• Korean Journal of Clinical Laboratory Science
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• v.48 no.3
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• pp.217-224
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• 2016

Acinetobacter baumannii (A. baumannii) is prevalent in hospital environments and is an important opportunistic pathogen of nosocomial infection. It is known that this pathogen cause herd infection in hospitals, and the mortality rate is remarkably higher for patients infected with this pathogen and already have other underlying diseases. Herein, we investigated the antibiotic resistance rate and the type of resistance genes in 85 isolates of multi-drug resistant A. baumannii from the samples commissioned to laboratory medicine in two university hospitals-in hospital A and hospital B-located in Cheonan and Chungcheong provinces, respectively, in Korea. As a result, $bla_{OXA-23-like}$ and $bla_{OXA-51-like}$ were detected in 82 stains (96.5%). These 82 strains of $bla_{OXA-23-like}$ producing A. baumannii were confirmed with the ISAba1 gene found at the top of the $bla_{OXA-23-like}$ genes by PCR, inducing the resistance against carbapenemase. The armA, AME gene that induces the resistance against aminoglycoside was detected in 34 strains out of 38 strains from Hospital A (89.5%), and in 40 strains out of 47 strains from Hospital B (85.1%), while AMEs were found in 33 strains out of 38 strains from Hospital A (70.2%) and in 44 strains out of 47 strains in Hospital B (93.6%). Therefore, it was found that most multi-drug resistant A. baumannii from the Cheonan area expressed both acethyltransferase and adenyltransferase. This study investigated the multi-drug resistant A. baumannii isolated from Cheonan and Chungcheong provinces in Korea, and it is thought that the results of the study can be utilized as the basic information to cure multi-drug resistant A. baumannii infections and to prevent the spread of drug resistance.

• Journal of Plant Biotechnology
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• v.44 no.4
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• pp.438-447
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• 2017

Flowering is one of the most important development traits related to the production of Brassica rapa crops. After planting, a sudden low temperature triggers premature flowering, which leads to a reduction in the yield and quality of harvested production. Therefore, understanding the mechanism of flowering control is important in the agricultural productivity for preventing Brassica rapa crops. Vernalization is generally known as the main factor of flowering in the Brassica plant. However, in the subspecies of Brassica rapa, some accession such as Yellow sarson and Komatsuna display the flowering phenotype without vernalization. Circadian genes, which diurnally regulate plant physiology, have a role for photoperiodic flowering but are related to the regulation of the vernalizarion mechanism. In this report, the 22 B. rapa accession were divided into two groups, vernalization and non-vernalization, and the sequenced circadian gene, BrPRR1s. Among them, the BrPRR1b gene was found to have deletion regions, which could classify the two groups. The PCR primer was designed to amplify a short band of 422bp in the vernalization type and a long band of 451bp in the non-vernalization type. This primer set was applied to distinguish the flowering types in the 43 B. rapa accession and 4 Brassica genus crop, Broccoli, cabbage, mustard, and rape. The PCR analysis results and flowering time information of each crop demonstrated that the primer set can be used as marker to discern the flowering type in Brassica crops. This marker system can be applied to the B. rapa breeding when selecting the flowering character of new progenies or introducing varieties at an early stage. In addition, these results displayed that the circadian clock genes can be a good strategy for the flowering control of B. rapa crops.

• Journal of Internet Computing and Services
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• v.5 no.5
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• pp.1-15
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• 2004

In this paper, we explain the design and implementation of GWB(Gene WorkBench), which is a web-based, integrated system for efficiently managing and analyzing genomic sequences, Most existing software systems handling genomic sequences rarely provide both managing facilities and analyzing facilities. The analysis programs also tend to be unit programs that include just single or some part of the required functions. Moreover, these programs are widely distributed over Internet and require different execution environments. As lots of manual and conversion works are required for using these programs together, many life science researchers suffer great inconveniences. in order to overcome the problems of existing systems and provide a more convenient one for helping genomic researches in effective ways, this paper integrates both managing facilities and analyzing facilities into a single system called GWB. Most important issues regarding the design of GWB are how to integrate many different analysis programs into a single software system, and how to provide data or databases of different formats required to run these programs. In order to address these issues, GWB integrates different analysis programs byusing common input/output interfaces called wrappers, suggests a common format of genomic sequence data, organizes local databases consisting of a relational database and an indexed sequential file, and provides facilities for converting data among several well-known different formats and exporting local databases into XML files.

