• Molecules and Cells
• /
• v.28 no.2
• /
• pp.87-92
• /
• 2009

Human SIRT3 gene contains an intronic VNTR enhancer. A T > C transition occurring in the second repeat of each VNTR allele implies the presence/absence of a putative GATA binding motif. A partially overlapping AP-1 site, not affected by the transition, was also identified. Aims of the present study were: 1) to verify if GATA and AP-1 sites could bind GATA2 and c-Jun/c-Fos factors, respectively; 2) to investigate whether such sites modulate the enhancer activity of the SIRT3-VNTR alleles. DAPA assay proved that GATA2 and c-Jun/c-Fos factors are able to bind the corresponding sites. Moreover, co-transfection experiments showed that the over-expression of GATA2 and c-Jun/c-Fos factors boosts the VNTR enhancer activity in an allelic-specific way. Furthermore, we established that GATA2 and c-Jun/c-Fos act additively in modulating the SIRT3-VNTR enhancer function. Therefore, GATA2 and AP-1 are functional sites and the T > C transition of the second VNTR repeat affects their activity.

• Molecules and Cells
• /
• v.39 no.9
• /
• pp.687-691
• /
• 2016

Transcription activator-like effector nucleases (TALENs) are powerful tools for targeted genome editing in diverse cell types and organisms. However, the highly identical TALE repeat sequences make it challenging to assemble TALEs using conventional cloning approaches, and multiple repeats in one plasmid are easily catalyzed for homologous recombination in bacteria. Although the methods for TALE assembly are constantly improving, these methods are not convenient because of laborious assembly steps or large module libraries, limiting their broad utility. To overcome the barrier of multiple assembly steps, we report a one-step system for the convenient and flexible assembly of a 180 TALE module library. This study is the first demonstration to ligate 9 mono-/dimer modules and one circular TALEN backbone vector in a one step process, generating 9.5 to 18.5 repeat sequences with an overall assembly rate higher than 50%. This system makes TALEN assembly much simpler than the conventional cloning of two DNA fragments because this strategy combines digestion and ligation into one step using circular vectors and different modules to avoid gel extraction. Therefore, this system provides a convenient tool for the application of TALEN-mediated genome editing in scientific studies and clinical trials.

• The Korean Journal of Physiology
• /
• v.28 no.1
• /
• pp.91-97
• /
• 1994

In order to produce a specific bombesin antiserum far very sensitive radioimmunoassay, synthetic $[lys^3]-bombesin$ conjugated to bovine serum albumin was subcutaneously injected into guinea pigs. The conjugation was performed using either carbodiimide or gIutaraldehyde as a coupling agent. The antisera were characterized by analysis of Scatchard and Sips plots. The antiserum LBE 2G/2 raised by repeat injection of the immunogen conjugated with carbodiimide showed the titer of 1 : 188,000, very low cross-reactivity to bombesin-like peptides except bombesin, with high affinity constant $(1.64{\times}10^{11}\;M^{-1})$ and high heterogeneity index (0.91). The antiserum LBG 1G/2 produced by repeat injection of the immunogen conjugated with glutaraldehyde possessed the titer of 1 : 43,000, high cross-reactivity to some bombesin-like peptides, high affinity constant $(1.19{\times}10^{11}\;M^{-1})$ and high heterogeneity index (0.79). These results indicate that the antiserum LBE 2G/2 is specific only to bombesin and that the antiserum LBG IG/2 binds to some bombesin-like peptides such as alytesin, gastrin releasing peptide and neuromedin C. The antiserum LBE 2G/2 is sufficient for the very sensitive radioimmunoassay of bombesin.

• Journal of the Korea Society of Computer and Information
• /
• v.13 no.3
• /
• pp.35-44
• /
• 2008

In this paper, we present an EST sequence annotation system based on Service Oriented Architecture, called SeqWeB. We developed the web services of eight applications (Phred, cross_match, RepeatMasker, TGICL, ICAtools, CAP3, Phrap and Blast) which are located in sequence annotation process and integrated the web services through BFEL. SeqWeB uses an XML file format for data input and output to maximize interoperability between each application. SeqWeB can be extended or modified easily through some modification such as insertion, deletion and replacement because service-oriented architecture allows loose coupling between applications.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.2
• /
• pp.380-387
• /
• 2017

