• Molecules and Cells
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• 제38권4호
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• pp.304-311
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• 2015

Most follicles in the mammalian ovary undergo atresia. Granulosa cell apoptosis is a hallmark of follicle atresia. Our previous study using a microRNA (miRNA) microarray showed that the let-7 microRNA family was differentially expressed during follicular atresia. However, whether the let-7 miRNA family members are related to porcine (Sus scrofa) ovary follicular apoptosis is unclear. In the current study, real-time quantitative polymerase chain reaction showed that the expression levels of let-7 family members in follicles and granulosa cells were similar to our microarray data, in which miRNAs let-7a, let-7b, let-7c, and let-7i were significantly decreased in early atretic and progressively atretic porcine ovary follicles compared with healthy follicles, while let-7g was highly expressed during follicle atresia. Furthermore, flow cytometric analysis and Hoechst33342 staining demonstrated that let-7g increased the apoptotic rate of cultured granulosa cells. In addition, let-7 target genes were predicted and annotated by TargetScan, PicTar, gene ontology and Kyoto encyclopedia of genes and genomes pathways. Our data provide new insight into the association between the let-7 miRNA family in granulosa cell programmed death.

• Journal of Ecology and Environment
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• 제45권2호
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• pp.88-96
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• 2021

Background: Sika deer, Cervus nippon, were originally introduced to South Korea from Japan and Taiwan for commercial farming purposes. Unfortunately, they were released into the wild during religious events and have since begun to impact the native ecosystem and species endemic to South Korea. The study of activity patterns can improve our understanding of the environmental impact of non-native species and their association with sympatric species. Using camera traps, we studied the diel and seasonal activity patterns of non-native sika deer and quantified the temporal overlap with sympatric mammalian species in the Muljangori-oreum wetlands of Hallasan National Park, South Korea. Results: A total of 970 trap events were recorded for five mammalian species from nine locations during the camera-trap survey. Siberian roe deer (Capreolus pygargus tianschanicus) had the highest number of recorded events (72.0%), followed by sika deer (Cervus nippon) (16.2%), wild boar (Sus scrofa) (5.0%), Asian badger (Meles leucurus) (4.5%), and the Jeju weasel (Mustela sibirica quelpartis) (2.0%). Sika deer had bimodal activity patterns throughout the year, with peaks throughout the spring-autumn twilight, and day and night time throughout the winter. Relating the daily activity of sika deer with other mammalian species, roe deer expressed the highest degree of overlap (Δ₄ = 0.80) while the Asian badger demonstrated the lowest overlap (Δ₄ = 0.37). Conclusions: Our data show that sika deer are a crepuscular species with seasonal variations in daily activity patterns. Additionally, we identified the temporal differences in activity peaks between different mammals in the Muljangori-oreum wetlands and found higher degree of overlap between sika deer and roe deer during twilight hours.

• Animal Bioscience
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• 제35권7호
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• pp.975-988
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• 2022

Objective: In this study, we aimed to identify long non-coding RNAs (lncRNAs) that play important roles in starvation stress, analyze their functions, and discover potential molecular targets to alleviate starvation stress to provide a theoretical reference for subsequent in-depth research. Methods: We generated a piglet starvation stress animal model. Nine Yorkshire weaned piglets were randomly divided into a long-term starvation stress group (starved for 72 h), short-term starvation stress group (starved for 48 h), and the control group. LncRNA libraries were constructed using high-throughput sequencing of piglet ileums. Results: We obtained 11,792 lncRNAs, among which, 2,500 lncRNAs were novel. In total, 509 differentially expressed (DE)lncRNAs were identified in this study. Target genes of DElncRNAs were predicted via cis and trans interactions, and functional and pathway analyses were performed. Gene ontology functions and Kyoto encyclopedia of genes and genomes analysis revealed that lncRNA-targeted genes mainly participated in metabolic pathways, cellular processes, immune system processes, digestive systems, and transport activities. To reveal the mechanism underlying starvation stress, the interaction network between lncRNAs and their targets was constructed based on 26 DElncRNAs and 72 DEmRNAs. We performed an interaction network analysis of 121 DElncRNA-DEmRNA pairs with a Pearson correlation coefficient greater than 0.99. Conclusion: We found that MSTRG.19894.13, MSTRG.16726.3, and MSTRG.12176.1 might play important roles in starvation stress. This study not only generated a library of enriched lncRNAs in piglets, but its outcomes also provide a strong foundation to screen key lncRNAs involved in starvation stress and a reference for subsequent in-depth research.

