• Korean Journal of Veterinary Research
• /
• v.40 no.1
• /
• pp.42-48
• /
• 2000

Akabane disease is transmitted through mosquitoes in cattle, sheep and goats. It shows congenital abnormalities including encephalomyetitis, hydranencephaly, neurogenic arthrogryposis, and deformed neonatal calves. Akabane viruses, 93FMX and K-9 strain, were isolated from fetal matrix of aborted cow and blood of healthy cow, respectively. S gene sequences of 93FMX and K-9 showed 100% homology with that of OBE-1 strain isolated in Japan. Based upon our sequencing data, we synthesized specific primers for PCR diagnosis. Using these primers, we were able to amplify the S gene of Akabane virus not only from the culture fluid of Vero cells but also from the brain tissue of suckling mouse inoculated with, Akabane virus. These PCR products were confirmed by Southern blot hybridization. Not only the sensitivity of PCR test was high enough to detect the viruses of $10^{1.0}TCID_{50}/ml$, but also the time for diagnosis was significantly shorter than that of the virus isolation by tissue culture method. This method was also effective for the detection of Akabane virus in the cerebrum of fetus. RT-PCR method may be used for a useful diagnostic test of the clinical cases of Akabane disease.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.3
• /
• pp.563-569
• /
• 2004

The DNA sequence of the chitosanase gene (choK) from $\beta$-Proteobacterium KNU3 showed an 1,158-bp open reading frame that encodes a protein of 386 amino acids with a novel 74 signal peptide. The degenerated primers based on the partial deduced amino acid sequences from MALDI- TOF MS analyses yielded the 820 bp of the PCR product. Based on this information, double inverse PCR cloning experiments, which use the two specific sets of PCR primers rather than single set primers, identified the unknown 1.2 kb of the choK gene. Subsequently, a 1.8 kb of full choK gene was cloned from another PCR cloning experiment and it was then subcloned into pGEM T-easy and pUC18 vectors. The recombinant E. coli clone harboring recombinant pUC18 vector produced a clear halo around the colony in the glycol chitosan plates. The recombinant ChoK protein was secreted into medium in a mature form while the intracellular ChoK was produced without signal peptide cleavage. The activity staining of PAGE showed that the recombinant ChoK protein was identical to the chitosanase of wild-type. The comparison of deduced amino acid sequences of choK revealed that there is 92% identity with that of Sphingobacterium multivorum chitosanase. Judging from the conserved module in other bacterial chitosanases, chitosanase of KNU3 strain (ChoK) belongs to the family 80 of glycoside hydrolases.

• Journal of Mushroom
• /
• v.7 no.4
• /
• pp.150-155
• /
• 2009

Because the import of Inonotus obliquus have been rapidly increased in Korea, we developed the Inonotus species-specific marker by using various sequences including ITS sequences, PCR-RFLP and STS primers and used this marker to determine both genetic relatedness and strains discrimination of Inonotus spp. Total 17 different Inonotus spp. were examined by using ITS sequences and classified into 2 different groups. One strain, ASI74008 isolated from Kamchaka island of Siberia, showed the high sequence identity (98%) at the nucleotide level to the other I. obliquus DSM strain, indicating the ASI74008 belong to I. obliquus species. Comparison of banding patterns after restriction enzyme digestions with PCR amplicons of ITS region revealed some variations depending on the species and strains. However, PCR products amplified with STS primer showed species specific patterns.Therefore, use of both STS primers and PCR-RFLP could help for better strain identification.

• The Plant Pathology Journal
• /
• v.35 no.3
• /
• pp.243-256
• /
• 2019

Field surveys for Plum pox virus (PPV) infection were conducted in stone fruit orchards all over Bulgaria. In total, 1168 out of 3020 leaf samples from cultivated Prunus spp. and wildly growing P. cerasifera trees reacted positive for PPV in DASI-ELISA with the universal monoclonal antibody (MAb) 5B. Further ELISA analyses showed that 987 and 127 isolates belonged to PPV-M and PPV-D serotypes, respectively. The plum and P. cerasifera showed 82.0% and 50.5% levels of infection, respectively followed by the peach (40.0%) and the apricot (32.0%). Five hundred fifty one PPV isolates were further typed by IC-RT-PCR with PPV-Rec, -M and -D-specific primers, targeting (Cter)NIb-(Nter) CP genome region, as 125 isolates were sequenced. The results revealed the presence of PPV-Rec, PPV-M and PPV-D and mixed infections of these strains. PPV-Rec was the most prevalent strain (49.0%), followed by PPV-M (40.1%), while PPV-D was the less spread strain (8.2%). PPV-Rec was the most common strain in plums, including the eight "old-aged" trees from the region of the first Sharka discovery. PPV-M was the most prevalent strain in peach and apricot. Phylogenetic analyses on (Cter)NIb-(Nter)CP of the isolates were performed. PPV-Rec isolates formed a homogeneous group, while PPV-M isolates split into PPV-Ma and PPV-Mb subgroups. Five separated clades were formed by the analyzed PPV-D isolates. Nucleotide sequences of the partial CP coding region of the analyzed isolates revealed a slightly higher intra-strain genetic variability in PPV-Rec and PPV-M isolates, while that of PPV-D strain isolates was higher from the reported for these strains.

• Genomics & Informatics
• /
• v.21 no.4
• /
• pp.52.1-52.10
• /
• 2023

Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.

