• Animal Bioscience
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• v.34 no.11
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• pp.1739-1748
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• 2021

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation. Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg's approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway. Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

• Applied Chemistry for Engineering
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• v.32 no.4
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• pp.461-466
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• 2021

In this article, a portable and cost-effective voltammetric biosensor with nanoparticles was developed for the measurements of heterogeneous nuclear ribonucleoprotein A1 protein (hnRNP A1) biomarker which can potentially be used for lung cancer diagnosis. Gold nanoparticles were first electrodeposited onto screen printed carbon electrode (SPCE) followed by immobilizing a single stranded DNA aptamer specific to hnRNP A1 onto the electrode surface. Ethanolamine was also used when immobilizing DNA aptamer on the surface to prevent signals from non-specific adsorption events. Sequential injection of hnRNP A1 biomarker and anti-hnRNP A1 conjugated with alkaline phosphatase (ALP) onto the aptamer chip surface allows to form the sandwich complex of DNA aptamer/hnRNP A1/ALP-anti-hnRNP A1 on the electrode surface which further reacted with 4-aminophenyl phosphate (APP). The electrocatalytic reaction of the enzyme, ALP, and the substrate, APP, resulting in the oxidative current response changes at -0.05 and -0.17 V (vs. Ag/AgCl) against the hnRNP A1 concentration was measured using cyclic and differential pulse voltammetry, respectively. The Au nanoparticles-integrated voltammetric biosensor was applied to analyze human normal serum solutions possibly suggesting potential applicability for lung cancer diagnosis.

• Animal Bioscience
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• v.35 no.4
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• pp.544-555
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• 2022

Objective: Spermatozoa are produced within the seminiferous tubules after sexual maturity. The expression levels of mRNAs and lncRNAs in testicular tissues are different at each stage of testicular development and are closely related to formation of the extracellular matrix (ECM) and spermatogenesis. Therefore, we set out to study the expression of lncRNAs and mRNAs during the different developmental stages of the goat testis. Methods: We constructed 12 RNA libraries using testicular tissues from goats aged 3, 6, and 12 months, and studied the functions of mRNAs and lncRNAs using the gene ontogeny (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. Relationships between differentially expressed genes (DEGs) were analyzed by lncRNA-mRNA co-expression network and protein-protein interaction network (PPI). Finally, the protein expression levels of matrix metalloproteinase 2 (MMP2), insulin-like growth factor 2 (IGF2), and insulin-like growth factor-binding protein 6 (IGFBP6) were detected by western blotting. Results: We found 23, 8, and 135 differentially expressed lncRNAs and 161, 12, and 665 differentially expressed mRNAs that were identified between 3 vs 6, 6 vs 12, and 3 vs 12 months, respectively. GO, KEGG, and PPI analyses showed that the differential genes were mainly related to the ECM. Moreover, MMP2 was a hub gene and co-expressed with the lncRNA TCONS-0002139 and TCONS-00093342. The results of quantitative reverse-transcription polymerase chain reaction verification were consistent with those of RNA-seq sequencing. The expression trends of MMP2, IGF2, and IGFBP6 protein were the same as that of mRNA, which all decreased with age. IGF2 and MMP2 were significantly different in the 3 vs 6-month-old group (p<0.05). Conclusion: These results improve our understanding of the molecular mechanisms involved in sexual maturation of the goat testis.

• Journal of Ginseng Research
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• v.47 no.1
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• pp.97-105
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• 2023

Background: Hyperactivated airway mucosa cells overproduce mucin and cause severe breathing complications. Here, we aimed to identify the effects of saponins derived from Panax ginseng on inflammation and mucin overproduction. Methods: NCI-H292 cells were pre-incubated with 16 saponins derived from P. ginseng, and mucin overproduction was induced by treatment with phorbol 12-myristate 13-acetate (PMA). Mucin protein MUC5AC was quantified by enzyme-linked immunosorbent assay, and mRNA levels were analyzed using quantitative polymerase chain reaction (qPCR). Moreover, we performed a transcriptome analysis of PMA-treated NCI-H292 cells in the absence or presence of Rg5, and differential gene expression was confirmed using qPCR. Phosphorylation levels of signaling molecules, and the abundance of lipid droplets, were measured by western blotting, flow cytometry, and confocal microscopy. Results: Ginsenoside Rg5 effectively reduced MUC5AC secretion and decreased MUC5AC mRNA levels. A systematic functional network analysis revealed that Rg5 upregulated cholesterol and glycerolipid metabolism, resulting in the production of lipid droplets to clear reactive oxygen species (ROS), and modulated the mitogen-activated protein kinase and nuclear factor (NF)-kB signaling pathways to regulate inflammatory responses. Rg5 induced the accumulation of lipid droplets and decreased cellular ROS levels, and N-acetyl-ⳑ-cysteine, a ROS inhibitor, reduced MUC5AC secretion via Rg5. Furthermore, Rg5 hampered the phosphorylation of extracellular signal-regulated kinase and p38 proteins, affecting the NF-kB signaling pathway and pro-inflammatory responses. Conclusion: Rg5 alleviated inflammatory responses by reducing mucin secretion and promoting lipid droplet-mediated ROS clearance. Therefore, Rg5 may have potential as a therapeutic agent to alleviate respiratory disorders caused by hyperactivation of mucosa cells.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.36-36
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• 2022

