• Animal Bioscience
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• v.34 no.9
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• pp.1439-1450
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• 2021

Objective: With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods: Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results: In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion: Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

• The Korea Journal of Herbology
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• v.34 no.1
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• pp.33-42
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• 2019

Objectives : This study aimed to be used as basic data for obtaining excellent quality of Salvia miltiorrhiza (SM) root. Methods : SM cultivated in Anhui Bozou, Henan, Shandong, Henan Wenxian, Zhejiang, Hebei, Liaoning, Shanxi, Shaanxi Shangluo, Sichuan Zhongjiang, Sichuan Minyang and Jiangsu in China were gathered and its internal morphology and physicochemical patterns were analyzed. Results : Cross-section of sang plants according to cultivated regions in China showed that cork layers consisted of cells with four to six layers, cortex width was wide, and phloem was semilunar-shaped. Although there are forms layers, yet boundary was vague. It was observed that eight to ten vascular bundles were arranged in wooden parts in all directions and as a single line of vascular was distributed nearby form layers as it nears to the center. Tanshinon IIA identified a spot in the same location with standard product near by Rf 0.9 in the test identifying TLC of SM according to cultivated areas in China. The largest amount was 0.535% identified in Shandong and the lowest amount of 0.05% in Hebei. Salvianolic acid B identified a spot in the same location with standard product near by Rf 0.7 in the test identifying TLC of SM according to cultivated areas in China. The largest amount was 2.72% identified in Liaoning and the lowest amount of 0.825% in Jiangsu. Conclusions : The results are assumed to be used as basic data for obtaining excellent quality of SM oriental medical hers and distinguishing authentic or fake herbs.

• Korean Journal of Clinical Pharmacy
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• v.32 no.4
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• pp.321-327
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• 2022

Background: To implement medication management service in Korean nursing home (NH), medication review tool for residents in Korean long-term care facilities was developed. This prospective pilot study aimed to verify the applicability of this newly developed tool and to evaluate the drug related problems (DRPs) identified by pharmacists' medication review in NH setting. Methods: This study was carried out in two NHs in Korea. The elderly residents (65 or older) using 5 or more medications were eligible. Pharmacists conducted medication review and identified the DRPs and potentially inappropriate medications (PIMs) based on the newly developed tool. Results: Among 43 NH residents, 27 residents agreed to participate. The median age was 87 and about 55.6% of them were taking 10 or more medications. Pharmacists identified a total of 37 PIMs in 18 NH residents (66.7%) and 54 DRPs in 22 residents (81.5%). The most frequent PIM was general-PIM (26 cases) followed by PIM under specific diseases or conditions (7 cases). Out of 77 items contained in the tool, 15 items were detected in study participants. 'Continued use or regular daily use of hypnotics' was the most highly detected item (9 cases) followed by 'multiple prescriptions within each class of hypnotics/sedatives' (5 cases). Among 54 DRPs identified, pharmacist intervened 39 cases (72.2%) and interventions were accepted in 18 cases (46.1%). Conclusion: This pilot study demonstrated that newly developed tool is feasible for the nursing home residents. However, further studies with larger population are warranted.

• Microbiology and Biotechnology Letters
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• v.50 no.4
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• pp.563-573
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• 2022

Xanthomonas arboricola pv. juglandis (Xaj) is a globally important bacterial pathogen of walnut trees that causes substantial economic losses in commercial walnut production. Although prophages are common in bacterial plant pathogens and play important roles in bacterial diversity and pathogenicity, there has been limited investigation into the distribution and function of prophages in Xaj. In this study, we identified and characterized 13 predicted prophages from the genomes of 12 Xaj isolates from around the globe. These prophages ranged in length from 11.8 kb to 51.9 kb, with between 11-75 genes and 57.82-64.15% GC content. The closest relatives of these prophages belong to the Myoviridae and Siphoviridae families of the Caudovirales order. The phylogenetic analysis allowed the classification of the prophages into five groups. The gene constitution of these predicted prophages was revealed via Roary analysis. Amongst 126 total protein groups, the most prevalent group was only present in nine prophages, and 22 protein groups were present in only one prophage (singletons). Also, bioinformatic analysis of the 13 identified prophages revealed the presence of 431 genes with an average length of 389.7 bp. Prokka annotation of these prophages identified 466 hypothetical proteins, 24 proteins with known function, and six tRNA genes. The proteins with known function mainly comprised prophage integrase IntA, replicative DNA helicase, tyrosine recombinase XerC, and IS3 family transposase. There was no detectable insertion site specificity for these prophages in the Xaj genomes. The identified Xaj prophage genes, particularly those of unknown function, merit future investigation.

