• The Plant Pathology Journal
• /
• v.29 no.1
• /
• pp.31-41
• /
• 2013

The presence of Citrus tristeza virus (CTV) has previously been reported in citrus growing regions of Turkey. All serologically and biologically characterized isolates including I$\breve{g}$d${\i}$r, which was the first identified CTV isolates from Turkey, were considered mild isolates. In this study, molecular characteristics of the I d r isolate were determined by different methods. Analysis of the I$\breve{g}$d${\i}$r isolate by western blot and BD-RT-PCR assays showed the presence of MCA13 epitope, predominantly found in severe isolates, in the I$\breve{g}$d${\i}$r isolate revealing that it contains a severe component. For further characterization, the coat protein (CP) and the RNA-depen-dent RNA polymerase (RdRp) genes representing the 3' and 5' half of CTV genome, respectively, were amplified from dsRNA by RT-PCR. Both genes were cloned separately and two clones for each gene were sequenced. Comparisons of nucleotide and deduced amino acid sequences showed that while two CP gene sequences were identical, two RdRp clones showed only 90% and 91% sequence identity in their nucleotide and amino acid sequences, respectively, suggesting a mixed infection with different strains. Phylogenetic analyses of the CP and RdRp genes of I$\breve{g}$d${\i}$r isolate with previously characterized CTV isolates from different citrus growing regions showed that the CP gene was clustered with NZRB-TH30, a resistance breaking isolate from New Zealand, clearly showing the presence of severe component. Furthermore, two different clones of the RdRp gene were clustered separately with different CTV isolates with a diverse biological activity. While the RdRp-1 was clustered with T30 and T385, two well-characterized mild isolates from Florida and Spain, respectively, the RdRp-2 was most closely related to NZRB-G90 and NZRB-TH30, two well-characterized resistance breaking and stem pitting (SP) isolates from New Zealand confirming the mixed infection. These results clearly demonstrated that the I$\breve{g}$d${\i}$r isolate, which was previously described as biologically a mild isolate, actually contains a mixture of mild and severe strains.

• Radiation Oncology Journal
• /
• v.11 no.2
• /
• pp.321-330
• /
• 1993

Purpose: A retrospective analysis was performed to evaluate the incidence of radiation induced lung damage after the radiation therapy for the patients with carcinoma of the lung. Method and Materials: Sixty-six patients with lung cancer (squamous cell carcinoma 27, adenocarcinoma 14, large cell carcinoma 2, small cell carcinoma 13, unknown 10) were treated with definitive, postoperative or palliative radiation therapy with or without chemotherapy between July 1987 and December 1991. There were 50 males and 16 females with median age of 63 years (range: 33~80 years). Total lung doses ranged from 500 to 6,660 cGy (median 3960 cGy) given in 2 to 38 fractions (median 20) over a range or 2 to 150 days (median in days) using 6 MV or 15 MV linear accelerator. To represent different fractionation schedules of equivalent biological effect, the estimated single dose (ED) model, $ED=D{\dot}N^{-0.377}{\dot}T^{-0.058}$ was used in which D was the lung dose in cGy, N was the number of fractions, and T was the overall treatment time in days. The range of ED was 370 to 1357. The endpoint was a visible increase in lung density within the irradiated volume on chest X-ray as observed independently by three diagnostic radiologists. Patients were grouped according to ED, treatment duration, treatment modality and age, and the percent incidence of pulmonary damage for each group was determined. Result: In 40 of 66 patients, radiation induced change was seen on chest radiographs between 11 days and 314 days after initiation of radiation therapy. The incidence of radiation pneumonitis was increased according to increased ED, which was statistically significant (p=0.001). Roentgenographic changes consistent with radiation pneumonitis were seen in $100\%$ of patients receiving radiotherapy after lobectomy or pneumonectomy, which was not statistically significant. In 32 patients who also received chemotherapy, there was no difference in the incidence of radiation induced change between the group with radiation alone and the group with radiation and chemotherapy, among the sequence of chemotherapy No correlation was seen between incidence of radiation pneumonitis and age or sex. Conclusions: The occurrence of radiation pneumonitis varies. The incidence of radiation pneumonitis depends on radiation total dose, nature of fractionation, duration of therapy, and modifying factors such as lobectomy or pneumonectomy.

