• Journal of Periodontal and Implant Science
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• v.32 no.2
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• pp.281-290
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• 2002

The purpose of this study is to develop species-specific DNA probe for detection and identification of Prevotella intermedia (P. intermedia) G8-9K-3. This study procedure includes (1) whole-genomic DNA extraction of P. intermedia G8-9K-3 (2) construction of the genomic DNA library, (3) screening of strain-specific DNA probe by reverse dot hybridization, (4) confirmation of strain-specific DNA probe by Southern blot hybridization, (5) determination of nucleotide sequences of strain-specific DNA probe. Twenty-eight recombinant plasmids containing Hind III-digested DNA fragments of P. intermedia G8-9K-3 were obtained. Reverse Dot Hybridization and Southern blot analysis data showed that one of them, Pig3, could be P. intermedia G8-9K-3-specific DNA probe. This datum indicates that this Pig3 DNA probe could be useful in detection and identification of the P. intermedia G8-9K-3 strain.

• The Journal of Korean Society of Virology
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• v.28 no.4
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• pp.337-345
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• 1998

Hantaviruses are distributed in rodent population world-widely even in geographical areas where hemorrhagic fever with renal syndrome (HFRS) has not been reported. Various species of Family Muridae and Arvicolidae serve as the natural reservoirs of hantaviruses. Hantaan virus, Seoul virus, Puumala virus, Prospect HII virus, Sin Nombre virus and New York virus are members of genus Hantavirus and isolated from lungs of A. agrarius, R. norvegicus, C. glareolus, M. pennsylvanicus, P. maniculatus and P. leucopus respectively. This experiment was intended to find the distribution of hantavirus infection among wild rodents and isolate the hantavirus from lung tissue of seropositve Apodemus peninsulae, and compared the nucleotide and amino acid sequences with prototype of hantaan virus 76-118 strain. Hantaviral sequences were amplified from lung tissues of A. peninsulae by reverse-transcriptase polymerase chain reaction. Alignment and comparison of the 324 nucleotide of G2 region of M-genomic segment diverged 4.6% and 0% at the nucleotide and amino acid levels, and complete N protein-coding region of S-genomic segment diverged 3.7% and 1.4% nucleotide and amino acid levels, respectively. This is the report to spill-over on the hantaan virus from A. agrarius to A. peninsulae in Korea.

• Journal of Food Hygiene and Safety
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• v.32 no.3
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• pp.171-178
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• 2017

This study evaluated the protective effect of Chungkookjang (CKJ) extract, a Korean traditional fermented soybean product made from Bacillus species in rice straw and boiled soybean, and one of its main flavonoids, genistein, against Trp-P-1 induced cytotoxicity and DNA damage in HepG2 cells. CKJ and genistein exhibited protective effect against Trp-P-1 induced cytotoxicity and Trp-P-1 induced DNA single strand breaks. CKJ and genistein inhibited Trp-P-1 induced CYP1A1 and CYP1A2 transcription in HepG2 cells. Our results indicated that CKJ and genistein have the protective effect against Trp-P-1 induced cytotoxicity and DNA damage. Via inhibiting expression of CYP1A1 and CYP1A2. CKJ can be used as a promising functional food material that prevents the genotoxicity induced by carcinogens produced by the heat treatment of foods such as heterocyclic amines (HCAs) that cause genomic instability.

• Fisheries and Aquatic Sciences
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• v.14 no.1
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• pp.22-30
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• 2011

