Korea Research Institute of Bioscience and Biotechnology
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Eleocharis kuroguwai Ohwi ameliorates LPS-mediated inflammation by suppressing MAPKs signaling
No full textIn rice agriculture, Eleocharis kuroguwai Ohwi (olbanggae) is a target for herbicidal intervention as a problem weed although it has also long been used clinically as a traditional medicine for jaundice, fever, and blood flow. E. kuroguwai has been evaluated in many clinical trials, but its molecular biological advantages are still unknown. Here, we investigate the anti-inflammatory effects of E. kuroguwai 80% ethanol extracts by screening NO production in LPS-induced macrophage activation. To find the most effective fractions, we partitioned five sub-fractions using HP20 column chromatography, namely 20%, 40%, 60%, 80%, and 100%. Of these, the 60% and 80% sub-fractions were found to significantly inhibit NO production; there were no toxicological effects at any concentration. In addition, the 80% sub-fraction inhibited significantly the iNOS and the mRNA of the pro-inflammatory mediators IL-6, TNF-α, and IL-1β by inhibiting the phosphorylation of JNK and ERK pathways associated with MAPKs signaling. Our results suggest that the 80% E. kuroguwai sub-fraction has the most significant anti-inflammatory effects of inhibiting iNOS and pro-inflammatory mediators and suppressing the phosphorylation of JNK and ERK. Therefore, the 80% sub-fraction of E. kuroguwai extract may be a therapeutic candidate for inflammatory diseases associated with the overexpression of MAPKs.
GMStool: GWAS-based marker selection tool for genomic prediction from genomic data
No full textThe increased accessibility to genomic data in recent years has laid the foundation for studies to predict various phenotypes of organisms based on the genome. Genomic prediction collectively refers to these studies, and it estimates an individual’s phenotypes mainly using single nucleotide polymorphism markers. Typically, the accuracy of these genomic prediction studies is highly dependent on the markers used; however, in practice, choosing optimal markers with high accuracy for the phenotype to be used is a challenging task. Therefore, we present a new tool called GMStool for selecting optimal marker sets and predicting quantitative phenotypes. The GMStool is based on a genome-wide association study (GWAS) and heuristically searches for optimal markers using statistical and machine-learning methods. The GMStool performs the genomic prediction using statistical and machine/deep-learning models and presents the best prediction model with the optimal marker-set. For the evaluation, the GMStool was tested on real datasets with four phenotypes. The prediction results showed higher performance than using the entire markers or the GWAS-top markers, which have been used frequently in prediction studies. Although the GMStool has several limitations, it is expected to contribute to various studies for predicting quantitative phenotypes. The GMStool written in R is available at www.github.com/JaeYoonKim72/GMStool.
The anti-inflammatory effect of Trichilia martiana C. DC. in the lipopolysaccharide-stimulated inflammatory response in macrophages and airway epithelial cells and in LPS-challenged mice
No full textA number of species of the genus Trichilia (Meliaceae) exhibit anti-inflammatory effects. However, the effect of Trichilia martiana C. DC. (TM) on lipopolysaccharide (LPS)-induced inflammation has not, to the best of our knowledge, yet been determined. Therefore, in the present study, the anti-inflammatory effect of TM on LPS-stimulated RAW264.7 macrophages was evaluated. The ethanol extract of TM (TMEE) significantly inhibited LPS-induced nitric oxide (NO), prostaglandin 2 (PGE2), inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). TMEE also reduced the levels of inflammatory cytokines, including tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1β and IL-6. The upregulation of mitogen-activated protein kinases (MAPKs) and NF-κB activation was revealed to be downregulated following TMEE pretreatment. Furthermore, TMEE was indicated to lead to the nucleus translocation of nuclear factor erythroid-derived 2-related factor 2 (Nrf2) and the expression of heme oxygenase-1 (HO-1). In H292 airway epithelial cells, the pretreatment of TMEE significantly downregulated the production of LPS-stimulated IL-1β, and TMEE was indicated to increase the expression of HO-1. In animal models exhibiting LPS-induced acute lung injury (ALI), treatment with TMEE reduced the levels of macrophages influx and TNF-α production in the bronchoalveolar lavage fluid (BALF) of ALI mice. Additionally, TMEE significantly downregulated the activation of ERK, JNK and IκB, and upregulated the expression of HO-1 in the lungs of ALI mice. In conclusion, the results of the current study demonstrated that TMEE could exert a regulatory role in the prevention or treatment of the endotoxin-mediated inflammatory response.
