• Journal of Microbiology and Biotechnology
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• 제32권2호
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• pp.195-204
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• 2022

Chinese chive (Allium tuberosum Rottler) has potential risks associated with pathogenic bacterial contamination as it is usually consumed raw. In this study, we investigated the microbiota of Chinese chives purchased from traditional markets and grocery stores in March (Spring) and June (Summer) 2017. Differences in bacterial diversity were observed, and the microbial composition varied across sampling times and sites. In June, potential pathogenic genera, such as Escherichia, Enterobacter, and Pantoea, accounted for a high proportion of the microbiota in samples purchased from the traditional market. A large number of pathogenic bacteria (Acinetobacter lwoffii, Bacillus cereus, Klebsiella pneumoniae, and Serratia marcescens) were detected in the June samples at a relatively high rate. In addition, the influence of the washing treatment on Chinese chive microbiota was analyzed. After storage at 26℃, the washing treatment accelerated the growth of enterohemorrhagic Escherichia coli (EHEC) because it caused dynamic shifts in Chinese chive indigenous microbiota. These results expand our knowledge of the microbiota in Chinese chives and provide data for the prediction and prevention of food-borne illnesses.

• Geomechanics and Engineering
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• 제30권6호
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• pp.551-564
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• 2022

Fragmenting the rock mass is considered as the most important work in open-pit mines. Ground vibration is the most hazardous issue of blasting which can cause critical damage to the surrounding structures. This paper focuses on developing an explicit model to predict the ground vibration through an multi objective evolutionary polynomial regression (MOGA-EPR). To this end, a database including 79 sets of data related to a quarry site in Malaysia were used. In addition, a gene expression programming (GEP) model and several empirical equations were employed to predict ground vibration, and their performances were then compared with the MOGA-EPR model using the mean absolute error (MAE), root mean square error (RMSE), mean (𝜇), standard deviation of the mean (𝜎), coefficient of determination (R²) and a20-index. Comparing the results, it was found that the MOGA-EPR model predicted the ground vibration more precisely than the GEP model and the empirical equations, where the MOGA-EPR scored lower MAE and RMSE, 𝜇 and 𝜎 closer to the optimum value, and higher R² and a20-index. Accordingly, the proposed MOGA-EPR model can be introduced as a useful method to predict ground vibration and has the capacity to be generalized to predict other blasting effects.

• Journal of Digestive Cancer Research
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• 제3권2호
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• pp.89-94
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• 2015

The role of adjuvant chemotherapy in patients with stage II colon cancer remains a controversial issue. Adjuvant chemotherapy aims to eliminate any micrometastatic disease that may have been missed, at the time of surgery. Although one prospective study showed a small but statistically significant benefit with respect to the overall survival for those who received adjuvant chemotherapy, multiple pooled data did not demonstrate any benefit of this therapy in patients with stage II colon cancer. Current national and international guidelines for the adjuvant treatment of stage II colon dose not advise routine implementation of adjuvant chemotherapy, but rather recommend selective use of this therapy for patients with high risk of recurrence. High risk features for recurrence include T4 disease, poorly differentiated histology, presence of lymphovascular invasion, presence of perineural invasion, inadequate retrieval of lymph nodes, bowel obstruction, localized perforation, or positive margins. More recently, prediction tools using gene expression cancer profiles are proposed to identify patients who are most likely to have recurrence and therefore may benefit from postoperative chemotherapy in stage II colon cancer. These novel methods together with conventional prognosticators, will allow us to implement more optimized personalizing adjuvant therapy in these patients.

• BMB Reports
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• 제40권5호
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• pp.625-635
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• 2007

The enzyme squalene synthase (EC 2.5.1.21) catalyzes a reductive dimerization of two farnesyl diphosphate (FPP) molecules into squalene, a key precursor for the sterol and triterpene biosynthesis. A full-length cDNA encoding squalene synthase (designated as TcSqS) was isolated from Taxus cuspidata, a kind of important medicinal plants producing potent anti-cancer drug, taxol. The full-length cDNA of TcSqS was 1765 bp and contained a 1230 bp open reading frame (ORF) encoding a polypeptide of 409 amino acids. Bioinformatic analysis revealed that the deduced TcSqS protein had high similarity with other plant squalene synthases and a predicted crystal structure similar to other class I isoprenoid biosynthetic enzymes. Southern blot analysis revealed that there was one copy of TcSqS gene in the genome of T. cuspidata. Semi-quantitative RT-PCR analysis and northern blotting analysis showed that TcSqS expressed constitutively in all tested tissues, with the highest expression in roots. The promoter region of TcSqS was also isolated by genomic walking and analysis showed that several cis-acting elements were present in the promoter region. The results of treatment experiments by different signaling components including methyl-jasmonate, salicylic acid and gibberellin revealed that the TcSqS expression level of treated cells had a prominent diversity to that of control, which was consistent with the prediction results of TcSqS promoter region in the PlantCARE database.

