scholarly journals Integrated Four Comparative-Omics Reveals the Mechanism of the Terpenoid Biosynthesis in Two Different Overwintering Cryptomeria fortunei Phenotypes

2021 ◽  
Vol 12 ◽  
Author(s):  
Yingting Zhang ◽  
Jiebing Cui ◽  
Hailiang Hu ◽  
Jinyu Xue ◽  
Junjie Yang ◽  
...  
Keyword(s):  
Essential Oil ◽  
Mirna Target ◽  
Economic Value ◽  
Terpenoid Biosynthesis ◽  
Wild Type ◽  
Metabolome Analysis ◽  
Differentially Expressed Mirnas ◽  
Target Regulation ◽  
Regulation Mechanisms ◽  
Diterpenoid Biosynthesis

Chinese cedar (Cryptomeria fortunei) is a tree species with important ornamental, medicinal, and economic value. Terpenoids extracted from the essential oil of C. fortunei needles have been considered valuable ingredients in the pharmaceutical and cosmetic industries. However, the possible gene regulation mechanisms that limit terpenoid biosynthesis in this genus are poorly understood. Here, we adopted integrated metabolome analysis, transcriptome, small-RNA (sRNA), and degradome sequencing to analyze the differences in terpenoid regulatory mechanisms in two different overwintering C. fortunei phenotypes (wild-type and an evergreen mutant). A total of 1447/6219 differentially synthesized metabolites (DSMs)/unigenes (DEGs) were detected through metabolome/transcriptome analyses, and these DSMs/DEGs were significantly enriched in flavonoid and diterpenoid biosynthesis pathways. In C. fortunei needles, 587 microRNAs (miRNAs), including 67 differentially expressed miRNAs (DERs), were detected. Among them, 8346 targets of 571 miRNAs were predicted using degradome data, and a 72-miRNA-target regulatory network involved in the metabolism of terpenoids and polyketides was constructed. Forty-one targets were further confirmed to be involved in terpenoid backbone and diterpenoid biosynthesis, and target analyses revealed that two miRNAs (i.e., aly-miR168a-5p and aof-miR396a) may be related to the different phenotypes and to differential regulation of diterpenoid biosynthesis. Overall, these results reveal that C. fortunei plants with the evergreen mutation maintain high terpenoid levels in winter through miRNA-target regulation, which provides a valuable resource for essential oil-related bioengineering research.

scholarly journals Integrative Analysis of Terpenoid Profiles and Hormones from Fruits of Red-Flesh Citrus Mutants and Their Wild Types

Molecules ◽  
2019 ◽  
Vol 24 (19) ◽  
pp. 3456
Author(s):  
Cuihua Liu ◽  
Min He ◽  
Zhuang Wang ◽  
Juan Xu
Keyword(s):  
Citrus Fruit ◽  
Isopentenyl Diphosphate ◽  
Citrus Fruits ◽  
Limited Extent ◽  
Terpenoid Biosynthesis ◽  
Wild Type ◽  
Flux Balance ◽  
Metabolite Profiles ◽  
Volatile Profiles ◽  
Low Levels

In citrus color mutants, the levels of carotenoid constituents and other secondary metabolites are different in their corresponding wild types. Terpenoids are closely related to coloration, bitterness, and flavor. In this study, terpenoid profiles and hormones in citrus fruits of two red-flesh mutants—Red Anliu orange and Red-flesh Guanxi pummelo—and their corresponding wild types were investigated using GC/MS, HPLC, and LC-MS/MS. Results showed that Red Anliu orange (high in carotenoids) and Anliu orange (low in carotenoids) accumulated low levels of limonoid aglycones but high levels of monoterpenoids; conversely, Red-flesh Guanxi pummelo (high in carotenoids) and Guanxi pummelo (deficient in carotenoids) accumulated high levels of limonoid aglycones but low levels of monoterpenoids. However, isopentenyl diphosphate was present at similar levels. A correlation analysis indicated that jasmonic and salicylic acids might play important roles in regulating terpenoid biosynthesis. Additionally, the similarities of carotenoid and volatile profiles between each mutant and its corresponding wild type were greater than those between the two mutants or the two wild types. The flux balance of terpenoid metabolism in citrus fruit tends toward stability among various citrus genera that have different terpenoid profiles. Bud mutations could influence metabolite profiles of citrus fruit to a limited extent.

scholarly journals Characteristic Analysis from Excessive to Deficient Syndromes in Hepatocarcinoma Underlying miRNA Array Data

