• Archives of Pharmacal Research
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• v.28 no.7
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• pp.854-858
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• 2005

A Lactobacillus isolate was collected from the feces of a healthy Korean individual and named as Lactobacillus ruminus SPM0211. It was further characterized by subjecting it to an antibiotic resistance test and genetic analysis. In the antibiotic resistance test, all tested Lactobacillus spp. were classified as 'high resistance' for multiple antibiotics, such as isoniazid, ethambutol, cycloserine, and vancomycin. L. ruminus SPM0211 was classified as 'high resistance' for streptomycin also, while the other tested Lactobacillus spp. were classified as low resistance. This suggests that the antimicrobial spectra may be a good indicator in the discrimination of this strain among the tested Lactobacillus spp. In a polymerase chain reaction-random amplified polymorphic DNA (PCR-RAPD) analysis using the Microbial Uniprimer kit, L. ruminus SPM0211, and L. suebicus were clustered as a group with a 74.3% similarity level, suggesting that these two species are genetically related. Thus, our data suggest that the PCR-RADP method using the Microbial Uniprimer kit may be valuable in discriminating L. ruminus SPM0211 from other Lactobacillus spp.

• Journal of dental hygiene science
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• v.19 no.2
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• pp.86-95
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• 2019

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.

• Journal of agriculture & life science
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• v.50 no.2
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• pp.53-59
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• 2016

Bacterial fruit blotch(BFB) of cucurbits caused by Acidovorax citrulli(Acc) continues to diminish fruit yields. The aim of this study was to address whether two genetically distinct populations of Acc are present in watermelon-growing fields in Korea. For this purpose, we used the enterobacterial repetitive intergenic consensus polymerase chain reaction(ERIC-PCR) profiling and substrate-utilization profiles. According to the results of ERIC-PCR, group I and II strains showed clearly differentiated PCR-based fingerprinting profiles. Differences between group I and II strains included amplification of unique, group-specific DNA fragments such as the 1.3-, 0.28-, and 0.25-kb fragments in ERIC-PCR. Acc stains belonging to group I did not use L-leucine, whereas group II strains did use the substrate. Our results support the genetic differentiation of Acc strains into two groups and demonstrate that Acc strains from both groups are previously existed in watermelon-growing fields in Korea. Information about the genetic diversity of Acc under the present study will help scientists and managers form strategies to control BFB.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.3
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• pp.253-258
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• 2010

In this study, a total of 25 lines consisting of five native ginseng collections from Poonggi area, five lines from Geumsam area and 15 varieties were analyzed and clustered for the selection of Poonggi native ginseng in Korea using DNA markers. The results indicated that the long cluster distance were observed between the collections of 331002, 331004, 331005, 331007 and 331026 from Poonggi area, and the collections of 332009, 332021, 332046, 332050 and 332066 from Geumsan area because of the sensible differences on the number of leaves per stem, stem color and petiole color. Thus, the collections from Poonggi area with specific characters consisting of one stem per plant, five leaves per stem and broad elliptic leaflet shape were finely classified using nine primers including OPD05, OPD20, OPG17, OPH05 and so on. In this study, the collection of 331007 from Poonggi area was considered as the respective collection with above characters. Thus, the nine primers such as OPD05 and so on, will be used to select the Poonggi ginseng in the future studies.

• Korean Journal of Microbiology
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• v.51 no.4
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• pp.398-406
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• 2015

Culture-dependent ARDRA and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Halichondria panicea collected from Jeju Island. A total of 120 bacterial strains associated with the sponge were cultivated using modified Zobell and Marine agar media. PCR amplicons of the 16S rRNA gene from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rRNA gene sequences derived from ARDRA patterns showed more than 96% similarities compared with known bacterial species, and the isolates belonged to four classes, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Firmicutes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rRNA genes amplified from the sponge-derived total gDNA showed 14 DGGE bands, and their sequences showed 100% similarities compared with the sequences available in GenBank. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of seven classes, including Alphaproteobacteria, Gammaproteobacteria, Acidobacteria, Actinobacteira, Bacteroidetes, Cyanobacteria, and Chloroflexi. According to both the ARDRA and DGGE methods, three classes, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, were commonly found in H. panicea. However, overall bacterial community in the sponge differed depending on the analysis methods. Sponge showed more various bacterial community structures in culture independent method than in culture-dependent method.

