• Journal of fish pathology
• /
• v.24 no.2
• /
• pp.53-64
• /
• 2011

In quantitative studies of clinical signs, rock bream of adults and juveniles infected with Megalocytivirus IVS-1 isolated from rock bream (Oplegnathus fasciatus) in Korea showed average $4.49{\pm}1.13$ and $4.85{\pm}1.06$ of spleen index respectively. In challenge experiments, Megalocytivirus IVS-1 induced 100% cumulative mortality in both adult and juvenile rock bream. However we found 60% cumulative mortality in juvenile red sea bream (Pagrus major) even after 30 days of injection, which contradicted with the results of other laboratories. Interestingly, IVS-1 infected red sea bream of the same juvenile size with rock bream showed lower spleen index compared to that of rock bream. In real-time PCR, there was continuous increasing of the numbers of viral copies ($2.03{\times}10^7$ copies/mg) in the spleen of juvenile rock bream infected, which were different from those in adult rock bream showing plateau level after reaching to the peak level. Moreover, enlarged cell numbers in the infected spleen were also increased continuously in the juvenile but not in adult of rock bream, even decreased after reaching to peak level. Consequently, significant differences in clinical signs: cumulative mortality. spleen index and viral copy number were found between rock bream and red sea bream, but not between adult and juvenile rock bream. Certainly quantitative expression of clinical sign as in this study may be a way to compare the progression of megalocitiviral disease more accurately in different species or physiological conditions.

• Genomics & Informatics
• /
• v.15 no.3
• /
• pp.87-97
• /
• 2017

Multiple myeloma (MM) is a malignant disease caused by an abnormal proliferation of plasma cells, of which the prognostic factors include chromosomal abnormality, ${\beta}$-2 microglobulin, and albumin. Recently, the term chromothripsis has emerged, which is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event. Many studies have shown an association of chromothripsis with the prognosis in several cancers; however, few studies have investigated it in MM. Here, we studied the association between chromothripsis-like patterns and treatment resistance or prognosis. First, we analyzed nine MM cell lines (U266, MM.1S, RPMI8226, KMS-11, KMS-12-BM, KMS-12-PE, KMS-28-BM, KMS-28-PE, and NCI-H929) and bone marrow samples of four patients who were diagnosed with MM by next-generation sequencing-based copy number variation analysis. The frequency of the chromothripsis-like pattern was observed in seven cell lines. We analyzed the treatment-induced chromothripsis-like patterns in KMS-12-BM and KMS-12-PE cells. As a result, breakpoints and chromothripsis-like patterns were increased after drug treatment in the relatively resistant KMS-12-BM. We further analyzed the patients' results according to the therapeutic response, which was divided into sensitive and resistant, as suggested by the International Myeloma Working Group. The chromothripsis-like pattern was more frequently observed in the resistant group. In the sensitive group, the frequency of the chromothripsis-like pattern decreased after treatment, whereas the resistant group showed increased chromothripsis-like patterns after the treatment. These results suggest that the chromothripsis-like pattern is associated with treatment response in MM.

• Journal of Plant Biotechnology
• /
• v.41 no.3
• /
• pp.127-133
• /
• 2014

Four transgenic rice lines harboring insect-resistant gene cry3A showed ideal field performances characterized by high considerable resistance to rice water weevil (Lissorhoptrus oryzophilus Kuschel). In this study, we estimated the insertion number of foreign genes, and analyzed the flanking sequences of T-DNAs in rice genome. As a result, T-DNA of BT12R1 line was inserted in exon region of rice chromosome 10. Two copies of T-DNAs were inserted in line BT12R2. BT12R3 line was analyzed at only left border flanking sequence. BT12R4 line was confirmed one copy of foreign gene insertion at the position 24,516,607 ~ 24,516,636 of rice chromosome 5, accompanied by a deletion of 30 bp known genomic sequences. This intergenic position was confirmed none of expressed gene and any deletion/addition of T-DNA sequence. In conclusion, these molecular data of rice water weevil resistant Bt rice would be used to conduct the biosafety and environment risk assessment for GM crop commercialization.

• Korean Journal of Microbiology
• /
• v.50 no.3
• /
• pp.210-215
• /
• 2014

Pseudomonas nitroreducens TX1 was isolated from a rice field drainage in Taiwan. The bacterium is of special interest because of its capability to use a group of nonionic surfactants such as alkylphenol polyethoxylates even at high concentrations as a sole carbon source. In this study, a small cryptic circular plasmid, pTX1, was characterized from P. nitroreducens TX1. It is 2,286 bp in length with a GC content of 63.3% and harbors three open reading frames, $Rep_{pTX1}$ and functionally unidentified ORF1 and ORF2. The predicted $rep_{pTX1}$ gene product is homologous to Rep proteins of plasmids belonging to the pC194/pUB110 family, which is predominantly found in Gram-positive bacteria and is known to replicate by the rolling-circle mechanism. The copy number of pTX1 was estimated to be about 150 in each cell. Based on the genetic fingerprints and comparison with other plasmids, it is concluded that pTX1 replicates by a rolling circle mechanism which is rarely found for Pseudomonas plasmids.