• Journal of Microbiology
• /
• v.40 no.4
• /
• pp.274-281
• /
• 2002

The competitive quantitative PCR method targeting pcbC gene was developed for monitoring 4-chlorobiphenyl(4CB)-degrading bacteria, Pseudomonas sp. strain DJ-12, in soil microcosms. The method involves extraction of DNA from soil contaminated with 4CB, PCR amplification of a pcbC gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the elec-trophoresed PCR product by densitometry. To test the adequacy of the method, Pseudomonas sp. strain DJ-12 was introduced into both contaminated and non-contaminated soil microcosms amended with 4CB. Pseudomonas sp. strain DJ-12 was monitored and quantified by a competitive quantitative PCR in comparison with 4CB degradation and the result was compared to those obtained by using the conventional cultivation method. We successfully detected and monitored 4CB-degrading bacteria in each microcosm and found a significant linear relationship between the number of 4CB-degrading bacteria and the capacity for 4CB biodegradation. The results of DNA spiking and cell-spreading experiments suggest that this competitive quantitative PCR method targeting the pcbC gene for monitoring 4CB- degrading bacteria appears to be rapid, sensitive and more suitable than the microbiological approach in estimating the capacity of 4CB biodegradation in environmental samples.

• Journal of Microbiology and Biotechnology
• /
• v.25 no.6
• /
• pp.863-871
• /
• 2015

Bifidobacterium longum subsp. longum BBMN68, isolated from centenarians in Guangxi, China, has been proved to be a promising probiotic strain for its health benefits. In this study, the biodistribution of this strain in the rat gut was first investigated using the quantitative realtime PCR assay and propidium monoazide. Strain-specific primers were originally designed based on the BBMN68 genome sequence. Healthy rats were orally inoculated with either a single dose of BBMN68 (10¹⁰ colony-forming units/kg), or with one dose per day for 7 days and bacterial concentrations were analyzed in detail from the intestinal contents and feces of four different gut locations, including stomach, small intestine, colon, and rectum. Results indicated that strain BBMN68 could overcome the rigors of passage through the upper gastrointestinal tract and transiently accumulate in the colon, even though survival in the stomach and small intestine was not high. A good level of BBMN8 could stay in vivo for 72 h following a 7-day oral administration, and a daily administration is suggested for a considerable and continuous population of BBMN68 to be maintained in the host intestine.

• International Journal of Oral Biology
• /
• v.41 no.4
• /
• pp.199-208
• /
• 2016

The aim of this study was to identify the non-Aggregatibacter actinomycetemcomitans bacteria grown on the tryptic soy-serum-bacitracin-vancomycin (TSBV) medium, an A. actinomycetemcomitans selective medium. A total of 82 unidentified bacterial isolates from the oral cavities of a Korean population were kindly provide by the Korean Collection for Oral Microbiology. All the clinical isolates were grown on TSBV medium and bacterial DNA purified from each isolate was subjected to PCR with universal primers specific for bacterial 16S rRNA genes (16S rDNAs) sequence. The each bacterial 16S rDNA was amplified by PCR and the nucleotide sequences of it was determined by the dideoxynucleotide chain termination method. They were identified by 16S rDNA sequence comparison method at the specie-level. The data showed that Neisseria spp. (42 strains), Fusobacterium spp. (10 strains), Capnocytophaga spp. (8 strains), Propionibacterium acnes (5 strains), Aggregatibacter aprophilus (4 strains), Campylobacter spp. (5 strains), Veillonella dispar (3 strains), Streptococcus sp. (1 strain), Haemophilus parainfluenzae (1 strain), Leptotrichia wadei (1 strain), Morococcus sp./Neisseria sp. (1 strain), and Staphylococcus sp. (1 strain) were identified. These results could be used to develop a new A. actinomycetemcomitans-selective medium which is more effective than the TSBV medium in future studies.

• Korean Journal of Veterinary Research
• /
• v.39 no.4
• /
• pp.778-785
• /
• 1999

To detect CDV RNA in clinical samples and differentiate prevailing CDV virulent strains affecting susceptible animals from attenuated vaccine strains, we performed RT-PCR, RFLP, and sequencing. CDV specific primers were generated from the middle part of nucleocapsid gene. The expected size of PCR products, 519 bp, was observed in tissues of Jindo dog, poodle dog, badger, fourteen of nineteen blood samples as well as 5 vaccine strains including domestic and imported products. The PCR products obtained from tissues and PBMCs of infected animals were digested to 317- and 202-bp fragments by Bam HI, but the products obtained from four of five vaccine strains and Lederle strain were not digesed by Bam HI. Only one vaccine strain of which the PCR products were digested by Bam HI was confirmed as imported vaccine, modified Synider Hill strain. Based on seqencing data obtained from the 519-bp products, it was confirmed that Bam HI restriction site tends to be conserved in field isolates compared to the commercially available attenuated vaccine strains. Partial nucleotide sequences of CDV NP gene obtained from tissues of Jindo dog, poodle and badger shared 100% homology each other, whereas the nucleotide sequences showed 96.3, 96.5, 93.6 and 93.4% homology with Yanaka (virulent), Han95 (virulent), Lederle (attenuated) and Onderstepoort (attenuated) strain, respectively.

• Korean Journal Plant Pathology
• /
• v.14 no.3
• /
• pp.223-228
• /
• 1998

Turnip mosaic virus)TuMV-Ca) was isolated from a Chinese cabbage showing severe mosaic and black necrotic spots symptoms in Korea. The virus was identified as a strain of TuMV by its host range test, particle morphology, serology, double stranded RNA analysis. For detection of the virus, reverse transcription and polymerase chain reaction(RT-PCR) was performed with a set of 18-mer TuMV-specific primers to amplify a 876 bp DNA fragment The virus was rapidly detected from total nucleic acids of virus infected tissues as well as native viral RNA of purified virion particles by RT-PCR. Detection limit of the viral RNA by RT-PCR was 10 fg.