• Archives of Pharmacal Research
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• 제19권6호
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• pp.450-455
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• 1996

The genomic DNA was prepared from trout liver which was treated with 3-methycholanthrene, and cloned into lambda EMBL3 at BamHl site. The genomic library was constructed via infections of these recombinant phages into E. coli K802, and screened by the most $5^I$-portion of trout CYP1A1 cDNA. After the screening of $10^9$ clones of the amplified library, 12 positive clones were isolated, and subjected to further screenings. The results of southern blot hybridization of genomic DNA prepared from the positive clone showed the presence of a single gene of CYP1A1, and 3.5 Kb PstI fragment that hybridizes with the most $5^I$-region DNA of CYP1A1 cDNA. The restriction map of PstI fragment was determined by the restriction digestion with various enzymes. The nucleotide sequence of the upstream genomic DNA of CYPIAI was determined by DNA sequencing of exonuclease III unidirectionally deleted PstI fragment DNA using $[^{35}/S]$dATP. This paper presented the upstream genomic DNA of CYP1A1 contained a part of coding region which was about 351 base pairs (from ATG to PstI site at 3563).

• Animal Systematics, Evolution and Diversity
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• 제36권4호
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• pp.336-346
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• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• Genomics & Informatics
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• 제20권3호
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• pp.30.1-30.9
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• 2022

Hereditary spastic paraplegia is a not common inherited neurological disorder with heterogeneous clinical expressions. ALDH18A1 (located on 10q24.1) gene-related spastic paraplegias (SPG9A and SPG9B) are rare metabolic disorders caused by dominant and recessive mutations that have been found recently. Autosomal recessive hereditary spastic paraplegia is a common and clinical type of familial spastic paraplegia linked to the SPG11 locus (locates on 15q21.1). There are different symptoms of spastic paraplegia, such as muscle atrophy, moderate mental retardation, short stature, balance problem, and lower limb weakness. Our first proband involves a 45 years old man and our second proband involves a 20 years old woman both are affected by spastic paraplegia disease. Genomic DNA was extracted from the peripheral blood of the patients, their parents, and their siblings using a filter-based methodology and quantified and used for molecular analysis and sequencing. Sequencing libraries were generated using Agilent SureSelect Human All ExonV7 kit, and the qualified libraries are fed into NovaSeq 6000 Illumina sequencers. Sanger sequencing was performed by an ABI prism 3730 sequencer. Here, for the first time, we report two cases, the first one which contains likely pathogenic NM_002860: c.475C>T: p.R159X mutation of the ALDH18A1 and the second one has likely pathogenic NM_001160227.2: c.5454dupA: p.Glu1819Argfs Ter11 mutation of the SPG11 gene and also was identified by the whole-exome sequencing and confirmed by Sanger sequencing. Our aim with this study was to confirm that these two novel variants are direct causes of spastic paraplegia.

• 대한임상검사과학회지
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• 제49권1호
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• pp.28-39
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• 2017

잔류성 유기 오염 물질은 후성학적 메커니즘과 비만의 발달에 영향을 줄 수가 있다. 폴리브롬화 디페닐 에테르는 주요한 잔류성 유기 오염 물질 중 하나이며, 난연제로 널리 쓰인다. 출생전 잔류성 유기 오염 물질과 같은 내분비교란물질에 노출시 LINE-1 (long interspersed nuclear elements)의 global DNA 메틸화와 비만 위험도의 증가에 영향을 미칠 수 있다. 따라서, 이번 연구는 임신한 스프라그-돌리 백서를 이용하여 태반과 모유를 통하여 전달된 BDE-47, BDE-209가 LINE-1에서의 후성학적인 변화와 obesogen으로서 발달과정에 따른 유전적 비만 감수성의 증가에 영향을 줄 수 있는지에 대해서 보고자 하였다. 어미와 새끼에서 LINE-1의 광범위 DNA 메틸화와 비만과 관련된 유전자 발현은 methylation-sensitive high resolution melting analysis (MS-HRM), direct bisulfite sequencing와 quantitative real time polymerase chain reaction (qPCR)을 사용하여 각각 분석하였다. MS-HRM 결과는 출생 후 4일의 노출군 새끼에서 (4마리 중 2마리) LINE-1의 광범위 DNA 저메틸화 양상을 보여주었지만, bisulfite sequencing은 노출군과 비노출군에서 차이가 없었다. ${\beta}$-산화 경로와 adipokines과 관련된 어미의 유전자 발현은 두 그룹간 차이를 보였다. 반면에, 새끼의 유전자 발현은 비슷한 양상을 나타내었다. ${\beta}$-산화 경로와 비만과 관련된 유전자 발현 중 $PPAR-{\alpha}$를 제외하고는 출생 시에 유의하게 증가하였다. 결론적으로, 이번 연구는 BDE-47, BDE-209의 동시 노출이 태반과 모유를 통해서 새끼에서의 후성학적인 변화와 비만과 관련된 유전자 발현 변화에 영향을 미칠 수 있는 것을 보여주었다.

