• 한국동물위생학회지
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• 제30권4호
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• pp.505-510
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• 2007

This study was conducted to detect ${\beta}$-lactam antibiotic-resistant genes in the 400 E coli isolates from porcine fecal samples in Korea by a DNA chip. The DNA chip contains the specific probe DNAs of the ${\beta}$-lactam antibiotic-resistant genes that had been labeled with a mixture of primer set designed to amplify specific genes (PSE, OXA, FOX, MEN, CMY, TEM, SHV, OXY and AmpC) using a multiplex polymerase chain reaction (PCR). Of 400 isolates 339 contained at least one ${\beta}$-lactamases gene. Resistance to ${\beta}$-lactamases was mediated mainly by AmpC (n = 339, 100%), and followed by TEM (n = 200, 59.0%), CMY (n = 101, 29.8%), PSE (n = 30, 8.9%) and both OXA and SHV genes (n = 20, 5.9%), while the FOX, MEN and OXY genes were not detected. The other sixty-one did not contain any ${\beta}$-lactamase genes even though they were resistant to antimicrobial drugs. In conclusion, the DNA chip system can be used as a rapid and reliable method for detecting of ${\beta}$-lactamases genes, which will help veterinarians select the antibiotics for monitoring and treating of animal diseases.

• 한국동물생명공학회지
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• 제34권2호
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• pp.111-116
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• 2019

This study was conducted to analyze the specific genes associated with sex-determination in Korean native cow. The highly organized spermatogenesis requires accurate spatial and temporal regulation of gene expression, which is governed by transcriptional, post-transcriptional, and epigenetic processes. Recently, farmers have been interested in determining the sexual identity of the calves in their farm. We analyzed the sperm of Korean native and Holstein cows, which were supplied from Hanwoo Improvement Center. We evaluated sperm motility and expression of sperm-specific genes after treating semen with both male- and female reagents. Sperm motility in Korean native cows decreased by approximately 10% in the first 30 minutes after treatment with sex-determination reagent. However, sperm motility of Holstein cows decreased to 60-70% after 15 minutes and to 20-30% after 30 minutes. We selected six specific genes expressing in the spermatozoa to analysis the gene expression level. The Real-time PCR results suggest that the selected genes (Gimap4, Tmeff1, Rac2, Abi2, Rac1, and Clu) were highly expressed in the group treated with the male reagent compared to the group treated the female reagent and to the untreated-group (control). In the present study, we suggest that the selected genes play a pivotal role in sex-determination.

• Toxicological Research
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• 제8권2호
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• pp.331-342
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• 1992

The chicken major histocompatibility complex (MHC), the B complex, is beginning to be analyzed at the DNA level. Inbred lines of chickens have been reported to possess 3~5 MHC class II genes. To further analyzed the molecular structure of the chicken MHC class II genes, cDNA clones coding for chicken MHC class II (B-L) ${\beta}$ chain molecules were isolated from chicken spleen and liver. Tissue-specific transcription of B-L ${\beta}$genes was studied by Northern blot analysis. A high level of expression was detected for spleen poly(A)$^+$ RNA whereas a faint signal was detected for liver poly(A)$^+$ RNA. Twenty-nine cDNA clones were isolated from the spleen and eight cDNA clones were isolated from the liver. Based on restriction maps, most clones could be clustered into one family of genes. Four cDNA clones were sequenced (S7, S10 and S19 from the spleen and L1, which was identical to S19, from the liver). Complete amino acid sequences of B-L ${\beta}$ chain molecules were predicated from the nucleotide sequences of the cDNA clones. Although both the nature and the location of the conserved residues were similar in chicken and mammalian sequences, some species-specific differences were found, suggesting that the structures of the B-L molecules are similar, but not identical to their mammalian counterparts.

• Journal of Microbiology and Biotechnology
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• 제30권3호
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• pp.341-351
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• 2020

To shed light on the genetic differences among food-originated coagulase-negative Staphylococcus (CNS), we performed pan-genome analysis of five species: Staphylococcus carnosus (two strains), Staphylococcus equorum (two strains), Staphylococcus succinus (three strains), Staphylococcus xylosus (two strains), and Staphylococcus saprophyticus (one strain). The pan-genome size increases with each new strain and currently holds about 4,500 genes from 10 genomes. Specific genes were shown to be strain dependent but not species dependent. Most specific genes were of unknown function or encoded restriction-modification enzymes, transposases, or prophages. Our results indicate that unique genes have been acquired or lost by convergent evolution within individual strains.

• Asian-Australasian Journal of Animal Sciences
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• 제32권12호
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• pp.1816-1825
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• 2019

Objective: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs. Methods: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of single nucleotide polymorphisms (SNPs) in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed. Results: Because of the low genome coverage (${\sim}4{\times}$) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (p<0.05) including three previously reported and four newly identified genes in this study. Conclusion: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.