• Korean Journal of Agricultural Science
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• v.5 no.2
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• pp.43-48
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• 1978

To information on the inheriance of heading date of rice under the short-day condition, the $F_2$ seeds obtained from all possible combinations of the diallel crosses between five leading rice varieties: Nongbaek, Tongil, Palgueng, Mangyeong and Gimmaze were grown under the short-day condition and natural condition. The days to heading were investigated and analysed for genetic components. The results obtained are summarized as follows. 1. Under the natural condition, the durations to heading of all combinations excluding Nong-baek x Palgueng and Nongbaek x Mangyeong were longer than those of their parents. mean. Whereas, under the short-day condition, the duration to heading of Mangyeong x Gimmaze combination was equal to that of their parents mean, and those of all other combinations were significantly shorter than those of their parents mean. 2. Under the natural condition, the non-allelic gene interactions were significant in days to heading, but under the short-day condition, the non-allelic gene interactions were not significant, and inheritance of days to heading revealed partial dominace in which additive effects were greater than dominant effects. 3. Tongil and Gimmaze were located on dominant zone under the natural day-length, and Nongbaek and Mangyeong were under the short-day condition. 4. Under the natual condition, dominant effects were greater than additive effects, and both heritabilities of the broad and the narrow senses were significantly low. Under the short-day condition, additive effects were significantly higher than dominant effects, and both heritabilities of the broad and the narrow senses were high.

• Journal of Mushroom
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• v.13 no.3
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• pp.217-222
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• 2015

This study was conducted to obtain a growth correlation of basal information from the development of disease resistant Flammulina velutipes cultivars through back-crossing between the strains of wild-type brown monokaryon 4019-20 and the derivative of commercial quality white monokaryons 3. The two strains were selected to back-cross for further enhancing their latent attributes and growth characteristics. The parents of 4019-$20{\times}M3$ back-crossed to reproduce $F_1$, M3-Sn. Using $F_1$, M3-Sn procured and isolated into 94 monokaryon strains. Further examination of growth characteristics carried out by back-crossing between M3 and $BC_1F_1$ from M3-n dikaryon. Monokaryon exhibited an irregular growth pattern and demonstrated to be sluggish development in the sawdust medium. However $BC_1F_1$(M3-n) dikaryon strains confirmed mostly regular growth pattern and demonstrated ordinary growth in the sawdust medium. The fruitbody of $BC_1F_1$ confirmed as light-brown colour to be the dominant gene. The colour distributions of fruitbody, $BC_1F_1$, resulted as follows; 7% of dark brown, 25% of brown, 27% of light brown, 16% of ivory and 25% of white. The ratio of the other color to white showed 3 to 1 which suggested two major genes were related to fruitbody color.

• Journal of Plant Biotechnology
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• v.42 no.3
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• pp.161-167
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• 2015

Sweetpotato [Ipomoea batatas (L.) Lam] grows well in harsh environmental conditions, and is cultivated as one of the top seven food crops in the world. Recently, sweetpotato is drawing interest from people as a healthy food because it is high in dietary fiber, vitamins, carotenoids and overall nutrition value. However, few studies have been conducted on sweetpotato genome sequencing in spite of its importance. This review is aimed at increasing the efficiency of sweetpotato genome sequencing research as well as establishing a base for gene utilization in order to control useful traits. Recently, animal and plant genome sequencing projects increased significantly. However, sweetpotato genome sequencing has not been performed due to polyploidy and heterogeneity problems in its genome. Meanwhile research on its transcriptome has been conducted actively. Recently, a draft of the diploid sweetpotato genome was reported in 2015 by Japanese researchers. In addition, the Korea-China-Japan Trilateral Research Association of Sweetpotato (TRAS) has conducted research on gene map construction and genome sequencing of the hexaploid sweetpotato Xushu 18 since 2014. The Bill & Melinda Gates Foundation launched the 'sweetpotato genomic sequencing to develop genomic tools for Sub-Sahara Africa breeding program'. The chloroplast genome sequence acquired during sweetpotato genome sequencing is used in evolutionary analyses. In this review, the trend of research in the sweetpotato genome sequencing was analyzed. Research trend analysis like this will provide researchers working toward sweetpotato productivity and nutrient improvement with information on the status of sweetpotato genome research. This will contribute to solving world food, energy and environmental problems.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3349-3355
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• 2012

Background and objectives: Chromosomal abnormalities play an important role in genesis of acute lymphoblastic leukemia (ALL) and have prognostic implications. Five major risk stratifying fusion genes in ALL are BCR-ABL, MLL-AF4, ETV6-RUNX11, E2A-PBX1 and SIL-TAL1. This work aimed to detect common chromosomal translocations and associated fusion oncogenes in adult ALL patients and study their relationship with clinical features and treatment outcome. Methods: We studied fusion oncogenes in 104 adult ALL patients using RT-PCR and interphase-FISH at diagnosis and their association with clinical characteristics and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL (t 9; 22), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (Del 1p32) were found in 82/104 (79%) patients. TCF3-PBX1 fusion gene was associated with lymphadenopathy, SIL-TAL1 positive patients had frequent organomegaly and usually presented with a platelets count of less than $50{\times}10^9/l$. Survival of patients with fusion gene ETV6-RUNX1 was better when compared to patients harboring other genes. MLL-AF4 and BCR-ABL positivity characterized a subset of adult ALL patients with aggressive clinical behaviour and a poor outcome. Conclusions: This is the first study from Pakistan which investigated the frequency of5 fusion oncogenes in adult ALL patients, and their association with clinical features, treatment response and outcome. Frequencies of some of the oncogenes were different from those reported elsewhere and they appear to be associated with distinct clinical characteristics and treatment outcome. This information will help in the prognostic stratification and risk adapted management of adult ALL patients.

