• Journal of Microbiology and Biotechnology
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• v.24 no.11
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• pp.1473-1483
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• 2014

Reports of herbicide resistance events are proliferating worldwide, leading to new cultivation strategies using combinations of pre-emergence and post-emergence herbicides. We analyzed the impact during a one-year cultivation cycle of several herbicide combinations on the rhizobacterial community of glyphosate-tolerant Bt-maize and compared them to those of the untreated or glyphosate-treated soils. Samples were analyzed using pyrosequencing of the V6 hypervariable region of the 16S rRNA gene. The sequences obtained were subjected to taxonomic, taxonomy-independent, and phylogeny-based diversity studies, followed by a statistical analysis using principal components analysis and hierarchical clustering with jackknife statistical validation. The resilience of the microbial communities was analyzed by comparing their relative composition at the end of the cultivation cycle. The bacterial communites from soil subjected to a combined treatment with mesotrione plus s-metolachlor followed by glyphosate were not statistically different from those treated with glyphosate or the untreated ones. The use of acetochlor plus terbuthylazine followed by glyphosate, and the use of aclonifen plus isoxaflutole followed by mesotrione clearly affected the resilience of their corresponding bacterial communities. The treatment with pethoxamid followed by glyphosate resulted in an intermediate effect. The use of glyphosate alone seems to be the less aggressive one for bacterial communities. Should a combined treatment be needed, the combination of mesotrione and s-metolachlor shows the next best final resilience. Our results show the relevance of comparative rhizobacterial community studies when novel combined herbicide treatments are deemed necessary to control weed growth.

• Journal of Microbiology and Biotechnology
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• v.22 no.2
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• pp.159-165
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• 2012

The rhizobacterial composition varies according to the soil properties. To test if the effect of herbicides on the rhizobacterial communities of genetically modified NK603 glyphosate-tolerant maize varies according to different soil locations, a comparison was made between the effects of glyphosate (Roundup Plus), a post-emergence applied herbicide, and a pre-emergence applied herbicide (GTZ) versus untreated soil. The potential effect was monitored by direct amplification, cloning, and sequencing of the soil DNA encoding 16S rRNA, and high-throughput DNA pyrosequencing of the bacterial DNA coding for the 16S rRNA hypervariable V6 region. The results obtained using three different methods to analyze the herbicide effect on the rhizobacterial communities of genetically modified NK603 maize were comparable to those previously obtained when glyphosate-tolerant maize was grown in soil with different characteristics. Both herbicides decreased the bacterial diversity in the rhizosphere, with Actinobacteria being the taxonomic group most affected. The results suggest that both herbicides affected the structure of the maize rhizobacterial community, but glyphosate was environmentally less aggressive.

• Korean Journal of Veterinary Research
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• v.38 no.4
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• pp.909-917
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• 1998

Six different sequences types(A through E and H) and a subtype(Bl) of the small subunit ribosomal RNA(SSUrRNA) gene were found in bovine Theileria isolates from different areas of Korea and Japan. The sequences were aligned and three hypervariable regions were observed in the nucleotide position ranges 212~231, 261~270 and 632~690. Five of the Theileria isolates yielded sequence type A; these were the field isolates KCB, KCN, and KCJ, and the laboratory stock KLS, all from Korea, and a single isolate from Japan (JHS). This sequence type is identical to the SSUrRNA gene sequence listed for Theileria buffeli (GenBank Accession No. Z15106) from Marula, Kenya. The Korean field isolate KKB yielded only a single sequence type (B), but multiple sequence types were found in some isolates. For example, KCB and JHS isolates yielded both types A and B ; isolate KKW showed types B and H; isolate KCN showed types A, C, and D ; and isolate KCJ showed types A, B, E, and a subtype B1. Finding of the multiple sequences SSUrRNA gene sequences suggests that bovine Theileria isolates from both Korea and Japan may consist of mixed populations.

