• Journal of Microbiology and Biotechnology
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• v.19 no.6
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• pp.610-615
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• 2009

As a provirus, polydnavirus has a segmented DNA genome on chromosome(s) of host wasp. It contains several genes in each segment that presumably play critical roles in regulating physiological processes of target insect parasitized by the wasp. A cysteine-rich protein 1 (CRP1) is present in the polydnavirus Cotesia plutellae bracovirus (CpBV) genome, but its expression and physiological function in Plutella xylostella parasitized by the viral host C. plutellae is not known. This CpBV-CRP1 encoding 189 amino acids with a putative signal peptide (20 residues) was persistently expressed in parasitized P. xylostella with gradual decrease at the late parasitization period. Expression of CpBV-CRP1 was tissue-specific in the fat body/epidermis and hemocyte, but not in the gut. Its physiological function was analyzed by inducing transient expression of a CpBV segment containing CpBV-CRP1 and its promoter, which caused significant reduction in hemocyte -spreading and delayed larval development. When the treated larvae were co-injected with double-stranded RNA of CpBV-CRP1, the expression of CpBV-CRP1 disappeared, whereas other genes encoded in the CpBV segment was expressed. These co-injected larvae significantly recovered the hemocyte-spreading capacity and larval development rate. This study reports that CpBV-CRP1 is expressed in P. xylostella parasitized by C. plutellae and its physiological function is to alter the host immune and developmental processes.

• Journal of Microbiology and Biotechnology
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• v.27 no.2
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• pp.207-218
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• 2017

Clustered regulatory interspaced short palindromic repeats (CRISPR) in association with CRISPR-associated protein (Cas) is an adaptive immune system, playing a pivotal role in the defense of bacteria and archaea. Ease of handling and cost effectiveness make the CRISPR-Cas system an ideal programmable nuclease tool. Recent advances in understanding the CRISPR-Cas system have tremendously improved its efficiency. For instance, it is possible to recapitulate the chronicle CRISPR-Cas from its infancy and inaugurate a developed version by generating novel variants of Cas proteins, subduing off-target effects, and optimizing of innovative strategies. In summary, the CRISPR-Cas system could be employed in a number of applications, including providing model systems, rectification of detrimental mutations, and antiviral therapies.

• BMB Reports
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• v.41 no.11
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• pp.771-777
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• 2008

Calmodulin (CaM) proteins, members of the EF-hand family of $Ca^{2+}$-binding proteins, represent important relays in plant calcium signals. Here, OsCam1-1 was isolated by PCR amplification from the rice genome. The gene contains an ORF of 450 base pairs with a single intron at the same position found in other plant Cam genes. A promoter region with a TATA box at position-26 was predicted and fused to a gus reporter gene, and this construct was used to produce transgenic rice by Agrobacterium-mediated transformation. GUS activity was observed in all organs examined and throughout tissues in cross-sections, but activity was strongest in the vascular bundles of leaves and the vascular cylinders of roots. To examine the properties of OsCaM1-1, the encoding cDNA was expressed in Escherichia coli. The electrophoretic mobility shift when incubated with $Ca^{2+}$ indicates that recombinant OsCaM1-1 is a functional $Ca^{2+}$-binding protein. In addition, OsCaM1-1 bound the CaMKII target peptide confirming its likely functionality as a calmodulin.

• BMB Reports
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• v.50 no.5
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• pp.247-256
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• 2017

CRISPR/Cas9 is the latest tool introduced in the field of genome engineering and is so far the best genome-editing tool as compared to its precedents such as, meganucleases, zinc finger nucleases (ZFNs) and transcription activator-like effectors (TALENs). The simple design and assembly of the CRISPR/Cas9 system makes genome editing easy to perform as it uses small guide RNAs that correspond to their DNA targets for high efficiency editing. This has helped open the doors for multiplexible genome targeting in many species that were intractable using old genetic perturbation techniques. Currently, The CRISPR system is revolutionizing the way biological researches are conducted and paves a bright future not only in research but also in medicine and biotechnology. In this review, we evaluated the history, types and structure, the mechanism of action of CRISPR/Cas System. In particular, we focused on the application of this powerful tool in autophagy research.

• Journal of Sensor Science and Technology
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• v.19 no.6
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• pp.403-420
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• 2010

Nano and micro structure-based biosensors are promising tool for label-free detection of biomolecular interactions with great accuracy. This review gives a brief survey on nano and micro platforms to sense a variety of analytes such as DNA, proteins and viruses. Among incredible nano and micro structure for bio-analytical applications, the scope of this paper will be limited to micro and nano resonators and nanowire field-effect transistors. Nanomechanical motion of the resonators transducers biological information to readable signals. They are commonly combined with an optical, capacitive or piezo-resistive detection systems. Binding of target molecule to the modified surface of nanowire modulates the current of the nanowire through electrical field-effect. Both detection methods have advantages of label-free, real-time and high sensitive detection. These structures can be extended to fabricate array-type sensors for multiplexed detection and high-throughput analysis. The biosensors based on these structures will be applied to lab-on-a-chip platforms and point-of-care diagnostics. Basic concepts including detection mechanisms and trends in their fields will be covered in this review.

