• 대한의생명과학회지
• /
• 제10권4호
• /
• pp.333-339
• /
• 2004

A multiplex PCR assay targeting the yst and 16S rRNA genes of Yersinia enterocolitica was developed to specifically identify pathogenic Y. enterocolitica from pure culture. Simultaneous amplification of 145 and 416 bp fragments of the yst and 16S rRNA genes of Y. enterocolitica was obtained using the primer pairs in a single reaction. Validation of the assay was performed with the reference Yersinia strains and other members of the family Enterobacteriaceae. The defined primer pairs amplified the targeted sequence from only pathogenic Y. enterocolitica strains, whereas none of the other bacterial species yielded any amplified fragments. Within an assay time of 4 h, this assay offers a very specific, reliable, and inexpensive alternative to the conventional phenotypic assays used in clinical laboratories to identify pathogenic Y. enterocolitica.

• 한국미생물학회:학술대회논문집
• /
• 한국미생물학회 2008년도 International Meeting of the Microbiological Society of Korea
• /
• pp.62-64
• /
• 2008

A major hurdle to the development of RNA interference as therapy for HIV infection is the delivery of siRNA to T lymphocytes which are difficult cells to transfect even in vitro. We have employed a single chain antibody to the pan T cell surface antigen CD7 was conjugated to an oligo-9-arginine peptide (scFvCD7-9R) for T cell-specific siRNA delivery in NOD/SCIDIL2${\gamma}$-/- mice reconstituted with human peripheral blood lymphocytes (Hu-PBL). Using a novel delivery, we first show that scFvCD7-9R efficiently delivered CD4 siRNA into human T cells in vitro. In vivo administration to Hu-PBL mice resulted in reduced levels of surface CD4 expression on T cells. Mice infected with HIV-1 and treated on a weekly basis with scFvCD7-9R-siRNA complexes targeting a combination of viral genes and the host coreceptor molecule CCR5 successfully maintained CD4/CD3 T cell ratios up to 4 weeks after infection in contrast to control mice that displayed a marked reduction in CD4 T cell numbers. p24 antigen levels were undetectable in 3 of the 4 protected mice. scFvCD7-9R/antiviral siRNA treatment also helped maintain CD4 T cell numbers with reduced plasma viral loads in Hu-PBL mice reconstituted with PBMC from donors seropositive for HIV, indicating that this method can contain viral replication even in established HIV infections. Our results show that scFvCD7-9R could be further developed as a potential therapeutic for HIV-1 infection.

• 한국어병학회지
• /
• 제17권2호
• /
• pp.91-98
• /
• 2004

본 연구의 목적은 국내 어류 연쇄구균증 병원체 동정에 있어서 Streptococcus iniae에 대한 구체적인 국내 연구 보고가 없어, 기존에 수행되고 있는 동정방법을 근간으로 16S-23S intergenic spacer region (ISR)의 염기서열을 분석하여 보다 명확한 동정을 실시하고자 하였다. API 20 strep system에 의한 생화학적 성상을 분석해본 결과 정확한 종 동정은 이루어지지 않았지만 기존의 연구에서 보고된 API 20 strep system에 의한 S. iniae의 생화학적 성상과 높은 유사성을 보이는 10균주를 분리할 수 있었다. S. iniae 16S rRNA gene 서열 유래 종 특이적 primer Sin-1 5'-CTAGAGTACACATGTACT(AGCT)AAG-3'와 Sin-2 5'-GGATTTTC CACTCCCATTAC-3'에 의한 PCR-assay 결과 시험균주 10 균주 모두 동일하게 약 300bp의 증폭산물이 관찰되었고, 비 특이적인 반응은 관찰되지 않았다. 시험균주 모두 3개의 16S-23S ISR operon 구조가 관찰되었으나 S. iniae 표준균주 (KCTC 3657)의 경우 단일 구조가 관찰되었다. 16S-23S intergenic spacer region (ISR)의 염기서열을 분석해본 결과 기존에 보고된 S. iniae (Genbank accession number AF 048773)와 96%의 상동성을 보였으며 전체서열에서 상동성을 보이는 근연종이나 근연속은 검색되지 않아 최종적으로 S. iniae로 동정하였다.