• Journal of Society of Preventive Korean Medicine
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• v.27 no.2
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• pp.35-48
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• 2023

Objective : We studied prognostic biomarkers discovery for lung cancer based on the pattern identification for the personalized Korean medicine. Methods : Using 30 tissue samples, we performed a whole exome sequencing to examine the genetic differences among three groups. Results : The exome sequencing identified among 23,490 SNPs germline variants, 12 variants showed significant frequency differences between Xu and Stasis groups (P<0.0005). As similar, 18 and 10 variants were identified in analysis for Xu vs. Gentleness group and Stasis vs. Gentleness group, respectively (P<0.001). Our exome sequencing also found 8,792 lung cancer specific variants and among the groups identified 6, 34, and 12 variants which showed significant allele frequency differences in the comparison groups; Xu vs. Stasis, Xu vs. Gentleness group, and Stasis vs. Gentleness group. As a result of PCA analysis, in germline data set, Xu group was divided from other groups. Analysis using somatic variants also showed similar result. And in gene ontology analysis using pattern identification variants, we found genes like as FUT3, MYCBPAP, and ST5 were related to tumorigenicity, and tumor metastasis in comparison between Xu and Stasis. Other significant SNPs for two were responsible for eye morphogenesis and olfactory receptor activity. Classification of somatic pattern identification variants showed close relationship in multicellular organism reproduction, anion-anion antiporter activity, and GTPase regulator activity. Conclusions : Taken together, our study identified 40 variants in 29 genes in association with germline difference of pattern identification groups and 52 variants in 47 genes in somatic cancer tissues.

• Journal of Ginseng Research
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• v.47 no.4
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• pp.593-603
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• 2023

Background: Korean Red Ginseng is a major source of bioactive substances such as ginsenosides. Efficacy of red ginseng extract (RGE), which contains not only saponins but also various non-saponins, has long been studied. In the water-soluble component-rich fraction of RGE (WS), a byproduct generated in the process of extracting saponins from the RGE, we identified previously unidentified molecules and confirmed their efficacy. Methods: The RGE was prepared and used to produce WS, whose components were isolated sequentially according to their water affinity. The new compounds from WS were fractionized and structurally analyzed using nuclear magnetic resonance spectroscopy. Physiological applicability was evaluated by verifying the antioxidant and anti-inflammatory efficacies of these compounds in vitro. Results: High-performance liquid chromatography confirmed that the obtained WS comprised 11 phenolic acid and flavonoid substances. Among four major compounds from fractions 1-4 (F1-4) of WS, two compounds from F3 and F4 were newly identified in red ginseng. The analysis results show that these compound molecules are member of the maltol-structure-based glucopyranose series, and F1 and F4 are particularly effective for decreasing oxidative stress levels and inhibiting nitric oxide secretion, interleukin (IL)-1β and IL-6, and tumor necrosis factor-α. Conclusion: Our findings suggest that a few newly identified maltol derivatives, such as red ginseng-derived non-saponin in the WS, exhibit antioxidant and anti-inflammatory effects, making them viable candidates for application to pharmaceutical, cosmetic, and functional food materials.

• ALGAE
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• v.38 no.2
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• pp.127-139
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• 2023

Cryptic stages of diverse macroalgae present in natural substrata, "the bank of microscopic forms", were isolated into clonal cultures and identified based on both morphological characteristics and DNA barcoding. Approximately 120 clonal isolates from 308 natural substratum samples were collected from the entire coastline of Kuwait. Amongst these isolates, 77 (64%) were identified through DNA barcoding using the nuclear ribosomal small subunit, RuBisCO spacer (ITS2, tufa, rbcL, psaA, and psbA) and sequencing. Twenty-six isolates (34%) were identified in the division Chlorophyta, 18 (23%) as Phaeophyceae, and 33 (43%) as Rhodophyta. For all DNA sequences in this study, species-level cut off applied was ≥98% homology which depend entirely on the markers used. Three putative new records of Chlorophyta new for the Arabian Gulf were made: Cladophora laetevirens (Dillwyn) Kützing, Ulva torta (Mertens) Trevisan and Ulvella leptochaete (Huber) R. Nielsen, C. J. O'Kelly & B. Wysor in Nielsen, while Cladophora gracilis Kützing and Ulva ohnoi M. Hiraoka & S. Shimada are new records for Kuwait. For Phaeophyceae, Ectocarpus subulatus Kützing and Elachista stellaris Areschoug were new records for the Gulf and Kuwait. In the Rhodophyta, Acrochaetium secundatum (Lyngbye) Nägeli in Nägeli & Cramer, Ceramium affine Setchell & N. L. Gardner, Gelidium pusillum var. pakistanicum Afaq-Husain & Shameel and Dasya caraibica Børgesen are new records for the Gulf and Kuwait, while the red alga Stylonema alsidii (Zanardini) K. Drew is a new record for Kuwait. Several isolates identified corresponded to genera not previously reported in Kuwait and / or the Arabian Gulf, such as Porphyrostromium Trevisan, a new genus from the Bangiales, and two unidentified species for the Planophilaceae Škaloud & Leliaert. The isolates cultivated from substrata enhance understanding of the marine macroalgal diversity in the region and confirmed that the Germling Emergence Method is suitable for determining the actual diversity of a given study area through isolation from cryptic life-history phases.

