http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/158 Mon, 06 Apr 2026 10:10:52 GMT 2026-04-06T10:10:52Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4723 Molecular Basis of the Pelvi-Ureteric Junction Obstruction in Children with Hydronephrosis SHADRUL ALAM, MOHAMMED ABSTRACT: Background: Pelvi-Ureteric Junction Obstruction (PUJO) represents a significant cause of congenital hydronephrosis that can lead to progressive renal damage if untreated. While the condition is well-characterized clinically, its molecular pathogenesis remains poorly understood. This study aimed to identify key genetic alterations in PUJO through comprehensive transcriptomic analysis. Methods: We conducted a prospective study from January 2016 to December 2023 involving 9 pediatric patients (18 tissue samples) undergoing Anderson-Hynes pyeloplasty. Paired samples were collected from stenotic PUJ segments and adjacent normal ureteral tissue. RNA sequencing was performed followed by bioinformatic analysis to identify differentially expressed genes (DEGs) and pathway enrichment. Clinical parameters including demographics, presentation, and postoperative outcomes were systematically recorded. Results: The cohort showed male predominance (3.5:1 ratio) with mean age 40.22±32.61 months and left-sided predominance (77.8%). Key clinical presentations included abdominal distension (55.6%) and urinary tract infections (33.3%). Postoperative complications occurred in 22.2% cases. Transcriptomic analysis revealed 590 significant DEGs (292 upregulated, 298 downregulated), with notable enrichment in neuroactive ligand-receptor interactions (141 genes) and olfactory transduction pathways (50 genes). Chromosomal analysis identified 29 enriched regions, particularly on chromosomes 19, 17, and 9. Key dysregulated genes included KRT8 (upregulated) and SEMA3F (downregulated), implicating defects in smooth muscle differentiation and ureteral development. Conclusion: This first Bangladeshi transcriptomic study of PUJO identifies distinct molecular signatures involving neural signaling, ion transport, and developmental pathways. The findings provide novel insights into PUJO pathogenesis and potential biomarkers for early diagnosis. These results establish a foundation for developing targeted therapies to prevent renal damage in affected children. This thesis is submitted for the degree of Doctor of Philosophy. Wed, 05 Nov 2025 00:00:00 GMT http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4723 2025-11-05T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4684 Impacts of pathogenic mutations and XmnI polymorphism on the severity of haemoglobin E β-thalassaemia patients in Bangladesh Aziz, Md. Abdul Background: Haemoglobin E β-thalassaemia is a common blood disorder in South Asia, especially Bangladesh. The disorder can range from mild and asymptomatic anemia to life-threatening anemia. Patients with asymptomatic anemia do not require blood transfusions in their lifetime. Mild Hb E beta thalassaemia patients require occasional blood transfusions. However, patients with life-threatening anemia need frequent blood transfusions. The presence of XmnI polymorphism with specific mutation led to a delay of blood transfusions, higher haemoglobin levels, better response to hydroxyurea treatment, and milder phenotypic presentation among Hb E β thalassaemia patients. Aims: The aim of this study is to examine how the HBB gene mutations and the XmnI polymorphism affect the severity and transfusion needs of haemoglobin E β thalassaemia patients. Methodology: In this study, a total of 360 Hb E β-thalassaemia patients were included. The seven common HBB mutations in Bangladesh were detected by amplification refractory mutation system (ARMS) method, and rare/novel mutations were detected by Sanger sequencing. Moreover, XmnI (PdmI) restriction site was detected by XmnI (PdmI) restriction enzyme digestion. Results: Among the subjects in this research, 62.5% (n=225) were regular transfusion dependent, 22.8% (n=82) were occasionally transfusion-dependent, 8.1% (n=29) were one-time transfusion patients, and 6.7% (n=24) were transfusion-independent patients. This study identified a total of thirteen pathogenic mutations among the 360 Hb E β thalassaemia patients. The most common mutation was IVS 1-5 (G>C), accounting for 57.8% (n=208) of cases, followed by Fr 41/42(-CTTT) 12.2% (n=44), codon 30 (G>C) 8.3% (n=30), Fr 8/9 (+G) 7.5% (n=27), codon 16 (-C) 3.9% (n=14), and codon 15 (G>A) 2.8% (n=10). The study also identified six rare mutations, including -90(C>T) 