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Qi-Long Chen ◽  
Yi-Yu Lu ◽  
Gui-Biao Zhang ◽  
Ya-Nan Song ◽  
Qian-Mei Zhou ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Hierarchical Cluster ◽  
Characteristic Analysis ◽  
Array Data ◽  
Mirna Array ◽  
Differentially Expressed Mirnas ◽  
Similar Complex

Traditional Chinese medicine (TCM) treatment is regarded as a safe and effective method for many diseases. In this study, the characteristics among excessive, excessive-deficient, and deficient syndromes of Hepatocellular carcinoma (HCC) were studied using miRNA array data. We first calculated the differentially expressed miRNAs based on random modulet-test and classified three TCM syndromes of HCC using SVM method. Then, the weighted miRNA-target networks were constructed for different TCM syndromes using predicted miRNA targets. Subsequently, the prioritized target genes of upexpression network of TCM syndromes were analyzed using DAVID online analysis. The results showed that there are distinctly different hierarchical cluster and network structure of TCM syndromes in HCC, but the excessive-deficient combination syndrome is extrinsically close to deficient syndrome. GO and pathway analysis revealed that the molecular mechanisms of excessive-deficient and deficient syndromes of HCC are more complex than excessive syndrome. Furthermore, although excessive-deficient and deficient syndromes have similar complex mechanisms, excessive-deficient syndrome is more involved than deficient syndrome in development of cancer process. This study suggested that miRNAs might be important mediators involved in the changing process from excessive to deficient syndromes and could be potential molecular markers for the diagnosis of TCM syndromes in HCC.

Determining differentially expressed miRNAs and validating miRNA—target relationships using the SPRET/Ei mouse strain

2014 ◽  
Vol 26 (1-2) ◽  
pp. 94-107 ◽  
Author(s):  
S. Timmermans ◽  
F. Van Hauwermeiren ◽  
L. Puimège ◽  
L. Dejager ◽  
E. Van Wonterghem ◽  
...  
Keyword(s):  
Mouse Strain ◽  
Mirna Target ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas

scholarly journals Cendana (Santalum album L.) sebagai tanaman penghasil minyak atsiri

Kultivasi ◽  
2018 ◽  
Vol 17 (1) ◽  
Author(s):  
Mira Ariyanti ◽  
Yenni Asbur
Keyword(s):  
Essential Oil ◽  
Oil Content ◽  
Genetic Factors ◽  
Economic Value ◽  
Volatile Oil ◽  
Oil Extraction ◽  
Santalum Album ◽  
Functional Value ◽  
Sandalwood Oil ◽  
Santalum Album L

Abstract. Sandalwood is source of essential oil and as non-wood commodity of forest, which is potential and considered luxurious due to its distinctiveness hard wood and containing specific oil scent. Sandalwood oil can be produced from its wood by extracting from its tree trunks, twigs, brances, or root. The economic value of sandalwood plan is derived from its oil content (santalol) which has unique scent. A volatile oil contained in sandalwood is the sesquiterpenoid compound; among them are α-santalol dan b-santalol. Interaction between genetic factors of plant with its environment is a major factor that determines the growth and development of sandalwood plant that eventually affecting the volatile oil that can be produced. Engineering efforts are required against factors that  related with oil extraction in order to obtain its maximum production in both in quantity and quality. Sandalwood oil has high functional value, some of them are as the material for aromatic therapy which is particularly beneficial for human health, as cosmetic material, and as material for medicines.Keywords : sandalwood, essential oil, santalol Sari. Cendana merupakan sumber penghasil minyak atsiri dan merupakan komoditi hasil hutan bukan kayu yang potensial dan tergolong mewah karena sifat kayu terasnya yang khas dan mengandung minyak dengan aroma yang spesifik. Pembuatan minyak cendana dapat dilakukan dengan memanfaatkan batang kayu, ranting, cabang ranting, dan akar pohon cendana. Nilai ekonomi tanaman cendana didapat dari kandungan minyak (santalol) dalam kayu yang beraroma wangi yang khas. Minyak atsiri yang terkandung pada kayu cendana merupakan golongan senyawa sesquiterpenoid diantaranya α-santalol dan b-santalol. Interaksi antara faktor genetik tanaman dengan ling-kungan merupakan faktor utama yang menentukan pertumbuhan dan perkembangan tanaman cendana yang pada akhirnya berpengaruh terhadap produksi minyak atsiri yang dihasilkan. Diperlukan upaya rekayasa terhadap faktor-faktor yang terkait dengan ektraksi minyak cendana sehingga produksi maksimal dicapai baik secara kuantitas maupun kualitas. Minyak cendana memiliki nilai fungsi yang tinggi diantaranya sebagai bahan aroma terapi yang sangat bermanfaat bagi kesehatan manusia, bahan kosmetik, dan bahan untuk obat-obatan.Kata kunci : tanaman cendana, minyak atsiri, santalol

