• Genomics & Informatics
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• 제9권1호
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• pp.28-36
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• 2011

Most statistical methods for finding interesting genes are focusing on the summary values with large fold-changes or large variations. Very few methods consider the probe level data. We developed a new measure to detect reliability that incorporates the probe level data. This reliability measure is useful for exploring the microarray data without ignoring the probe level data. It is easy to calculate, and it can be used for all the other statistical methods as a good guideline to find real differentially expressed genes. Instead of filtering out genes before the analysis, we use whole genes in the analysis and make decisions with new reliability measures.

• Korean Chemical Engineering Research
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• 제47권5호
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• pp.538-545
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• 2009

본 총설에서는 주사형프로브현미경의 원리와 응용에 관하여 간략히 설명하고 최근 본 그룹에 의하여 활발하게 연구되고 있는 나노탐침과 AFM(원자간력현미경 atomic force microscopy)을 이용한 저침습성(low-invasive) 단일세포 조작기술과 고효율 유전자 도입기술을 소개하고자 한다. 시판 AFM 탐침을 침상구조로 가공한 나노탐침과 AFM을 이용하였을 경우, 탐침의 세포삽입의 성공여부를 force-distance curve 상의 척력소실의 유무로 판단할 수 있다. 침상 나노탐침을 사용하면 대부분의 세포에서 80~90%의 고효율 세포삽입이 가능하여 마이크로인젝션용 미세관을 이용하는 경우보다 세포삽입효율이 높았다. 또한 나노탐침의 직경이 400 nm 이하의 경우에는 세포 종류에 관계없이 장시간 나노탐침의 삽입에도 세포활성에 큰 영향이 없었다. 침상나노탐침을 이용하여 DNA를 도입하였을 경우에도 기존의 DNA 도입방법과 비교하여 높은 도입효율과 유전자 발현율로 DNA를 도입할 수 있는 가능성을 확인하였다.

• 한국미생물·생명공학회지
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• 제18권6호
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• pp.640-646
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• 1990

E.coli의 cytidine deaminase(cytidine/2'-deoxy-cytidine aminohydrolas` EC 3.5.4.5)를 코딩하는 cdd 유전자를 E.coli cdd- pyr- 결손 변이주를 cloning host로 하여 southern blotting과 colony hybridization을 통하여 클로닝하였다. cdd 유전자가 단편인, cdd 유전자의 transcription initiation 부위의 23개 nucleotide를 합성한 후 probe로 사용하여 Southern hybridization에 의해 회수된 cdd 유전자를 함유한 단편을 얻었으며, 이를 pBR322에 삽입한 후 형질전환하여 colony hybridization한 결과 cdd+ cell을 얻었다. 삽입된 DNA 단편의 size는 27kb이었으며 이를 결실 및 subcloning을 연속 수행한 결과 2.1kb의 SalI/ DraI fragment(pTK605)에 cdd 유전자가 location 되어 있음을 알게 되었다. Mini cell 실험결과 합성된 cytidine deaminase의 활성이 pBR322에서 증폭시킴으로서 37배 정도 배가되었으며, pBR322에 비해 pUC vector계에서 다시 활성이 7배 정도 증가됨을 알 수 있었다.

• Journal of Microbiology and Biotechnology
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• 제27권1호
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• pp.72-76
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• 2017

Detection of exon 19 deletion mutation in the epidermal growth factor receptor (EGFR) gene, which results in increased and sustained phosphorylation of EGFR, is important for diagnosis and treatment guidelines in non-small-cell lung cancer. Here, we have developed a simple and convenient detection system using the interaction between G-quadruplex and fluorophore thioflavin T (ThT) for discriminating EGFR exon 19 deletion mutant DNA from wild type without a label and quencher. In the presence of exon 19 deletion mutant DNA, the probe DNAs annealed to the target sequences were transformed into G-quadruplex structure. Subsequent intercalation of ThT into the G-quadruplex resulted in a light-up fluorescence signal, which reflects the amount of mutant DNA. Due to stark differences in fluorescence intensity between mutant and wild-type DNA, we suggest that the induced G-quadruplex structure in the probe DNA can report the presence of cancer-causing deletion mutant DNAs with high sensitivity.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2002년도 하계학술대회 논문집 C
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• pp.1569-1571
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• 2002

The determination of DNA hybridization can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and other application area. So, The determination of hybridization is very important for the improvement of DNA detection system. In this study, we report the characterization of the DNA hybridization by the electricalchemical methods. A new electrochemical biosensor is described for voltammetric detection of gene sequence related to probe oligonucleotide of bacterium Escherichia coli O157:H7. The biosensor involves the immobilization of a 18-mer probe oligonucleotide, which is complemetary to a specific gene sequence related to Escherichia coli O157:H7 on a gold electrode through specific adsorption. The probe oligonucleotide was used to determine the amount of target oligonucleotide in solution using mitoxantrone(MTX) as the electrochemical indicators. The cathodic peak currents $(I_{peak})$ of MTX were linearly related to the concentration of the target oligonucleotide sequence in the range $1[{\mu}M]{\sim}0.1[nM]$. The detection limit of this approach was 0.01[nM]. In addition, these indicators were capable of selectivity discriminating against various mismatching condition.