• Food Science of Animal Resources
• /
• v.28 no.1
• /
• pp.82-90
• /
• 2008

Two strains of pure lactic acid bacteria capable of forming both acid and slime were isolated from the kefir made of goat milk. The isolated strains observed by morphological and physiological properties, and their 16S rDNA partial sequence were identified as Streptococcus salivarius subsp. thermophilus(LFG-1) and Lactococcus lactis subsp. lacits(LFG-2) with over 99% homology. The optimum temperature of Str. salivarius subs. thermophilus LFG-1 for growth was $40-45^{\circ}C$, and its generation time was 40.6 minutes. The final pH of cultured broth by Str. salivarius subsp. thermophilus LFG-1 and the commercial strain Str. thermophilus Body-1 for 24hr at $37^{\circ}C$ were 4.30 and 4.55, respectively. The coagulative activity of Str. salivarius subsp. thermophilus LFG-1 was almost as strong as that of commercial strain Str. thermophilus Body-1. However, the LFG-2 strain showed lower coagulative activity than Str. thermophilus Body-1. The survival rate of lactic acid bacteria were between 22-29% in 0.3% bile extract. At pH 1.0 all of the bacteria were killed, and most of lactic acid bacteria died against pH 3.0. However, all lactic acid bacteria survived well at pH 4.5.

• Journal of KIISE:Databases
• /
• v.34 no.5
• /
• pp.396-408
• /
• 2007

After the Human Genome Project finished the sequencing of a human DNA sequence, the concerns on protein functions are increasing. Since the structures of proteins are conserved in divergent evolution, their functions are determined by their structures rather than by their amino acid sequences. Therefore, if similarities between two protein structures are observed, we could expect them to have common biological functions. So far, a lot of researches on protein structure alignment have been performed. However, most of them use RMSD(Root Mean Square Deviation) as a similarity measure with which it is hard to judge the similarity level of two protein structures intuitively. In addition, they retrieve only one result having the highest alignment score with which it is hard to satisfy various users of different purpose. To overcome these limitations, we propose a novel protein structure alignment algorithm based on MRPD(Maximum of Residue Pair Distance) and SG (Similarity Graph). MRPD is more intuitive similarity measure by which fast tittering of unpromising pairs of protein pairs is possible, and SG is a compact representation method for multiple alignment results with which users can choose the most plausible one among various users' needs by providing multiple alignment results without compromising the time to align protein structures.

• Journal of Biomedical Engineering Research
• /
• v.23 no.1
• /
• pp.61-72
• /
• 2002

In this parer, a new harmonic imaging technique is Proposed and evaluated experimentally. In the Proposed method. a weighted chirp signal with a hanning window is transmitted. The RF samples obtained on each array element are individually compressed by correlating with the reference signal defined as the 2nd harmonic component($2f_0$) of a transmitted chirp signal generated in a square-law system. The correlator output will then consist of the compressed version of the $2f_0$ component generated in tissue and the crosscorrelation sequence of the fundamental($f_0$) and 2f$_{0}$components. The Proposed method uses the compressed $2f_0$ component to form an image. for which the crosscorrelation term should be suppressed below at least -50dB. The Proposed method has two process, 2f$_{0}$-correlation and $2f_0$-correlation(PI) . $2f_0$-correlation can successfully eliminate the $f_0$ component with a single transmit-receive events and therefore is more efficient than the conventional Pulse inversion method in terms of the frame rate. 2i)-correlation(Pl) Performs pulse compression after applying pulse inversion method for the 2nd harmonic image with high resolution and SNR. Another advantage of the proposed method is that the SNR of 2nd harmonic imaging can be improved without limitation by increasing the duration of the chirp signal. The proposed method was verified through both the computer simulations and actual experiments .ts .

