• BMB Reports
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• v.52 no.9
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• pp.540-547
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• 2019

Immune repertoire is a collection of enormously diverse adaptive immune cells within an individual. As the repertoire shapes and represents immunological conditions, identification of clones and characterization of diversity are critical for understanding how to protect ourselves against various illness such as infectious diseases and cancers. Over the past several years, fast growing technologies for high throughput sequencing have facilitated rapid advancement of repertoire research, enabling us to observe the diversity of repertoire at an unprecedented level. Here, we focus on B cell receptor (BCR) repertoire and review approaches to B cell isolation and sequencing library construction. These experiments should be carefully designed according to BCR regions to be interrogated, such as heavy chain full length, complementarity determining regions, and isotypes. We also highlight preprocessing steps to remove sequencing and PCR errors with unique molecular index and bioinformatics techniques. Due to the nature of massive sequence variation in BCR, caution is warranted when interpreting repertoire diversity from error-prone sequencing data. Furthermore, we provide a summary of statistical frameworks and bioinformatics tools for clonal evolution and diversity. Finally, we discuss limitations of current BCR-seq technologies and future perspectives on advances in repertoire sequencing.

• Journal of Electrochemical Science and Technology
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• v.10 no.3
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• pp.257-270
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• 2019

The inhibition performance of sodium gluconate (SG), cetyltrimethylammonium bromide (CTAB) and their mixture (SG/CTAB) on the corrosion behavior of ${\alpha}$-brass in 0.5 M $H_2SO_4$ solution has been investigated by potentiodynamic polarization, electrochemical impedance spectroscopy (EIS), Scanning Electron Microscope with Energy-Dispersive Spectrometer (SEM-EDS), Inductively Coupled Plasma Spectrometry (ICPS) and molecular dynamics (MD) simulation techniques. The results reveal that SG with 5ppm CTAB, noted SG/CTAB, acts as a good corrosion inhibitor and its inhibition efficiency reached 89% after 24 h immersion in sulfuric acid solution, but slightly decreased at higher temperatures. The polarization curves displayed that SG/CTAB acts as a cathodic-kind inhibitor. Electrochemical impedance spectroscopy (EIS) studies revealed that the addition of 5ppm CTAB to different concentrations of SG considerably increases the corrosion resistance of ${\alpha}$-brass. The SEM-EDS and ICPS analyses support the experimental results. Further, molecular dynamics (MD) simulations were used to understand the adsorption profiles of SG/CTAB on Cu(111) and Zn(111) surfaces.

• BMB Reports
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• v.52 no.3
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• pp.163-164
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• 2019

The ribosomal synthesis of proteins in the eukaryotic cytosol has always been thought to start from the unformylated N-terminal (Nt) methionine (Met). In contrast, in virtually all nascent proteins in bacteria and eukaryotic organelles, such as mitochondria and chloroplasts, Nt-formyl-methionine (fMet) is the first building block of ribosomal synthesis. Through extensive approaches, including mass spectrometric analyses of the N-termini of proteins and molecular genetic techniques with an affinity-purified antibody for Nt-formylation, we investigated whether Nt-formylated proteins could also be produced and have their own metabolic fate in the cytosol of a eukaryote, such as yeast Saccharomyces cerevisiae. We discovered that Nt-formylated proteins could be generated in the cytosol by yeast mitochondrial formyltransferase (Fmt1). These Nt-formylated proteins were massively upregulated in the stationary phase or upon starvation for specific amino acids and were crucial for the adaptation to specific stresses. The stress-activated kinase Gcn2 was strictly required for the upregulation of Nt-formylated proteins by regulating the activity of Fmt1 and its retention in the cytosol. We also found that the Nt-fMet residues of Nt-formylated proteins could be distinct N-terminal degradation signals, termed fMet/N-degrons, and that Psh1 E3 ubiquitin ligase mediated the selective destruction of Nt-formylated proteins as the recognition component of a novel eukaryotic fMet/N-end rule pathway, termed fMet/N-recognin.