Vitellogenin (Vg) is the precursor of vitellin (Vn), which is the major yolk protein in nearly all oviparous species, including fish, amphibians, reptiles, and most invertebrates. It is one of the most important factors during reproduction, and numerous studies have shown that Vg genes are markers of the reproductive cycle and effecter genes induced by endocrine-disrupting chemicals (EDCs). Previously, we isolated two distinct cDNAs encoding vitellogenin homologs Pj-Vg1 and Pj-Vg2 from Pandalus shrimp Pandalopsis japonica. In this study, full-length genomic sequences of Pj-Vg1 and Pj-Vg2 were determined using a PCR-based genome walking strategy. Isolated Pj-Vg1 and Pj-Vg2 genes were 11,910 and 11,850 bp long, respectively. Both Pj-Vg genes had 15 exons and 14 introns, and the splicing sites were also the same, suggesting that they arose via gene duplication. The similar structural characteristics of decapod Vg genes suggest that they are all orthologs that evolved from the same ancestral gene. Analysis of Pj-Vg1 and Pj-Vg2 expression revealed that the relative copy numbers of Pj-Vg1 and Pj-Vg2 were similar in the hepatopancreas, whereas Pj-Vg2 transcripts were also detected in the ovary. Expression of both Pj-Vg genes was induced in hepatopancreas of mature individuals, whereas only Pj-Vg2 transcripts were upregulated in the ovaries from mature animals, suggesting that both Pj-Vgs are important for oocyte development. A strong positive correlation was found between Pj-Vg1 and Pj-Vg2 transcripts in the same individual, indicating they are under the same control mechanisms. Additionally, a positive correlation was found between ovarian and hepatopancreatic Pj-Vg2 transcripts, suggesting that its dual expression is regulated by similar physiological conditions. Knowledge of the similarities and differences between the two vitellogenin-like genes, Pj-Vg1 and Pj-Vg2, would help us to understand their roles in reproduction and other physiological effects.

• Journal of Microbiology and Biotechnology
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• v.25 no.12
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• pp.1971-1976
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• 2015

Oceanobacillus kimchii is a member of the genus Oceanobacillus within the family Bacillaceae. Species of the Oceanobacillus possess moderate haloalkaliphilic features and originate from various alkali or salty environments. The haloalkaliphilic characteristics of Oceanobacillus advocate they may have possible uses in biotechnological and industrial applications, such as alkaline enzyme production and biodegradation. This study presents the draft genome sequence of O. kimchii X50^T and its annotation. Furthermore, comparative genomic analysis of O. kimchii X50^T was performed with two previously reported Oceanobacillus genome sequences. The 3,822,411 base-pair genome contains 3,792 protein-coding genes and 80 RNA genes with an average G+C content of 35.18 mol%. The strain carried 67 and 13 predicted genes annotated with transport system and osmoregulation, respectively, which support the tolerance phenotype of the strain in high-alkali and high-salt environments.

• Environmental Engineering Research
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• v.25 no.1
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• pp.62-70
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• 2020

Here in this work, a 4-chlorophenol (4-CP)-degrading bacterial strain Bacillus subtilis (B. subtilis) MF447840.1 was isolated from the drain outside the Hyundai car service center, Agartala, Tripura, India. 16S rDNA technique used carried out for genomic recognition of the bacterial species. Isolated bacterial strain was phylogenetically related with B. subtilis. This strain was capable of breaking down both phenol and 4-CP at the concentration of 1,000 mg/L. Also, the isolated strain can able to metabolize five diverse aromatic molecules such as 2-chlorophenol, 2,4-dichlorophenol, 2,4,6-trichlorophenol, 4-nitrophenol, and pentachlorophenol for their growth. An extensive investigation was performed to portray the kinetics of cell growth along with 4-CP degradation in the batch study utilizing 4-CP as substrate. Various unstructured models were applied to evaluate the intrinsic kinetic factors. Levenspiel's model demonstrates a comparatively enhanced R² value (0.997) amongst every analyzed model. The data of specific growth rate (μ), saturation constant (K_S), and Y_X/S were 0.11 h^-1, 39.88 mg/L, along with 0.53 g/g, correspondingly. The isolated strain degrades 1,000 mg/L of 4-CP within 40 h. Therefore, B. subtilis MF447840.1 was considered a potential candidate for 4-CP degradation.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.74-74
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• 2018

