Conference Presentations

1. Ealam Selvan, M., Lim, K. S., Teo, C. H., Lim, Y. (2022) Genome Wide Identification and Characterisation of Host Circular RNAs Involved in Monocyte-derived Macrophages in response to H1N1 Influenza A virus induced innate immune response. Paper presented at the 27th Biological Sciences Graduate Congress (BSGC), 15th-17th December 2022, Bangkok, Thailand.

2. Ealam Selvan, M., Lim, K. S., Teo, C. H., Lim, Y. (2023) Genome Wide Identification and Characterisation of Host Circular RNAs Involved in Monocyte-derived Macrophages in response to H1N1 Influenza A virus induced innate immune response. Paper presented at the 27th Biological Sciences Graduate Congress (BSGC), 14th-15th December 2023, Bangkok, Thailand.

Abstracts

Masters Thesis:

Lung epithelial cells serve as the primary entry points for influenza A virus (IAV) and play a key role in its pathogenesis. Simultaneously, IAV infection triggers the recruitment of monocytes, which differentiate into macrophages (MDM) upon entering the lungs. These macrophages express pro-inflammatory cytokines and pro-apoptotic mediators essential for IAV clearance. Circular RNAs (circRNAs) are non-coding RNA molecules that participate in various biological processes, including the regulation of innate immune responses and viral pathogenesis. While previous studies have predominantly focused on profiling and understanding the role of circRNAs in lung epithelial cells infected with H1N1 influenza A virus (IAV), no such investigations has been conducted in MDM. Here, a novel in-house pipeline, developed and benchmarked in this study for improved identification and quantification of putative circRNAs through pooled reads – referred to as CIRI2 Superdepth approach followed by CIRIquant, was employed to identify and analyse for the differential expression (DE) of circRNAs in a public RNA-seq dataset of MDM cells infected H1N1 IAV. A total of 66, 402 distinct circRNAs were detected with 2, 905 and 502 being differentially expressed (DE) at 6 hrs, 12 hrs and 18 hrs post infection (hpi), respectively. No DE circRNA was detected at 3 hpi. Most of the circRNAs, including DE, were derived from exonic regions, overlapped a single host parental gene and annotated in circBase and circAtlas databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses of DE circRNA parental genes highlighted pathways related to ubiquitination, TNF signaling, endocytosis, and chemokine signaling. In addition, a competing endogenous RNA (ceRNA) network analysis conducted through in-silico tools to explore the circRNA-miRNA-mRNA interactions, identified 129 DE circRNAs that potentially sponge 955 miRNAs, which in turn regulate 389 DE mRNAs. Functional enrichment of ceRNA-regulated mRNAs revealed GO terms and KEGG pathways associated with chemokine and cytokine signaling, mononuclear differentiation, leukocyte recruitment, and NOD-like receptor signaling. Notably, circCTSB_1, circAKIRIN2_1, and circAFF4_1 emerged as key circRNAs due to their high expression levels and the presence of multiple binding sites. Further focused analysis of the DE circRNAs associated with GO BP subontology: antiviral innate immune signaling revealed circUSP18_2_2 and several circRNAs derived from DDX58 (circDDX58_1, circDDX58_2, circDDX58_3, and circDDX58_5) as potential ceRNA regulators. GO enrichment analysis of the genes regulated by these DE circRNA suggests overall negative regulation of leukocyte development, activation and adhesion. Together, this study provides valuable insights into the circRNA landscape of MDM cells during IAV-induced innate immune response, including their characterisation, functional enrichment of parental host genes and potential downstream interactions.

Undergraduate Thesis:

Sewage effluents can carry many opportunistic bacteria (e.g., Salmonella, Shigella, Vibrio, Campylobacter and E. coli) which are capable of infecting people. Treatment of these bacterial infections is becoming more difficult due to the emergence of multidrug resistant (MDR) bacteria. However, studies concerning the antibiotic resistance patterns of bacteria in sewage effluents are very scarce in Malaysia. The aim of this study is to determine the antibiotic resistance profiles of bacteria isolated from a sewage effluent and to also determine their identity using molecular approach on 16S rRNA gene sequences phylogenetic analysis. A sample of sewage effluent was collected at a sewage located in Kuala Lumpur. Antibiotic sensitivity was ascertained using the Kirby-Bauer disk diffusion technique according to Clinical Laboratory Standards Institute (CLSI) 2019 guidelines. All 14 isolates tested were Gram negative bacteria. Out of 14 bacterial isolates, only seven isolates have undergone antibiotic sensitivity testing and showed common resistance to minocycline, ampicillin, clindamycin and vancomycin. However, only three isolates were identified where one is a novel isolate of family Pseudomonadaceae and remaining two strains are Enterobacter mori. Isolate of family Pseudomonadaceae showed the highest number of antibiotic resistances with resistance to 11 out of 15 antibiotics tested. It also showed an unusual resistance to imipenem which are usually effective against this particular bacterial family. Two strains of Enterobacter mori which are plant pathogenic bacteria were also identified. The present study showed that antibiotic resistance profiles and 16S rRNA gene sequences phylogenetic analysis of culturable bacteria from sewage effluents are needed to keep track of the growing rate of MDR bacteria.