to maintain the commercial value of the crop. To detect the cap color mutant Gonji7ho, molecular markers were developed based on insertion/deletions (InDels) derived from the comparison of mitogenomes of Gonji7ho and Gonji7hoM mushrooms. Sequencing, assembly, and comparative analysis of the two mitogenomes revealed genome sizes of 73,212 bp and 72,576 bp with 61 and 57 genes or open reading frames (ORFs) in P. ostreatus Gonji7ho and Gonji7hoM, respectively. Fourteen core protein-encoding genes, two rRNA, and 24 tRNA with some OFRs were predicted. Of the 61 genes or OFRs in the wild type, dpo, rpo, and two orf139 were missing (or remnant) in the mutant strain. Molecular markers were developed based on the sequence variations (InDels) between the two mitogenomes. Six polymorphic molecular markers could detect the mutated mitochondria by PCR. These results provide basic knowledge of the mitogenomes of wild-type and mutant P. ostreatus, and can be applied to discriminate mutated mitochondria.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.6871-6876
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• 2015

Background: The meningeal hemangiopericytoma (MHPC) is a vascular tumor arising from pericytes. Most intracranial MHPCs resemble meningiomas (MNGs) in their clinical presentation and histological features and may therefore be misdiagnosed, despite important differences in prognosis. Materials and Methods: We report 8 cases of MHPC and 5 cases of MNG collected from 2007 to 2011 from the Neuro-Surgery and Histopathology departments. All 13 samples were re reviewed by two independent pathologists and investigated by immunohistochemistry (IHC) using mesenchymal, epithelial and neuro-glial markers. Additionally, we screened all tumors for a large panel of chromosomal alterations using multiplex ligation probe amplification (MLPA). Presence of the NAB2-STAT6 fusion gene was inferred by immunohistochemical staining for STAT6. Results: Compared with MNG, MHPCs showed strong VIM (100% of cases), CD99 (62%), bcl-2 (87%), and p16 (75%) staining but only focal positivity with EMA (33%) and NSE (37%). The p21 antibody was positive in 62% of MHPC and less than 1% in all MNGs. MLPA data did not distinguish HPC from MNG, with PTEN loss and ERBB2 gain found in both. By contrast, STAT6 nuclear staining was observed in 3 MHPC cases and was absent from MNG. Conclusions: MNG and MHPC comprise a spectrum of tumors that cannot be easily differentiated based on histopathology. The presence of STAT6 nuclear positivity may however be a useful diagnostic marker.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4581-4585
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• 2012

Fms-like tyrosine kinase 3 (FLT3) performs a vital role in the pathogenesis of hematopoietic malignancies. Therefore in recent times, the focus of several studies was on use of FLT3 as a prognostic marker. The present study investigated the molecular characterization and incidence of FLT3 mutations in acute leukemia patients in Pakistan. A total of 55 patients were studied, of which 25 were suffering from acute lymphoblastic leukemia (ALL) and 30 were suffering from acute myeloid leukemia (AML). The polymerase chain reaction demonstrated FLT3/ITD mutations in 1 (4%) of 25 ALL patients, a male with the L2 subtype. In AML cases the rate was 4 (13.3%) of 30, three males and one female. The AML-M4 subtype was found in three and the AML M2 subtype in the other. In the AML cases, a statistically significant (p=0.009) relationship was found between WBC (109/L) and FLT3/ITD positivity. However, no significant relationship was found with other clinical parameters (p>0.05). In acute myeloid leukemia (AML) $FLT3/ITD^+$ mutation was more prevalent in elderly patients 31-40 age groups, 21-30 and 51-60 age groups respectively. In acute lymphoblastic leukemia (ALL) statistically no significant relationship was found between clinical features and FLT3/ITD positivity (p>0.05). However, in acute lymphoblastic leukemia (ALL) $FLT3/ITD^+$ mutation was more commonly found in age groups of 21-30.

• Reproductive and Developmental Biology
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• v.34 no.3
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• pp.263-270
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• 2010

Luteal cells produce progesterone that supports pregnancy. Steroidogenesis requires coordination of the anabolic and catabolic pathways of lipid metabolism. In the present study, the corpus luteum (CL) in early pregnancy established from luteal phase and pregnant phase was analyzed. The first study determined progesterone changes in the bovine CL at day 19 (early maternal recognition period) and day 90 in mid-pregnancy and compared them to the CL from day 12 of the estrous cycle. CL alternation was tested using two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Comparing CL from luteal phase to those from pregnant phase counterparts, significant changes in expression level were found in 23 proteins. Of these proteins 17 were not expressed in pregnant phase CL but expressed in luteal phase counterpart, whereas, the expression of the other 6 proteins was limited only in pregnant phase CL. Among these proteins, vimentin is considered to be involved in regulation of post-implantation development. In particular, vimentin may be used as marker for CL development during pregnancy because the expression level changed considerably in pregnant phase CL tissue compared with its luteal phase counterpart. Data from 2-DE suggest that protein expression was disorientated in mid pregnancy from luteal phase, but these changes was regulated with progression of pregnancy. These findings demonstrate CL development during mid-pregnancy from luteal phase and suggest that alternations of specific CL protein expression may be involved in maintenance of pregnancy.