3.1% (n=11), IVS-I-130(G>A) 3.1% (n=11), IVS II-654 (C>T) 0.6% (n=2), and -30 (T>C) 0.3% (n=1), codon 14/15 (+G) 0.3% (n=1) and -29 (A>G) 0.3% (n=1). Of these, -29 (A>G) had not been reported previously in Bangladesh. Page | v This study found that those with codon 16 (-C) mutation required regular transfusions, while those with codon 30 (G>C) mutations had the least transfusion dependency (6.7%). Patients with codon 30 (G>C) mutations had the highest response to hydroxyurea therapy (76.7% (n=23)) (p=0.051), while patients with Codon 16 (-C) mutations had the lowest response (0% (n=14)) (p=0.057). Codon 16 (-C) mutation was associated with the least HbF (mean ± SD= 24.8±7.7%), while codon 30 (G>C) mutation was associated with the highest HbF (mean ± SD= 41.9±16.10%). Regarding XmnI polymorphism, Codon 16 (-C) mutation was associated with the highest wild type (-/-) (n=11) genotype (p=0.153), while codon 30 (G>C) mutation was associated with the highest homozygous mutated (+/+) (n=11) and the least wild type (-/-) (n=4) of XmnI polymorphism genotype (p=0.157). Conclusion: The outcomes of this study will be useful for developing treatment strategies involving HU therapy and for managing Hb E β-thalassemia patients in Bagladesh. This thesis is submitted for the degree of Doctor of Philosophy. Mon, 07 Jul 2025 00:00:00 GMT http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/4684 2025-07-07T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/3591 Metabolomics Profiling for Amino Acidopathies of Infants in Hospital Based Settings in Bangladesh and Development of Easy-to-Use Kit for Disease Diagnosis and Monitoring Hossain, Md. Shawkat This study aimed to address the challenges associated with identifying inborn errors of metabolism (IEM) in resource-constrained environments, focusing on amino acid and galactose metabolism disorders in the Bangladeshi infant population. Liquid Chromatography Mass Spectrometry (LC-MS) is a robust diagnostic tool but faces limitations due to cost, complexity, and accessibility. Therefore alternative approaches, including enzyme assays, genetic testing, and metabolite profiling, were explored for effective IEM detection. In pursuit of an affordable diagnostic solution, a low-cost kit was developed for early detection and intervention of amino acid and galactose-related disorders. A validated HPLC-based method was established for accurate quantification of amino acids. The method exhibited strong linearity (R2 = 0.9999) and high accuracy (99.10% average recovery), establishing its suitability for amino acid analysis. Precision was confirmed through repeatability and intermediate precision tests, with low RSD values (0.30% to 1.53% and 0.23% to 0.66%, respectively). Amino acid cutoff ranges were determined for the Bangladeshi population using the validated HPLC method. Noteworthy variations in amino acid counts were observed in positive samples, emphasizing the importance of accurate cutoff values. A lateral flow paper-based diagnostic kit was designed for phenylalanine detection, offering a cost-effective means for phenylketonuria (PKU) monitoring. The kit demonstrated a minimum detection limit of 2 mg/dL, catering to PKU therapy needs. The study also concentrated on Galactosemia as a model disorder, underlining the necessity of early intervention. Molecular analysis of the GALT gene unveiled specific mutations in the Bangladeshi population, contributing to Galactosemia's molecular diversity. Evaluation of silent mutations' impact on splicing shed light on potential gene expression and protein function alterations, influencing Galactosemia outcomes. An easy-to-use lateral flow diagnostic kit for Galactosemia was developed, showing specificity for galactose and delivering rapid results within 5 minutes. Stability assessment revealed promising results at 2-8°C storage over a year, with signal degradation at higher temperatures, emphasizing proper storage conditions. The study highlights the potential of the HPLC method for amino acid detection, paving the way for accessible and cost-effective amino acidopathy detection facilities. The Galactosemia kit, with further refinement, holds promise for broader use. Insights into alternate GALT gene splicing patterns provide avenues for therapeutic exploration. Future research should fine-tune kits and establish precise phenylalanine and galactose cutoff ranges for the Bangladeshi population, contributing to improved IEM management. A DESSERTATION SUBMITTED TO THE UNIVERSITY OF DHAKA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN