• Journal of Korean Dental Science
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• v.16 no.1
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• Journal of Biosystems Engineering
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• v.41 no.3
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• pp.263-272
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• 2016

Purpose: Pulse crop damage due to wild birds is a serious problem, to the extent that the rate of damage during the period of time between seeding and the stage of cotyledon reaches 45.4% on average. This study investigated a method of fundamentally blocking birds from eating crops by conducting vinyl mulching after seeding and identifying the growing locations for beans to perform punching. Methods: Infrared (IR) sensors that could measure the temperature without contact were used to recognize the locations of soybean cotyledons below vinyl mulch. To expand the measurable range, 10 IR sensors were arranged in a linear array. A sliding mechanical device was used to reconstruct the two-dimensional spatial variance information of targets. Spatial interpolation was applied to the two-dimensional temperature distribution information measured in real time to improve the resolution of the bean coleoptile locations. The temperature distributions above the vinyl mulch for five species of soybeans over a period of six days from the appearance of the cotyledon stage were analyzed. Results: During the experimental period, cases where bean cotyledons did and did not come into contact with the bottom of the vinyl mulch were both observed, and depended on the degree of growth of the bean cotyledons. Although the locations of bean cotyledons could be estimated through temperature distribution analyses in cases where they came into contact with the bottom of the vinyl mulch, this estimation showed somewhat large errors according to the time that had passed after the cotyledon stage. The detection results were similar for similar types of crops. Thus, this method could be applied to crops with similar growth patterns. According to the results of 360 experiments that were conducted (five species of bean ${\times}$ six days ${\times}$ four speed levels ${\times}$ three repetitions), the location detection performance had an accuracy of 36.9%, and the range of location errors was 0-4.9 cm (RMSE = 3.1 cm). During a period of 3-5 days after the cotyledon stage, the location detection performance had an accuracy of 59% (RMSE = 3.9 cm). Conclusions: In the present study, to fundamentally solve the problem of damage to beans from birds in the early stage after seeding, a working method was proposed in which punching is carried out after seeding, thereby breaking away from the existing method in which seeding is carried out after punching. Methods for the accurate detection of soybean growing locations were studied to allow punching to promote the continuous growth of soybeans that had reached the cotyledon stage. Through experiments using multiple IR sensors and a sliding mechanical device, it was found that the locations of the crop could be partially identified 3-5 days after reaching the cotyledon stage regardless of the kind of pulse crop. It can be concluded that additional studies of robust detection methods considering environmental factors and factors for crop growth are necessary.

• Parasites, Hosts and Diseases
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• v.57 no.1
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• pp.9-15
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• 2019

Melting temperature shift ($T_m-shift$) is a new detection method that analyze the melting curve on real-time PCR thermocycler using SYBR Green I fluorescent dye. To establish a $T_m-shift$ method for the detection of Ancylostoma ceylanicum and A. tubaeforme in cats, specific primers, with GC tail of unequal length attached to their 5' end, were designed based on 2 SNP loci (ITS101 and ITS296) of the internal transcribed spacer 1 (ITS1) sequences. The standard curve of $T_m-shift$ was established using the standard plasmids of A. ceylanicum (AceP) and A. tubaeforme (AtuP). The $T_m-shift$ method stability, sensitivity, and accuracy were tested with reference to the standard curve, and clinical fecal samples were also examined. The results demonstrated that the 2 sets of primers based on the 2 SNPs could accurately distinguish between A. ceylanicum and A. tubaeforme. The coefficient of variation (CV) of $T_m$- values of AceP and AtuP was 0.07% and 0.06% in ITS101 and was 0.06% and 0.08% in ITS296, respectively. The minimum detectable DNA concentration was $5.22{\times}10^{-6}$ and $5.28{\times}10^{-6}ng/{\mu}l$ samples of AceP and AtuP, respectively. The accuracy of $T_m-shift$ method reached 100% based on examination of 10 hookworm DNA samples with known species. In the clinical detection of hookworm in 69 stray cat fecal sample, the $T_m-shift$ detection results were consistent with the microscopic examination and successfully differentiated between the 2-hookworm species. In conclusion, the developed method is a rapid, sensitive and accurate technique and can provide a promising tool for clinical detection and epidemiological investigation of cat-derived hookworms.

