• Design & Manufacturing
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• v.17 no.1
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• pp.20-26
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• 2023

Lab-on-a-disc is a circular disc shape of cartridge that can be used for blood-based liquid biopsy to diagnose an early stage of cancer. Currently, liquid biopsies are regarded as a time-consuming process, and require sophisticated skills to precisely separate cell-free DNA (cfDNA) and circulating tumor cells (CTCs) floating in the bloodstream for accurate diagnosis. However, by applying the lab-on-a-disc to liquid biopsy, the entire process can be operated automatically. To do so, the lab-on-a-disc should be designed to prevent blood leakage during the centrifugation, transport, and dilution of blood inside the lab-on-a-disc in the process of liquid biopsy. In this study, the main components of lab-on-a-disc for liquid biopsy are fabricated by injection molding for mass production, and ultrasonic welding is employed to ensure the bonding strength between the components. To guarantee accurate ultrasonic welding, the flatness of the components is optimized numerically by using the response surface methodology with four main injection molding processing parameters, including the mold & resin temperatures, the injection speed, and the packing pressure. The 27 times finite element analyses using Moldflow® reveal that the injection time and the packing pressure are the critical factors affecting the flatness of the components with an optimal set of values for all four processing parameters. To further improve the flatness of the lab-on-a-disc components for stable mass production, a quarter-disc shape of lab-on-a-disc with a radius of 75 mm is used instead of a full circular shape of the disc, and this significantly decreases the standard deviation of flatness to 30% due to the reduced overall length of the injection molded components by one-half. Moreover, it is also beneficial to use a quarter disc shape to manage the deviation of flatness under 3 sigma limits.

• Animal cells and systems
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• v.2 no.1
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• pp.117-122
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• 1998

D-raf, a Drosophila homolog of the human c-raf-1, is known as a signal transducer in cell proliferation and differentiation. A previous study found that the D-raf gene expression is regulated by the DNA replication-related element (DRE)/DRE-binding factor (DREF) system. In this study, we found the sequences homologous to transcription factor C/EBP, MyoD, STAT and Myc recognition sites in the D-raf promoter. We have generated various base substitutional mutations in these recognition sites and subsequently examined their effects on D-raf promoter activity through transient CAT assays in Kc cells with reporter plasmids p5'-878DrafCAT carrying the mutations in these binding sites. Through gel mobility shift assay using nuclear extracts of Kc cells, we detected factors binding to these recognition sites. Our results show that transcription factor C/EBP, STAT and Myc binding sites in D-raf promoter region play a positive role in transcriptional regulation of the D-raf gene and the Myo D binding site plays a negative role.

• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1778-1782
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• 2017

To identify and discriminate the bacterial species at the subspecific level, rep-PCR is a reliable genomic fingerprinting tool. Fourteen strains of bacteria were isolated from different food sources, identified as Leuconostoc citreum using 16S rRNA gene sequencing, and amplified using rep-primers (REP, ERIC, and $(GTG)_5$). Fingerprinting patterns generated bands in the range of 300-6,000 bp with REP, 150-6,000 bp with ERIC, and 200-1,700 bp with $(GTG)_5$ primers. In UPGMA dendrogram analysis, 14 strains were clustered into three clades (I, II, and III) with all the primers, thus differentiating them at the molecular level. The present study revealed the differentiation of L. citreum strains using rep-PCR.

• BMB Reports
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• v.42 no.12
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• pp.823-828
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• 2009

Techniques for analyzing protein-DNA interactions on a genome-wide scale have recently established regulatory roles for distal enhancers. However, the large sizes of higher eukaryotic genomes have made identification of these elements difficult. Information regarding sequence conservation, exon annotation and repetitive regions can be used to reduce the size of the search region. However, previously developed resources are inadequate for consolidating such information. CONVIRT is a web resource for the identification of transcription factor binding sites and also features comparative genomics. Genomic information on ortholog-independent conserved regions, exons, repeats and sequences is integrated into the virtual chromosome, and statistically over-represented single or combinations of transcription factor binding sites are sought. CONVIRT provides regulatory network analysis for several organisms with long promoter regions and permits inter-species genome alignments. CONVIRT is freely available at http://biosoft.kaist.ac.kr/convirt.

• BMB Reports
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• v.47 no.9
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• pp.518-523
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• 2014

The maternal transcription factor Dorsal (Dl) functions as both an activator and a repressor in a context-dependent manner to control dorsal-ventral patterning in the Drosophila embryo. Previous studies have suggested that Dl is an intrinsic activator and its repressive activity requires additional corepressors that bind corepressor-binding sites near Dl-binding sites. However, the molecular identities of the corepressors have yet to be identified. Here, we present evidence that Capicua (Cic) is involved in Dl-mediated repression in the zerkn$\ddot{u}$llt (zen) ventral repression element (VRE). Computational and genetic analyses indicate that a DNA-binding consensus sequence of Cic is highly analogous with previously identified corepressor-binding sequences and that Dl failed to repress zen expression in lateral regions of cic mutant embryos. Furthermore, electrophoretic mobility shift assay (EMSA) shows that Cic directly interacts with several corepressor-binding sites in the zen VRE. These results suggest that Cic may function as a corepressor by binding the VRE.