• Journal of Photoscience
• /
• 제7권2호
• /
• pp.73-78
• /
• 2000

To analyze molecular traits determining pigmentation between Pharbitis nill violet and white, Amplified Fragment Length Polymorphism(AFLP) and Differential Display Reverse Transcription(DDRT) experiments were carried out with either genomic DNAs or total RNAs isolated from both plants. Results of AFLP experiment in combination of 8 EcoRⅠ primers with 6 MseⅠ primers showed 41 violet-and 60 white-specific DNA bands. In the subsequent experiment, 22 violet-and 22 white-specific DNA fragments were amplified by PCR with DNAs eluted. The sizes of the fragments range from 200 to 600bp. DDRT using total RNA produced 19 violet-and 17 white-specific cDNA fragments, ranging from 200 to 600bp. The fragments obtained by both AFLP and DDRT had been cloned into pGEM T-easy vector, amplified and subjected to the nucleotide sequence analyses. As a result of Blast sequence analysis, most of them sequenced up to date showed no similarity to any Known gene, while few has similarity to known animal or plant genes. An AFLP clone V6, for example, has a strong sequence similarity to the human transcription factor LZIP-alpha mRNA and a DDRT clone W19 to Solanum tuberosum 3-hydroxy-3-methylglutaryl coenzyme A reductase mRNA.

• Journal of the Korean Data and Information Science Society
• /
• 제27권1호
• /
• pp.225-243
• /
• 2016

Thanks to recent advance of next generation sequencing techniques, RNA-seq enabled to have an unprecedented opportunity to identify transcript variants with isoform diversity and allelic imbalance (Anders et al., 2012) by different transcriptional rates. To date, it is well known that those features might be associated with the aberrant patterns of disease complexity such as tissue (Anders and Huber, 2010; Anders et al., 2012; Nariai et al., 2014) specific differential expression at isoform levels or tissue specific allelic imbalance in mal-functionality of disease processes, etc. Nevertheless, the knowledge of post-transcriptional modification and AI in transcriptomic and genomic areas has been little known in the traditional platforms due to the limitation of technology and insufficient resolution. We here stress the potential of isoform variability and allelic specific expression that are relevant to the abnormality of disease mechanisms in transcriptional genetic regulatory networks. In addition, we systematically review how robust Bayesian approaches in RNA-seq have been developed and utilized in this regard in the field.

• Journal of Plant Biology
• /
• 제39권4호
• /
• pp.279-286
• /
• 1996

To know the changes of rbcL mRNA level by illumination, Northern hybridization analysis was performed with maize (Zea mays L.cv. Golden X Bantam). The average level of rbcL. mRNA in the light-grown shoots was 3.1 times higher than that of the dark-grown shoots after 6 to 10 growth days. The maximum difference of rbcL mRNA level between the dark-grown and the light-grown shoots was 5.1 folds. These results indicate that accumulation of rbcL mRNAin maize shoots is induced by light. Since the transcriptional DNA binding proteins and their cognate promoter elements, we carried out gel-retardation assays to elucidate the specific binding proteins on the rbcL promoter. It was found that plastid proteins of light-grown shoots bound to the R2 DNA fragment (-33 to -229) and R3 DNA fragment (-230 to -418 from ATG) of the rbcL promoter. From the results of competitive binding assays and heat or protease treatments, it was demonstrated that the bindings were sequence-specific DNA-protein interactions. Therefore, it could be concluded that the rbcL promoter region has at least two specific recognition sites for plastid proteins.