• Asian Pacific Journal of Cancer Prevention
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• 제14권6호
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• pp.3503-3507
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• 2013

Background: Although the majority of investigations concerned with TP53 and its protein have focused on coding regions, recently a set of studies highlighted significant roles of regulatory elements located in p53 mRNA, especially 5'UTR. The wrap53${\alpha}$ transcript is one of those that acts as a natural antisense agent, forming RNA-RNA hybrids with p53 mRNA and protecting it from degradation. Materials and Methods: In this study, we focused on the mutation status of exon $1{\alpha}$ of the WRAP53 gene (according to exon 1 of p53) in 160 breast tumor tissue samples and conducted a bioinformatics search for probable miRNA binding site in the p53/wrap53 overlapping region. Mutations were detected, using single stranded conformation polymorphism (SSCP) and sequencing. We applied the miRBase database for prediction of miRNAs which target overlapping region of p53/wrap53 transcripts. Results: Our results showed all samples to have wild type alleles in exon 1 of TP53 gene. We could detect a novel and unreported intronic mutation (IVS1+56, G>C) outside overlapping regions of p53/wrap53 genes in breast cancer tissues and also predict the presence of a binding site for miR-4732-5p in the 5'UTR of Wrap53 mRNA. Conclusions: From our findings we propose designing further studies focused on overexpression of miRNA-4732-5p and introducing different mutations in the overlapping region of wrap53 and p53 genes in order to study their effects on p53 and its ${\Delta}N$ isoform (${\Delta}$40p53) expression. The results may provide new pieces in the p53 targeting puzzle for cancer therapy.

• Asian-Australasian Journal of Animal Sciences
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• 제28권6호
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• pp.870-875
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• 2015

The purpose of this study was to investigate the alternative splicing in equine cordon-bleu WH2 repeat protein-like 1 (COBLL1) gene that was identified in horse muscle and blood leukocytes, and to predict functional consequences of alternative splicing by bioinformatics analysis. In a previous study, RNA-seq analysis predicted the presence of alternative spliced isoforms of equine COBLL1, namely COBLL1a as a long form and COBLL1b as a short form. In this study, we validated two isoforms of COBLL1 transcripts in horse tissues by the real-time polymerase chain reaction, and cloned them for Sanger sequencing. The sequencing results showed that the alternative splicing occurs at exon 9. Prediction of protein structure of these isoforms revealed three putative phosphorylation sites at the amino acid sequences encoded in exon 9, which is deleted in COBLL1b. In expression analysis, it was found that COBLL1b was expressed ubiquitously and equivalently in all the analyzed tissues, whereas COBLL1a showed strong expression in kidney, spinal cord and lung, moderate expression in heart and skeletal muscle, and low expression in thyroid and colon. In muscle, both COBLL1a and COBLL1b expression decreased after exercise. It is assumed that the regulation of COBLL1 expression may be important for regulating glucose level or switching of energy source, possibly through an insulin signaling pathway, in muscle after exercise. Further study is warranted to reveal the functional importance of COBLL1 on athletic performance in race horses.

• Asian-Australasian Journal of Animal Sciences
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• 제32권9호
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• pp.1340-1348
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• 2019

