• Journal of the Korea Organic Resources Recycling Association
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• v.18 no.3
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• pp.31-37
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• 2010

Chitinases (EC 3.2.1.14) hydrolyze the ${\beta}$-1,4-linkages in chitin, the second most abundant polymer of N-acetyl-${\beta}$-D-glucosamine which is a structural component of protective biological matrices such as fungal cell walls and insect exoskeletons. The glycosyl hydrolases 18 family including chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Since earthworms live in the soil with a lot of microbial activities and fungi are supposed to be a major component of the diet of earthworm, it has been reported that there would be appropriate immune system to protect themselves from microorganisms attacks. In this study, the novel chitinase, EaChi, from the midgut of earthworm, Eisenia andrei, were identified and characterized. To obtain full-length cDNA sequence of chitinase, RT-PCR and RACE-PCR analyses were carried out by using the previously identified EST sequence amongst cDNA library established from the midgut of E. andrei. EaChi, a partial chitinase gene, was composed of 927 nucleotides encoding 309 amino acids. By the multiple sequence alignments of amino acids with other different species, it was revealed that EaCHI is a member of glycosyl hydrolases 18 family, which has two highly conserved domains, substrate binding and catalytic domain.

• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.131-140
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• 2020

Solanum stoloniferum, one of the wild tetraploid Solanum species belonging to the Solanaceae family, is an excellent resource for potato breeding owing to its resistance to several important pathogens. However, the sexual hybridization of S. stoloniferum with S. tuberosum (potato) is hampered due to the sexual incompatibility between the two species. To overcome this and introgress the various novel traits of S. stoloniferum in cultivated potatoes, cell fusion can be performed. The identification of the fusion products is crucial and can be achieved with the aid of molecular markers. In this study, the chloroplast genome sequence of S. stoloniferum was obtained by next-generation sequencing technology, and compared with that of six other Solanum species to identify S. stoloniferum-specific molecular markers. The length of the complete chloroplast genome of S. stoloniferum was found to be 155,567 bp. The structural organization of the chloroplast genome of S. stoloniferum was similar to that of the six other Solanum species studied. Phylogenetic analysis of S. stoloniferum with nine other Solanaceae family members revealed that S. stoloniferum was most closely related to S. berthaultii. Additional comparison of the complete chloroplast genome sequence of S. stoloniferum with that of five Solanum species revealed the presence of six InDels and 39 SNPs specific to S. stoloniferum. Based on these InDels and SNPs, four PCR-based markers were developed to differentiate S. stoloniferum from other Solanum species. These markers will facilitate the selection of fusion products and accelerate potato breeding using S. stoloniferum.

• Microbiology and Biotechnology Letters
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• v.32 no.3
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• pp.256-264
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• 2004

A new primer set was developed for the detection and identification of Xanthomonas oryzae pv. oryzae, the bacterial leaf blight (BLB) pathogen in rice plant. The nucleotide sequence of hpaA gene was determined from X. o. pv. oryzae str. KACC10331, and the sequence information was used to design primers for the application of the polymerase chain reaction (PCR). The nucleotide sequence of hpaA from X. o. pv. oryzae str. KACC 10331 was aligned with those of X. campestris pv. vesicatoria, X. campestris pv. campestris, X. axonopodis pv. citri, and X. axonopodis pv. glycines. Based on these results, a primer set(XOF and XOR) was designed for the specific detection of hpaA in X. o. pv. oryzae. The length of PCR products amplified using the primer set was 534-bp. The PCR product was detected from only X. o. pv. oryzae among other Xanthomonas strains and reference bacteria. This product was used to confirm the conservation of hpaA among Xanthomonas strains by Southern-blotting. Furthermore, PCR amplification with XOF and XOR was used to detect the pathogen in an artificially infected leaf. The sensitivity of PCR detection in the pure culture suspension was also determined. This PCR-based detection methods will be a useful method for the detection and identification of X. o. pv. oryzae as well as disease forecasting.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.5
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• pp.216-222
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• 2020