• Horticultural Science & Technology
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• v.32 no.4
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• pp.525-534
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• 2014

Microsatellite markers were used to identify 58 major commercial melon cultivars, and to assess hybrid seed purity of a melon breeding line known as '10H08'. A set of 412 microsatellite primer pairs were utilized for fingerprinting of the melon cultivars. Twenty-nine markers showed hyper-variability and could discriminate all cultivars on the basis of marker genotypes, representing the genetic variation within varietal groups. Cluster analysis based on Jaccard's distance coefficients using the UPGMA algorithm categorized 2 major groups, which were in accordance to morphological traits. The DNA bulks of female and male parents of breeding line '10H08' were tested with 29 primer pairs based on microsatellites to investigate purity testing of $F_1$ hybrid seeds, and 5 primer pairs exhibited polymorphism. One microsatellite primer pair (CMGAN12) produced unambiguous polymorphic bands among the parents. Among 192 seeds tested with CMGAN12, progeny possibly generated by self-pollination of the female parent were clearly distinguished from the hybrid progeny. These markers will be useful for fingerprinting melon cultivars and can help private seed companies to improve melon seed purity.

• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.1971-1982
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• 2017

Piliated Lactobacillus rhamnosus (pLR) strains possess higher adherent capacity than non-piliated strains. The objective of this study was to isolate and characterize probiotic pLR strains in human fecal samples. To this end, mouse polyclonal antiserum (anti-SpaA) against the recombinant pilus protein (SpaA) of L. rhamnosus strain GG (LGG) was prepared and tested for its reactivity and specificity. With the anti-SpaA, a method combining the de Man, Rogosa, and Sharpe (MRS) agar plating separation and colony immunoblotting (CIB) was developed to isolate pLR from 124 human fecal samples. The genetic and phenotypic characteristics of the resultant pLR isolates were compared by randomly amplified polymorphic DNA (RAPD) fingerprinting, and examination of adhesion to Caco-2 cells, hydrophobicity, autoaggregation, and in vitro gastrointestinal tolerance. Anti-SpaA specifically reacted with three pLR strains of 25 test strains, as assessed by western blotting, immunofluorescence flow cytometry, and immunoelectron microscopy (IEM) assays. The optimized MRS agar separation plus anti-SpaA-based CIB procedure could quantitatively detect $2.5{\times}10^3CFU/ml$ of pLR colonies spiked in $10^6CFU/ml$ of background bacteria. Eight pLR strains were identified in 124 human fecal samples, and were confirmed by 16S RNA gene sequencing and IEM identification. RAPD fingerprinting of the pLR strains revealed seven different patterns, of which only two isolates from infants showed the same RAPD profiles with LGG. Strain PLR06 was obtained with high adhesion and autoaggregation activities, hydrophobicity, and gastrointestinal tolerance. Anti-SpaA-based CIB is a rapid and inexpensive method for the preliminary screening of novel adherent L. rhamnosus strains for commercial purposes.

• Journal of Embryo Transfer
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• v.16 no.3
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• pp.193-201
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• 2001

