Browsing by Author "Nor Afiqah-Aleng"

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    Protein–protein interaction network: an emerging tool for understanding fish disease in aquaculture
    (John Wiley & Sons Australia, Ltd, 2020-06) Khor Waiho; Nor Afiqah-Aleng; Mat Taib Mimi Iryani; Hanafiah Fazhan
    Protein–protein interactions (PPIs) play integral roles in a wide range of biological processes that regulate the overall growth, development, physiology and disease in living organisms. With the advancement of high-throughput sequencing technologies, increasing numbers of PPI networks are being predicted and annotated, and these contribute greatly towards the understanding of pathogenesis and the discovery of novel drug targets for the treatment of diseases. The use of this tool is gaining popularity in the identification, understanding and treatment of diseases in humans and plants. Due to the importance of aquaculture in tackling the global food crisis by producing cheap and high-quality protein source, the maintenance of the overall health status of aquaculture species is essential. With the increasing omics data on aquaculture species, the PPI network is an emerging tool for fish health maintenance. In this review, we first introduce the concept of PPI network, how they are discovered and their general application. Then, the current status of aquaculture and disease in aquaculture are discussed. The different applications of PPI network in aquaculture fish disease management such as biomarker identification, mechanism prediction, understanding of host–pathogen interaction, understanding of pathogen co-infection interaction, and potential development of vaccines and treatments are subsequently highlighted. It is hoped that this emerging tool – PPI network – would deepen our understanding of the pathogenesis of various diseases and hasten the prevention and treatment processes in aquaculture species.
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    Transcriptomics in advancing portunid aquaculture: A systematic review
    (John wiley & Sons Australia, Ltd., 2022-04) Khor Waiho; Mhd Ikhwanuddin; Nor Afiqah-Aleng; Alexander Chong Shu-Chien; Youji Wang; Hongyu Ma; Hanafiah Fazhan
    The rapid advancement of next-generation sequencing technologies has promoted the use of transcriptomics in non-model organisms, including species in the aquaculture sector. Compared to that of other crustacean species, portunid crab aquaculture is impeded by the insufficient knowledge of their biological and physiological processes. This systematic review summarised the advances in transcriptomics in cultured portunid crabs using a systematic literature review methodology. The filtered transcriptome dataset comprised 66 articles from four genera: Scylla, Portunus, Callinectes and Charybdis. At the species level, Scylla paramamosain and Portunus trituberculatus were the two most studied species, highlighting their importance in the aquaculture sector. The affordable cost of RNA sequencing (RNA-Seq) led to an increase in transcriptome-related research in portunid crabs and made available a huge repertoire of differentially expressed genes (DEGs) and single nucleotide polymorphisms (SNPs). We further discussed the transcriptomic advances based on six main functional categories, that is, ‘growth and moulting’, ‘gonadal development and reproduction’, ‘nutrition metabolism’, ‘disease and immunity’, ‘toxicology and stress’ and ‘general transcriptomic profiling’. In general, transcriptomic studies of portunid crabs, specifically the DEGs and pathways allow an in-depth understanding of the biological and physiological processes involved at different growth stages or under various conditions based on the difference in gene transcriptional activity. SNPs obtained from the transcriptome data are useful in many genetic improvementrelated downstream applications, including the construction of genetic linkage maps and as population genetic markers. Future directions, such as hybrid approaches of long-read and common RNA-Seq, and the incorporation of other omics were also discussed.