• Journal of Life Science
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• v.27 no.10
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• pp.1215-1224
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• 2017

Until now, various oncogenic pathways were idenfied. The accumulation of DNA mutation induces genomic instability in the cell, and it makes cancer. The development of bioinformatics and genomics, to find the precise and reliable biomarker is available. This biomarker could be applied the early-dignosis, prediction and convalescence of cancer. Recently, Transposable elements (TEs) have been attracted as the regulator of genes, because they occupy a half of human genome, and the cause of various diseases. TEs induce DNA mutation, as well as the regulation of gene expression, that makes to cancer development. So, we confirmed the relationship between TEs and colon cancer, and provided the clue for colon cancer biomarker. First, we confirmed long interspersed nuclear element-1 (LINE-1), Alu, and long terminal repeats (LTRs) and their relationship to colon cancer. Because these elements have large composition and enormous effect to the human genome. Interestingly, colon cancer specific patterns were detected, such as the hypomethylation of LINE-1, LINE-1 insertion in the APC gene, hypo- or hypermethylation of Alu, and isoform derived from LTR insertion. Moreover, hypomethylation of LINE-1 in proto-oncogene is used as the biomarker of colon cancer metastasis, and MLH1 mutation induced by Alu is detected in familial or hereditary colon cancer. The genes, effected by TEs, were analyzed their expression patterns by in silico analysis. Then, we provided tissue- and gender-specific expression patterns. This information can provide reliable cancer biomarker, and apply to prediction and diagnosis of colon cancer.

• Journal of Plant Biotechnology
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• v.33 no.3
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• pp.153-160
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• 2006

Brassica rape is an important species used as a vegetable, oil, and fodder worldwide. It is related phylogenically to Arabidopsis thaliana, which has already been fully sequenced as a model plant. The 'Multinational Brassica Genome Project (MBGP)'was launched by the international Brassica community with the aim of sequencing the whole genome of B. rapa in 2003 on account of its value and the fact that it has the smallest genome among the diploid Brassica. The genome study was carried out not only to know the structure of genome but also to understand the function and the evolution of the genes comprehensively. There are two mapping populations, over 1,000 molecular markers and a genetic map, 2 BAC libraries, physical map, a 22 cDHA libraries as suitable genomic materials for examining the genome of B. rapa ssp. pekinensis Chinese cabbage. As the first step for whole genome analysis, 220,000 BAC-end sequences of the KBrH and KBrB BAC library are achieved by cooperation of six countries. The results of BAC-end sequence analysis will provide a clue in understanding the structure of the genome of Brassica rapa by analyzing the gene sequence, annotation and abundant repetitive DHA. The second stage involves sequencing of the genetically mapped seed BACs and identifying the overlapping BACs for complete genome sequencing. Currently, the second stage is comprises of process genetic anchoring using communal populations and maps to identify more than 1,000 seed BACs based on a BAC-to-BAC strategy. For the initial sequencing, 629 seed BACs corresponding to the minimum tiling path onto Arabidopsis genome were selected and fully sequenced. These BACs are now anchoring to the genetic map using the development of SSR markers. This information will be useful for identifying near BAC clones with the seed BAC on a genome map. From the BAC sequences, it is revealed that the Brassica rapa genome has extensive triplication of the DNA segment coupled with variable gene losses and rearrangements within the segments. This article introduces the current status and prospective of Korea Brassica Genome Project and the bioinformatics tools possessed in each national team. In the near future, data of the genome will contribute to improving Brassicas for their economic use as well as in understanding the evolutional process.

• Investigative Magnetic Resonance Imaging
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• v.17 no.3
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• pp.207-214
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• 2013

Purpose : To evaluate the MRI findings of breast cancer with BRCA mutation. Materials and Methods: We collected information of the breast cancer patients who underwent the test for BRCA gene mutation as well as preoperative breast MRI from January 2007 to December 2010. A total of 185 patients were enrolled; 33 of these patients had BRCA mutations and 152 patients did not. Among them, a total of 231 breast cancers were detected. Images of the 47 breast cancers with BRCA mutation and of the 184 breast cancers without mutations were evaluated to compare the morphologic and enhancement features on MRI. Results: With MR imaging, there were no significant difference in morphologic characteristic between two groups. However, enhancement pattern in the group with BRCA mutation were more likely to have persistent enhancement (p < 0.233), and LN metastasis was more common in breast cancers without BRCA mutation. Breast cancers with BRCA 2 mutation tend to show more persistent enhancement pattern than BRCA 1 mutation. Conclusion: In breast cancer patients with BRCA mutation, MRI didn't show significant difference in morphologic characteristics, however breast cancers with BRCA gene mutation carriers tend to have benign morphologic features on MRI, such as Type 1 kinetic curve enhancement.