• Korean Journal of Veterinary Service
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• v.44 no.2
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• pp.119-124
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• 2021

The report describes an avian mycobacteriosis in a captive wild bird. A 7-year-old female Indian peafowl (Pavo cristatus) maintained in a zoo of Korea presented a gradual cachexia and eventually was found dead. At necropsy, severely atrophied pectoral muscles exposing the keel bone were noticed. Yellowish thick nodules in varying sizes were scattered in all lobes of lungs, liver and spleen, suggesting mycobacteriosis. Histopathologically, multifocal to coalescing granulomas surrounded by multinucleated giant cells were observed. Numbers of acid-fast bacilli were revealed in granulomas. Then, a series of molecular diagnostic techniques were followed: a nested PCR, DNA sequencing and bioinformatics analysis. It resulted as Mycobacterium genavense. The identification of M. genavense as an etiological agent suggested that it might serve as a risk factor for other captive wild animals, and for a potential zoonotic risk since M. genavense have been a definite cause of disseminated mycobacterial infection in immunocompromised people. To the authors' knowledge, this is the first report of avian mycobacteriosis with M. genavense in a captive Indian peafowl.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.616-628
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• 2022

Resistance to pyraclostrobin due to a single nucleotide polymorphism at 143rd amino acid position on the cytochrome b gene has been a major source of concern in red pepper field infected by anthracnose in Korea. Therefore, this study investigated the response of 24 isolates of C. acutatum and C. gloeosporioides isolated from anthracnose infected red pepper fruits using agar dilution method and other molecular techniques such as cytochrome b gene sequencing, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and allele-specific polymerase chain reaction (PCR). The result showed that four isolates were resistant to pyraclostrobin on agar dilution method and possessed GCT (alanine) codon at 143rd amino acid position, whereas the sensitive isolates possessed GGT (glycine). Furthermore, this study illustrated the difference in the cytochrome b gene structure of C. acutatum and C. gloeosporioides. The use of cDNA in this study suggested that the primer Cacytb-P2 can amplify the cytochrome b gene of both C. acutatum and C. gloeosporioides despite the presence of various introns in the cytochrome b gene structure of C. gloeosporioides. The use of allele-specific PCR and PCR-RFLP provided clear difference between the resistant and sensitive isolates. The application of molecular technique in the evaluation of the resistance status of anthracnose pathogen in red pepper provided rapid, reliable, and accurate results that can be helpful in the early adoption of fungicide-resistant management strategies for the strobilurins in the field.

• The Korean Journal of Food & Health Convergence
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• v.9 no.2
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• pp.1-6
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• 2023

As oil palm trees are an important economic source in many countries, particularly in Southeast Asia and Africa, the study of Ganoderma boninense is crucial for the sustainability of the oil palm industry. This study aims to understand the biology and ecology of the fungus, its pathogenesis, and the impact it has on oil palm trees. This knowledge can be used to develop management strategies to mitigate the damage caused by the fungus, such as the use of resistant varieties, chemical and biological control methods, and cultural practices. This study is to ensure the long-term productivity and sustainability of the oil palm industry. The main method of recent academic studies on this pathogen is molecular biology, with a focus on genetic analysis and functional genomics. Researchers have used techniques such as PCR, DNA sequencing, and transcriptomics to identify genes and pathways involved in pathogenesis and better understand the fungus's interactions with its host plant. Other methods used in recent studies include biochemical analysis, microscopy, and phytohormonal assays to investigate the biochemistry and physiology of the interaction between G. boninense and oil palm. This study is intended to provide implications from a new perspective by organizing and integrating studies on Ganoderma boninense.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.7 no.1
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• pp.22-32
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• 2021

