University of Colombo e-Repository

UCER (University of Colombo Electronic Repository) is a collection of scientific research publications by researchers at the University of Colombo, Sri Lanka. This e-Repository serves to manage, preserve and make available the academic works of the faculty, postgraduate students, and research groups. The collection includes faculty publications, master's and doctoral theses abstracts. This repository is updated regularly, and new works are added to collections on a continuous basis

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Recent Submissions

Anti-glycemic activity of ethanolic extract and essential oils obtained by solvent-free microwave extraction and hydro-distillation of rhizomes and leaves of Alpinia calcarata Roscoe
(University of Colombo, 2025) Aazif, N.M.T.; Samarasekera, J.K.R.R.; Liyanaarachchi, G.D.; Fernando, N.
Alpinia calcarata Roscoe is a rhizomatous herb used in Ayurveda and traditional Sri Lankan indigenous medicine for treatment of metabolic disorders, including diabetes. Although its anti-diabetic properties have been preliminarily investigated, comprehensive studies evaluating the glycemic regulatory properties of both rhizomes and leaves have not been reported. This study evaluated the anti-glycemic activity of rhizomes and leaves of A. calcarata ethanolic extracts (EE) and essential oils (EOs) obtained by hydro-distillation (HD), and Solvent-Free Microwave Extraction (SFME). HD was performed with a Clevenger apparatus, while SFME used a NEOS GR microwave extractor to obtain EOs. EEs of rhizomes and leaves were obtained following standard protocols. Anti-glycemic activity of EOs and EEs were assessed through α-glucosidase and α-amylase inhibition, and an advanced glycation end product (AGE) formation assay with acarbose as the positive control. The leaf EE exhibited the highest α-glucosidase inhibitory activity (IC₅₀ = 7.05 ± 0.37 μg/mL), followed by the rhizome EE (IC₅₀ = 23.79 ± 0.56 μg/mL) and both were more active than the standard drug acarbose (IC₅₀ = 430.55 ± 0.14 μg/mL). α-amylase inhibitory activity of the rhizome EE was notably higher IC₅₀ = 5.70 ± 0.09 μg/mL) compared to acarbose (IC₅₀ = 76.28 ± 0.25 μg/mL). In contrast, the EOs extracted by HD and SFME showed weak inhibition in both enzyme assays, with inhibition values below 10% at 500 μg/mL. However, in the anti-AGE formation assay, EOs from leaf HD (13.08 mg RE/g) and leaf SFME (10.17 mg RE/g) showed higher inhibition compared to leaf EE (4.5 mg RE/g) and rhizome EE (3.42 mg RE/g). The EEs of A. calcarata rhizomes and leaves are rich in bioactive compounds and indicate strong anti-hyperglycemic effects. Additionally, the moderate anti-AGE activity observed in the EOs may further enhance therapeutic potential of this plant. Overall, these results highlight A. calcarata as a promising candidate for studies to identify phytochemicals, isolation and characterization of bioactive constituents and in vivo studies for development of natural anti-diabetic formulations.
Diagnostic value of BAT-25 and BAT-26 qPCR markers for microsatellite instability in colon cancer
(University of Colombo, 2025) Yadeeshani, H.D.L.; Abeysuriya, V.; Rajagopalan, U.; Abeysuriya, V.; Akram, F.N.
Colon cancer is a leading cause of cancer-related morbidity and mortality worldwide. Microsatellite instability (MSI), reflecting deficient DNA mismatch repair, is present in a subset of colon cancers and may serve as a useful diagnostic marker. This study aimed to detect MSI in colon cancer patients by analyzing BAT-25 and BAT-26 microsatellite markers using quantitative PCR (qPCR) in a Sri Lankan cohort. In a cross-sectional design, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissues of ten patients who were confirmed as colon cancer patients by histopathological investigations. Five patients whose biopsy samples were confirmed negative for colon cancers, colon or rectal polyps were selected as controls. Comorbidities which effect the MSI status were not reported in the cohort. qPCR was performed to determine cycle threshold (Ct) values for BAT-25 and BAT-26. Group comparisons used t-tests, Mann-Whitney U, and ANOVA as appropriate. Logistic regression assessed the diagnostic potential of Ct values. ROC analysis determined the discriminatory performance of BAT 25 and BAT-26. Both BAT-25 and BAT-26 showed significantly different Ct values between patients and controls (p < 0.05). Lower (more negative) BAT-25 and BAT-26 values were associated with earlier T, N, and M stages. Logistic regression identified BAT-25 as a significant predictor of patient status (p = 0.041, OR = 0.82, 95% CI: 0.50–0.94). ROC analysis showed good discriminatory power for both markers, with area under the curve (AUC) values of 0.72 (BAT-25) and 0.80 (BAT-26), and specificity up to 80% in BAT 25 and 100% for BAT-26. qPCR-based analysis of BAT-25 and BAT-26 effectively distinguishes colon cancer patients from controls and correlating with disease stage. These findings support the utility of BAT-25 and BAT-26 as molecular markers for MSI detection in colon cancer, with potential diagnostic applications in clinical practice.