scholarly journals Identification and validation of key miRNAs and miRNA–mRNA regulatory network associated with uterine involution in postpartum Kazakh sheep

2021 ◽  
Vol 64 (1) ◽  
pp. 119-129
Author(s):  
Heng Yang ◽  
Lin Fu ◽  
Qifeng Luo ◽  
Licai Li ◽  
Fangling Zheng ◽  
...  
Keyword(s):  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Gene Prediction ◽  
Biological Effects ◽  
Differentially Expressed ◽  
Illumina Hiseq ◽  
Go Annotation ◽  
Uterine Involution ◽  
Differentially Expressed Mirnas

Abstract. MicroRNAs (miRNAs) are widely expressed in different mammalian tissues and exert their biological effects through corresponding target genes. miRNA target genes can be rapidly and efficiently identified and screened by combining bioinformatics prediction and experimental validation. To investigate the possible molecular regulatory mechanisms involving miRNAs during uterine involution in postpartum ewes, we used Illumina HiSeq sequencing technology to screen for the number and characteristics of miRNAs in faster uterine involution and normal uterine involution group. A total of 118 differentially expressed miRNAs, including 33 known miRNAs and 85 new miRNAs, were identified in the hypothalamic library, whereas 54 miRNAs, including 5 known miRNAs and 49 new miRNAs, were identified in the uterine library. Screening with four types of gene prediction software revealed 73 target genes associated with uterine involution, and subsequently, GO annotation and KEGG pathway analysis were performed. The results showed that, in the hypothalamic–uterine axis, uterine involution in postpartum ewes might primarily involve two miRNA-target gene pairs, namely, miRNA-200a–PTEN and miRNA-133–FGFR1, which can participate in GnRH signal transduction in the upstream hypothalamus and in the remodeling process at the downstream uterus, through the PI3K–AKT signaling pathway to influence the recovery of the morphology and functions of the uterus during the postpartum period in sheep. Therefore, identification of differentially expressed miRNAs in this study fills a gap in the research related to miRNAs in uterine involution in postpartum ewes and provides an important reference point for a comprehensive understanding of the molecular mechanisms underlying the regulation of postpartum uterine involution in female livestock.

scholarly journals Ekstraksi Minyak Gaharu dengan Pelarut Etanol secara Maserasi

2021 ◽  
Vol 2 (2) ◽  
pp. 36
Author(s):  
Muhammad Zulfikar Luthfi ◽  
Jerry Jerry
Keyword(s):  
Particle Size ◽  
Essential Oil ◽  
Essential Oils ◽  
Economic Value ◽  
Forest Products ◽  
Microbial Infection ◽  
Physical Damage ◽  
Active Compounds

Agarwood is one of the forest products that can be utilized and has a high selling value. Agarwood contains essential oils which have many active compounds and contains a specific aromatic resin that is naturally formed as a form of defense against physical damage or microbial infection. Agarwood essential oil with good quality has a high economic value. This study aims to extract agarwood essential oil using ethanol as a solvent. The optimal yield of agarwood essential oil can be obtained by varying the particle size, the ratio of the weight of the agarwood biomass (kg) to the volume of the solvent (L), and the length of maceration (h). The results showed that the particle size of agarwood did notaffect the yield of agarwood essential oil. The results of the comparison of agarwood biomass with the volume of the solvent showed that the ratio of 1:9 (w/v) obtained the highest yield of 4.02% and the longest maceration time with the highest yield of 4.12% for 72 hours. However, 48 hours of maceration had a greater increase in yield compared to 72 hours of maceration. The increase in yield at 48 hours to 72 hours of maceration was only 0.22% when compared to the increase in yield at 24 hours to 48 hours of maceration, which was 0.56%.

scholarly journals Fourier Transform Infrared Spectroscopy Analysis Of Oil Of Menthaarvensis Grown At Sites Varying With Vehicular Traffic Loads In Lucknow City, India