Fluorine-18 is by far the most widely exploited radionuclide in PET (positron emission tomography) radiochemistry. The physical half-life of fluorine-18 allows for chemical manipulation within a restricted timeframe, and cyclotron-produced fluoride ion has been widely applied in aliphatic and aromatic nucleophilic radiofluorinations to produce a variety of established radiotracers. Radiotracers have become more structurally complicated to address diverse targets in physiobiological systems. There is therefore an unmet need to complement traditional C-¹⁸F bond-forming radiofluorination with new and efficient radiolabeling techniques to tackle the myriad of possible chemical environments. This review discusses recent advances in organometallic fluorine-18 bond creation in ¹⁸F-radiochemistry. Although not widely employed, new radiolabeling strategies for constructing boron-¹⁸F, silicon-¹⁸F, aluminum-¹⁸F, and other metal-¹⁸F bonds are described in view of their potential use in the development of novel radiopharmaceuticals.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.15 no.1
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• pp.36-40
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• 2010

Ballast water has been known as a major vector for global dispersal of toxic dinoflagellates and other microalgae. In this study, biodiversity in ships’ ballast water was examined using a dinoflagellate-oriented PCR primer set and species-specific real-time PCR. While motile dinoflagellates could be observe at very low cell densities by light microscopy,a wide range of dinoflagellate taxa including parasitic and phototrophic pico-dinoflagellates as well as harmful species to marine fish/shellfish was detected when techniques for cloning/sequencing of SSU rDNA of sample cells were used. Present result suggests that molecular methods including species-specific PCR primers may offer rapid and accurate detection of invasive species in ballast water.

• Journal of Korea Artificial Intelligence Association
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• v.2 no.1
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• pp.7-14
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• 2024

In this paper, we explore the application of RNA-sequencing data and ensemble machine learning to predict lung cancer and treatment strategies for lung cancer, a leading cause of cancer mortality worldwide. The research utilizes Random Forest, XGBoost, and LightGBM models to analyze gene expression profiles from extensive datasets, aiming to enhance predictive accuracy for lung cancer prognosis. The methodology focuses on preprocessing RNA-seq data to standardize expression levels across samples and applying ensemble algorithms to maximize prediction stability and reduce model overfitting. Key findings indicate that ensemble models, especially XGBoost, substantially outperform traditional predictive models. Significant genetic markers such as ADGRF5 is identified as crucial for predicting lung cancer outcomes. In conclusion, ensemble learning using RNA-seq data proves highly effective in predicting lung cancer, suggesting a potential shift towards more precise and personalized treatment approaches. The results advocate for further integration of molecular and clinical data to refine diagnostic models and improve clinical outcomes, underscoring the critical role of advanced molecular diagnostics in enhancing patient survival rates and quality of life. This study lays the groundwork for future research in the application of RNA-sequencing data and ensemble machine learning techniques in clinical settings.

• IMMUNE NETWORK
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• v.22 no.1
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• pp.9.1-9.23
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• 2022

In the past few decades, biological drugs and small molecule inhibitors targeting inflammatory cytokines, immune cells, and intracellular kinases have become the standard-of-care to treat autoimmune diseases. Inhibition of TNF, IL-6, IL-17, and IL-23 has revolutionized the treatment of autoimmune diseases, such as rheumatoid arthritis, ankylosing spondylitis, and psoriasis. B cell depletion therapy using anti-CD20 mAbs has shown promising results in patients with neuroinflammatory diseases, and inhibition of B cell survival factors is approved for treatment of systemic lupus erythematosus. Targeting co-stimulatory molecules expressed on Ag-presenting cells and T cells is also expected to have therapeutic potential in autoimmune diseases by modulating T cell function. Recently, small molecule kinase inhibitors targeting the JAK family, which is responsible for signal transduction from multiple receptors, have garnered great interest in the field of autoimmune and hematologic diseases. However, there are still unmet medical needs in terms of therapeutic efficacy and safety profiles. Emerging therapies aim to induce immune tolerance without compromising immune function, using advanced molecular engineering techniques.