• Asian-Australasian Journal of Animal Sciences
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• 제31권2호
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• pp.189-197
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• 2018

Objective: Hemicastration is a unilateral orchiectomy to remove an injured testis, which can induce hormonal changes and compensatory hypertrophy of the remaining testis, and may influence spermatogenesis. However, the underlying molecular mechanisms are poorly understood. Here, we investigated the impact of hemicastration on remaining testicular function. Methods: Prepubertal mice (age 24 days) were hemicastrated, and their growth was monitored until they reached physical maturity (age 72 days). Subsequently, we determined testis DNA methylation patterns using reduced representation bisulfite sequencing of normal and hemicastrated mice. Moreover, we profiled the testicular gene expression patterns by RNA sequencing (RNA-seq) to examine whether methylation changes affected gene expression in hemicastrated mice. Results: Hemicastration did not significantly affect growth or testosterone (p>0.05) compared with control. The genome-wide DNA methylation pattern of remaining testis suggested that substantial genes harbored differentially methylated regions (1,139) in gene bodies, which were enriched in process of protein binding and cell adhesion. Moreover, RNA-seq results indicated that 46 differentially expressed genes (DEGs) involved in meiotic cell cycle, synaptonemal complex assembly and spermatogenesis were upregulated in the hemicastration group, while 197 DEGs were downregulated, which were related to arachidonic acid metabolism. Integrative analysis revealed that proteasome 26S subunit ATPase 3 interacting protein gene, which encodes a protein crucial for homologous recombination in spermatocytes, exhibited promoter hypomethylation and higher expression level in hemicastrated mice. Conclusion: Global profiling of DNA methylation and gene expression demonstrated that hemicastration-induced compensatory response maintained normal growth and testicular morphological structure in mice.

• KSBB Journal
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• 제16권1호
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• pp.36-40
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• 2001

In order to study the molecular mechanism of $\gamma$-aminobutyric acid (GABA) production in plants, we cloned and sequenced a partial glutamate decarboxylase (GAD) cDNA from the Arabidopsis thaliana cDNA library, using primers targeted at highly conserved sequences of the petunia GAD gene. The cDNA fragment was inserted into TA cloning vector with T7 promoter and the recombinant plasmid obtained was used to transform E. coli. The plasmid DNA purified from the transformed E. coli was digested with EcoRI and the presence of the insert was confirmed. Nucleotide sequence analysis showed that the fragment is a partial Arabidopsis thaliana GAD gene and that the sequence showed 98% and 78% identity to the region of the putative Arabidopsis thaliana GAD sequences deposited in GenBank, Accession nos: U46665 and U10034, respectively. The amino acid sequence deduced from the partial Arabidopsis thaliana GAD gene showed 99% and 91% identities to the GAD sequences deduced from the genes of the U46665 and U10034, respectively. The partial cDNA sequence determined may facilitate the study of the molecular mechanism of GABA metabolism in plants.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2001년도 하계학술대회 논문집 C
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• pp.1869-1871
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• 2001

