• Parasites, Hosts and Diseases
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• 제48권3호
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• pp.231-236
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• 2010

Anopheles fluviatilis James (Oiptera: Culicidae) is one of the known malaria vectors in south and southeastern Iran. Earlier ITS2 sequences analysis of specimens from Iran demonstrated only a single genotype that was identical to species Y in India, which is also the same as species T. We identified 2 haplotypes in the An. fluviatilis populations of Iran based on differences in nucleotide sequences of D3 domain of the 28S locus of ribosomal DNA (rDNA). Comparison of sequence data from 44 Iranian specimens with those publicly available in the Genbank database showed that all of the 288-D3 sequences from Kazeroun and Khesht regions in Fars Province were identical to the database entry representing species U in India. In other regions, all the individuals showed heterozygosity at the single nucleotide position, which identifies species U and T. It is argued that the 2 species may co-occur in some regions and hybridize; however, the heterozygosity in the 288-D3 locus was not reflected in ITS2 sequences and this locus for all individuals was identical to species T. This study shows that in a newly diverged species, like members of An. fluviatilis complex, a single molecular marker may not be sufficiently discriminatory to identify all the taxa over a vast geographical area. In addition, other molecular markers may provide more reliable information for species discrimination.

• 농업과학연구
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• 제46권1호
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• pp.27-31
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• 2019

It is well documented that intensive selection in dairy cattle for economic value such as increased milk yield led to a decline in reproductive performance. Recent studies using genome-wide association studies (GWASs) discovered candidate genes involved in the lower fertility including embryo development and conception rates. However, the information, which showed a lower reproductive performance, is limited to dairy cattle, especially Holstein, and the candidate genes were not examined in the Korean native cattle Hanwoo which has been intensively selected and bred for meat in the last few decades. We selected the candidate genes WBP1 and PARM1 reported to be associated with cow and/or heifer conception in dairy cattle and analyzed the genotype because those genes have non-synonymous single nucleotide polymorphisms (SNPs). To determine the single base change, we used the high resolution melting (HRM) assay which is rapid and cost-effective for a small number of genes. We found that most heifers with higher conception (1: service per conception) have the AA genotype coding Threonine rather than Proline in the WBP1 gene. We did not detect an association for a SNP in PARM1 in our analysis. In conclusion, the genetic variation of WBP1 can be used as a selective marker gene to improve reproductive performance, and HRM assay can be used to identify common SNP genotypes rapidly and cost effectively.

• BMB Reports
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• 제32권5호
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• pp.492-496
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• 1999

We have investigated the biochemical properties of the herpes simplex virus type 1 (HSV-1) DNA polymerase without the UL42 protein (Pol), purified from insect cells infected with a recombinant baculovirus containing the UL30 gene. BSA and DTT have inhibitory effects on dAMP incorporation. Pol showed a greater turnover rate of steady-state single nucleotide incorporation at 12 mM $MgCl_2$ than at 2 mM $MgCl_2$. However, it showed a greater processivity of DNA synthesis at lower $MgCl_2$ concentration (1 mM, 2 mM) than at a higher $MgCl_2$ concentration (12.5 mM). These results are consistent with a slow DNA dissociation at lower $MgCl_2$ concentrations. Pol does not incorporate a correct nucleotide into the primer with an incorrect nucleotide at the end; instead, it preferentially excises the incorrect nucleotide at the 3' end of the primer. Pol has DNA polymerase activity at pHs 6.5 and 7.5 but little at pHs 5.5, 8.5, and 9.5. It has exonuclease activity at pHs 6.5, 7.5, and 8.5 but little at pHs 4.5, 5.5, and 9.5. The finding that Pol has exonuclease activity but not DNA polymerase at pH 8.5 suggests that DNA binds to Pol, but deoxynucleotide binding or incorporation does not occur at pH 8.5.

