• BMB Reports
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• v.56 no.3
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• pp.153-159
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• 2023

Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between trans-acting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cis-regulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.788-796
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• 2023

Canine parvovirus type 2 (CPV-2) has high morbidity and mortality rates in canines. Nonstructural protein 1 (NS1) of CPV-2 has endonuclease activity, initiates viral DNA replication, and is highly conserved. Thus, it is a promising target for antiviral inhibitor development. We overexpressed a 41.9 kDa active recombinant endonuclease in Escherichia coli and designed a nicking assay using carboxyfluorescein and quencher-linked ssDNA as substrates. The optimal temperature and pH of the endonuclease were 37℃ and pH 7, respectively. Curcumin, bisdemethoxycurcumin, demethoxycurcumin, linoleic acid, tannic acid, and α-tocopherol inhibited CPV-2 NS1 endonuclease with IC₅₀ values of 0.29 to 8.03 µM. The extracted turmeric, yerba mate, and sesame cake suppressed CPV-2 NS1 endonuclease with IC₅₀ values of 1.48, 7.09, and 52.67 ㎍/ml, respectively. The binding affinity between curcumin, the strongest inhibitor, and CPV-2 NS1 endonuclease by molecular docking was -6.4 kcal/mol. Curcumin inhibited CPV-2 NS1 endonuclease via numerous hydrophobic interactions and two hydrogen bonds with Lys97 and Pro111 in the allosteric site. These results suggest that adding curcuminoids, linoleic acid, tannic acid, α-tocopherol, extracted turmeric, sesame cake, and yerba to the diet could prevent CPV-2 infection.

• Journal of Animal Science and Technology
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• v.65 no.3
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• pp.652-663
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• 2023

The rumen fluids contain a wide range of bacteria, protozoa, fungi, and viruses. The various ruminal microorganisms in the rumen provide nutrients by fermenting the forage they eat. During metabolic processes, microorganisms present in the rumen release diverse vesicles during the fermentation process. Therefore, in this study, we confirmed the function of rumen extracellular vesicles (EVs) and their interaction with the host. We confirmed the structure of the rumen EVs by transmission electron microscope (TEM) and the size of the particles using nanoparticle tracking analysis (NTA). Rumen EVs range in size from 100 nm to 400 nm and are composed of microvesicles, microparticles, and ectosomes. Using the Caenorhabditis elegans smart animal model, we verified the interaction between the host and rumen EVs. Exposure of C. elegans to rumen EVs did not significantly enhance longevity, whereas exposure to the pathogenic bacteria Escherichia coli O157:H7 and Staphylococcus aureus significantly increased lifespan. Furthermore, transcriptome analysis showed gene expression alterations in C. elegans exposed to rumen EVs, with significant changes in the metabolic pathway, fatty acid degradation, and biosynthesis of cofactors. Our study describes the effect of rumen EV interactions with the host and provides novel insights for discovering biotherapeutic agents in the animal industry.

• Molecules and Cells
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• v.46 no.4
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• pp.231-244
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• 2023

Leucine-rich repeat containing 15 (LRRC15) has been identified as a contributing factor for cartilage damage in osteoarthritis; however, its involvement in rheumatoid arthritis (RA) and the underlying mechanisms have not been well characterized. The purpose of this study was to explore the function of LRRC15 in RA-associated fibroblast-like synoviocytes (RA-FLS) and in mice with collagen-induced arthritis (CIA) and to dissect the epigenetic mechanisms involved. LRRC15 was overexpressed in the synovial tissues of patients with RA, and LRRC15 overexpression was associated with increased proliferative, migratory, invasive, and angiogenic capacities of RA-FLS and accelerated release of pro-inflammatory cytokines. LRRC15 knockdown significantly inhibited synovial proliferation and reduced bone invasion and destruction in CIA mice. Runt-related transcription factor 1 (RUNX1) transcriptionally represses LRRC15 by binding to core-binding factor subunit beta (CBF-β). Overexpression of RUNX1 significantly inhibited the invasive phenotype of RA-FLS and suppressed the expression of proinflammatory cytokines. Conversely, the effects of RUNX1 were significantly reversed after overexpression of LRRC15 or inhibition of RUNX1-CBF-β interactions. Therefore, we demonstrated that RUNX1-mediated transcriptional repression of LRRC15 inhibited the development of RA, which may have therapeutic effects for RA patients.