• Journal of Life Science
• /
• v.26 no.1
• /
• pp.42-49
• /
• 2016

The retinoic acid (RA) plays an important role in the growth and development of many cells, and bioactive RA concentration is regulated by several enzymes, including CYP26A1. The expression of the CYP26A1 gene is regulated by RA, and the CYP26A1 gene is one of the candidates for RA-responsive genes. Although CYP26A1 genes are cloned from several animals, cloning of the CYP26A1 gene from cows has not been reported yet. The promoter region of CYP26A1 from cows was cloned by PCR and analyzed by sequence alignment with human and mouse CYP26A1. The RA-responsive element (RARE), DR-5 (ttggg), was located in this region and was perfectly conserved. The promoter region of bovine CYP26A1, which contains DR-5, was ligated to the luciferase reporter gene on transient transfection assays. The expression of CYP26A1-Luc promoter was activated by ATRA treatment in lung-derived mtCC cells. Co-transfection with RAR-α or -β with ATRA significantly activates the expression of CYP26A1-Luc promoter; however, it was less effective with either RAR-γ or RXR-γ. In addition, the endogenous gene expressions measured by Q-RT-PCR in mtCC cells were not significantly affected by ATRA treatment for 2 days; however, the expression of the endogenous CYP26A1 gene was diminished sharply at day 3 with ATRA treatment. In conclusion, the promoter region of bovine CYP26A1 contains conserved DR-5 RARE, which functions as a binding site for RAR-α or -β, and it is involved in the regulation of CYP26A1 gene expression and the control of RA signaling in mtCC cells.

• Journal of Life Science
• /
• v.17 no.7 s.87
• /
• pp.970-975
• /
• 2007

For the screening of ${\gamma}-aminobutyric$ acid (CABA)-producing bacteria, 86 bacterial strains which produce GABA were isolated from Kimchi and Salted fisk .Among these, three strains designated AML15, AML45-1, AML72 with relatively high GABA productivity were selecled by thin layer chromatography (TLC). To elucidate the relationship between isolated strains and the genus Lactobacillus, their 16S rDNA sequence were examined. The result of their DNA sequences showed 99% similarity with Lactobacillus brevis ATCC 367. On the basis of the these results, isolated strains were identified as Lactobacillus brevis and designated L. brevis AML15. In order to determine the optimum conditions for GABA production, the isolated strains were cultivated in pyridoxal phosphate (PLP) and monosodium glutami. acid (MSG). Results showed that L. brevis AML15 had the highest CABA productivity with 10,424 $nM/{\mu}l$ concentration in MRS broth containing 5% (w/v) MSG and 10 ${\mu}M$ PLP at pH 5.0. The results imply that L. brevis AML15 has the potential to be developed as a strain for GABA hyper-production.

• Korean Journal of Microbiology
• /
• v.36 no.4
• /
• pp.273-278
• /
• 2000

The aacCl, aacC2, aacC3, and aacC4 genes, which encode aminoglycoside acetyltransferase AAC(3)-I, AA(3)-II, AAC(3)-III, and AAC(3)-IV, respectively, and aerolysin genes in water samples from Juam lake were surveyed by polymerase chain reaction. Surface water was collected from January 1996 to December 1998, and then bacterial DNA was extracted from the water. Twelve samples were tested by PCR to servey the genes for aminoglycoside acetyltransferase and aerolysin in the lake water. The aacC2 gene was detected in 9 of 12 DNA samples. Among 9 samples showing aacC2 positive, 7 samples were associated with Tn3 sequence. However, none of the twelve samples amplified the expected DNA fragment for aacC1, aacC3, and aacC4 genes. PCR primer to detect the aerolysin gene was designed using the conserved region of the genes for aerolysin and hemolysin of Aeromonas spp. This primer set successfully amplified the expected 414 bp PCR product with the DNA samples from the lake water. The aerolysin gene was detected in 7 of 12 DNA samples. When Southern hybridization of the gel with probe was performed, the aerolysin gene was detected in 10 of 12 DNA samples. However, the seasonal fluctuation of these genes was not found.