• Asian Pacific Journal of Cancer Prevention
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• 제15권10호
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• pp.4217-4224
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• 2014

Cholangiocarcinoma (CCA), a slow growing but highly metastatic tumor, is highly prevalent in Northeast Thailand. Specific tests that predict prognosis of CCA remain elusive. The present study was designed to investigate whether peripheral blood leukocyte (PBL) transcriptional profiles might be of use as a prognostic test in CCA patients. Gene expression profiles of PBLs from 9 CCA and 8 healthy subjects were conducted using the Affymetrix HG_U133 Plus 2.0 GeneChip. We indentified informative PBLs gene expression profiles that could reliably distinguish CCA patients from healthy subjects. Of these CCA specific genes, 117 genes were up regulated and 60 were down regulated. The molecular and cellular functions predicted for these CCA specific genes according to the Gene Ontology database indicated differential PBL expression of host immune response and tumor progression genes (EREG, TGF ${\beta}1$, CXCL2, CXCL3, IL-8, and VEGFA). The expression levels of 9 differentially expressed genes were verified in 36 CCA vs 20 healthy subjects. A set of three tumor invasion related genes (PLAU, CTSL and SERPINB2) computed as "prognostic index" was found to be an independent and statistically significant predictor for CCA patient survival. The present study shows that CCA PBLs may serve as disease predictive clinically accessible surrogates for indentifying expressed genes reflective of CCA disease severity.

• Molecules and Cells
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• 제39권9호
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• pp.692-698
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• 2016

Advances in next generation sequencing (NGS) technologies have enabled population-level studies for many animals to unravel the relationships between genotypic differences and traits of specific populations. The objective of this study was to perform evolutionary analysis of single nucleotide polymorphisms (SNP) in genes of Korean native cattle Hanwoo in comparison to SNP data from four other cattle breeds (Jersey, Simmental, Angus, and Holstein) and four related species (pig, horse, human, and mouse) obtained from public databases through NGS-based resequencing. We analyzed population structures and differentiation levels for the five cattle breeds and estimated species-specific SNPs with their origins and phylogenetic relationships among species. In addition, we identified Hanwoo-specific genes and proteins, and determined distinct changes in protein-protein interactions among five species (cattle, pig, horse, human, mouse) in the STRING network database by additionally considering indirect protein interactions. We found that the Hanwoo population was clearly different from the other four cattle populations. There were Hanwoo-specific genes related to its meat trait. Protein interaction rewiring analysis also confirmed that there were Hanwoo-specific protein-protein interactions that might have contributed to its unique meat quality.

• The Plant Pathology Journal
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• 제38권6호
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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.

• 한국축산식품학회지
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• 제27권3호
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• pp.351-356
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• 2007

본 연구는 포유류의 Y-염색체상에 존재하는 SRY 및 ZFY의 웅성 특이적 성 결정 유전자를 이용하는 PCR 기법으로 쇠고기 성판별 기술을 개발하고자 수행하였다. 성 결정 유전자 영역의 특정 염기서열을 포함하는 primer를 각각 설계 합성하고 이들 primer를 이용하여 PCR증폭을 실시한 다음, 각각의 증폭산물을 1.5% agarose gel에 전기영동하여 웅성 특이적 DNA band의 증폭여부를 확인하였다. SRY 유전자에서 웅성개체 쇠고기는 1,348 bp 크기의 단편을 가진 DNA band가 검출되었으나, 자성개체의 경우 DNA band가 전혀 검출되지 않은 것을 확인 할 수 있었다. 또한, ZFY 유전자에서 웅성개체의 쇠고기는 979 bp 크기의 단편을 가진 DNA band가 모두 검출되었으나, 자성개체의 쇠고기에서는 역시 DNA band가 전혀 검출되지 않았다. 즉, SRY 및 ZFY 유전자는 모두 숫소에서 유래한 쇠고기에서 웅성 특이적인 DNA band가 정확히 검출된 반면 암소에서 유래한 쇠고기에서는 웅성 특이적 DNA band가 전혀 검출되지 않았다. 또한 쇠고기 성 감별법을 도축 후 가공 유통판매단계에 실제 활용 가능성을 검증하고자 시중에 유통되고 있는 등심 및 갈비 포장육 350시료를 무작위 추출하여 성 판별을 실시한 결과 숫소가 252시료(72%) 그리고 암소가 98두(28%)로 조사되었다. 따라서 본 연구에서 개발한 SRY 또는 ZFY의 웅성 특이적 성 결정 유전자를 이용하는 쇠고기 성 감별기술은 생산단계는 물론 도축 후 가공 유통 판매되고 있는 모든 쇠고기의 암수 성감별을 위한 유용한 DNA 표지인자로 활용할 수 있을 것으로 기대된다.

• Genomics & Informatics
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• 제4권2호
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• pp.80-86
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• 2006

It is clear that the construction of large insert DNA libraries is important for map-based gene cloning, the assembly of physical maps, and simple screening for specific genomic sequences. The bacterial artificial chromosome (BAC) system is likely to be an important tool for map-based cloning of genes since BAC libraries can be constructed simply and analyzed more efficiently than yeast artificial chromosome (YAC) libraries. BACs have significantly expanded the size of fragments from eukaryotic genomes that can be cloned in Escherichia coli as plasmid molecules. To facilitate the isolation of molecular-biologically important genes in Ashbya gossypii, we constructed Ashbya chromosome-specific BAC libraries using pBeloBAC11 and pBACwich vectors with an average insert size of 100 kb, which is equivalent to 19.8X genomic coverage. pBACwich was developed to streamline map-based cloning by providing a tool to integrate large DNA fragments into specific sites in chromosomes. These chromosome-specific libraries have provided a useful tool for the further characterization of the Ashbya genome including positional cloning and genome sequencing.