• Journal of Microbiology and Biotechnology
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• 제26권4호
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• pp.799-805
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• 2016

Methicillin-resistant Staphylococcus aureus (MRSA), the major causative agent of nosocomial infection, has also been reported from non-human sources. A sequence type (ST) 541 MRSA isolate designated K12PJN53 was isolated from a healthy pig in 2012. The genome of K12PJN53 consists of 44 contiguous sequences (contigs), totalling 2,880,108 bases with 32.88% GC content. Among the annotated contigs, 14, 17, and 18 contained genes related to antimicrobial resistance, adherence, and toxin genes, respectively. The genomic distance of strain K12PJN53 was close to the ST398 strains. This is the first report of the draft genome sequence of a novel livestock-associated MRSA ST541 strain.

• Genomics & Informatics
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• 제8권2호
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• pp.81-85
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• 2010

The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR ) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR ) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.

• Genomics & Informatics
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• 제18권2호
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• pp.18.1-18.5
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• 2020

Finding publications that propose alternative methods to animal experiments is an important but time-consuming task since researchers need to perform various queries to literature databases and screen many articles to assess two important aspects: the relevance of the article to the research question, and whether the article's proposed approach qualifies to being an alternative method. We are currently developing a Web application to support finding alternative methods to animal experiments. The current (under development) version of the application utilizes external tools and resources for document processing, and relies on the PubAnnotation ecosystem for annotation querying, annotation storage, dictionary-based tagging of cell lines, and annotation visualization. Currently, our two PubAnnotation repositories for discourse elements contain annotations for more than 110k PubMed documents. Further, we created an annotator for cell lines that contain more than 196k terms from Cellosaurus. Finally, we are experimenting with TextAE for annotation visualization and for user feedback.

• 한국발생생물학회지:발생과생식
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• 제19권2호
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• pp.79-84
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• 2015

The Korean native pig (KNP) have been considered as animal models for animal biotechnology research because of their relatively small body size and their presumably highly inbred status due to the closed breeding program. However, little is reported about the use of KNP for animal biotechnology researches. This study was performed to establish the somatic cell nuclear transfer (SCNT) protocol for the production of swine leukocyte antigens (SLA) homotype-defined SCNT KNP. The ear fibroblast cells originated from KNP were cultured and used as donor cell. After thawing, the donor cells were cultured for 1 hour with 15 ${\mu}M$ roscovitine prior to the nuclear transfer. The numbers of reconstructed and parthenogenetic embryos transferred were $98{\pm}35.2$ and $145{\pm}11.2$, respectively. The pregnancy and delivery rate were 3/5 (60%) and 2/5 (40%). One healthy SLA homotype-defined SCNT KNP was successfully generated. The recipient-based individual cloning efficiency ranged from 0.65 to 1.08%. Taken together, it can be postulated that the methodological establishment of the production of SLA homotype-defined cloned KNP can be applied to the generation of transgenic cloned KNP as model animals for human disease and xenotransplantation researches.

• Asian-Australasian Journal of Animal Sciences
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• 제27권9호
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• pp.1345-1354
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• 2014

Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

• Journal of Animal Science and Technology
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• 제63권6호
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• pp.1232-1246
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• 2021

Recently, the cattle genome sequence has been completed, followed by developing a commercial single nucleotide polymorphism (SNP) chip panel in the animal genome industry. In order to increase statistical power for detecting quantitative trait locus (QTL), a number of animals should be genotyped. However, a high-density chip for many animals would be increasing the genotyping cost. Therefore, statistical inference of genotype imputation (low-density chip to high-density) will be useful in the animal industry. The purpose of this study is to investigate the effect of the reference population size and marker density on the imputation accuracy and to suggest the appropriate number of reference population sets for the imputation in Hanwoo cattle. A total of 3,821 Hanwoo cattle were divided into reference and validation populations. The reference sets consisted of 50k (38,916) marker data and different population sizes (500, 1,000, 1,500, 2,000, and 3,600). The validation sets consisted of four validation sets (Total 889) and the different marker density (5k [5,000], 10k [10,000], and 15k [15,000]). The accuracy of imputation was calculated by direct comparison of the true genotype and the imputed genotype. In conclusion, when the lowest marker density (5k) was used in the validation set, according to the reference population size, the imputation accuracy was 0.793 to 0.929. On the other hand, when the highest marker density (15k), according to the reference population size, the imputation accuracy was 0.904 to 0.967. Moreover, the reference population size should be more than 1,000 to obtain at least 88% imputation accuracy in Hanwoo cattle.

