• Korean Journal of Ecology and Environment
• /
• v.53 no.3
• /
• pp.265-274
• /
• 2020

Silver croaker (Pennahia argentata) is a turbulent species that is widely distributed worldwide and is mainly found in the bottom of the ocean. In the study, we characterized the cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA (mtDNA) on P. argentata inhabiting Gwangyang Bay and analyzed the phylogenetic location of marine fish species. As a result of multiple arrangement of 605 bp COI sequences, high homology of mtDNA nucleotide sequences was confirmed in the silver croakers from Gwangyang Bay (98~100%). However, the nucleotide variation was different according to the catching points of the inland and the open seas of Gwangyang Bay. The nucleotide sequence variation in COI was high in P. argentata from the open seas of Gwangyang Bay (43.2~70.3%). Furthermore, the phylogenetic analysis of 13 fish showed that P. argentata from Gwangyang Bay were grouped into one clade with P. argentata reported in Taiwan, and the evolutionary distance was 0.036. In addition, it was identified that the evolutionary distance was close to that of fish belonging to the Mi-iuy croaker (Miichthys miiuy) and the Big-head pennah croaker (Pennahia Macrocephalus) (0.041~0.048). The result of these studies will be used as the key genetic information for fisheries resources monitoring and species diversity management according to the coastal environment.

• Korean Journal of Ecology and Environment
• /
• v.53 no.3
• /
• pp.286-294
• /
• 2020

The Chironomus(Diptera: Chironomidae) is a freshwater benthic invertebrate that is an important indicator organism used for environmental pollution and water quality monitoring. In this study, we performed morphological classification and genetic species identification using the cytochrome c oxidase subunit I (COI) gene on mitochondrial DNA for an accurate species classification of Chironomus larvae found in tap water purification plants in Incheon, Korea. Twenty larvae in six water purification plants consist of four species, including twelve Chironomus kiiensis, six Chironomus flaviplumus, one Chironomus dorsalis, and one Polypedilum yongsanensis (not included Genus Chironomus). Morphological characteristics of each larvae were identified based on the head capsule, the mentum, the mandible, the antenna, and the claw. Based on the COI sequences of 21 individuals of 17 Chironomus species registered in NCBI Genbank, phylogenetic analysis indicated that the 20 individuals investigated in this study consist of the same clade with corresponding species of the high homology (99~100%) including C. kiiensis, C. flaviplumus, C. dorsalis, and P. yongsanensis. These results will be used as main classification indicator for monitoring freshwater ecosystems by providing integrated morphological and genetic information for the species identification of Korean Chironomus.

• Journal of Science Education
• /
• v.42 no.1
• /
• pp.12-26
• /
• 2018

This study examined the effects of SSI argumentation program on the preservice biology teachers' decision-making types and communication ability. The SSI argumentation program was developed based on 'Social Decision-Making & Problem-Solving strategy' and Toulmin's argumentation pattern. The preservice teachers had opportunities of SSI argumentation through small group discussions. They were asked to identify the issues regarding SSI, think of solutions, and make a decision along with claims, warrants, data, and rebuttals. The preservice biology teachers experienced four SSI topics of abortion, euthanasia, gene manipulation, artificial intelligence. The results indicated that the preservice biology teachers significantly improved the communication ability after the intervention, but they did not change their types of decision-making. In addition, after the intervention, the Pearson correlation results indicated that 'the logical type' of decision-making significantly relates to the communication ability(p<.01). The preservice biology teachers mentioned that they improved their ability of considering warrants, data, background information, context, and rebuttals. Further, the preserivce biology teachers mentioned that they became take an interest in socioscientific issues and improved their ability of accepting criticism from others as well as caring about others when they argue each other. This study implicated that the SSI argumentation program has effects on improving personality education in school science.