Tumor necrosis factor receptor associated factor 4 (TRAF4) is found to be overexpressed in human breast cancer. It plays a role in cancer metastasis, production of reactive oxygen species, and cell polarity at membranes. The characteristics and functions of TRAF4 in pigs have not yet been identified. As the first step of research, the mRNA sequence of TRAF4 in porcine cells has been determined. To obtain the full-length sequence, rapid amplification of cDNA ends (RACE) has been carried out. Upon cloning, 2,030 bp of nucleotides were found to encode 470 amino acids, and 8 and 12 amino acids were different from those of the human and mouse TRAF4, respectively. The coding region of porcine TRAF4 was shown to be 93% and 90% homologous to human and mouse TRAF4, respectively. qPCR was conducted to determine the relative expression level of TRAF4. TRAF4 expression in pK15 was enhanced by cell-cell contacts. The mRNA levels of CLDN4, OCLN, and TJP1 at 60% and 80% confluency were significantly higher than at 40% confluency. Further, TRAF4 and tight junction-related genes were down-regulated upon treatment with TRAF4 siRNA. Thus, TRAF4 may affect the function of tight junctions in pig.

• Korean Journal of Plant Taxonomy
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• v.37 no.4
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• pp.419-430
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• 2007

This study was conducted to know the taxonomic features of nuclear ribosomal ITS DNA sequences, ITS1, ITS3 and 5.8S regions, as to nine individuals belonging to four Oxalis species in Korea and an induced species. Sequences of the same regions of sixteen taxa deposited in GenBank were also aligned with those of Korean species as outgroups. The length of ITS sequences aligned in this study is 679 by in total. Evidences, from not only the sequence similarities and divergences but also the phylogenetic and statistical treatments with ITS sequences aligned, were useful for the taxonomy of the genus. The similarity of sequences, among both cauline and acauline taxa, is high as 89% and 95% respectively, but between cauline and acauline taxa, relatively low in the range of 64~69%. The sequence divergences, among both cauline and acauline taxa, is also high as much as 0.36~0.42, but between both cauline and both acauline taxa, low as 0.04~0.06. Two groups between cauline and acauline taxa are paraphyletic, and each group makes a single Glade with a high bootstrap value. The analysis of variance, using ITS sequence aligned, revealed that taxa are significantly different in the level of 0.5%, and O. corymbosa, an induced speices, is also separated from the Korean taxa in the Duncan analysis.

• Journal of the Korean earth science society
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• v.39 no.3
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• pp.260-274
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• 2018

The purpose of this study was to propose curriculum and teaching sequence for seasonal change by exploring a learning progression. For the purpose, 4 steps of construct modeling approach (specifying construct, item design, outcome space, and measurement model) proposed by Wilson (2005) was applied. In the stage of specifying construct, 'length of shadow according to seasons', 'position of constellation according to seasons', 'seasons of the southern hemisphere and northern hemisphere', 'cause and phenomenon of seasonal change' were selected as the subconstructs of seasonal changes, and constructed a construct map showing the level of development from level 1 to level 4 for each subconstruct based on the results of the previous research. In the item design stage, we developed five assessment items consisting of 3 items in the form of C-E (choose and explain) and two items in the form of CR (constructed response), applied it to 383 elementary, middle and high school students. In the outcome space stage, the students' responses to the assessment items were categorized based on the construct map. The categories were classified into 4 levels according to student ability and scores of 1-4 were given. In the measurement model stage, we applied the partial credit model of the Rasch model and compared whether the learning pathway created from the results of students' response coincides with the construct map. Based on the results of the research, we modified the construct map and finally created hypothetical learning progression on seasonal change. Finally, we proposed an orientation of curriculum amendment and effective teaching sequence for seasonal change.