A preliminary study targeting exon 12 MSH2 mutations in FFPE rectal tumors: feasibility and challenges
(University of Colombo, 2025) Nufla, M.A.F.; Yadeeshani, H.D.L.; Abeysuriya, V.; De Silva, S.; Abeysuriya, V.
Rectal cancer constitutes a major burden of colorectal malignancies in Sri Lanka. Despite growing disease burden, Sri Lanka lacks molecular data and genomic profiles, particularly on Mismatch repair (MMR) gene mutations. MSH2 is a frequently mutated MMR gene, associated with microsatellite instability-high (MSI-H) tumors. This pilot study explores the feasibility and limitations of detecting MSH2 exon 12 mutations using formalin-fixed paraffin-embedded (FFPE) tissue the most accessible archival resource in local clinical settings. Twelve FFPE tumor samples and four control blocks were sectioned and processed using the QIAamp DNA FFPE Tissue Kit. DNA was quantified via NanoDrop spectrophotometry and agarose gel electrophoresis. Primers targeting exon 12 (471 bp) were designed using Primer-BLAST, BioEdit, and IDT OligoAnalyzer. PCR optimization was initially conducted with high-quality blood-derived DNA, then adapted for FFPE DNA using incremental changes in annealing temperature, MgCl₂ concentration (2.0-3.5 mM), and template pre-treatment (dilution, 95 °C incubation). Amplified products were visualized, gel-purified using low-melting agarose, and sequenced via Sanger method. Blood DNA consistently yielded specific 471 bp products. In contrast, FFPE DNA yielded smeared products or weak bands, often accompanied by primer-dimers. Gel purified products from FFPE samples were successfully extracted but sequencing chromatograms showed poor peak resolution, baseline noise, and unreadable sequences, confirming insufficient template quality for Sanger sequencing. Amplification and sequencing of MSH2 exon 12 from FFPE rectal tumor DNA proved technically unviable due to extensive fragmentation and chemical modifications inherent to formalin fixation. Large-amplicon PCR from FFPE was not consistently achievable despite multi-parameter optimization, indicating that prolonged/formalin fixation and block age are dominant constraints on amplifiability in this setting. Future efforts should employ standardizing fixation, enforcing block-age thresholds shorter amplicon designs, FFPE-specific polymerases, and enzymatic repair steps to enable reliable mutation detection from archival tissue. By systematically confronting the technical barriers of FFPE tissue genomics in a Sri Lankan context, this pioneering study not only highlights the urgent need for protocol innovation but also lays the foundation for accessible, population-scale molecular diagnostics in underrepresented cancer cohorts.
Identification of genetic variants of PHEX gene in a cohort of children with hereditary hypophosphatemic rickets in Sri Lanka
(University of Colombo, 2025) Milhan, M.M.; Hewage, A.S.; De Silva, S.; Atapattu, N.