• Journal of Microbiology and Biotechnology
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• v.22 no.10
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• pp.1350-1358
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• 2012

Viral pathogens, alongside other pathogens, have major effects on crustacean aquaculture. Hepatopancreatic parvovirus (HPV) is an emerging virus in the shrimp industry and has been detected in shrimp farms worldwide. The HPV genome has greater diversity than other shrimp viruses owing to its wide host range and geographical distribution. Therefore, developing diagnostic tools is essential to detect even small copy numbers from the target region of native HPV isolates. We have developed two easy to use quantitative real-time PCR kits, called Green Star and Dual Star, which contain all of the necessary components for real-time PCR, including HPV primers, using the primers obtained from the sequences of HPV isolates from Korea, and analyzed their specificity, efficiency, and reproducibility. These two kits could detect from 1 to $1{\times}10^9$ copies of cloned HPV DNA. The minimum detection limits obtained from HPV-infected shrimp were $7.74{\times}10^1$ and $9.06{\times}10^1$ copies in the Green Star and Dual Star assay kits, respectively. These kits can be used for rapid, sensitive, and efficient screening for HPV isolates from Korea before the introduction of postlarval stages into culture ponds, thereby decreasing the incidence of early development of the disease.

• Journal of Korean Society of Water and Wastewater
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• v.33 no.5
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• pp.379-388
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• 2019

Chlorination and UV illumination are being widely applied to inactivate a number of pathogenic microbials in the environment. Here, we evaluated the inactivation efficiency of individual and combined treatments of chlorination and UV under various aqueous conditions. UV dosage was required higher in waste water than in phosphate buffer to achieve the similar disinfecting efficiency. Free chlorine generated by electrolysis of waste water was abundant enough to inactivate microbials. Based on these, hybrid system composed of sequential treatment of electrolysis-mediated chlorination and UV treatment was developed under waste water conditions. Compared to individual treatments, hybrid system inactivated bacteria (i.e., E. coli and S. typhimurium) and viruses (i.e., MS-2 bacteriophage, rotavirus, and norovirus) more efficiently. The hybrid system also mitigated the photo re-pair of UV-driven DNA damages of target bacteria. The combined results suggested the hybrid system would achieve high inactivation efficiency and safety on various pathogenic microbials in wastewater.

• Molecules and Cells
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• v.44 no.5
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• pp.342-355
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• 2021

The microphthalmia-associated transcription factor family (MiT family) proteins are evolutionarily conserved transcription factors that perform many essential biological functions. In mammals, the MiT family consists of MITF (microphthalmia-associated transcription factor or melanocyte-inducing transcription factor), TFEB (transcription factor EB), TFE3 (transcription factor E3), and TFEC (transcription factor EC). These transcriptional factors belong to the basic helix-loop-helix-leucine zipper (bHLH-LZ) transcription factor family and bind the E-box DNA motifs in the promoter regions of target genes to enhance transcription. The best studied functions of MiT proteins include lysosome biogenesis and autophagy induction. In addition, they modulate cellular metabolism, mitochondria dynamics, and various stress responses. The control of nuclear localization via phosphorylation and dephosphorylation serves as the primary regulatory mechanism for MiT family proteins, and several kinases and phosphatases have been identified to directly determine the transcriptional activities of MiT proteins. In different immune cell types, each MiT family member is shown to play distinct or redundant roles and we expect that there is far more to learn about their functions and regulatory mechanisms in host defense and inflammatory responses.

• Genomics & Informatics
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• v.16 no.4
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• pp.29.1-29.5
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• 2018

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.54 no.3
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• pp.280-286
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• 2021

This study was performed to screen the antimicrobial activities and proteolytic enzyme stability of the acidified extract of the Blue mussel Mytilus edulis. The acidified extract showed potent antimicrobial activities against Gram-positive bacteria, Bacillus subtilis, and Gram-negative bacteria, Escherichia coli D31, but had no activity against Candida albicans. Treatment of extract with trypsin completely abolished all or significant antibacterial activity against the tested bacteria, but slightly decreased antimicrobial activity against B. subtilis, and treatment of extract with chymotrypsin retained almost antibacterial activity against the tested bacteria except for E. coli D31. To confirm the additional enzyme stability of the extract, antimicrobial activity of the extract was tested after treated with several enzymes. Enzymes treated extract showed potent antimicrobial activity against B. subtilis and its activity was also retained for 5 h after trypsin treatments. Non-proteinaceous materials in the acidified extract also showed strong DNA-binding ability but did not show bacterial membrane permeabilizing ability. All our results indicate that mussel extract might contain the proteinaceous or non-proteinaceous antibacterial materials target not bacterial membrane but intracellular components. These results could be used to develop mussel extract as an additive for the improvement of stability or antimicrobial activity of antibiotics against specific bacteria.