Objective: The objectives were to compare variance components, genetic parameters, prediction accuracies, and genomic-polygenic estimated breeding value (EBV) rankings for milk yield (MY) and fat yield (FY) in the Thai multibreed dairy population using five single nucleotide polymorphism (SNP) sets from GeneSeek GGP80K chip. Methods: The dataset contained monthly MY and FY of 8,361 first-lactation cows from 810 farms. Variance components, genetic parameters, and EBV for five SNP sets from the GeneSeek GGP80K chip were obtained using a 2-trait single-step average-information restricted maximum likelihood procedure. The SNP sets were the complete SNP set (all available SNP; SNP100), top 75% set (SNP75), top 50% set (SNP50), top 25% set (SNP25), and top 5% set (SNP5). The 2-trait models included herd-year-season, heterozygosity and age at first calving as fixed effects, and animal additive genetic and residual as random effects. Results: The estimates of additive genetic variances for MY and FY from SNP subsets were mostly higher than those of the complete set. The SNP25 MY and FY heritability estimates (0.276 and 0.183) were higher than those from SNP75 (0.265 and 0.168), SNP50 (0.275 and 0.179), SNP5 (0.231 and 0.169), and SNP100 (0.251and 0.159). The SNP25 EBV accuracies for MY and FY (39.76% and 33.82%) were higher than for SNP75 (35.01% and 32.60%), SNP50 (39.64% and 33.38%), SNP5 (38.61% and 29.70%), and SNP100 (34.43% and 31.61%). All rank correlations between SNP100 and SNP subsets were above 0.98 for both traits, except for SNP100 and SNP5 (0.93 for MY; 0.92 for FY). Conclusion: The high SNP25 estimates of genetic variances, heritabilities, EBV accuracies, and rank correlations between SNP100 and SNP25 for MY and FY indicated that genotyping animals with SNP25 dedicated chip would be a suitable to maintain genotyping costs low while speeding up genetic progress for MY and FY in the Thai dairy population.

• Animal Bioscience
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• 제35권1호
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• pp.115-125
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• 2022

Objective: Intramuscular fat (IMF) is a critical economic indicator of pork quality. Studies on IMF among different pig breeds have been performed via high-throughput sequencing, but comparisons within the same pig breed remain unreported. Methods: This study was performed to explore the gene profile and identify candidate long noncoding RNA (lncRNAs) and mRNAs associated with IMF deposition among Laiwu pigs with different IMF contents. Based on the longissimus dorsi muscle IMF content, eight pigs from the same breed and management were selected and divided into two groups: a high IMF (>12%, H) and low IMF group (<5%, L). Whole-transcriptome sequencing was performed to explore the differentially expressed (DE) genes between these two groups. Results: The IMF content varied greatly among Laiwu pig individuals (2.17% to 13.93%). Seventeen DE lncRNAs (11 upregulated and 6 downregulated) and 180 mRNAs (112 upregulated and 68 downregulated) were found. Gene Ontology analysis indicated that the following biological processes played an important role in IMF deposition: fatty acid and lipid biosynthetic processes; the extracellular signal-regulated kinase cascade; and white fat cell differentiation. In addition, the peroxisome proliferator-activated receptor, phosphatidylinositol-3-kinase-protein kinase B, and mammalian target of rapamycin pathways were enriched in the pathway analysis. Intersection analysis of the target genes of DE lncRNAs and mRNAs revealed seven candidate genes associated with IMF accumulation. Five DE lncRNAs and 20 DE mRNAs based on the pig quantitative trait locus database were identified and shown to be related to fat deposition. The expression of five DE lncRNAs and mRNAs was verified by quantitative real time polymerase chain reaction (qRT-PCR). The results of qRT-PCR and RNA-sequencing were consistent. Conclusion: These results demonstrated that the different IMF contents among pig individuals may be due to the DE lncRNAs and mRNAs associated with lipid droplets and fat deposition.

• 대한한의학회지
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• 제44권2호
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• pp.106-118
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• 2023

Objectives: Network pharmacology is a method of constructing and analyzing a drug-compound-target network to predict potential efficacy and mechanisms related to drug targets. In that large-scale analysis can be performed in a short time, it is considered a suitable tool to explore the function and role of herbal medicine. Thus, we investigated the potential functions and pathways of Chongmyunggongjin-dan (CMGJD) on Alzheimer's disease (AD) via network pharmacology analysis. Methods: Using public databases and PubChem database, compounds of CMGJD and their target genes were collected. The putative target genes of CMGJD and known target genes of AD were compared and found the correlation. Then, the network was constructed using Cytoscape 3.9.1. and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms. Results: The result showed that total 104 compounds and 1157 related genes were gathered from CMGJD. The network consisted of 1157nodes and 10034 edges. 859 genes were interacted with AD gene set, suggesting that the effects of CMGJD are closely related to AD. Target genes of CMGJD are considerably associated with various pathways including 'Positive regulation of chemokine production', 'Cellular response to toxic substance', 'Arachidonic acid metabolic process', 'PI3K-Akt signaling pathway', 'Metabolic pathways', 'IL-17 signaling pathway' and 'Neuroactive ligand-receptor interaction'. Conclusion: Through a network pharmacological method, CMGJD was predicted to have high relevance with AD by regulating inflammation. This study could be used as a basis for effects of CMGJD on AD.

• Animal Bioscience
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• 제37권8호
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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.