DNA 센서의 중요한 역할 중의 하나는 염기서열을 분석함으로써 유전적인 질병이나 돌연변이를 찾아낸다는 점이다. 염기서열 분석법으로 질량, 광학, 전기 화학적 측정법 등이 있는데, 그 중 전기 화학적 측정방법이 타 방법에 비해 간편하고 비용도 저렴해서 전망이 매우 밝다. 전기 화학적 측정을 위해서는 전극의 표면 처리 공정과 전극 표면에서의 DNA immobilization, hybridization 공정 및 전기적 신호를 발생시키는 intercalator, 그리고 전기적 신호 검출을 위한 측정 장비가 필요하다. 본 논문에서는 전극의 표면 처리 물질로서 2-mercaptoethanol을 사용했고 double strand DNA의 intercalator로써 methylene blue를 사용했으며, methylene blue의 환원 전류값을 측정하여 double strand DNA를 bare Au 또는 single strand DNA와 구분할 수 있었다. 이러한 연구 결과를 토대로 하여 전기 화학적 신호 검출을 이용한 DNA 센서의 가능성과 개발 방향을 제시하고자 한다.

• 인터넷정보학회논문지
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• 제19권2호
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• pp.1-7
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• 2018

기술의 발전에 따라 유전 정보를 수월하게 얻을 수 있게 되었으며, 이것의 활용도 및 미래 가치는 매우 높다. 하지만, 유전 정보는 한 번 유출되면 변경할 수 없으며, 피해의 정도도 개인에만 국한되지 않고, 대용량 데이터이기 때문에 이를 고려한 처리 기술 또한 필요하다. 즉, 대용량에서도 프라이버시를 고려하며 유전 정보를 처리할 수 있는 기술의 개발이 필요하다. 본 논문에서는 Gentry 등의 준동형 암호 기법을 사용하여 먼저 대용량에서 프라이버시를 보호하는 내적 연산 프로토콜을 제안하고, 이 프로토콜을 활용하여 효율적인 프라이버시를 보호하는 DNA 매칭 프로토콜을 제안한다. 우리가 제안하는 프라이버시를 보호하는 DNA 매칭 프로토콜은 효율적이며, 정확성, 기밀성, 프라이버시를 만족한다.

• BMB Reports
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• 제38권6호
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• pp.690-694
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• 2005

Transcription termination of the human mitochondrial genome requires specific binding to termination factor mTERF. In this study, mTERF was produced in E. coli and purified by two-step chromatography. mTERF-binding DNA sequences were isolated from a pool of randomized sequences by the repeated selection of bound sequences by gel-mobility shift assay and polymerase chain reaction. Sequencing and comparison of the 23 isolated clones revealed a 16-bp consensus sequence of 5'-GTG$\b{TGGC}$AGANCCNGG-3' in the light-strand (underlined residues were absolutely conserved), which nicely matched the genomic 13-bp terminator sequence 5'-$\b{TGGC}$AGAGCCCGG-3'. Moreover, mTERF binding assays of heteroduplex and single-stranded DNAs showed mTERF recognized the light strand in preference to the heavy strand. The preferential binding of mTERF with the light-strand may explain its distinct orientation-dependent termination activity.

• Journal of Plant Biotechnology
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• 제3권3호
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• pp.131-134
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• 2001

In $\lambda$-Zap II vector system, a cDNA library was constructed for the developing secondary xylem mRNA from hybrid poplar, Populus nigra x maximowiczii. A cDNA clone of 1.5 kb in size, pOMTB1.4 encoding a lignin-bispecific O-methyltransferase was screened by plaque hybridization using a probe of 540 bp cDNA amplified by polymerase chain reaction from the cDNA library and identified by nucleotide sequencing. Its nucleotide sequence contains one open reading frame of 366 amino acids. The deduced amino acid sequence in comparison with that of Populus tremuloides showed the differences of 9 amino acids and revealed 85-99% homology among alfalfa, poplar and aspen.