• Molecules and Cells
• /
• 제39권5호
• /
• pp.375-381
• /
• 2016

MicroRNAs (miRNAs) are small non-coding RNAs (~22 nucleotides) regulating gene expression at the post-transcriptional level. By directing the RNA-induced silencing complex (RISC) to bind specific target mRNAs, miRNA can repress target genes and affect various biological phenotypes. Functional miRNA target recognition is known to majorly attribute specificity to consecutive pairing with seed region (position 2-8) of miRNA. Recent advances in a transcriptome-wide method of mapping miRNA binding sites (Ago HITS-CLIP) elucidated that a large portion of miRNA-target interactions in vivo are mediated not only through the canonical "seed sites" but also via non-canonical sites (~15-80%), setting the stage to expand and determine their properties. Here we focus on recent findings from transcriptome-wide non-canonical miRNA-target interactions, specifically regarding "nucleation bulges" and "seed-like motifs". We also discuss insights from Ago HITS-CLIP data alongside structural and biochemical studies, which highlight putative mechanisms of miRNA target recognition, and the biological significance of these non-canonical sites mediating marginal repression.

• Journal of Microbiology and Biotechnology
• /
• 제15권5호
• /
• pp.1100-1105
• /
• 2005

Previous work has identified a Streptomyces coelicolor gene, rns, encoding a 140 kDa protein (RNase ES) that exhibits the endoribonucleolytic cleavage specificity characteristic of RNase E and confers viability on and allows the propagation of E. coli cells lacking RNase E. Here, we identify a putative S. coelicolor 9S rRNA sequence and sites cleaved by RNase ES. The cleavage of the S. coelicolor 9S rRNA transcript by RNase ES resulted in a 5S rRNA precursor (p5S) that had four and two additional nucleotides at the 5' end and 3' ends of the mature 5S rRNA, respectively. However, despite the similarities between RNase E and RNase ES, these enzymes could accurately process 9S rRNA from just their own bacteria, indicating that these ancient enzymes and the rRNA segments that they attack appear to have co-evolved.

• 식물조직배양학회지
• /
• 제27권5호
• /
• pp.379-385
• /
• 2000

tRNA and 7SL RNA based antisense vehicles were prepared by inserting conserved anti-viral and anti-viroid domains. Anti-PVS coat protein leader sequence (ACPL) and antistructural antihairpin domain of PSTVd (AHII) were inserted in tRNA cassette; anti- zing finger domain of PVS, AHII and anti hop latent viroid ribozyme were inserted in 7SL RNA gene isolated from A. thaliana. These constructs were shown to be transcribed both, in in vitro and in in vivo conditions. However, it followed from our work that closely linked position of PoIII reference genes and PoIIII antisense genes within T-DNA lead to the impairment of RNA expression in transgenic plants. To assay in vivo transcription of antisense genes, hairy root potato cultures were established using h. tumefaciens A4-24 bearing both, Ri plasmid and PoIII-promoterless plant expression vectors with antisense RNA genes. Expression of antisense RNA in transgenic potato tissues was proven by specific RT-PCR reactions.

• Genomics & Informatics
• /
• 제7권4호
• /
• pp.181-186
• /
• 2009

Myotonic dystrophy type 1 (DM1), which is a dominantly inherited neurodegenerative disorder, results from a CTG trinucleotide repeat expansion in the 3'-untranslated region (3'-UTR) of the myotonic dystrophy protein kinase (DMPK) gene. Retention of mutant DMPK (mDMPK) transcripts in the nuclei of affected cells has been known to be the main cause of pathogenesis of the disease. Thus, reducing the RNA toxicity through elimination of the mutant RNA has been suggested as one therapeutic strategy against DM1. In this study, we suggested RNA replacement with a trans -splicing ribozyme as an alternate genetic therapeutic approach for amelioration of DM1. To this end, we identified the regions of mDMPK 3'-UTR RNA that were accessible to ribozymes by using an RNA mapping strategy based on a trans-splicing ribozyme library. We found that particularly accessible sites were present not only upstream but also downstream of the expanded repeat sequence. Repair or replacement of the mDMPK transcript with the specific ribozyme will be useful for DM1 treatment through reduction of toxic mutant transcripts and simultaneously restore wild-type DMPK or release nucleus-entrapped mDMPK transcripts to the cytoplasm.