The foamy viruses are currently considered essential for development as vectors for gene delivery. Previous studies demonstrated that prototype foamy virus (PFV) can infect and replicate prevalently in a variety of cell types for its exclusive replication strategy. However, the virus-host interaction, especially PFV-transportin3 (TNPO3), is still poorly understood. In our investigation of the role of TNPO3 in PFV infection, we found lower virus production in TNPO3 knockdown (KD) cells compared with wild-type 293T cells. PCR analysis revealed that viral DNAs were mostly altered to circular forms: both 1-long terminal repeat (1-LTR) and 2-LTR in TNPO3 KD cells. We therefore suggest that TNPO3 is required for successful PFV replication, at least at/after the nuclear entry step of viral DNA. These findings highlight the obscure mysteries of PFV-host interaction and the requirement of TNPO3 for productive infection of PFV in 293T cells.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.38-38
• /
• 2018

The genus Carduus (Asteraceae), containing ca. 90 species, is mainly distributed in Eurasia and Africa. Carduus species are one of the most hazardous invasive species, which causes serious environmental threats and biodiversity damages in North America. Thus, the member of Carduus are targeted for classical biological control in this region. Here, we provide the complete cp genome of Carduus crispus using next-generation sequencing technology. The size of cp genomes of C. crispus is 152,342 bp. It shows a typical quadripartite structure, consisting of the large single copy (LSC; 83,254 bp), small single copy (SSC; 18,706 bp), separated by a pair of inverted repeats (IRs; 25,191 bp). It contains 115 unique genes of which 21 genes duplicated in the IR regions. The cpSSR regions of Carduus species were searched through the complete chloroplast genome sequence using a tandem repeat search tool in Geneious with the parameters set to ${\geq}7$ mononucleotide repeats, ${\geq}4$ di- and trinucleotide repeats, and ${\geq}3$ tetra-, penta-, and hexanucleotide repeats. A total of 22 repeat motifs were identified, which may be useful for molecular identification of Korean Carduus species (C. cripus), and providing a guideline for its conservation.

• Korean Journal of Plant Taxonomy
• /
• v.48 no.3
• /
• pp.195-200
• /
• 2018

Genetic assessments of rare and endangered species are among the first steps necessary to establish the proper management of natural populations. Transcriptome-derived single-sequence repeat markers were developed for the Korean endangered species Astilboides tabularis (Saxifragaceae) to assess its genetic diversity. A total of 96 candidate microsatellite loci were isolated based on transcriptome data using Illumina pair end sequencing. Of these, 26 were polymorphic, with one to five alleles per locus in 60 individuals from three populations of A. tabularis. The observed and expected heterozygosity per locus ranged from 0.000 to 0.950 and from 0.000 to 0.741, respectively. These polymorphic transcriptome-derived simple sequence repeat markers would be invaluable for future studies of population genetics and for ecological conservation of the endangered species A. tabularis.

• Molecules and Cells
• /
• v.27 no.2
• /
• pp.237-241
• /
• 2009

Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens.

• Molecules and Cells
• /
• v.27 no.2
• /
• pp.199-203
• /
• 2009

The somatic Sertoli cells play an essential role in testis determination and spermatogenesis by providing nutrition and structural support. In the current study, we report on the novel Ankrd7 gene that contains five ankyrin repeat domains. This gene was specifically expressed in Sertoli cells and was regulated in a maturation-dependent manner. Its expression was restricted to testicular tissue, and its mRNA could be detected in testes at as early as 14 dpp (days post partum) using RT-PCR analysis. In both testicular tissue sections and in vitro cultured Sertoli cells, the Ankrd7 protein was localized to the nucleus of the Sertoli cell. Immunohistochemistry and immunocytochemistry investigations showed that the protein was detectable in testicular tissues at 20 dpp, at which time Sertoli cells were gradually differentiating into their mature cellular form. These results suggest that Ankrd7 is probably involved in the process of Sertoli cell maturation and in spermatogenesis.

• Journal of Communications and Networks
• /
• v.18 no.3
• /
• pp.333-339
• /
• 2016

A multi-stage turbo equalization scheme based on the bit-level combining (BLC) is proposed for multiple-input multiple-output (MIMO) systems with hybrid automatic repeat request (HARQ). In the proposed multi-stage turbo equalization scheme, the minimum mean-square-error equalizer at each iteration calculates the extrinsic log-likelihood ratios for the transmitted bits in a subpacket and the subpackets are sequentially replaced at each iteration according to the HARQ rounds of received subpackets. Therefore, a number of iterations are executed for different subpackets received at several HARQ rounds, and the transmitted bits received at the previous HARQ rounds as well as the current HARQ round can be estimated from the combined information up to the current HARQ round. In addition, the proposed multi-stage turbo equalization scheme has the same computational complexity as the conventional bit-level combining based turbo equalization scheme. Simulation results show that the proposed multi-stage turbo equalization scheme outperforms the conventional BLC based turbo equalization scheme for MIMO systems with HARQ.