• Journal of Embryo Transfer
• /
• v.28 no.3
• /
• pp.215-222
• /
• 2013

Bovine coat color is decided by the melanocortin receptor 1 (MC1R) genotype mutation and melanogenesis. Specially, in the various cattle breeds, dominant black coat color is expressed by dominant genotype of $E^D$, red or brown is expressed in the frame shift mutation of recessive homozygous e by base pair deletion and wild type of $E^+$ is expressed in various coat colors. However, not very well known about the effected of MC1R genotype mutation on the coat color through family lines in KBC. Therefore, this study were to investigate effect of MC1R genotype mutation on the coat color, and to suggest mating breed system in accordance with of MC1R genotype for increased on brindle coat color appearance. Parents (sire 2 heads and dam 3 heads) and offspring (total : 54 heads) from crossbreeding in KBC family line with the MC1R genotype and phenotype records were selected as experimental animals. The relationship between melanocortin 1 receptor (MC1R) genotypes expression verified by PCR-RFLP, and brindle coat color appearance to the family line of the cross mating breed from MC1R genotype pattern was determined. As a result, 4MC1R genetic variations, $E^+/E^+$ (sire 1), $E^+/e$ (sire 2 and dam 3), $E^+/e$ with 4 bands of 174, 207 and 328 bp (dam 1) and $E^+/e$ with 3 bands of 174, 207, 328 and 535 bp (dam 2) from parents (sire and dam) of KBC. However, 3 genetic variations, e/e (24%), $E^+/E^+$ (22%) and $E^+/e$ (56%) were identified in offspring. Also, brindle coat color expressrated was the e/e with the 0%, $E^+/E^+$ with 67% and $E^+/e$ with 77% from MC1R genotype in offspring on the cross mating of KBC. Furthermore, when the sire had $E^+/e$ genotype and the dam had $E^+/E^+$ with the 3 bands or $E^+/e$ genotype, and both had whole body-brindle coat color, 62% of the offspring had whole body-brindle coat color. Therefore, the seresults, the mating system from MC1R genotype patterns of the sires ($E^+/e$) and dams ($E^+/E^+$ with the 3 bands or $E^+/e$) with brindle coat color may have the highest whole body-brindle coat color expression in their offspring.

• Journal of Embryo Transfer
• /
• v.28 no.3
• /
• pp.207-213
• /
• 2013

This study was carried out to examine a molecular marker system for parentage test in Jeju Black cattle (JBC). Based on the preliminarily studies, we finally selected for construction of a novel genetic marker system for molecular traceability, identity test, breed certification, and parentage test in JBC and its related industrial populations. The genetic marker system had eight MS markers, five indel markers, and two single nucleotide polymorphisms (SNPs; g.G299T and g.del310G) within MC1R gene which is critical to verify the breed specific genotypes for coat color of JBC differing from those of exotic black cattle breeds such as Holstein and Angus. The results showed lower level of a combined non-exclusion probability for second parent (NE-P2) of $4.1202{\times}10^{-4}$ than those previously recommended by International Society of Animal Genetics (ISAG) of $5.000{\times}10^{-4}$ for parentage, and a combined non-exclusion probability for sib identity (NE-SI) of $2.679{\times}10^{-5}$. Parentage analysis has been successfully identified the JBC offspring in the indigenous population and cattle farms used the certified AI semens for production using the JBC-derived offspring for commercial beef. This combined molecular marker system will be helpful to supply genetic information for parentage test and traceability and to develop the molecular breeding system for improvement of animal productivity in JBC population.

• Genomics & Informatics
• /
• v.6 no.1
• /
• pp.18-28
• /
• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.12
• /
• pp.2021-2030
• /
• 2020

Objective: Quantitative polymerase chain reaction (qPCR) has been extensively used in the field of mesenchymal stem cell (MSC) research to elucidate their characteristics and clinical potential by normalization of target genes against reference genes (RGs), which are believed to be stably expressed irrespective of various experimental conditions. However, the expression of RGs is also variable depending on the experimental conditions, which may lead to false or contradictory conclusions upon normalization. Due to the current lack of information for a clear list of stable RGs in bovine MSCs, we conducted this study to identify suitable RGs in bovine MSCs. Methods: The cycle threshold values of ten traditionally used RGs (18S ribosomal RNA [18S], beta-2-microglobulin [B2M], H2A histone family, member Z [H2A], peptidylprolyl isomerase A [PPIA], ribosomal protein 4 [RPL4], succinate dehydrogenase complex, subunit A [SDHA], beta actin [ACTB], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], TATA box binding protein [TBP], and hypoxanthine phosphoribosyltrasnfrase1 [HPRT1]) in bovine bone marrow-derived MSCs (bBMMSCs) were validated for their stabilities using three types of RG evaluation algorithms (geNorm, Normfinder, and Bestkeeper). The effect of validated RGs was then verified by normalization of lineage-specific genes (fatty acid binding protein 4 [FABP4] and osteonectin [ON]) expressions during differentiations of bBMMSCs or POU class 5 homeobox 1 (OCT4) expression between bBMMSCs and dermal skins. Results: Based on the results obtained for the three most stable RGs from geNorm (TBP, RPL4, and H2A), Normfinder (TBP, RPL4, and SDHA), and Bestkeeper (TBP, RPL4, and SDHA), it was comprehensively determined that TBP and RPL4 were the most stable RGs in bBMMSCs. However, traditional RGs were suggested to be the least stable (18S) or moderately stable (GAPDH and ACTB) in bBMMSCs. Normalization of FABP4 or ON against TBP, RPL4, and 18S presented significant differences during differentiation of bBMMSCs. However, although significantly low expression of OCT4 was detected in dermal skins compared to that in bBMMSCs when TBP and RPL4 were used in normalization, normalization against 18S exhibited no significance. Conclusion: This study proposes that TBP and RPL4 were suitable as stable RGs for qPCR study in bovine MSCs.