• Reproductive and Developmental Biology
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• 제38권3호
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• pp.123-127
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• 2014

This study was conducted for SNPs in the 5'-regions of estrogen receptor-${\alpha}$ (ESR-${\alpha}$), and association with calving interval (CI), service per conception (SPC) and 305 days milk yield in Hanwoo and Holstein dairy cattle. The genetic improvement was incurred low reproduction performance. The objective of this study was to investigate connections between single nucleotide polymorphisms (SNP) of Estrogen receptor-${\alpha}$ (ESR-${\alpha}$) with reproduction performance (calving interval, service per conception, and 305 d milk yield) in Hanwoo and Holstein dairy cattle. Hanwoo and Holstein blood samples were collected from 183 and 124 dam of breeding farms and DNA was extracted. Primer design was based on NCBI GenBank (Accession No. AY340579). The PCR-RFLP method with Bgl I was used to genotype the cattle. The result showed two variants of the ESR-${\alpha}$ gene. The Bgl I cut the 492 bp amplification product into 322 bp and 170 bp fragments for allele G, while allele A remained uncut, resulting in two restriction fragments for homozygote G/G and three fragments for heterozygote A/G. We found two of different genotypes in these breeds, A/G and G/G. In Hanwoo, the A/G genotype frequency was 0.13, and G/G was 0.87. The CI of A/G was $382.18{\pm}10.03$ days, and G/G was $381.69{\pm}5.22$ days. The SPC of A/G was $1.62{\pm}0.16$, and G/G was $1.32{\pm}0.04$. While CI showed no significance difference, SPC exhibited significant difference (p<0.05). In Holstein cattle, the frequency of genotype A/G was 0.02 and G/G was 0.98. The 305 days milk yield of A/G was $7,253.00{\pm}936.00kg$ and of G/G was $8,747.51{\pm}204.88kg$, showing no significant difference.

• Clinical and Experimental Reproductive Medicine
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• 제32권3호
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• pp.279-286
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• 2005

Objective: Although several genetic factors have been associated with defects in human spermatogenesis, the unambiguous causative genes have not been elucidated. The male infertility by haploinsufficiency of PRM1 or PRM2 has been reported in mouse model. The aim of this study was to identify the single nucleotide polymorphisms (SNPs) of PRM1 and PRM2, related to the genotype of Korean infertile men. Methods: Genomic DNAs were extracted from peripheral bloods of infertile men with oligozoospermia or azoospermia, and analyzed using polymerase chain reaction (PCR) and direct sequencing. We carried out the direct sequencing analysis of amplified fragments in PRM1 (557 nucleotides from -42 to 515) and PRM2 (599 nucleotides from 49 to 648) genes, respectively. Results: Three SNPs of coding region in the PRM1 gene was found in the analysis of 130 infertile men. However, the SNPs at a133g (aa 96.9%, ag 3.1% and gg 0.0%), c160a (cc 99.2%, ca 0.8% and aa 0.0%) and c321a (cc 56.9%, ca 35.4% and aa 7.7%) coded the same amino acids, in terms of silence phenotypes. On the other hand, as results of the PRM2 gene sequencing in 164 infertile men, only two SNPs, g398c (gg 62.2%, gc 31.1% and ga 6.7%) and a473c (aa 63.4%, ac 29.9% and cc 6.7%), were identified in the intron of the PRM2 gene. Conclusions: There was no mutation and significant SNPs on PRM1 and PRM2 gene in Korean infertile men. These results suggest that the PRM1 and PRM2 genes are highly conserved and essential for normal fertility of men.

• Asian-Australasian Journal of Animal Sciences
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• 제31권12호
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• pp.1852-1862
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• 2018

Objective: The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods: The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results: The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion: The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.2077-2080
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• 2010

• 융합정보논문지
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• 제8권6호
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• pp.201-207
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• 2018

유전체는 생명체가 가지고 있는 모든 유전적 정보를 담고 있다. 특정 종 내에서는 개체별로 고유의 특성이 나타나며, 이 특성은 유전체의 염기서열 분석을 통해 확인할 수 있다. 종내 개체들 사이에 조금씩 다른 염기에 대해 유전적 연관성을 규명 짓고, 더 나아가 질병과의 연관성을 찾는 전장유전체 연관분석 연구가 많이 진행되고 있다. 종 내의 조금씩 발생하는 염기변이를 파악하는 것은 개체의 다형성을 파악하기 위해 중요하다. 이 논문에서는 종 내 여러 개체의 염기서열에서 대립형질 빈도의 특정변화패턴을 쉽게 파악할 수 있는 분석 및 시각화 도구를 제안한다. 그리고 수두 대상포진 바이러스의 계대 배양한 pOka strain 염기서열 데이터를 이용해 실험하여 분석과 시각화의 실용성을 보인다. 본 제안도구를 통해 종 내의 대립형질 빈도의 변화를 탐색하고 유전적 요인을 찾는 연구효율의 증진을 기대할 수 있다.