• The Plant Pathology Journal
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• v.25 no.4
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• pp.381-388
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• 2009

On screening pathogen-resistant soybean, we identified a WRKY type transcription factor named a Glycine max WRKY1 (GmWRKY1). Expression of GmWRKY1 gene was induced in the soybean sprout by Pseudomonas infection. The GmWRKY1 was expressed in all of the tissues with high levels in stems, leaves and developing seeds. The protein Gm WRKY1 contains highly conserved two WRKY DNA-binding domains having two $C_2-H_2$ zinc-finger motif ($C-X_{4-5}-C-X_{22-23}-H-X-H$) in its N-terminal and C-terminal amino acid sequences. In electrophoresis mobility shift assay, the GmWRKY1 protein bound specifically to W-box elements in the promoters of defense related genes. These results demonstrated that GmWRKY1 is one of the soybean WRKY family genes and the plant-specific transcription factors for defense processes.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.3
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• pp.302-307
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• 1999

Hamlet (PI549276) possessing 2RL was obtained by cross between a wheat cultivar ND7532 (Froid/Centurk) and a rye cultivar Chaupon. Chaupon was known to have resistant gene to biotype L of Hessian fly [Mayetiola destructor (Say)] larvae. The wheat-rye translocation line (Coker797*4/Hamlet) was also known to be resistant to biotype L of Hessian fly larvae. We analysed a set of 96 ESTs from the wheat-rye translocation line (2BS/2RL). ESTs were classified by various physiological processings, such as primary metabolism, secondary metabolism, transcription, translation, transport, signal transduction, defense, transposable element, and others. Three sequences encoding thioredoxin peroxidase, 26S rRNA, and rubisco small subunits were homologous to registered genes in rye. Although limited number of clones were used to develop ESTs, these clones and their sequence information may be useful for researchers studying general physiology and molecular biology on the translocation line.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.109-115
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• 2002

Gene therapy is to treat and cure diseases by an introduction of therapeutic genes in defective cells or tissues of human body. Gene delivery system, gene expression system, and therapeutic gene are three core elements for gene therapy. The efficient delivery of therapeutic genes and appropriate gene expression are the crucial issues for therapeutic outcome of gene delivery. Because it can be used in common for the treatment and cure of various diseases, gene delivery system is the most important core element for a successful gene therapy. Viruses are naturally evolved to transfer their genomes into host cells efficiently. This ability has made vectorologists exploit viruses as attractive vehicles for the delivery of therapeutic genes. Viral vectors based on adenovirus (Ad) and adeno-associated virus (AAV) have been often used for gene delivery in laboratory. Ad and AAV vectors derived from human DNA viruses differ greatly in their life cycle, expression level and duration of transgenes, immunogenicity, and vector preparation. Both vectors can be used as effective tools for gene therapy and more recently in functional genomics. Here, the characteristics of Ad and AAV vectors are discussed.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2199-2205
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• 2016

Vibrio cholerae O1 serogroup Wave 3 El Tor strains are presently prevalent worldwide. The Wave 3 El Tor strains contain a TLC:RS1:CTX array on chromosome 1, and no element is integrated on chromosome 2. A multiplex PCR optimized to identify the TLC:RS1:CTX array of Wave 3 strains has been developed in this study. By using eight primers, the multiplex PCR can identify the characteristic CTX and RS1 array of Wave 3 strains from various arrays of strains belonging to other Waves. The four amplified DNA fragments of Wave 3 strains have been cloned in a vector, which could be used as a positive control for the multiplex PCR. This multiplex PCR and the positive control set could be useful tools for rapid recognition of Wave 3 El Tor strains.

• Genomics & Informatics
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• v.13 no.4
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• pp.152-155
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• 2015

Recently, the Encyclopedia of DNA Elements (ENCODE) Analysis Working Group converted data from ChIP-seq analyses from the Broad Histone track into 15 corresponding chromatic maps that label sequences with different kinds of histone modifications in promoter regions. Here, we publish a frequency profile of the three ChromHMM promoter states, at 200-bp intervals, with particular reference to the existence of sequence patterns of promoter elements, GC-richness, and transcription starting sites. Through detailed and diligent analysis of promoter regions, researchers will be able to uncover new and significant information about transcription initiation and gene function.