• Parasites, Hosts and Diseases
• /
• v.51 no.3
• /
• pp.269-277
• /
• 2013

Amoebic keratitis (AK) caused by Acanthamoeba is one of the most serious corneal infections. AK is frequently misdiagnosed initially as viral, bacterial, or fungal keratitis, thus ensuring treatment delays. Accordingly, the early detection of Acanthamoeba would contribute significantly to disease management and selection of an appropriate anti-amoebic therapy. Recently, the loop-mediated isothermal amplification (LAMP) method has been applied to the clinical diagnosis of a range of infectious diseases. Here, we describe a rapid and efficient LAMP-based method targeting Acanthamoeba 18S rDNA gene for the detection of Acanthamoeba using clinical ocular specimens in the diagnosis of AK. Acanthamoeba LAMP assays detected 11 different strains including all AK-associated species. The copy number detection limit for a positive signal was 10 DNA copies of 18S rDNA per reaction. No cross-reactivity with the DNA of fungi or other protozoa was observed. The sensitivity of LAMP assay was higher than those of Nelson primer PCR and JDP primer PCR. In the present study, LAMP assay based on directly heat-treated samples was found to be as efficient at detecting Acanthamoeba as DNA extracted using a commercial kit, whereas PCR was only effective when commercial kit-extracted DNA was used. This study showed that the devised Acanthamoeba LAMP assay could be used to diagnose AK in a simple, sensitive, and specific manner.

• Journal of Plant Biotechnology
• /
• v.34 no.4
• /
• pp.347-354
• /
• 2007

Commercialization of genetically modified (GM) plants will be required the assessment of risks associated with the release of GM plants that should include a detailed risk assessment of their impacts in human health and the environment. Prior to GM plant release, applicants should provide the information on GM crops for approval. We carried out this study to provide the molecular data for risk assessment of the GM Chinese cabbage plants with insect-resistance gene, modified CryIAc, which we obtained by Agrobacterium-transformation. From the molecular analysis with GM Chinese cabbage, we confirmed the transgene copy number and stability, the expression of the transgene, and integration region sequences between the transgene and the Chinese cabbage genome. Based on the unique integration DNA sequences, we designed specific primer set to detect GM Chinese cabbage and set up the GM cabbage detection method by qualitative PCR analysis. Qualitative analysis with GM Chinese cabbage progenies analysis was revealed the same as the result of herbicide treatment. Our results provided the molecular data for risk assessment analysis of GM Chinese cabbage and demonstrated that the primer set proposed could be useful to detect GM Chinese cabbage.

• Journal of Plant Biotechnology
• /
• v.36 no.4
• /
• pp.384-391
• /
• 2009

Previously, two events (H15 and B20) of transgenic pepper (Capsicum annuum L.) that enhanced resistance to Cucumber mosaic virus (CMV) by the introduction of CMV coat protein (CP) gene were constructed. Presently, a single copy number of the CP gene was revealed in H15 and B20 by Southern blot. To predict possible unintended effects due to transgene insertion in an endogenous gene, we carried out sequencing of the 5'-flanking region of the CP gene and a Blastbased search. The results revealed that insertion of the transgene into genes encoding putative proteins may occur in the H15 and B20 transgenic event. Mutiplex polymerase chain reaction (PCR) for simultaneous detection and identification of transgenic pepper was conducted with a set of nine primers. Both transgenic event were differentiated from non-transgenic event by the presence of 267 bp and 430 bp PCR products indicative of CP gene specific primer pairs and primer pairs targeting the CP gene and 35S promoter. H15 and B20 uniquely possessed a 390 bp and 596 bp PCR product, respectively. The presence of a 1115 bp product corresponding to intrinsic pepper actin gene confirmed the use of pepper DNA as the PCR template. The primer set and PCR conditions used presently may allow the accurate and simple identification of CMV resistant transgenic pepper.