• BMB Reports
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• v.37 no.2
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• pp.213-222
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• 2004

A randomly amplified polymorphic DNA (RAPD) analysis was used to identify the species- and population-specific markers of abalone; Haliotis asinina, H. ovina, and H. varia in Thai waters. Fifteen species-specific and six population-specific RAPD markers were identified. In addition, an 1650 bp band (UBC195) that was restricted to H. ovina from the Gulf of Thailand (east) was also found. All of the specific RAPD markers were cloned and sequenced. Twenty pairs of primers were designed and specificity-tested (N = 12 and 4 for target and non-target species, respectively). Seven primer pairs (CUHA1, 2, 4, 11, 12, 13, and 14) were specifically amplified by H. asinina DNA, whereas a single pair of primers showed specificity with H. ovina (CUHO3) and H. varia (CUHV1), respectively. Four primer pairs, including CUHA2, CUHA12, CUHO3, and CUHV1, were further examined against 216 individuals of abalone (N = 111, 73, and 32, respectively). Results indicated the species-specific nature of all of them, except CUHO3, with the sensitivity of detection of 100 pg and 20 pg of the target DNA template for CUHA2 and CUHA12 and CUHV1, respectively. The species-origin of the frozen, ethanol-preserved, dried, and boiled H. asinina specimens could also be successfully identified by CUHA2.

• BMB Reports
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• v.37 no.4
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• pp.493-502
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• 2004

The genetic diversity and species-diagnostic markers in the introduced apple snail, Pomacea canaliculata and in the native Thai apple snails; Pila ampullacea, P. angelica, P. pesmei, and P. polita, were investigated by restriction analysis of COI and are reported for the first time. Twenty-one composite haplotypes showing non-overlapping distributions among species were found. Genetic heterogeneity analysis indicated significant differences between species (P < 0.0001) and within P. pesmei (P < 0.0001) and P. angelica (P < 0.0004). No such heterogeneity was observed in Pomacea canaliculata (P > 0.0036 as modified by the Bonferroni procedure), P. ampullacea (P = 0.0824-1.000) and P. polita (P = 1.0000). A neighbor-joining tree based on genetic distance between pairs of composite haplotypes differentiated all species and indicated that P. angelica and P. pesmei are closely related phylogenetically. In addition, the 16S rDNA of these species was cloned and sequenced. A species-specific PCR for P. canaliculata was successfully developed with a sensitivity of detection of approximately 50 pg of the target DNA template. The amplification of genomic DNA (50 pg and 25 ng) isolated from the fertilized eggs, and juveniles (1, 7, and 15 d after hatching) of Pomacea canaliculata was also successful, and suggested that Pomacea canaliculata and Pila species can be discriminated from the early stages of development.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.656-664
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• 2022

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

• Applied Biological Chemistry
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• v.46 no.2
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• pp.74-78
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• 2003

To determine the urease inhibitory activity of various heavy metal ions, a photometric cuvette assay for measuring ammonia production was developed. In this assay, the absorbance values at 630 m were linearly increased according to the ammonia concentrations up to 3.0 mg/l (r : 0.998). The urease inhibitions upon addition of a single species of heavy metal ions were in the decreasing order of Hg(II) > Pb(II) > Cu(II) > Cd(II) > Zn(II) ions. As expected, the urease inhibitions at a fixed concentration of a single species and at varying concentrations of other species occurred in the additive way. The above results show the applicability of the current method to the selective detection on Hg(II) ions as well as the screening of heavy metal ions possibly present at various samples.