Hereditary hypophosphatemic rickets (HHR) comprises a group of rare genetic disorders characterized by renal phosphate wasting leading to chronic hypophosphatemic rickets. The most common form, X linked hypophosphatemic rickets (XLHR), arises from inactivating mutations in the phosphate regulating endopeptidase homolog X-linked (PHEX) gene, which disrupts phosphate homeostasis through dysregulation of the phosphaturic hormone FGF23. Although more than 800 pathogenic PHEX variants have been reported globally, the genetic variants in Sri Lankan patients remain unexplored. This study aimed to identify the genetic variants of XLHR in Sri Lankan pediatric patients. Eleven children clinically diagnosed with hypophosphatemic rickets underwent comprehensive evaluation, including biochemical analyses, radiological assessments, and phenotypic characterization. PCR amplification followed by targeted Sanger sequencing was performed on PHEX exons 17, 19, and 22, along with flanking intronic regions. Pathogenicity predictions were conducted using MutationTaster and SpliceAI algorithms. The index patient (Male) harboring a novel variant was diagnosed at one year and five months of age and exhibited hypophosphatemia (0.9 mmol/L, approximately 25% below the normal lower limit for age), markedly elevated alkaline phosphatase (682 U/L, nearly twofold above normal range), serum calcium within normal limits (2.31 mmol/L), and elevated parathyroid hormone (8.06 pmol/L). Radiographs revealed classic rickets features. Genetic analysis identified a novel intronic deletion variant, c.1900-31_1900-30del, within the polypyrimidine tract 30 base pairs upstream of exon 19. This two-nucleotide deletion reduces a consecutive thymine stretch from 12 to 10 bases, potentially disrupting splice acceptor site recognition and pre-mRNA splicing. MutationTaster predicted the variant as disease-causing with possible cryptic splice site generation, while SpliceAI assigned low pathogenicity scores, illustrating the complexity of non-coding variant interpretation. This is the first report of an intronic polypyrimidine tract deletion in the PHEX gene in Sri Lankan patients. The variant’s associated clinical phenotype supports its pathogenicity. Functional validation studies are needed to confirm these findings.
Synergistic anticancer potential of Andrographis paniculata and Datura metel combined with Doxorubicin in inhibiting breast cancer cells
(University of Colombo, 2025) Kanagasundaram, A.; Rajagopalan, U.
Breast cancer remains one of the prevalent malignancies affecting women worldwide. This study investigates the synergistic anticancer potential of triple-combinatorial phytotherapeutic agents, Andrographis paniculata and Datura metel, along with the chemotherapeutic drug doxorubicin (DOX), on estrogen-receptor-positive (MCF-7) and triple-negative (MDA-MB-231) breast carcinoma cells and normal breast epithelial cells (MCF-10A). The objective was to identify a synergistic drug–natural product combination that enhances cytotoxic efficacy while minimizing off-target toxicity. Sequential ultrasound-assisted extractions were performed using hexane, ethyl acetate, methanol, and aqueous ethanol. SRB-based cytotoxic screening revealed that ethyl acetate extract of A. paniculata (AP) and methanolic extract of D. metel (DM) were most potent, demonstrating IC₅₀ values at 168.2 µg/mL (MCF-7) and 90.26 µg/mL (MDA-MB-231) for A. paniculata, and 0.23 µg/mL (MCF-7) and 21.59 µg/mL (MDA-MB-231) for D. metel after 72 h, with relatively low cytotoxicity toward MCF 10A. Bioactivity-guided fractionation of A. paniculata ethyl acetate extract was performed using normal-phase column chromatography with a 10% gradient solvent system consisting of hexane and ethyl acetate. Methanolic extract of D. metel was subjected to Kupchan’s solvent-solvent partitioning to isolate active constituents. Fraction C8 of A. paniculata (AP-C8) exerted denotable cytotoxicity with IC₅₀ values at 32.99 ± 15.27 µg/mL on MCF-7 and 4.674 ± 0.73 µg/mL on MDA-MB-231 at 48 h post treatment. The chloroform fraction of D. metel (DM-F2) demonstrated the highest cytotoxicity with IC₅₀ at 16.04 ± 0.33 µg/mL and 2.535 ± 0.09 µg/mL on MCF-7 and MDA-MB-231, respectively. Triple combination treatments (DOX + AP-C8 + DM-F2) were assessed in various fixed dose ratios using the SRB assay. CompuSyn software analysis confirmed that the highest synergistic interactions were observed at a ratio of 1:64:256 on MCF-7 (combination index [CI]=0.71846) and at 1:1.25:10 on MDA MB-231 (CI=0.77291). Both combinations demonstrated higher dose reduction index (DRI) values in a favorable range, especially for DOX, indicating potential for therapeutic dose minimization. Mainly, the combinations exhibited minimal cytotoxic effects in MCF-10A cells, supporting their selective anticancer potential in the selected combination ratios.