• Journal of Animal Science and Technology
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• v.46 no.4
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• pp.537-546
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• 2004

Adiponectin is adipocyte complement-related protein which is highly specialized to play important roles in metabolic and honnonal processes. This protein, called GBP-28, AdipoQ, and Acrp30, is encoded by the adipose most abundant gene transcript 1 (APM1) which locates on human chromosome 3q27 and mouse chromosome 16. In order to determine chromosomal localization of the porcine APM1, we carried out PCR analysis using somatic cell hybrid panel as well as porcine whole genome radiation hybrid (RH) panel. The result showed that the porcine APM1 located on chromosome 13q41 or 13q46-49. These locations were further investigated with the two point analysis of RH panel, revealed the most significant linked marker (LOD score 20.29) being SIAT1 (8 cRs away), where the fat-related QTL located. From the SSCP analysis of APM1 using 8 pig breeds, two distinct SSCP types were detected from K~ native and Korean wild pigs. The determined sequences in Korean native and Korean wild pigs showed that two nucleotide positions (T672C and C705G) were substituted. The primary sequence of the porcine APM1 has 79 to 87% identity with those of human, mouse, and bovine APM1. The domain structures of the porcine APM1 such as signal sequence, hypervariable region, collagenous region. and globular domain are also similar to those of mammalian genes.

• Korean Journal of Poultry Science
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• v.36 no.4
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• pp.323-328
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• 2009

In order to determine the origin and genetic diversity among chicken breeds, mitochondrial (mt) DNA D-loop sequences have been widely used. In this study, 41 individuals from four breeds (Korean native chicken (Black and Brown) and two imported breeds, Rhode Island Red and Cornish) were used for identifying genetic relationships with other chicken breeds. We obtained ten haplotypes and the highest number of haplotype was represented by eight individuals each from haplotype 1 and haplotype 2. Neighbor-joining phylogenetic tree indicates that the black and brown Korean native chicken breeds were mixed in haplotype 2 and they were closely related with the red jungle fowl (Gallus gallus). We also investigated whether the D-loop hypervariable region in chicken mtDNA can be used for the breed identification marker. The results indicated that the combination of the SNPs in the D-loop region can be possibly used for the breed discriminating markers. The results obtained in this study can be used for designing proper breeding and conservation strategies for Korean native chicken, as well as development of breed identification markers.

• Analytical Science and Technology
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• v.18 no.4
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• pp.362-367
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• 2005

The human mitochondrial genome (mtDNA) has been an important tool in the field of forensic investigations. Within the entire mtDNA molecule, the non-coding control region which is approximately 1,100 bp including hypervariable region I and II (HV1 and HV2) is widely studied because it is highly polymorphic and useful for human identification purposes. In this study, 360 unrelated Koreans were analyzed in HV1. The number of polymorphic sites and genetic lineage were 124 and 210, respectively. The most prevalent substitution was C-T and 75.8% of DNA showed C-T substitution at 16223. There were 20 kinds of polymorphism between 16180 and 16193 including insertion and deletion. The most frequent haplotype was [16223T, 16362C] representing 5%. Approximately 25.9% of DNA showed the same haplotype in at least two samples. The gene diversity was calculated to 0.996 and the probability of two unrelated perosons having the same haplotype was determined to 0.7%.

• Korean Journal of Veterinary Research
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• v.43 no.3
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• pp.439-448
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• 2003

The VP2 gene of infectious bursal disease virus (IBDV) Chinju which was previously detected in Chinju, Korea was cloned and sequenced to establish the information for the development of genetically engineered vaccines and diagnostic reagents against IBDV. The nucleotide sequence of the entire Chinju VP2 gene consisted of 1,356 bases long encoding 452 amino acids in a single open reading frame (ORF). It consisted of 368 adenine (27.1%), 363 cytosine (26.8%), 339 guanine (25.0%) and 286 thymine (21.1%) residues. The predicted $M_r$ of the Chinju VP2 protein was 48 kDa, and the protein contained 13 phosphorylation sites by protein kinase C, casein kinase II or tyrosine kinase, whereas 3 asparagine-linked glycosylation sites were recognized. The nucleotide sequence of Chinju VP2 ORF had a very close phylogenetic relationship with 98-99% homology to that of the very virulent IBDVs (vvIBDVs) HK46, OKYM, D6948, UK661, UPM97/61 and BD3/99. Also, the Chinju VP2 protein revealed a very close phylogenetic relationship with 99-100% homology to that of these vvIBDVs. The Chinju VP2 protein had 100% amino acid identity in the variable region of residues 206-360 with that of the D6948, HK46, OKYM and UK661, as well as 100% identity in two hypervariable regions of residues 212-224 and 314-324 with those of the D6948, HK46, OKYM, UK661, UPM97/61 and BD3/99. The amino acid sequence of the chinju VP2 protein contained a serine-rich heptapeptide of SWSASGS as in these vvIBDVs.