• Journal of Forest and Environmental Science
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• 제38권2호
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• pp.128-132
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• 2022

Wild boars (Sus scrofa) not only cause crop damage and human casualties, but also facilitate the spread of many infectious diseases in domestic animals and humans. To determine the efficiency of a fencing system in blocking the movement of wild boars, long-term monitoring was performed in a fenced area in Bukhansan National Park using camera traps. Upon monitoring for a period of 46 months, there was a 72.6% reduction in the number of wild boar appearances in the fence-enclosed area, compared to that in the unenclosed area. For 20 months after the fence installation, the blocking effect of the fence was effective enough to reduce the appearance of wild boars by 92.6% in the fence-enclosed area, compared to that in the unenclosed area. The blocking effect of the fence remained effective for 20 months after its installation, after which its effectiveness decreased. Maintaining a fence for a long time is likely to lead to habitat fragmentation. It can also block the movement of other wild animals, including the endangered species - the long-tailed goral. This study suggests a 20-month retention period for the fences installed to inhibit the movement of wild boars in wide forests such as Gangwon-do in South Korea. To identify how long the blocking effect of the fences lasts, further studies are needed focusing on the length and height of the fence, and the conditions of the ground surface.

• 한국동물위생학회지
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• 제46권1호
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• pp.59-66
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• 2023

Wild boar is closely related to domestic pigs in terms of genetic homogeneity and the possibility of a source of infection by contact. This study investigated the prevalence of viral diseases from wild boars inhabiting Gyeongsangnam-do, South Korea. A total of 374 blood samples were collected and subjected to antigen tests to detect African swine fever virus (ASFV), Porcine circovirus type-2 (PCV2), Porcine reproductive and respiratory syndrome virus (PRRSV). For seroprevalence, PCV2, PRRS, classical swine fever virus (CSFV), Aujezsky's disease (ADV), and foot and mouth disease virus (FMDV) were investigated. The antigenic analysis revealed 73 positive cases (19.5%) for PCV2, while no positive cases for ASFV and PRRSV. For the antibody test, 225 (60.2%), 2 (0.5%), and 48 (12.8%) cases were detected against PCV2, PRRSV, and CSFV, respectively. There were no antibodies detected against both ADV and FMDV. Our results suggest that the viruses infecting both wild boar and domestic pig, mainly PCV2, are circulating in the wild boar population thus, the consistent monitoring of prevalence in wild boar will be needed for transboundary spillover to the domestic pig.

• Journal of Ecology and Environment
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• 제46권1호
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• pp.54-61
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• 2022