• Smart Structures and Systems
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• v.31 no.1
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• pp.57-68
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• 2023

Bridge hangers, such as those in suspension and cable-stayed bridges, suffer from cumulative fatigue damage caused by dynamic loads (e.g., cyclic traffic and wind loads) in their service condition. Thus, the identification of damage to hangers is important in preserving the service life of the bridge structure. This study develops a new method for condition assessment of bridge hangers. The tension force of the bridge and the damages in the element level can be identified using the Bayesian optimization method. To improve the number of observed data, the additional mass method is combined the Bayesian optimization method. Numerical studies are presented to verify the accuracy and efficiency of the proposed method. The influence of different acquisition functions, which include expected improvement (EI), probability-of-improvement (PI), lower confidence bound (LCB), and expected improvement per second (EIPC), on the identification of damage to the bridge hanger is studied. Results show that the errors identified by the EI acquisition function are smaller than those identified by the other acquisition functions. The identification of the damage to the bridge hanger with various types of boundary conditions and different levels of measurement noise are also studied. Results show that both the severity of the damage and the tension force can be identified via the proposed method, thereby verifying the robustness of the proposed method. Compared to the genetic algorithm (GA), particle swarm optimization (PSO), and nonlinear least-square method (NLS), the Bayesian optimization (BO) performs best in identifying the structural damage and tension force.

• Food Science and Preservation
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• v.30 no.6
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• pp.944-959
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• 2023

This study investigated the essential oil composition of fresh Panax ginseng root and identified novel compounds from ginseng oil. The oil was divided into five fractions (neutral, basic, phenolic, acidic, and aldehydic). In total, 149 constituents, including 29, 19, and 38 compounds in the basic, phenolic, and aldehydic fractions, respectively, were identified by gas chromatography (GC) and GC-mass spectrometry (MS). The primary constituents of the total ginseng volatile oil were α-humulene (13.91% as a peak area), bicyclogermacrene (13.59%), β-caryophyllene (8.24%), α-neoclovene (7.78%), and α- and β-panasinsenes (5.14% and 7.53%). The primary constituents of the basic fraction were 2-isopropyl-3-methoxypyrazine (35.51%), 3-sec-butyl-2-methoxy-5-methylpyrazine (31.54%), 2-isobutyl-3-methoxypyrazine (8.64%), and 2-methoxy-3-methylpyrazine (8.40%), whereas in the phenolic fraction, these were benzoic (25.40%), octanoic (11.57%), nonanoic (9.16%), propionic (6.35%), and decanoic acids (6.16%). The primary constituents of the aldehydic fraction were 4-(2-furyl)-3-buten-2-one (23.41%), benzaldehyde (10.18%), cis-2-heptanal (9.42%), 3-(α-furyl)-propenal (8.51%), and 2-phenyl-2-butenal (7.28%). Among these, the phenylalkenal compounds, including 2-phenyl-2-butenal, 2-methyl-3-phenyl-2-propenal, 5-methyl-2-phenyl-2-pentenal, 5-methyl-2-phenyl-2-hexenals, 2-phenyl-2-octenal, and 2-phenyl-2-nonenal, were newly identified in this study as ginseng volatile constituents. Furthermore, 2-phenyl-2-nonenal was identified as a plant-based volatile constituent for the first time in this study.

• International Journal of Industrial Entomology and Biomaterials
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• v.48 no.1
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• pp.42-47
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• 2024

The value of silkworms as functional health food materials has increased, as has the interest in its disease control for stable production, and in the economic value of entomopathogenic microorganisms. In this study, we isolated and identified disease-causing fungi from white muscardine silkworms, and confirmed whether this strain could produce white muscardine silkworms. For the analysis of the cause of white muscardine disease in the infected silkworms, the fungi and prokaryotes causing the disease were identified, isolated, and identified using metagenome analysis. Metagenomic analysis detected a large amount of the fungus Metarhizium rileyi in silkworms, and a large amount of the bacterium Enterococcus mundtii, which was presumed to be the causative agent of the disease. For accurate identification of the fungi, these were purified by culture medium, and sequencing and phylogenetic tree analyses were performed using an internal transcribed spacer. As a result, M. rileyi, Cladosporium cladosporioides, and C. tenuissimum were identified. In general, M. rileyi is known to form green conidia, but in this study, white-yellow conidia were formed, indicating that the exact causative agent of the fungal disease cannot be estimated by diagnosing the symptoms. Thus, a diagnostic method is necessary for the continuously collection of required pathogens, and identifying their morphological and genetic characteristics.