The molecular understanding of resistance and susceptibility of host plants to scab, a most threatful disease to pome fruit production worldwide, is very limited. Comparing resistant line '93-3-98' to susceptible one 'Sweet Skin' at seven time points of 0, 0.5, 1, 2, 3, 4, 8 days post inoculation, RNA-sequencing data derived from infected and mock-inoculated young leaves were analyzed to evaluate the tolerant response and to mine candidate genes of pear to the scab pathogen Venturia nashicola. Analysis of the mapped reads showed that the infection of V. nashicola led to significant differential expression of 17,827 transcripts with more than 3-fold change in the seven pairs of libraries, of which 9,672 (54%) are up- and 8,155(46%) are down-regulated. These included mainly receptor (NB-ARC domains-containing, CC-NBS-LRR, TIR-NBS-LRR, seven transmembrane MLO family protein) and transcription factor (ethylene responsive element binding, WRKY DNA-binding protein) related gene. An arsenal of defense response of highly resistant pear accessions derived from European pear was probably supposed no sooner had V. nashicola infected its host than host genes related to disease suppression like Polyketide cyclase/dehydrase and lipid transport protein, WRKY family transcription factor, lectin protein kinase, cystein-rich RLK, calcium-dependent phospholipid-binding copine protein were greatly boosted and eradicated cascade reaction induced by pathogen within 24 hours. To identify transcripts specifically expressed in response to V. nashicola, RT-PCRs were conducted and compare to the expression patterns of seven cultivars with a range of highly resistant to highly susceptible symptom. A DEG belonging to the PR protein family genes that were higher expressed in response to V. nashicola suggesting extraordinary role in the resistance response were led to the identification. This study provides the first transcriptional profile by RNA-seq of the host plant during scab disease and insights into the response of tolerant pear plants to V. nashicola.

• Journal of Yeungnam Medical Science
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• v.40 no.4
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• pp.388-393
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• 2023

Background: Differentiating between bacterial and nonbacterial colitis remains a challenge. We aimed to evaluate the value of serum procalcitonin (PCT) and C-reactive protein (CRP) in differentiating between bacterial and nonbacterial colitis. Methods: Adult patients with three or more episodes of watery diarrhea and colitis symptoms within 14 days of a hospital visit were eligible for this study. The patients' stool pathogen polymerase chain reaction (PCR) testing results, serum PCT levels, and serum CRP levels were analyzed retrospectively. Patients were divided into bacterial and nonbacterial colitis groups according to their PCR. The laboratory data were compared between the two groups. The area under the receiver operating characteristic curve (AUC) was used to evaluate diagnostic accuracy. Results: In total, 636 patients were included; 186 in the bacterial colitis group and 450 in the nonbacterial colitis group. In the bacterial colitis group, Clostridium perfringens was the commonest pathogen (n=70), followed by Clostridium difficile toxin B (n=60). The AUC for PCT and CRP was 0.557 and 0.567, respectively, indicating poor discrimination. The sensitivity and specificity for diagnosing bacterial colitis were 54.8% and 52.6% for PCT, and 52.2% and 54.2% for CRP, respectively. Combining PCT and CRP measurements did not increase the discrimination performance (AUC, 0.522; 95% confidence interval, 0.474-0.571). Conclusion: Neither PCT nor CRP helped discriminate bacterial colitis from nonbacterial colitis.

• Animal Bioscience
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• v.37 no.8
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• pp.1345-1354
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• 2024

Objective: The objective of this study was to identify candidate genes that play important roles in skeletal muscle development in ducks. Methods: In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized lines: Liancheng white ducks (female) and Cherry valley ducks (male) hybrid Line A (LCA) and Line C (LCC) ducks. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes signaling pathways were further analyzed. Finally, a protein-to-protein interaction network was analyzed by using the target genes to gain insights into their potential functional association. Results: A total of 1,428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p<0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly enriched (p<0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including integrin b3 (Itgb3), pyruvate kinase M1/2 (Pkm), insulin-like growth factor 1 (Igf1), glucose-6-phosphate isomerase (Gpi), GABA type A receptor-associated protein-like 1 (Gabarapl1), and thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by quantitative real-time polymerase chain reaction (qRT-PCR). The result of qRT-PCR was consistent with that of transcriptome sequencing. Conclusion: This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.