Background: In South Korea, African swine fever virus (ASFV) has spread among wild boars through Gangwon-do to Dangyang-gun, Chungcheongbuk-do on the southern border of Gangwon-do. To prevent the spread of ASFV to African swine fever (ASF)-free areas, it is necessary to identify areas with a high probability of finding ASFV-infected carcasses and to reduce the density of wild boars in those areas. In this study, we described the propagation trend of ASFV among wild boars, constructed the habitat suitability maps for ASFV-infected carcasses, and suggested areas with a high probability of finding ASFV-infected carcasses and an important route of ASFV transmission. Results: Despite the active quarantine policies in Korea to prevent the spread of ASFV through wild boars, there was no significant difference in the monthly average of number of ASFV-infected carcasses observed between 2020 and 2021. The ASFV-infected carcasses were found more in winter and spring (January to April). Since the first ASF outbreak in wild boars on October 2, 2019, the maximum width of ASFV-infected carcass distribution area was 222.7 km for about 26 months till November 20, 2021. The habitat suitability map, based on GPS coordinates of ASFV-infected wild boar carcasses, shows that highly detectable areas of ASFV-infected carcasses were sporadically dispersed in western and southwestern parts of Gangwon-do, and ranged from north to south of the province along the Baekdudaegan Mountains, whereas poorly detectable areas ranged along the north to the south in the middle parts of the province. Conclusions: Our suitability model, based on the GPS coordinates of ASFV-infected carcasses, identifies potential habitats where ASFV-infected carcasses are likely to be found and ponential routes where ASFV is likely to spread. Among ASF-free areas, the areas with high suitability predicted in this study should be given priority as survey areas to find ASFV-infected carcasses and hunting areas to reduce wild boar populations.

• Animal Bioscience
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• 제35권9호
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• pp.1289-1302
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• 2022

The next generation sequencing has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the male-specific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in Bos taurus, 5 and 7 in Bubalus bubalis, 5 and 24 in Ovis aries, 5 and 19 in Capra hircus, 10 and 16 in Sus scrofa, 46 and 18 in Equus caballus. While in Vicugna pacos only 10 loci are reported in the PAR region. The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.

• 한국환경생태학회지
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• 제37권6호
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• pp.429-438
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• 2023

두만강 하류의 숲은 북한, 중국, 러시아를 연결하는 중요한 산림생태계로서, 국제적인 멸종위기종인 호랑이(Panthera tigris)와 표범(Panthera pardus)을 포함한 다양한 야생동물들에게 서식환경과 이동경로를 제공하여 준다. 본 연구는 두만강 하류, 특히 중국과 북한을 연결하는 잠재적인 생태통로로서 한반도의 생물다양성 보전과 복원에 중요한 역할을 할 수 있는 밀강 지역에 초점을 맞추고 있다. 2019년 5월부터 2021년 5월까지 이 지역에 설치한 48대의 무인센서카메라를 통해 출현하는 포유류 종을 확인하고 그들의 상대개체수와 점유율 및 분포 현황을 파악하는 것을 목표로 하였다. 그 결과 총 18종의 포유류가 밀강 지역에 서식하고 있으며, 그 중에는 호랑이와 표범 등 대형 육식동물도 포함되고 있음을 확인하였다. 이 지역의 주요 포유류인 유제류 4종에 대한 점유율과 탐지율, 분포를 추정한 결과, 특히 노루(Capreolus pygargus)와 멧돼지(Sus scrofa)가 높은 점유율을 보였다. 노루는 모든 지역에 분포하며 예측 점유율은 0.97로 높게 나타났으나, 고도, 도시 주거용지, 패치 밀도 등의 영향을 받는 것으로 나타났다. 멧돼지는 0.73의 예측 점유율을 보이며 전 지역에 분포했으며, 습지 비율, 방목 강도, 사면에 대한 공간이질성 등의 인자가 점유율과 탐지율에 영향을 주었다. 꽃사슴(Cervus nippon)의 예측 점유율은 0.48로서 특정 지역에 국한되어 분포하였으며, 경사도와 서식지 파편화 다양성이 탐지율에, 방목 강도와 개방된 숲의 비율이 점유율에 각각 영향을 주었다. 고라니(Hydropotes inermis)는 아주 낮은 점유율(0.06)을 보이며 두만강 유역을 따라 분포했으며, 고도가 낮은 곳의 점유율이 높고 사면의 공간이질성이 높은 곳에서 탐지율이 높았다. 본 연구는 밀강 지역이 두만강 하류의 다양한 포유류 개체군을 유지하는 서식지인 동시에, 동물의 이동성과 서식지의 연결성을 유지하는 잠재적 생태통로로서 중요한 역할을 할 수 있음을 확인하였다. 동시에 본 연구에서 개발된 점유율 예측 모형은 향후 인간의 교란에 노출된 두만강 유역의 포유류 분포를 예측하고 국경지대의 생태통로를 파악하고 보호하는 데 기여할 수 있을 것으로 기대된다.