• Genomics & Informatics
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• v.21 no.3
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• pp.38.1-38.8
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• 2023

Non-small cell lung cancer (NSCLC) is an important cause of cancer-associated deaths worldwide. Therefore, the exact molecular mechanisms of NSCLC are unidentified. The present investigation aims to identify the miRNAs with predictive value in NSCLC. The two datasets were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEmiRNA) and mRNAs (DEmRNA) were selected from the normalized data. Next, miRNA-mRNA interactions were determined. Then, co-expression network analysis was completed using the WGCNA package in R software. The co-expression network between DEmiRNAs and DEmRNAs was calculated to prioritize the miRNAs. Next, the enrichment analysis was performed for DEmiRNA and DEmRNA. Finally, the drug-gene interaction network was constructed by importing the gene list to dgidb database. A total of 3,033 differentially expressed genes and 58 DEmiRNA were recognized from two datasets. The co-expression network analysis was utilized to build a gene co- expression network. Next, four modules were selected based on the Z_summary score. In the next step, a bipartite miRNA-gene network was constructed and hub miRNAs (let-7a-2-3p, let-7d-5p, let-7b-5p, let-7a-5p, and let-7b-3p) were selected. Finally, a drug-gene network was constructed while SUNITINIB, MEDROXYPROGESTERONE ACETATE, DOFETILIDE, HALOPERIDOL, and CALCITRIOL drugs were recognized as a beneficial drug in NSCLC. The hub miRNAs and repurposed drugs may act a vital role in NSCLC progression and treatment, respectively; however, these results must validate in further clinical and experimental assessments.

• Genomics & Informatics
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• v.21 no.3
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• pp.30.1-30.13
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• 2023

Ephs belong to the largest family of receptor tyrosine kinase and are highly conserved both sequentially and structurally. The structural organization of Eph is similar to other receptor tyrosine kinases; constituting the extracellular ligand binding domain, a fibronectin domain followed by intracellular juxtamembrane kinase, and SAM domain. Eph binds to respective ephrin ligand, through the ligand binding domain and forms a tetrameric complex to activate the kinase domain. Eph-ephrin regulates many downstream pathways that lead to physiological events such as cell migration, proliferation, and growth. Therefore, considering the importance of Eph-ephrin class of protein in tumorigenesis, 7,620 clinically reported missense mutations belonging to the class of variables of unknown significance were retrieved from cBioPortal and evaluated for pathogenicity. Thirty-two mutations predicted to be pathogenic using SIFT, Polyphen-2, PROVEAN, SNPs&GO, PMut, iSTABLE, and PremPS in-silico tools were found located either in critical functional regions or encompassing interactions at the binding interface of Eph-ephrin. However, seven were reported in nonsmall cell lung cancer (NSCLC). Considering the relevance of receptor tyrosine kinases and Eph in NSCLC, these seven mutations were assessed for change in the folding pattern using molecular dynamic simulation. Structural alterations, stability, flexibility, compactness, and solvent-exposed area was observed in EphA3 Trp790Cys, EphA7 Leu749Phe, EphB1 Gly685Cys, EphB4 Val748Ala, and Ephrin A2 Trp112Cys. Hence, it can be concluded that the evaluated mutations have potential to alter the folding pattern and thus can be further validated by in-vitro, structural and in-vivo studies for clinical management.

• The Plant Pathology Journal
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• v.40 no.3
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• pp.310-321
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• 2024

Tomato yellow leaf curl virus (TYLCV) and tomato spotted wilt virus (TSWV) are well-known examples of the begomovirus and orthotospovirus genera, respectively. These viruses cause significant economic damage to tomato crops worldwide. Weeds play an important role in the ongoing presence and spread of several plant viruses, such as TYLCV and TSWV, and are recognized as reservoirs for these infections. This work applies a comprehensive approach, encompassing field surveys and molecular techniques, to acquire an in-depth understanding of the interactions between viruses and their weed hosts. A total of 60 tomato samples exhibiting typical symptoms of TYLCV and TSWV were collected from a tomato greenhouse farm in Nonsan, South Korea. In addition, 130 samples of 16 different weed species in the immediate surroundings of the greenhouse were collected for viral detection. PCR and reverse transcription-PCR methodologies and specific primers for TYLCV and TSWV were used, which showed that 15 tomato samples were coinfected by both viruses. Interestingly, both viruses were also detected in perennial weeds, such as Rumex crispus, which highlights their function as viral reservoirs. Our study provides significant insights into the co-occurrence of TYLCV and TSWV in weed reservoirs, and their subsequent transmission under tomato greenhouse conditions. This project builds long-term strategies for integrated pest management to prevent and manage simultaneous virus outbreaks, known as twindemics, in agricultural systems.

• Development and Reproduction
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• v.27 no.4
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• pp.205-211
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• 2023

INTS14/VWA9, a component of the integrator complex subunits, plays a pivotal role in regulating the fate of numerous nascent RNAs transcribed by RNA polymerase II, particularly in the biogenesis of small nuclear RNAs and enhancer RNAs. Despite its significance, a comprehensive mutation model for developmental research has been lacking. To address this gap, we aimed to investigate the expression patterns of INTS14 during zebrafish embryonic development. We generated ints14 mutant strains using the CRISPR/Cas9 system. We validated the gRNA activity by co-injecting Cas9 protein and a single guide RNA into fertilized zebrafish eggs, subsequently confirming the presence of a 6- or 9-bp deletion in the ints14 gene. In addition, we examined the two mutant alleles through PCR analysis, T7E1 assay, TA-cloning, and sequencing. For the first time, we used the CRISPR/Cas9 system to create a model in which some sequences of the ints14 gene were removed. This breakthrough opens new avenues for in-depth exploration of the role of ints14 in animal diseases. The mutant strains generated in this study can provide a valuable resource for further investigations into the specific consequences of ints14 gene deletion during zebrafish development. This research establishes a foundation for future studies exploring the molecular mechanisms underlying the functions of ints14, its interactions with other genes or proteins, and its broader implications for biological processes.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.57 no.3
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• pp.239-252
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• 2024

