Displaying publications 61 - 62 of 62 in total

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  1. In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions
    Ealam Selvan M, Lim KS, Teo CH, Lim YY
    J Vis Exp, 2022 Oct 21.
    PMID: 36342167 DOI: 10.3791/64565
    Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as regulators of various biological processes. Notably, emerging evidence demonstrates that host circRNAs can be differentially expressed (DE) upon infection with pathogens (e.g., influenza and coronaviruses), suggesting a role for circRNAs in regulating host innate immune responses. However, investigations on the role of circRNAs during pathogenic infections are limited by the knowledge and skills required to carry out the necessary bioinformatic analysis to identify DE circRNAs from RNA sequencing (RNA-seq) data. Bioinformatics prediction and identification of circRNAs is crucial before any verification, and functional studies using costly and time-consuming wet-lab techniques. To solve this issue, a step-by-step protocol of in silico prediction and characterization of circRNAs using RNA-seq data is provided in this manuscript. The protocol can be divided into four steps: 1) Prediction and quantification of DE circRNAs via the CIRIquant pipeline; 2) Annotation via circBase and characterization of DE circRNAs; 3) CircRNA-miRNA interaction prediction through Circr pipeline; 4) functional enrichment analysis of circRNA parental genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). This pipeline will be useful in driving future in vitro and in vivo research to further unravel the role of circRNAs in host-pathogen interactions.
    Matched MeSH terms: Gene Expression Profiling/methods
  2. Fulltext Floral micromorphology and transcriptome analyses of a fragrant Vandaceous Orchid, Vanda Mimi Palmer, for its fragrance production sites
    Toh C, Mohd-Hairul AR, Ain NM, Namasivayam P, Go R, Abdullah NAP, et al.
    BMC Res Notes, 2017 Nov 02;10(1):554.
    PMID: 29096695 DOI: 10.1186/s13104-017-2872-6
    BACKGROUND: Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known regarding the fragrance production and emission sites on the flowers.

    RESULTS: Olfactory perception detected fragrance only from the petals and sepals. Light and Environmental Scanning Electron microscopy analyses on fresh tissues showed distributions of stomata and trichomes concentrated mostly around the edges. These results paralleled the rich starch deposits and intense neutral red stain, indicating strong fragrance and trichomes as potential main fragrance release sites. Next Generation Sequencing (NGS) transcriptomic data of adaxial and abaxial layers of the tissues showed monoterpene synthase transcripts specifically linalool and ocimene synthases distributed throughout the tissues. qPCR analyses taken at different time points revealed high levels of linalool and ocimene synthases transcripts in the early morning with maximal level at 4.00 am but remained low throughout daylight hours.

    CONCLUSIONS: Knowledge of the VMP floral anatomy and its fragrance production characteristics, which complemented our previous molecular and biochemical data on VMP, provided additional knowledge on how fragrance and flower morphology are closely intertwined. Further investigation on the mechanisms of fragrance biosynthesis and interaction of potential pollinators would elucidate the evolution of the flower morphology to maximize the reproduction success of this plant.

    Matched MeSH terms: Gene Expression Profiling/methods*
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