• Bioinformatics and Biosystems
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• 제1권2호
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• pp.99-102
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• 2006

BLAST(Basic Local Alignment Search Tool)는 서열 데이터베이스 탐색을 위하여 가장 많이 사용되는 프로그램이다. 전체 서열간의 최적 글로벌 정렬을 수행하는 대신에 지역적 유사성이 있는 부분을 찾아 서열 짝짓기를 수행하는 특징을 갖는다. 일반적인 연구자들은 서열 상동성 검색을 위해 NCBI에 접속하여 웹 브라우저를 통해 온라인으로 BLAST를 수행하게 되는데, 이 경우 사용자 각각의 네트워크 환경이나 입력할 데이터양에 따른 검색속도의 지연 및 제한 등과 같은 여러 문제에 부딪히게 되고, 또한 보안유지가 필요한 서열 데이터의 유출 가능성이 존재한다. 그러므로 대량의 서열 데이터에 대하여 빠르고 안전하게 BLAST 상동성 검색이 가능한 Local BLAST 검색 시스템의 필요성이 증대되고 있다. 본 연구에서는 NCBI의 Genbank에서 공개된 동물의 발현 유전자 단편들(ESTs)에 대한 데이터를 이용하여 소, 돼지, 닭, 등의 경제형질과 연관된 유용 유전자만을 추출하여 이들만으로 구성된 새로운 데이터베이스를 구축하였고, 또한 이들을 사용할 수 있는 새로운 검색시스템을 개발하였다 자체 제작한 Perl script를 사용하여 필요한 데이터를 축종별로 추출 하여 새로운 DB를 구축하였으며 이 속에는 소의 경우 650,046개, 돼지의 경우 368,120개, 닭의 경우 693,005개의 발현 유전자 단편들(ESTs)이 포함된다. 또한 이들 DB 분석이 가능한 Local Animal BLAST Web 검색시스템(http://bioinfo.kohost.net)을 고성능 병렬 PC Cluster 시스템과 연동하도록 자체 구축함으로써 본 시스템이 보다 효율적인 생물정보학 연구수행이 기여할 것으로 기대된다.

• 한국수정란이식학회지
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• 제31권3호
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• pp.235-242
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• 2016

This study tested the association between genotypes of the single nucleotide polymorphism (SNP) marker, rs81437607 and capric acid (FA_C10_0) compositions in longissimus dorsi muscle in pigs. Eighteen fatty acid (FA) compositions were measured in a total of 974 $F_2$ animals among 1,106 $F_2$ progeny produced between Landrace and Jeju Black Pig (JBP). Among FA compositions tested, we identified a cluster of highly significant SNPs for capric acid compositions on 58 Mb position of Sus scrofa chromosome 12 (SSC12) using genome-wide association study (GWAS) with $F_2$ genotypes from SNP panel analysis. GWAS results showed that the rs81437607 was the highest trait-related SNP marker with capric acid levels. Three genotypes (C/C, C/T and T/T) of rs81437607 marker were found in $F_2$ population by further pyrosequencing. Association analysis results showed the significant differences between rs81437607 genotypes and capric acid compositions (P<0.05). The $F_2$ pigs harboring rs81437607 C/C ($0.119{\pm}0.002%$) and C/T ($0.116{\pm}0.002%$) genotypes showed additively higher levels of capric acid content than those of T/T homozygotes ($0.109{\pm}0.002%$) ($P=1.30{\times}10^{-12}$). These results suggested that the genetic variations of rs81437607 may be helpful to find causative variants and assist as molecular genetic markers for improving the capric acid contents in longissimus dorsi muscle in pigs.