Recombination activating genes (RAGs) play a crucial role in initiating V(D)J recombination, which is essential for developing adaptive immunity in vertebrates. In this study, we cloned and characterized RAG1/2 cDNA from the marine medaka Oryzias dancena (OdRAG1/2) and investigated their mRNA expression patterns during ontogenetic developmental stages. The OdRAG1 and OdRAG2 cDNA contained open reading frames (ORFs) encoding proteins containing 1,078 and 531 amino acids, respectively. Multiple sequence alignment and phylogenetic analysis revealed that OdRAG1 and OdRAG2 are highly conserved with their corresponding orthologs, featuring distinct core and non-core regions. Notably, expression analysis showed that, in contrast to other fish RAGs studied, OdRAG1/2 expression peaked at 0 days post-hatching (DPH). Additionally, for the expression of T and B cell differentiation markers, CD3γ and CD20, also peaked at 0 DPH. Collectively, adaptive immunity in O. dancena potentially begins during embryonic development, which is critical for V(D)J recombination and essential immune component development, suggesting the early ontogenetic stage interactions between innate and adaptive immunity.

• Journal of the Korean Chemical Society
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• v.39 no.1
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• pp.66-70
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• 1995

The soil humic acid was subdivided into four subfractions by molecular weight (F1: >100.000 dalton; F2: >100.000 dalton; F3: >10.000 dalton; F4: >2.000 dalton) using MP-dual hollow fiber ultrafiltration system. The characterization using IR, 1H and 13C NMR spectroscopy, showed similar spectroscopic features of HA, demonstrating that the bulk properties of HA subfractions are very similar to one another. IR spectral data showed a decrease in polysaccharide contents and increase in carboxylate functionality as molecular weight become smaller.functions. The structure of (NO) can be described by two interactions (N${\cdot}{\cdot}{\cdot}$N, N${\cdot}{\cdot}{\cdot}$O). One is the ONNO structure with an (N${\cdot}{\cdot}{\cdot}$N) interaction. In this structure, acyclic cis-ONNO with $C_{2v}$-symmetry, acyclic trans-ONNO with $C_{2h}$, and cyclic ONNO with trapezoidal structure ($C_{2v}$) are optimized at the MP2 level. The other structure is the ONON structure with an (N${\cdot}{\cdot}{\cdot}$O) interaction. In the structure, acyclic cis-ONON with Cs$^{-symmetry}$ and cyclic ONON of the rectangular ($C_{2h}$), square $(D_{2h})$, rhombic $(D_{2h})$, and parallelogramic $(D_{2h})$ geometries are also optimized. It is found that acyclic cis-ONNO $(^1A_1$) is the most stable structure and cyclic ONNO ($^3A_1$) is the least stable. Acyclic trans-ONNO ($^3A_1$) with an (N${\cdot}{\cdot}{\cdot}$N) interaction, acyclic trans-ONON and bicyclic ONON $(C_{2v})$ with (N${\cdot}{\cdot}{\cdot}$O) interaction, and acyclic cis- and trans-NOON with an (O${\cdot}{\cdot}{\cdot}$O) interaction can not be optimized at the MP2 level. Particularly, acyclic trans-ONNO with $C_{2h}$-symmetry can not be optimized at the CCSD(T) level. Meanwhile, acyclic NNOO ($^1A_1$, $C_s)$ and trianglic NNOO ($^1A_1$,$C_{2v})$ formed by the (O${\cdot}{\cdot}{\cdot}$N) interaction between $O_2$and $N_2$are optimized at the MP2 level. The binding energies and the relative energy gaps among the isomers are found to be relatively small./sec. Spiral CT scans during the arterial phase were obtained 35 seconds after the injection of contrast medium. CT findings of 78 lesions less than 4cm in diameter were correlated with angiographic findings. Results : The attenuation of lesions was high(n = 69), iso(n = 5), and low(n = 4) compared with liver parenchyma during the arterial phase of spiral CT. In lesions with high-, iso-, and low-attenuation during the arterial phase of spiral CT, hypervascularity on angiograms was found in 63 of 69(91.3%), three of five(60%), and three of four lesions(75%), respectively. Six lesions with high-attenuation on the arterial phase of spiral CT were not seen on angiography. Two iso-attenuated and one low-attenuated lesion were hypovascular on angiograms. Conclusion : The results of this study suggest that with some exceptions there was good correlation between the arterial phase of spiral CT and angiography.