• Microbiology and Biotechnology Letters
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• v.36 no.2
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• pp.96-100
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• 2008

Diversity of lactic acid bacteria involved in 5 Korean fermented vegetables (Cot kimchi, Dongchimi, Baechu kimchi, Oisobagi, and Chonggak kimchi) was investigated using PCR-based method. PCR primer pairs targeted the recA gene were used for the detection of 7 species of lactic acid bacteria mainly found in kimchi and Lactobacillus acidophilus involved in dairy fermentation. Lactobacillus plantarum and Lactobacillus sakei were detected in all samples tested but Lactobacillus paraplantarum, Lactobacillus pentosus, and Lb. acidophilus were not detected. Lactobacillus brevis and Leuconostoc citreum were detected only from Baechu kimchi and Leuconostoc mesenteroides was detected from Got kimchi, Dongchimi, Baechu kimchi, and Oisobagi. The difference of detected species from fermented vegetables may be originated from the difference of main materials. Lb. plantarum and Lb. sakei are supposed to be broadly involved in Korean fermented vegetables.

• Korean Journal of Veterinary Research
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• v.43 no.4
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• pp.677-681
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• 2003

Currently, both the indirect fluorescent antibody test (IFAT) and enzyme linked immunosorbent assay (ELISA) have been used to detect Neospora caninum antibodies. Several factors such as the buffers, the conjugate, the pattern of fluorescence, and the cross reactivity with other apicornplexan protozoan, may result in poorly correlated data. The present study was undertaken to develop and evaluate the Neospora agglutination test (NAT) for the detection and quantification of IgG antibodies to N. caninum from various animal species. Compared to the ELISA method, the NAT with a cutoff value of 1:512 gave a high index of coincidence (kappa=0.807) and no cross reactivity to Toxoplasma gondii antiserum. Hence, this NAT method, which did not require a species-specific secondary antibody and expensive tools, would be easily available for the detection of antibodies to N. caninllm of various animal species.

• ALGAE
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• v.17 no.2
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• pp.95-104
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• 2002

Population dynamics of Anabaena and the anatoxin-a concentration were monitored with physicochemical parameters at 3 sites in the lower Naktong River from May to September in 2000. Total 4 species of Anabaena (A. flosaquae, A. smithii, A. ucrainica and A. mucosa) were identified with morphological characterisitcs. Anabaena flos-aquae was most abundant among the populations. The standing crop of Anabaena ranged from 10 to 11,220 cells · $ml^{-1}$ and biomass of Anabaena more 1,000 cells · $ml^{-1}$ was obseved once at St. Mulgeum and St. Seonam, twice at St. Hagueon out of total 9 samplings. There were not significant correlations between the standing crop of Anabaena and other physicochemical parameters such as temperature, nitrate, total nitrogen, phosphate, total phophorus and N/P ratios. The frequency of trichomes with akinetes was low and ranged from 0 to 4% in the total Anabaena population and A. smithii showed highest frequency of 2.8% among all species. The population at St. Seonam showed highest frequency of 1.4% among all sampling sties. The population in September showed the highest frequency of 3.0% among all sampling period. The frequency of trichomes with heterocysts was low and ranged from 1 to 87% inthe total Anabaena population and A. smithii showed highest frequency of 55.1% among all species. The population at St. Mulgeum showed highest frequency of 17.6% among all sampling sites. The population in August showed the highest frequency of 21.4% among all sampling period. The frequency of trichomes with akinetes and/or heterocysts was not related to all the physicochemical parameters of temperature, nitrate, total nitrogen, phosphate, total phosphorus and N/P ratios. The anatoxin-a concentations were determined in algal materials dominated by Microcystis and Anabaena from June though August by derivatization using 7-fluoro-4-nitro-2, 1,3-benzoxadiazole (NBD-F) and HPLC analysis with fluorimetric detection. All the concentrations were below the detection limit of 0.1 ㎍ · $l^{-1}$ in the present study.