This study was designed to examine the factors affecting in fertilization and development of embryos in vitro, and to examine whether zone drilling by laser irradiation can improve the hatching rate of IVF embryos from DNA marker-proved Hanwoo. DNA markers related to marbling score were identified using DNA fingerprinting with Ml3 probe and restriction enzyme Hae III. Oocytes were aspirated from immature ovarian follicles using a combined method of rectal ovarian-palpation and transvaginal ultrasound-guidance(6.5MHz) under local anesthesia. The aspirated oocytes were washed twice with fresh D-PBS containing 5% FBS and were rewashed 4 to 5 times with TCM-199 containing 5% FBS. A morphological grade of I to IV was assigned to each oocyte. Data were analyzed using the GLM procedure of SAS. Sperm separation methods did not have any significant effect on cleavage or developmental abilities of IVF embryos. Significantly(P<0.05) higher cleavage rate was observed in embryos from GI(60.0%, 3/5), GII(69.2%, 18/26) and GIII(62.1%, 59/95) compared to embryos from GIV oocytes(36.2%, 25/69). And the developmental rate to blastocyst stage was higher(P<0.05) in embryos from GI(33.3%, 1/3) and GII oocytes(38.9%, 7/18) than those from GIII(16.9%,10/59) and GIV oocytes(4.0%, 1/25). There was no significant difference in development of IVF embryos to blastocyst by media for in vitro culture. Proportion of hatched blastocyst was significantly(P<0.05) higher in embryos received zona drilling by laser than those of non-drilled.

• Journal of Embryo Transfer
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• v.16 no.3
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• pp.183-191
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• 2001

This study was designed to establish the superior method for IVF embryos from DNA marker-proved Hanwoo cattle. DNA markers related to marbling score were identified using DNA fingerprinting with Ml3 probe and restriction enzyme Hae III. Oocytes were aspirated from unstimulated. immature ovarian follicles using a combined method of rectal ovarian-palpation and transvaginal ultrasound-guidance(6.5MHz) under local abesthesia. The aspirated oocytes were washed twice with fresh D-PBS containing 5% FBS and were rewashed 4 to 5 times with TCM-199 containing 5% FBS. A morphological grade of I to IV was assigned to each oocyte. Data were analysed using the GLM procedure of SAS. Mean number of follicles identified on ultrasound was 5.5 $\pm$2.9 in right and 4.3 $\pm$2.8 in left ovaries, respectively. The highest follicles(16.6$\pm$2.6) were found in 5101 cow compared to others. Recovery rate of follicular oocytes in individual cow was highest in 5101 cow with 89.3% in > 2mm and 94.0% in $\leq$ 2mm follicles. Total recovery rate was significantly(P<0.01) higher in $\leq$ 2mm(85.7%, 130/154) than > 2mm follicles(74.2%, 201/271). Significantly more oocytcs of Grade IV were recovered from > 2mm follicles. Mean number follicles recovered was 4.8$\pm$3.7. 3.0$\pm$3.4 and 0.3$\pm$0.6 in $\leq$2mm, 2~6mm and $\geq$6mm follicles. respectively. Our results imply that the more fertilizablc oocytes can be recovered from invisible-immature follicles by the combination of simultaneous rectal ovarian-palpation and ultrasound-guided approach in Hanwoo cattle.

• The Plant Pathology Journal
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• v.31 no.3
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• pp.203-211
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• 2015

Maize is the dominant cereal crop produced in the US. One of the main fungal pathogens of maize is Fusarium verticillioides, the causative agent of ear and stalk rots. Significantly, the fungus produces a group of mycotoxins - fumonisins - on infested kernels, which have been linked to various illnesses in humans and animals. Nonetheless, durable resistance against F. verticillioides in maize is not currently available. In Texas, over 2.1 million acres of maize are vulnerable to fumonisin contamination, but understanding of the distribution of toxigenic F. verticillioides in maize-producing areas is currently lacking. Our goal was to investigate the genetic variability of F. verticillioides in Texas with an emphasis on fumonisin trait and geographical distribution. A total of 164 F. verticillioides cultures were isolated from 65 maize-producing counties. DNA from each isolate was extracted and analyzed by PCR for the presence of FUM1- a key fumonisin biosynthesis gene - and mating type genes. Results showed that all isolates are in fact F. verticillioides capable of producing fumonisins with a 1:1 mating-type gene ratio in the population. To further study the genetic diversity of the population, isolates were analyzed using RAPD fingerprinting. Polymorphic markers were identified and the analysis showed no clear correlation between the RAPD profile of the isolates and their corresponding geographical origin. Our data suggest the toxigenic F. verticillioides population in Texas is widely distributed wherever maize is grown. We also hypothesize that the population is fluid, with active movement and genetic recombination occurring in the field.