• Journal of the Korea Academia-Industrial cooperation Society
• /
• v.19 no.6
• /
• pp.375-381
• /
• 2018

This study was performed to investigate the residual characteristics of the insecticide dinotefuran in asparagus under greenhouse conditions from July to August and consequentially to obtain basic data for guidelines on the safe use of this pesticide in asparagus. Residues of dinotefuran in young stem of asparagus before and after growing mother stem were analyzed from samples collected at 0, 1, 3, 5, and 7 days after single application of a commercial formulation of dinotefuran (wettable powder, 10%) at the recommended dose (2,000 times dilution). The residue of dinotefuran in young stem of asparagus was analyzed by HPLC-UVD, and recovery of dinotefuran in young stem was tested at 0.5 and 1.0 mg/kg concentrations. As a result, the limit of quantitation (LOQ) of dinotefuran was 0.01 mg/kg, and the recovery of dinotefuran was in the range of 83.3-94.0% with a coefficient of variation less than 10%. Residues of dinotefuran in young stem of asparagus before and after growing the mother stem were lower than the tentative limit (0.05 mg/kg) from 5 and 3 days after single application, respectively. Based on these results, single application of dinotefuran (wettable powder, 10%) at the recommended dose at 7 days before harvest would have no deleterious effects on safety issues concerning pesticide residue. This result might provide basic information to construct guidelines for the safe use of dinotefuran in asparagus.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.3
• /
• pp.316-327
• /
• 2007

In this study, a Korean native cattle strain (Hanwoo) evidencing high performance in terms of both meat quality and quantity was employed in the generation of 150,000 BAC clones with an average insert size of 140 kb, and corresponding to about a 6X coverage of bovine chromosomal DNA. The BAC clones were pooled in a mini-scale via three rounds of a pooling protocol, and the efficiency of this pooling protocol was evaluated by testing the accuracy of accessibility to the positive clones, via a PCR-based screening method. Two sets of primers designed from each of two known genes were tested, and each yielded 2 or 3 positive clones for each gene, thereby indicating that the BAC library pooling system was appropriate with regard to the accession of the target BAC clones. Analyses of $3.3{\times}10^6$ base pairs obtained from the 7,090 BAC end sequence (BES) showed that 34.88% of the DNA sequence harbored the repetition sequence. Analysis of the 7,090 BES to the $1^{st}$ and $2^{nd}$ generation radiation hybrid map of the cattle genome, using the COMPASS program designed for the construction of a cattle-human comparative mapping, resulted in the localization of a total of 1,374 clones proximal to 339 $1^{st}$ generation markers, and 1,721 clones proximal to 664 $2^{nd}$ generation markers. Collectively, the BAC library and pooling system of the BAC clones from the Korean cattle, coupled with the chromosome-localized BAC clones, will provide us with novel tools for the excavation of desired clones for genome mapping and sequencing, and will also furnish us with additional information regarding breed differences in cattle.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.11
• /
• pp.1643-1650
• /
• 2017

Objective: The control of psychrotrophic bacteria causing milk spoilage and illness due to toxic compounds is an important issue in the dairy industry. In South Korea, Gangwon-do province is one of the coldest terrains in which eighty percent of the area is mountainous regions, and mainly plays an important role in the agriculture and dairy industries. The purposes of this study were to analyze the indigenous microbiota of raw milk in Gangwon-do and accurately investigate a putative microbial group causing deterioration in milk quality. Methods: We collected raw milk from the bulk tank of 18 dairy farms in the Hoengseong and Pyeongchang regions of Gangwon-do. Milk components were analyzed and the number of viable bacteria was confirmed. The V3 and V4 regions of 16S rRNA gene were amplified and sequenced on an Illumina Miseq platform. Sequences were then assigned to operational taxonomic units, followed by the selection of representative sequences using the QIIME software package. Results: The milk samples from Pyeongchang were higher in fat, protein, lactose, total solid, and solid non-fat, and bacterial cell counts were observed only for the Hoengseong samples. The phylum Proteobacteria was detected most frequently in both the Hoengseong and Pyeongchang samples, followed by the phyla Firmicutes and Actinobacteria. Notably, Corynebacterium, Pediococcus, Macrococcus, and Acinetobacter were significantly different from two regions. Conclusion: Although the predominant phylum in raw milk is same, the abundances of major genera in milk samples were different between Hoengseong and Pyeongchang. We assumed that these differences are caused by regional dissimilar farming environments such as soil, forage, and dairy farming equipment so that the quality of milk raw milk from Pyeongchang is higher than that of Hoengseong. These results could provide the crucial information for identifying the microbiota in raw milk of South Korea.