Little millet (Panicum sumatrense) is well known for its salt and drought stress tolerance and high nutritional value, but very limited knowledge of genetic variation and genomic information is available. This study was to develop highly polymorphic EST-SSR markers based on cross-species transferability of derived SSRs from switchgrass EST databases and characterize newly developed EST - SSRs to better understand the genetic diversity of collected 37 germplasm accessions of little millet. A total of 779 primer pairs were designed from the 22,961 EST sequences of switchgrass (Pancium virgatum), of which 48 EST - SSR markers were developed based on the trials of transferability of these primers in little millet. The EST - SSR amplicons showed reproducible single band polymorphism and produced a total of 160 alleles with an average of 3.3 alleles per locus in 37 accessions of little millet. T he average values of expected and observed heterozygosities were 0.266 and 0.123, respectively. T he polymorphic information content (PIC) values were observed in range of 0.026 to 0.549 with an average of 0.240. The genetic relatedness among the little millet accessions was evaluated by neighbor-joining dendrogram, which grouped all accessions into two distinct groups. The validation thus demonstrated the utility of the switchgrass EST - SSR markers in assessing genomic relationships in little millet. T he findings from this study could be useful for designing strategies for the identification of diverse germplasm for conservation and future molecular breeding programs for little millet.

• International Journal of Oral Biology
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• v.35 no.1
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• pp.13-19
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• 2010

The DNA probes Pn17 and Pn34 were evaluated for their ability to specifically detect clinical strains of P. intermedia and P. nigrescens from a Korean population by dot blot hybridization. These probes were sequenced by extension termination and their specificity was determined by Southern blot analysis. The results revealed that the Pn17 sequence (2,517 bp) partially encodes an RNA polymerase beta subunit (rpoB) and that Pn34 (1,918 bp) partially encodes both rpoB (1-169 nts) and the RNA polymerase beta subunit (rpoB'; 695-1918 nts). These probes hybridized with both HindIII- and PstI-digested genomic DNAs from the strains of P. intermedia and P. nigrescens used in this study. Interestingly, each of the hybrid bands generated from the HindIII-digested genomic DNAs of the two bacterial species could be used to distinguish between them via restriction fragment length polymorphism. These results thus indicate that Pn17 and Pn34 can simultaneously detect P. intermedia and P. nigrescens.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.8
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• pp.1063-1072
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• 2012

Effective population size ($N_e$) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate $N_e$ in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The $N_e$ estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for $N_e$ estimation, i.e. pair-wise $r^2$ values using a simple expectation of distance and $r^2$ values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise $N_e$ estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average $N_e$ estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past $N_e$ at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant $N_e$ reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase $N_e$, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.5
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• pp.686-690
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• 2015

The adrenergic receptor beta 2 (ADRB2) plays a role in various physiological responses of the muscle to exercise, such as contraction and relaxation. Given its important role in muscle function, we investigated the structure of the horse ADRB2 gene and its expression pattern after exercise to determine if it can serve as a putative biomarker for recovery. Evolutionary analyses using synonymous and non-synonymous mutation ratios, were compared with other species (human, chimpanzee, mouse, rat, cow, pig, chicken, dog, and cat), and revealed the occurrence of positive selection in the horse ADRB2 gene. In addition, expression analyses by quantitative polymerase chain reaction exhibited ubiquitous distribution of horse ADRB2 in various tissues including lung, skeletal muscle, kidney, thyroid, appendix, colon, spinal cord and heart, with the highest expression observed in the lung. The expression of ADRB2 in skeletal muscle was significantly up-regulated about four folds 30 minutes post-exercise compared to pre-exercise. The expression level of ADRB2 in leukocytes, which could be collected with convenience compared with other tissues in horse, increased until 60 min after exercise but decreased afterward until 120 min, suggesting the ADRB2 expression levels in leukocytes could be a useful biomarker to check the early recovery status of horse after exercise. In conclusion, we identified horse ADRB2 gene and analyzed expression profiles in various tissues. Additionally, analysis of ADBR2 gene expression in leukocytes could be a useful biomarker useful for evaluation of early recovery status after exercise in racing horses.