• Asian-Australasian Journal of Animal Sciences
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• 제29권7호
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• pp.1044-1051
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• 2016

The present study compared the differential functions of two groups of adjuvants, Montanide incomplete Seppic adjuvant (ISA) series and Quil A, cholesterol, dimethyl dioctadecyl ammonium bromide, and Carbopol (QCDC) formulations, in chicken by analyzing published microarray data associated with each type of vaccine adjuvants. In the biological function analysis for differentially expressed genes altered by two different adjuvant groups, ISA series and QCDC formulations showed differential effects when chickens were immunized with a recombinant immunogenic protein of Eimeria. Among the biological functions, six categories were modified in both adjuvant types. However, with respect to "Response to stimulus", no biological process was modified by the two adjuvant groups at the same time. The QCDC adjuvants showed effects on the biological processes (BPs) including the innate immune response and the immune response to the external stimulus such as toxin and bacterium, while the ISA adjuvants modified the BPs to regulate cell movement and the response to stress. In pathway analysis, ISA adjuvants altered the genes involved in the functions related with cell junctions and the elimination of exogenous and endogenous macromolecules. The analysis in the present study could contribute to the development of precise adjuvants based on molecular signatures related with their immunological functions.

• Safety and Health at Work
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• 제3권2호
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• pp.85-91
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• 2012

The occupations involved in food animal production have long been recognized to carry significant health risks for workers, with special attention to injuries. However, risk of pathogen exposure in these occupations has been less extensively considered. Pathogens are a food safety issue and are known to be present throughout the food animal production chain. Workers employed at farms and slaughterhouses are at risk of pathogen exposure and bacterial infections. The industrialization of animal farming and the use of antimicrobials in animal feed to promote growth have increased the development of antimicrobial resistance. The changed nature of these pathogens exposes workers in this industry to new strains, thus modifying the risks and health consequences for these workers. These risks are not yet recognized by any work-related health and safety agency in the world.

• 생명과학회지
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• 제17권11호
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• pp.1505-1510
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• 2007

본 연구는 돼지 4번 염색체에서 FAT1 좌위의 후보유전자인 Adipocyte Fatty-Acid 결합단백질 (FABP4) 유전자에서 8개의 Single Nucleotide Polymorphisms (SNPs)를 발견하였다. Duroc, Landrace, Berkshire, Yorkshire를 기초 축으로 이용한 800두에 대해 FABP4 유전자의 단일염기 분석과 PCR-RFLP를 이용하여 그 다형성을 조사하고 돼지의 일당증체량, 등지방두께, 사료요구율, 정육율과 그 유전자형간의 연관성을 규명하고자 실시하였다. FABP4 유전자에 대해 각 단일염기에 관한 PCR-RFLP를 이용하여 $400{\sim}800\;bp$ 산물을 증폭한 후 각각의 제한효소로 사용하여, 얻어진 FABP4 유전자의 빈도는 품종별로 다르게 나타났다. 통계적 분석을 통하여 각 유전자형에 대한 경제 형 질과 연관성을 분석한 결과 일당증체량, 등지방두께, 정육율, 사료요구량은 다른 유전자형을 가진 개체들이 유의적으로 우수한 능력을 보였다 (P<0.05). FABP4유전자는 일당증체량, 정육율, 등지방두께에 높은 연관성이 있음을 관찰하였다. 따라서 돼지의 성장과 정육율에 관련된 선발력을 높이기 위해서 FABP4 유전자의 다형성 분석에서 검증된 PCR marker를 우량돼지육종 계획에 있어 분자생물학적 선발 marker로 사용할 수 있을 것으로 사료된다.

• 생명과학회지
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• 제15권6호
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• pp.968-971
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• 2005

본 연구는 Duroc, Landrace, Berkshire, Yorkshire를 기초 축으로 이용한 1003두에 대해 MC4R유전자의 PCR-RFLP를 이용하여 그 다형성을 조사하고 돼지의 일당증체량, 등지방 두께, 사료 요구율, 정육율과 그 유전자형 간의 연관성을 규명하고자 실시하였다. MC4R유전자에 대해 PCR-RFLP를 이용하여 226bp산물을 증폭한후 Taq I 체한효소로 사용하였다. 얻어진 MC4R gene의 유전자 빈도는 품종별로 다르게 나타났다. 통계적 분석을 통하여 각 유전자형에 대한 경제형질과 관련성을 분석한 결과 일당 증체량과 사료요구량은 NN 유전자형을 가진 개체들이 DN이나 DD유전자형을 가진 개체들에 비해 유의적으로 우수한 능력을 보였다(P < 0.05). 하지만 D 대립유전자는 높은 정육율과 낮은 등지방두께에 연관성이 있음을 관찰하였다. 따라서 돼지의 성장과 정육율과 관련된 선발력을 높이기 위해서 MC4R유전자의 다형성분석에서 검증된 PCR marker를 우량돼지육종 계획에 있어 분자생물학적 선발 marker로 사용할 수 있을 것으로 사료된다.