Gene expression profile in similar tissues using transcriptome sequencing data of whole-body horse skeletal muscle
No full textHorses have been studied for exercise function rather than food production, unlike most livestock. Therefore, the role and characteristics of tissue landscapes are critically understudied, except for certain muscles used in exercise-related studies. In the present study, we compared RNA-Seq data from 18 Jeju horse skeletal muscles to identify differentially expressed genes (DEGs) between tissues that have similar functions and to characterize these differences. We identified DEGs between different muscles using pairwise differential expression (DE) analyses of tissue transcriptome expression data and classified the samples using the expression values of those genes. Each tissue was largely classified into two groups and their subgroups by k-means clustering, and the DEGs identified in comparison between each group were analyzed by functional/pathway level using gene set enrichment analysis and gene level, confirming the expression of significant genes. As a result of the analysis, the differences in metabolic properties like glycolysis, oxidative phosphorylation, and exercise adaptation of the groups were detected. The results demonstrated that the biochemical and anatomical features of a wide range of muscle tissues in horses could be determined through transcriptome expression analysis, and provided proof-of-concept data demonstrating that RNA-Seq analysis can be used to classify and study in-depth differences between tissues with similar properties.
Anti-obesity activity of anthocyanin and carotenoid extracts from color-fleshed sweet potatoes
No full textThe anti？obesity effects of anthocyanin and carotenoid extracts from color？fleshed potatoes were studied with 3T3？L1 cells in vitro and high？fat diet (HFD)？induced obese mice in vivo. Treatment of 3T3？L1 adipocytes with anthocyanin and carotenoid extracts, respectively, after differentiation induction significantly inhibited fat accumulation by 63.1 and 83.5%. Studies of adipogenesis inhibition showed that the anthocyanin extract acts at intermediate stages, whereas the carotenoid extract influences all the stages. The extracts significantly diminished triglyceride (TG) content and peroxisome proliferator？activated receptor gamma (PPARγ) protein expression during adipogenesis of the intermediate stage. Oral administration of anthocyanin and carotenoid extracts, respectively, to HFD？fed mice significantly reduced weight gain and restored TG levels to normal or lower as compared to the HFD？fed group with improvement of a lipid profile, TG to HDL？C ratio. Histological differences in liver tissues revealed that the extracts protected the liver tissue from adipogenesis by HFD fed. This research presents the first direct demonstration that the two pigment extracts from sweet potato exhibit anti？obesity activities.
Regulation of stomatal development by stomatal lineage miRNAs
No full textStomata in the plant epidermis play a critical role in growth and survival by controlling gas exchange, transpiration, and immunity to pathogens. Plants modulate stomatal cell fate and patterning through key transcriptional factors and signaling pathways. MicroRNAs (miRNAs) are known to contribute to developmental plasticity in multicellular organisms; however, no miRNAs appear to target the known regulators of stomatal development. It remains unclear as to whether miRNAs are involved in stomatal development. Here, we report highly dynamic, developmentally stage-specific miRNA expression profiles from stomatal lineage cells. We demonstrate that stomatal lineage miRNAs positively and negatively regulate stomatal formation and patterning to avoid clustered stomata. Target prediction of stomatal lineage miRNAs implicates potential cellular processes in stomatal development. We show that miR399-mediated PHO2 regulation, involved in phosphate homeostasis, contributes to the control of stomatal development. Our study demonstrates that miRNAs constitute a critical component in the regulatory mechanisms controlling stomatal development.
Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer
No full textImmunotherapy for metastatic colorectal cancer is effective only for mismatch repair-deficient tumors with high microsatellite instability that demonstrate immune infiltration, suggesting that tumor cells can determine their immune microenvironment. To understand this cross-talk, we analyzed the transcriptome of 91,103 unsorted single cells from 23 Korean and 6 Belgian patients. Cancer cells displayed transcriptional features reminiscent of normal differentiation programs, and genetic alterations that apparently fostered immunosuppressive microenvironments directed by regulatory T cells, myofibroblasts and myeloid cells. Intercellular network reconstruction supported the association between cancer cell signatures and specific stromal or immune cell populations. Our collective view of the cellular landscape and intercellular interactions in colorectal cancer provide mechanistic information for the design of efficient immuno-oncology treatment strategies.
Study on the inhibitory mechanism of the Dlk1-Dio3 miRNA cluster in muscle aging
No full text노화 근육에서 Dlk1-Dio3 마이크로 RNA 클러스터 발현억제 기전 연구KFM058191
Rugosic acid A, derived from Rosa rugosa Thunb., is novel inhibitory agent for NF-κB and IL-6/STAT3 axis in acute lung injury model
No full textRosa rugosa Thunb., is as a medicinal plant known for anti-diabetic, and anti-inflammatory activities. However, the specific active compounds responsible for the individual pharmacological effects of in R. rugosa extract (95% EtOH) remain unknown. Here, we hypothesized that terpenoid structure, the most abundant constituents in R. rugosa extract, are responsible for its anti-inflammatory activity. We investigated the phytochemical substituents (compounds 1-13) and newly purified 11-methoxy polisin A, and 13-methoxy bisaborosaol F using NMR and ESI-MS and to screened their effects on NO production in LPS-induced macrophages. Rugosic acid A (RA) induced to ameliorate NO production, iNOS, and pro-inflammatory cytokines associated with the NF-κB. And, RA suppressed IL-6 secretion and IL-6-mediated STAT3 activation in LPS-mediated inflammation. In addition, RA was evaluated in LPS-mediated acute lung injury (ALI) model similar to acute pneumonia. Our results suggested that RA was suppressed to translocate nuclear NF-κB and IL-6-mediated STAT3 activation. Finally, RA led to amelioration of ALI by decreasing myeloperoxidase (MPO) and inhibiting phosphorylation of NF-κB and STAT3. Our group originally found that R. rugosa extract had new methoxy compounds and RA may be alternative natural agent for acute pneumonia similar to severe acute respiratory syndrome by coronavirus.
Herbicide-based weed management for soybean production in the Far Eastern region of Russia
No full textThis study was conducted to establish a weed management system based on the sequential application of pre-emergence (PRE) and post-emergence (POST) herbicides for soybean production in Primorsky krai. Field experiments were conducted for two years in a field located in Bogatyrka, Primorsky krai, Russia (N43°49′, E131°36′). No herbicide application resulted in significant soybean yield loss, 0.03？0.3 t ha？1, which is more than 91.6% yield loss compared with that of the weed-free plot. The PRE application of acetochlor showed good weed control efficacy (greater than 90% weed control) with acceptable soybean safety (less than 10% soybean damage), while the other PRE herbicides performed poorly in terms of weed control. The POST application of bentazon + acifluorfen, bentazon, and imazamox at 30 days after soybean sowing (DAS) showed good weed control efficacy with good soybean safety. Neither the PRE nor POST application alone showed a sufficient soybean yield protection, resulting in much lower soybean yield than the weed-free plot. The sequential application of acetochlor (PRE), followed by either bentazon + acifluorfen (POST) at 30 DAS in 2012 or bentazon + imazamox (POST) at 60 DAS in 2013 showed the best performance in soybean yields, 1.7 t and 1.9 t ha？1, respectively, provided with 724.5 US ha？1 of economic returns. For alternative PRE herbicides of acetochlor, which is now banned, our tests of the sequential application of S-metolachlor with other POST herbicides and the sole application of other PRE herbicides revealed that S-metolachlor and clomazone could also be considered. Our results thus demonstrate that the sequential applications of PRE and POST herbicides should be incorporated into the weed management system for soybean production in Primorsky krai, Russia.