• Journal of Biomedical Engineering Research
• /
• v.32 no.3
• /
• pp.245-250
• /
• 2011

Parallel imaging technique can provide several advantages for a multitude of MRI applications. Especially, in SENSE technique, sensitivity maps were always required in order to determine the reconstruction matrix, therefore, a number of difference approaches using sensitivity information from coils have been demonstrated to improve of image quality. Moreover, many filtering methods were proposed such as adaptive matched filter and nonlinear diffusion technique to optimize the suppression of background noise and to improve of image quality. In this study, we performed SENSE reconstruction using computer simulations to confirm the most suitable method for the feasibility of filtering effect and according to changing order of polynomial fit that were applied on variation of spatial resolution of sensitivity map. The image was obtained at 0.32T(Magfinder II, Genpia, Korea) MRI system using spin-echo pulse sequence(TR/TE = 500/20 ms, FOV = 300 mm, matrix = $128{\times}128$, thickness = 8 mm). For the simulation, obtained image was multiplied with four linear-array coil sensitivities which were formed of 2D-gaussian distribution and the image was complex white gaussian noise was added. Image processing was separated to apply two methods which were polynomial fitting and filtering according to spatial resolution of sensitivity map and each coil image was subsampled corresponding to reduction factor(r-factor) of 2 and 4. The results were compared to mean value of geomety factor(g-factor) and artifact power(AP) according to r-factor 2 and 4. Our results were represented while changing of spatial resolution of sensitivity map and r-factor, polynomial fit methods were represented the better results compared with general filtering methods. Although our result had limitation of computer simulation study instead of applying to experiment and coil geometric array such as linear, our method may be useful for determination of optimal sensitivity map in a linear coil array.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.1
• /
• pp.106-112
• /
• 2014

Very few plant growth-promoting rhizobacteria (PGPR) are known to produce gibberellins (GAs). The current study aimed to isolate a phytohormone-producing PGP rhizobacterium from soil and assess its potential to enhance plant growth. The newly isolated bacterium was identified as Leifsonia soli sp. SE134 on the basis of partial 16S ribosomal RNA gene sequence. Application of L. soli culture filtrate significantly increased the biomass, hypocotyl, and root lengths of cucumber seeds as compared with non-inoculated sole medium and distilled water treated controls. Furthermore, the PGPR culture was applied to the GA-deficient mutant rice cultivar Waito-C. Treatment with L. soli SE134 significantly increased the growth of Waito-C rice seedlings as compared with controls. Upon chromatographic analysis of L. soli culture, we isolated, detected and quantified different GAs; namely, $GA_1$ ($0.61{\pm}0.15$), $GA_4$ ($1.58{\pm}0.26$), $GA_7$ ($0.54{\pm}0.18$), $GA_8$ ($0.98{\pm}0.15$), $GA_9$ ($0.45{\pm}0.17$), $GA_{12}$ ($0.64{\pm}0.21$), $GA_{19}$ ($0.18{\pm}0.09$), $GA_{20}$ ($0.78{\pm}0.15$), $GA_{24}$ ($0.38{\pm}0.09$), $GA_{34}$ ($0.35{\pm}0.10$), and $GA_{53}$ ($0.17{\pm}0.05$). Plant growth promotion in cucumber, tomato, and young radish plants further evidenced the potential of this strain as a PGP bacterium. The results suggest that GA secretion by L. soli SE134 might prove advantageous for its ameliorative role in crop growth. These findings can be extended for improving the productivity of different crops under diverse environmental conditions.