• Journal of Periodontal and Implant Science
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• v.52 no.5
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• pp.394-410
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• 2022

Purpose: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples. Methods: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis. Results: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples. Conclusions: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.

• Restorative Dentistry and Endodontics
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• v.36 no.6
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• pp.498-505
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• 2011

Objectives: The purpose of this in vivo study was to investigate the microbial diversity in symptomatic and asymptomatic canals with primary endodontic infections by using GS FLX Titanium pyrosequencing. Materials and Methods: Sequencing was performed on 6 teeth (symptomatic, n = 3; asymptomatic, n = 3) with primary endodontic infections. Amplicons from hypervariable region of the small-subunit ribosomal RNA gene were generated by polymerized chain reaction (PCR), and sequenced by means of the GS FLX Titanium pyrosequencing. Results: On average, 10,639 and 45,455 16S rRNA sequences for asymptomatic and symptomatic teeth were obtained, respectively. Based on Ribosomal Database Project Classifier analysis, pyrosequencing identified the 141 bacterial genera in 13 phyla. The vast majority of sequences belonged to one of the seven phyla: Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria, Spirochetes, and Synergistetes. In genus level, Pyramidobacter, Streptococcus, and Leptotrichia constituted about 50% of microbial profile in asymptomatic teeth, whereas Neisseria, Propionibacterium, and Tessaracoccus were frequently found in symptomatic teeth (69%). Grouping the sequences in operational taxonomic units (3%) yielded 450 and 1,997 species level phylotypes in asymptomatic and symptomatic teeth, respectively. The total bacteria counts were significantly higher in symptomatic teeth than that of asymptomatic teeth (p < 0.05). Conclusions: GS FLX Titanium pyrosequencing could reveal a previously unidentified high bacterial diversity in primary endodontic infections.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1561-1569
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• 2006

Denaturing gradient gel electrophoresis (DGGE) is one of the most frequently used methods for analysis of soil microbial community structure. Unbiased PCR amplification of target DNA templates is crucial for efficient detection of multiple microbial populations mixed in soil. In this study, DGGE profiles were compared using different pairs of primers targeting different hypervariable regions of thirteen representative soil bacteria and clones. The primer set (1070f-1392r) for the E. coli numbering 1,071-1,391 region could not resolve all the 16S rDNA fragments of the representative bacteria and clones, and moreover, yielded spurious bands in DGGE profiles. For the E. coli numbering 353-514 region, various forward primers were designed to investigate the efficiency of PCR amplification. A degenerate forward primer (F357IW) often yielded multiple bands for a certain single 16S rDNA fragment in DGGE analysis, whereas nondegenerate primers (338f, F338T2, F338I2) differentially amplified each of the fragments in the mixture according to the position and the number of primer-template mismatches. A forward primer (F352T) designed to have one internal mismatch commonly with all the thirteen 16S rDNA fragments efficiently produced and separated all the target DNA bands with similar intensities in the DGGE profiles. This primer set F352T-519r consistently yielded the best DGGE banding profiles when tested with various soil samples. Touchdown PCR intensified the uneven amplification, and lowering the annealing temperature had no significant effect on the DGGE profiles. These results showed that PCR amplification bias could be much improved by properly designing primers for use in fingerprinting soil bacterial communities with the DGGE technique.