• Journal of Life Science
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• v.19 no.3
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• pp.311-316
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• 2009

The brown algae, or phaeophytes, are a large group of multicellular algae, including many notable types of seaweed. We analysed intra- and interspecific phylogenic studies within the genus Pelvetia in Korea and compared them with results of both same and different species in GenBank. The sequences for P. babingtonii in Korea were generally similar to those for P. babingtonii AF102957, and the sequences of P. siliquosa in Korea were also similar to those of P. siliquosa AF102958. Sequence variation within the Pelvetia is mostly due to nucleotide substitutions, although several small indels and some large indels can be found. Another source of sequence divergence is length variation due to stretches of short repeats that occur at the ITS1 or ITS2 in all the Pelvetia. NJ analysis consists mainly of two clades. One of them contains P. canaliculata and P. limitata, and is sister to the rest of the genus (P. siliquosa, P. compressa, and P. babingtonii). P. babingtonii is not grouped one clade. In the MP analysis, ten accessions or populations were fully resolved and all accessions from the same species formed with 99% or 100% bootstrap supports.

• Proceedings of the KIEE Conference
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• 2007.04a
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• pp.58-60
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• 2007

Magnetic Resonance Imaging(MRI) has become a very widely used medical procedur e. Clo.sed and open systems are typically used with static magnetic fields at or below 2 Tesla. BWhole body SAR(specific absorbsion rate) is the value of SAR averaged over the entire body of the patient over any period of 15 minutes. Head SAR is the value of SAR averaged over the head of the patient for any period of 10 minutes. SAR is a measure of the absorption of electromagnetic energy in the body' (typically in watts per kilogram (W/kg)). The normal operating mode comprises values of head SAR not higher than 3 W/kg. The second level controlled operating mode comprises values higher than 3 W/kg. Current FDA guidance limits the SAR in the whole body. including the head to a range of 1.5 to 4.0 W/kg, depending on the patient's clinical condition. SAR, limit restrictions are incorporated in all MRI systems. and domestic' s guidance limits the SAR in a part body. including the head to 3.2w/kg and less. The purpose of this study is to evaluate on change of head SAR in using MRI pulse sequence and to check if exceed 3.2(w/kg) level in domestic a part exposure through measured head SAR. 23 patient's the average head SAR of pulse sequence is that T2WI sagittal is 0.5375. T2WI axial(FSE) is 0.4817, T1WI axial(SE) is, 0.8179. FLAIR axial is 0.4580. GRE axial is 0.0077, Diffusion is 0.0824w/kg. The head SAR exposed per patient was proved 2.3845w/kg less than the international standard. Coefficient of correlation for the relations body weight and SAR or for the relations ETL(echo train length) and SAR is 1 value. Coefficient of correlation for the relations between TR(time to repeat) and SAR is -0.602 value. so SAR increased relative to weight body and ETL. But the relations between TR and SAR is negative definite.

• Biomedical Science Letters
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• v.9 no.3
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• Journal of KIISE:Software and Applications
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• v.34 no.5
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• pp.397-406
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• 2007

The problem of finding an optimal alignment between sequence A and B can be solved by dynamic programming algorithm(DPA) efficiently. But, if the length of string was longer, the problem might not be solvable because it requires O(m*n) time and space complexity.(where, $m={\mid}A{\mid},\;n={\mid}B{\mid}$) For space, Hirschberg developed a linear space and quadratic time algorithm, so computer memory was no longer a limiting factor for long sequences. As computers's processor and memory become faster and larger, a method is needed to speed processing up, although which uses more space. For this purpose, we present an algorithm which will solve the problem in quadratic time and linear space. By using division method, It computes optimal alignment faster than LSA, although requires more memory. We generalized the algorithm about division problem for not being divided into integer and pruned additional space by entry/exit node concept. Through the proofness and experiment, we identified that our algorithm uses d*(m+n) space and a little more (m*n) time faster than LSA.