GENETIC ENGINEERING AND BIOTECHNOLOGY. Sun, 09 Feb 2025 00:00:00 GMT http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/3591 2025-02-09T00:00:00Z http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/1747 Inborn errors of metabolism screening and profiling of amino acids, acylcarnitines and glucose-6-phosphate dehydrogenase deficiency in Bangladesh population Sarker, Suprovath Kumar Similar to other lower and lower middle income countries, Bangladesh is facing the accelerated demographic shift from communicable diseases to non-communicable diseases (NCDs) including genetic disorders (GDs). Approximately 10,000 single-gene disorders have been identified which affects millions of people worldwide. One of the major categories of phenotypically and genotypically heterogeneous group of genetic disorders are inborn errors of metabolism (IEM). Liquid Chromatography tandem mass spectrometry (LC-MS/MS) is commonly used for the diagnosis of more than 30 IEM. Accurate and reliable diagnosis of IEM by quantifying amino acids (AAs) and acylcarnitines (ACs) using LC-MS/MS systems depend on the establishment of age-specific cut-off values of the analytes for the population under investigation. Thus, the first objective of the study was to (1) determine the age-specific cut-off values of AAs and ACs in Bangladesh and (2) validate the LC-MS/MS method for diagnosis of the patients with IEM. A total of 570 healthy participants were enrolled in this study. They were divided into 3 age groups, namely, (1) newborns (1-7 days), (2) 8 days–7 years, and (3) 8–17 years, to establish the age-specific cut-offs for AAs and ACs. In addition, 273 suspected patients with IEM were enrolled to evaluate the reliability of the established cut-off values. Among these patients, nine cases came out as screening positive by LC-MS/MS and seven cases were confirmed by urinary GC-MS analysis including 3 cases with phenylketonuria, 1 with methylmalonic acidemia, 1 with isovaleric acidemia, 1 with citrullinemia type II, and 1 with carnitine uptake defect. Two borderline positive cases with medium-chain acyl-CoA dehydrogenase deficiency were negative by urinary GC-MS analysis. The second objective of the study was to detect mutations in glucose-6-phosphate dehydrogenase (G6PD) gene that are responsible for G6PD deficiency in Bangladeshi individuals because G6PD deficiency is also very common like IEM in the Indian subcontinent. Among 121 clinically suspected patients, 12 (11 males and one female) patients were found to be G6PD deficient, suggesting the frequency of G6PD deficiency among suspected patients is 9.9%. Sanger sequencing revealed c.C131G substitution (exon-3: Ala44Gly) in six samples, c.G487A substitution (exon 6: Gly163Ser) in five samples and c.G949A substitution (exon-9: Glu317Lys) in the coding sequence in one sample. From the study, it appears that Ala44Gly and Gly163Ser are the most common G6PD mutations in Bangladesh The third objective of the study was to establish a real-time PCR-based approach called high-resolution melt (HRM) analysis as a rapid and reliable method for the detection of G6PD variants in heterozygous females. Although hemizygous males and homozygous females are easily detected by the conventional G6PD enzyme assay method, the heterozygous state can be missed by the conventional methods as the mosaic population of both normal and deficient RBCs circulate in the blood. Sixty-three clinically suspected females were evaluated for G6PD status using both enzyme assay and HRM analysis. Four out of sixty-three participants came out as G6PD deficient by the enzyme assay method, whereas the HRM approach could identify nine participants with different G6PD variants, namely one homozygous and eight heterozygous. In conclusion, along with the establishment of a validated LC-MS/MS method for the quantitation of amino acids and acylcarnitines from the DBS cards, the study also demonstrates the presence of predominant IEM in Bangladesh. In addition, this study is the first report for the underlying genetic defects of the G6PD gene that causes G6PD deficiency in the Bangladeshi population and the establishment of a rapid and reliable HRM-based method for identification of G6PD variants among heterozygous females in Bangladesh. THIS DISSERTATION SUBMITTED TO THE UNIVERSITY OF DHAKA IN PARTIAL ULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF HILOSOPHY IN GENETIC ENGINEERING AND BIOTECHNOLOGY. Sun, 29 Aug 2021 00:00:00 GMT http://reposit.library.du.ac.bd:8080/xmlui/xmlui/handle/123456789/1747 2021-08-29T00:00:00Z