• Animal Bioscience
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• v.37 no.2
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• pp.193-202
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• 2024

Objective: Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS. Methods: The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT-PCR) to examine the mechanism of oxidative damage. Results: A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS. Conclusion: Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum's response to OS.

• Parasites, Hosts and Diseases
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• v.24 no.1
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• pp.25-41
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• 1986

The applicability of micro-ELISA was evaluated in human neuro-cysticercosis using paired samples of serum and CSF. A total of 355 cases who were mostly neurologic patients was subjected. Cystic fluid of C. cellulosae was used as antigen in protein concentration of $2.5{\;}{\mu}g/ml$. Serum was diluted to 1 : 100 and CSF was undiluted in the assay for the specific IgG antibody level. The differential criterion of the positive reaction was the abs. of o. 18 in both samples. The results were summarized as follows: 1. The overall sensitivity of the micro-ELISA in 71 confirmed neurocysticercosis was 90.1% ; the sensitivity by serum was 77.5% and that by CSF was 83.1%. CSF was a more sensitive and valuable material. Most of the false negative cases of neuro-cysticercosis showed far lower level of abs. rather than marginal. 2. The overall specificity of the micro-ELISA in 52 confirmed other neurologic diseases was 88.5%; the specificities by serum and by CSF were 94.2% respectively. Cases of other neurologic diseases did not show false positive reactions in both samples. 3. When serum was assayed, taeniasis(2/18), sparganosis(2/20), paragonimiasis(1/56), clonorchiasis(1/15) and fascioliasis(1/1) cases showed cross reactions. When CSF was assayed, 2 ot 10 neuro-sparganosis showed cross reactions while none of 9 neuro-paragonimiasis showed it. Out of 71 confirmed neuro-cysticercosis cases, 6 and 11 showed cross reactions by serum and CSF to crude extract antigen of sparganum; but no case did show it to crude extract antigen of Paragonimus westermani. 4. Ventricular CSF showed low or negative levels of IgG antibody than lumbar CSF unless the lesion was at the lateral ventricle itself. 5. Out of 4 racemose cysticercosis cases, 3 showed positive reaction in serum while all of 3 examined CSF were positive. The above results indicated that the serological test for detecting the specific IgG antibody by micro-ELISA using paired samples of serum and CSF was very helpful for clinical differentiation of neuro-cysticercosis from neurologic diseases of other causes.

• Korean Journal of Food Science and Technology
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• v.39 no.5
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• pp.534-540
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• 2007

In this study, waxy rice starch was chemically modified using phosphorous oxychloride ($POCl_3$, 0.002-0.008%). Then the physicochemical properties of resulting cross-linked waxy rice starches were investigated in order to reduce the steeping time of Yukwa (a Korean oil-puffed rice snack) processing. The swelling powers of the cross-linked waxy rice starch samples were higher than the native waxy rice starch at temperatures above $60^{\circ}C$, and their increases were proportional to the $POCl_3$, concentration. The solubility of the cross-linked waxy rice starch was lower (1.6-3.4%) than the native waxy rice starch (2.7-6.1%). However, the moisture sorption isotherm of the cross-linked waxy rice starch was not significantly different from the native waxy rice starch. The rapid visco analyze. (RVA) pasting temperatures $(65.4-67^{\circ}C)$ of the cross-linked waxy rice starch were lower than those of the native starch $(67^{\circ}C)$. The RVA peak viscosities (287-337 RVU) of the cross-linked waxy rice starch were higher than that of native starch (179 rapid visco units (RVU)), and increased with increasing $POCl_3$ concentration. For the differential scornning calorimeter thermal characteristics, although Tc shifted toward higher temperatures with cross-linking, the To, Tp, and amylopectiin melting enthalpy of the cross-linked waxy rice starch showed no differences compared to the native waxy rice starch. The X-ray diffraction patterns of both the native and cross-linked waxy rice starches showed typical A-type crystal patterns, suggesting that cross-linking mainly occurs in the amorphous regions of starch granules. Therefore, the cross-linking reaction did not change the crystalline region, but altered the amorphous region of the waxy rice starch molecules, resulting in changes of solubility and RVA pasting properties in the cross-linked waxy rice starch. In summary, since cross-linked waxy rice starch has a high puffing efficiency and no browning reaction, it may be applicable for Yukwa processing without a long steeping process.