• Journal of Plant Biotechnology
• /
• v.38 no.2
• /
• pp.105-116
• /
• 2011

Transgenic zoysiagrass (Zoysia japonica Steud.) expressing the bar gene inserted in the plant genome has been generated previously through Agrobacterium tumefaciens-mediated transformation. The GM zoysiagrass (event: JG21) permits efficient management of weed control of widely cultivated zoysiagrass fields, reducing the frequency and cost of using various herbicides for weed control. Now we have carried out the environmental risk assessment of JG21 prior to applying to the governmental regulatory agency for the commercial release of the GM turf grass outside of test plots. The morphological phenotypes, molecular analysis, weediness and gene flow from each test plot of JG21 and wild-type zoysiagrasses have been evaluated by selectively analyzing environmental effects. There were no marked differences in morphological phenotypes between JG21 and wild-type grasses. The JG21 retained its stable integration in the host plant in T1 generation, exhibiting a 3:1 segregation ratio according to the Mendelian genetics. We confirmed the copy number (1) of JG21 by using Southern blot analysis, as the transgenic plants were tolerant to ammonium glufosinate throughout the culture period. From cross-fertilization and gene flow studies, we found a 9% cross-pollination rate at the center of JG21 field and 0% at distances over 3 m from the field. The JG21 and wild-type zoysiagrass plants are not considered "weed" because zoysiagrasses generally are not dominant and do not spread into weedy areas easily. We assessed the horizontal gene transfer (HGT) of the transgene DNA to soil microorganisms from JG21 and wild-type plants. The bar gene was not detected from the total genomic DNA extracted from each rhizosphere soil of GM and non-GM Zoysia grass fields. Through the monitoring of JG21 transgene's unintentional release into the environment, we found no evidence for either pollen mediated gene flow of zoysiagrass or seed dispersal from the test field within a 3 km radius of the natural habitat.

• Korean Journal of Microbiology
• /
• v.44 no.2
• /
• pp.93-97
• /
• 2008

RraA is a recently discovered protein inhibitor that regulates the enzymatic activity of RNase E, which plays a major role in the decay and processing of RNAs in Escherichia coli. It has also been shown to regulate the activity of RNase ES, a functional Streptomyces coelicolor ortholog of RNase E, which has 36% identity to the amino-terminal region of RNase E. There are two open reading frames in S. coelicolor genome that can potentially encode proteins having more than 35.4% similarity to the amino acid sequence of RraA. DNA fragment encoding one of these RraA orthologs, designated as RraAS2 here, was amplified and cloned in to E. coli vector to test whether it has ability to regulate RNase E activity in E. coli cells. Co-expression of RraAS2 partially rescued E. coli cells over-producing RNase E from growth arrest, although not as efficiently as RraA, induced by the increased ribonucleolytic activity in the cells. The copy number of ColEl-type plasmid in these cells was also decreased by 14% compared to that in cells over-producing RNase E only, indicating the ability of RraAS2 to inhibit RNase E action on RNA I. We observed that the expression level of RraAS2 was lower than that of RraA by 4.2 folds under the same culture condition, suggesting that because of inefficient expression of RraAS2 in E. coli cells, co-expression of RraAS2 was not efficiently able to inhibit RNase E activity to the level for proper processing and decay of all RNA species that is required to restore normal cellular growth to the cells over-producing RNase E.

• The Journal of Korean Academy of Prosthodontics
• /
• v.40 no.2
• /
• pp.131-139
• /
• 2002

There have been many studies about marginal discrepancy of single restorations made by various systems and materials. But many of statistical inferences are not definite because of sample size, measurement number, measuring instruments. etc. The purpose of this study was to compare the marginal adaptations of the anterior single restorations made by different systems and to consider more desirable statistical methods in analysing the marginal fit. The in vitro marginal discrepancies of three different all-ceramic crown systems (Celay In-Ceram. Conventional In-Ceram. IPS Empress 2 layering technique) and one control group (PFM) were evaluated and compared. The crowns were made from one extracted maxillary central incisor prepared with a 1mm shoulder margin and $6^{\circ}$ taper walls by milling machine. 10 crowns per each system were fabricated. Measurements or a crown were recorded at 50 points that were randomly selected for marginal gap evaluation. Non-parametric statistical analysis was performed for the results. Within the limits of this study, the following conclusions were drawn: 1 Mean gap dimensions and standard deviations at the marginal opening for the maxillary incisor crowns were $98.2{\pm}40.6{\mu}m$ for PFM, $83.5{\pm}18.7{\mu}m$ for Celay In-Ceram, $104.9{\pm}44.1{\mu}m$ for conventional In-Ceram, and $45.5{\pm}11.5{\mu}m$ for IPS Empress 2 layering technique. The IPS Empress 2 system showed the smallest marginal gap (P<0.05). The marginal openings of the other three groups were not significantly different (P<0.05). 2 The marginal discrepancies found in this study were all within clinically acceptable standards ($100\sim150{\mu}m$). 3. When the variable is so controlled that the system may be the only one, mean value is interpreted to be the marginal discrepancy of a restoration which is made by each system and standard deviation is to be technique-sensitivity of each one. 4. From the standard deviations. the copy-milling technique (Celay/In-Ceram) was not considered to be technique-sensitive in comparison with other methods. 5. Parametric analysis is more reliable than non-parametric one in interpretation of the mean and standard deviation. The sample size of each group has to be more than 30 to use parametric statistics. The level of clinically acceptable marginal fit has not been established. Further studies are needed.