• 한국축산식품학회지
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• 제39권1호
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• pp.93-101
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• 2019

Nucleotides play important roles in numerous intracellular biochemical processes and are used in infant formulas and other dairy products. However, domestic analytical methods for assessing nucleotide content in products have not yet been established, and therefore, methods for determining nucleotide content are urgently required. A rapid and simple analytical method for determining the content of five types of nucleotides in dairy products was improved using solid phase extraction clean-up and high-performance liquid chromatography with diode array detector. The extraction solvent used in the AOAC method was not well dissolved and was changed to hydrophilic EDTA-Na. In addition, the results obtained using the isocratic elution method and a single wavelength were similar to those obtained using the AOAC method, and the time taken for analysis was shortened from 40 min to 25 min. The process of method validation revealed the following parameters: accuracy (84.69%-102.72%), precision (1.51%-6.82%), linearity (0.999), and limit of detection (cytidine 5'-monophosphate, 0.09 mg/L; uridine 5'-monophosphate, 0.11 mg/L; adenosine 5'-monophosphate, 0.12 mg/L; guanosine 5'-monophosphate, 0.11 mg/L; and inosine 5'-monophosphate, 0.14 mg/L). The method was also used to determine the nucleotide concentration in 25 samples (infant formulas, 1.99-29.39 mg/100 g; and cow milk, 0.28-0.83 mg/100 g). The newly improved method was appropriate for analyzing nucleotides in infant formulas and other dairy products faster when compared to conventional methods.

• 대한임상검사과학회지
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• 제55권2호
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• pp.93-104
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• 2023

이전 연구에서 83명의 한국인 폐선암 환자의 차세대 염기서열 분석법(next generation sequencing, NGS) 분석 결과 돌연변이 빈도가 높은 상위 5개 유전자 TP53 (60%), EGFR (48%), KRAS (14%), PIK3CA (8%), CDKN2A (6%)를 확인했다. 본연구는 NGS 분석을 이용하여 최근 한국인의 폐선암에서 돌연변이 발생 빈도가 높은 상위 5개 유전자에 대한 돌연변이 핫스팟을 분석하여 폐선암을 유발하는 새로운 표지자를 확인하고자 했으며 가장 많은 돌연변이가 발생한 TP53 유전자의 돌연변이 유형과 패턴을 폐암의 주요 원인인 흡연과의 연관성을 분석했으며 TP53 P72R SNP가 발생한 폐선암 환자의 임상병리학적 특성을 분석하고자 했다. TP53, EGFR, KRAS, PIK3CA, CDKN2A의 돌연변이 핫스팟을 분석한 결과 이전에 보고된 결과와 일치했으나 TP53의 경우 약간의 차이를 나타냈다. TP53 돌연변이 핫스팟은 DBD에 집중하여 발생하는 점은 기존 연구 결과와 같았으나 코돈 72에서 발생하는 높은 돌연변이 빈도는 이전에 보고된 연구 결과와 다르게 나타났다. TP53 돌연변이가 발생한 폐선암 환자의 임상 특성을 분석한 결과 남성보다 여성, 흡연자보다 비흡연자에게 더 많이 발생했다. 또한, TP53 돌연변이 유형은 흡연 여부와 상관없이 전환의 비율이 가장 높았으며 전환 또는 결실 그리고 전환과 결실이 동시에 발생하는 비율이 전이의 발생 비율보다 높게 나타났다. 한국인의 폐선암 증례에서 흡연 여부와 상관없이 가장 발생 빈도가 높은 돌연변이 핫스팟은 TP53 코돈 72 뉴클레오타이드 염기가 C에서 G로의 전환되어 아미노산이 proline에서 arginine으로 치환되는 TP53 P72R SNP 발생 비율이 가장 높게 나타났다. TP53 P72R SNP가 발생한 폐선암 증례들의 임상병리학적 특성을 분석한 결과 환자의 연령, 성별, 흡연 유무 그리고 종양의 분화도와 유의한 상관관계를 보이지 않았지만 낮은 병기와 유의한 상관관계를 나타냈다(P-value=0.026). 본연구는 NGS를 통해 한국인의 폐선암에서 돌연변이 발생 빈도가 가장 많이 보고되었던 EGFR이 아닌 TP53의 증가를 확인했고 그중에서도 흡연 여부와 관계없이 TP53 P72R SNP의 발생 빈도가 가장 높음을 보고하는 바이다.