2013 ◽  
Vol 2 (1) ◽  
pp. 16-25 ◽  
Author(s):  
Nidhi Prakash ◽  
Mohhamad Yumus
Keyword(s):  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Essential Oil ◽  
Fourier Transform Infrared Spectroscopy ◽  
Heavy Traffic ◽  
Economic Value ◽  
Fourier Transform Infrared ◽  
Chemical Components ◽  
Vehicular Emissions ◽  
Traffic Loads

The demand of the essential oil of mint species; widely used in food, pharmaceutical and cosmetic industries, is growing throughout the world. Owing its significance, it was felt important to know the changes in chemical characteristics of the oil, if any, for economic value when the crop of Mentha is grown near highways, railway tracks or areas having heavy traffic loads. To assess the effect of vehicular emissions on menthol (mint oil), transfer experiment study was conducted. Firstly, within the municipal premises of Lucknow city, five sites (Road stretches) were identified based on survey of Lucknow city and the available data on air pollution loads. Sites were selected which were differing from each other significantly in terms of the number of vehicles (source of pollution) plying on them but were quite similar to each other in other eco-physiological factors. On the select sites equal number of potted Menthaarvensis plants of the same age, height and vigour of saccham variety obtained from CSIR-CIMAP was kept to get exposed to auto-exhaust pollutants for one year. Irrigation regime at all sites was kept uniform to avoid the influence of any other variable other than vehicular emissions. An analysis of hydro-distillated essential oil of Menthaarvensis variety Sascham under FTIR (Fourier Transform Infrared Spectroscopy) revealed some qualitative changes in the organic-compounds of the oil from plants grown at sites of Lucknow city loaded with high vehicular load (auto-exhaust pollutants) over plants kept under relatively pollution free site. Several indicator bands that are pertained to functional groups represent chemical components or metabolic products. The quantity of the peppermint oil extracted from plants of site having highest traffic loads, in turn maximum ambient pollutants (NO2, SO2, O3, SPM & RSPM) was also found less as compared to plants grown in less polluted site. International Journal of Environment, Volume-2, Issue-1, Sep-Nov 2013, Pages 16-25 DOI: http://dx.doi.org/10.3126/ije.v2i1.9204

scholarly journals Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

2014 ◽  
Vol 15 (1) ◽  
pp. R9 ◽  
Author(s):  
Thalia A Farazi ◽  
Jelle J ten Hoeve ◽  
Miguel Brown ◽  
Aleksandra Mihailovic ◽  
Hugo M Horlings ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mirna Target ◽  
Molecular Subtypes ◽  
Target Regulation

scholarly journals Immune-Related lncRNA Risk Signatures Predict Survival of IDH Wild-Type and MGMT Promoter Unmethylated Glioblastoma

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Xiaozhi Li ◽  
Yutong Meng
Keyword(s):  
Prognostic Factors ◽  
Cox Regression ◽  
Wild Type ◽  
Tumor Treatment ◽  
Cox Regression Analysis ◽  
Mgmt Promoter ◽  
Ppar Signaling ◽  
Risk Scoring ◽  
Regulation Mechanisms ◽  
Malignant Grade

Introduction. Glioblastoma is the most malignant grade of glioma, and it is also the most common primary tumor in the brain. Immunotherapy is a kind of precise tumor treatment. However, there are limited studies about immune-related lncRNA. This study is aimed at analyzing immune-related lncRNAs in glioblastoma and screening out prognostic factors, providing new potential targets for glioblastoma immunology research. Material and Methods. Gene expression data and clinical data of IDH wild-type with MGMT promoter unmethylated glioblastoma were acquired from the TCGA and CGGA databases. Immune-related lncRNAs were identified with the help of data from the InnateDB database. Immune prognostic factors were recognized by Cox regression analysis. GSEA analysis pursued their potential functions. Results. We found 318 immune-related lncRNAs. Among them, there were 137 immune-related lncRNAs that were upregulated and 181 that were downregulated. 15 prognostic lncRNAs were identified by Cox regression, and a total of 6 molecules were included in the following risk scoring model. GSEA showed that these lncRNAs participated in functions such as protein digestion and absorption and the PPAR signaling pathway. Conclusion. There are limited studies about immune regulation mechanisms of lncRNA in IDH wild-type with MGMT promoter unmethylated glioblastoma. The identified immune-related lncRNAs in glioblastoma might contribute new targets and research directions for immunological molecular studies of glioblastoma.

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