• Journal of Microbiology and Biotechnology
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• 제19권11호
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• pp.1464-1469
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• 2009

To achieve more accurate and rapid detection of macrolide-lincosamide-streptogramin B resistance genes, erm(A), erm(B), and erm(C), we developed a TaqMan probe-based real-time PCR (Q-PCR) method and compared it with conventional PCR (C-PCR), which is the most widely using erm gene identification method. The detection limit of Q-PCR was 5 fg of genomic DNA or 5-8 CFU of bacterial cells of Staphylococcus aureus. The utilization of Q-PCR might shorten the time to erm detection from 3-4 h to about 50 min. These data indicated that Q-PCR assay appears to be not only highly sensitive and specific, but also the most rapid diagnostic method. Therefore, the appropriate application of the Q-PCR assay will permit rapid and accurate identification of erm genes from clinical and other samples.

• Journal of Microbiology and Biotechnology
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• 제34권3호
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• pp.681-688
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• 2024

The accurate and rapid detection of methicillin-resistance of Staphylococcus aureus (SA) holds significant clinical importance. However, the methicillin-resistance detection strategies commonly require complicated cell lysis and gene extraction. Herein, we devised a novel colorimetric approach for the sensitive and accurate identification of methicillin-resistance of SA by combining allosteric probe-based target recognition with self-primer elongation-based target recycling. The PBP2a aptamer in the allosteric probe successfully identified the target MRSA, leading to the initiation of self-primer elongation based-cascade signal amplification. The peroxidase-like hemin/G-quadruplex undergo an isothermal autonomous process that effectively catalyzes the oxidation of ABTS2- and produces a distinct blue color, enabling the visual identification of MRSA at low concentrations. The method offers a shorter duration for bacteria cultivation compared to traditional susceptibility testing methods, as well as simplified manual procedures for gene analysis. The overall amplification time for this test is 60 min, and it has a detection limit of 3 CFU/ml. In addition, the approach has exceptional selectivity and reproducibility, demonstrating commendable performance when tested with real samples. Due to its advantages, this colorimetric assay exhibits considerable potential for integration into a sensor kit, thereby offering a viable and convenient alternative for the prompt and on-site detection of MRSA in patients with skin and soft tissue infections.

• BMB Reports
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• 제47권2호
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• pp.92-97
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• 2014

We have examined the effect of bithorax complex genes on the expression of castor gene. During the embryonic stages 12-15, both Ultrabithorax and abdominal-A regulated the castor gene expression negatively, whereas Abdominal-B showed a positive correlation with the castor gene expression according to real-time PCR. To investigate whether ABD-B protein directly interacts with the castor gene, electrophoretic mobility shift assays were performed using the recombinant ABD-B homeodomain and oligonucleotides, which are located within the region 10 kb upstream of the castor gene. The results show that ABD-B protein directly binds to the castor gene specifically. ABD-B binds more strongly to oligonucleotides containing two 5'-TTAT-3' canonical core motifs than the probe containing the 5'-TTAC-3' motif. In addition, the sequences flanking the core motif are also involved in the protein-DNA interaction. The results demonstrate the importance of HD for direct binding to target sequences to regulate the expression level of the target genes.

• 미생물학회지
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• 제35권3호
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• pp.192-196
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• 1999

Fusarium 균 중에서 section Liseola 에 속하는 8균주에 대하여 CHEF-PFGE를 이용하여 핵형을 분석비교하였다. 0.75 Mb에서 6.45Mb 크기의 DNA band가 9~13개로 분리되었고 전체 genome 크기는 38.19 Mb에서 43.22Mb 였으며 종간, 종내에서 염색체 길이 다형성을 볼 수 있었다. F. moniliforme 로부터 얻은 IGS sequence(2.6Kb), Neurospora crassa 의 chs-2 gene(2.8Kb) 과 trp-3gene(3.8 Kb)을 probe로 하여 hybridization을 통하여 이들 gene 의 위치를 확인하고자 하였다.

• Journal of Ginseng Research
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• 제19권1호
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• pp.51-55
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• 1995

The DNA fragment containing ginseng ribulose-1,5-bisphosphate carboxytase/oxygenase large subunit(rbcL) gene was cloned from the ginseng chloroplast EcoRl library by colony lift hybridization with tobacco rbcL gene probe. From the screened clone, the DNA fragment containing ginseng rbcL gene was digested with several restriction enzyme and analyzed by Southern blot hybridization for the construction of restriction map. The ginseng rbcL gene fragment was subcloned in pBluescript II SK + vector and sequence analysis was performed. The nucleotide sequence of ginseng rbcL gene was compared with those of petunia, tobacco, alfalfa, rice and barley, which showed a homology of 93.1%, 95.2%, 90.5%, 85.5% and 84.3%, respectively.