Saudi Cultural Missions Theses & Dissertations
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Item Restricted The Impact Of Dilated Cardiomyopathy on Cell-Type Diversity and Gene Expression(The University of Manchester, 2024) Alammari, Eman; Eales, James; Eales, JamesBackground: Dilated cardiomyopathy (DCM) is a leading cause of heart failure characterised by enlarged ventricles and reduced cardiac function. Despite advancements, understanding the cellular and molecular processes related to DCM remains challenging. Objectives: This study uses single-cell transcriptomics to identify unique gene expression patterns and cellular diversity in DCM to improve patient stratification and clinical care. Methods: Publicly available single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) data from normal cardiac tissues and DCM patients were obtained from the GEO dataset GSE183852. The analysis included 269,794 samples from 45 participants, comprising 36,488 DCM cells, 66,669 DCM nuclei, 12,554 healthy cells, and 154,083 healthy nuclei. Data analysis involved quality control, normalisation, data integration, dimensionality reduction, clustering, DE analysis, and Gene set enrichment analysis (GSEA). Results: Principal component analysis identified 50 principal components. Unsupervised cluster annotation revealed 21 cell types in nuclei samples and 15 in cell samples. The analysis showed an underrepresentation of cardiomyocytes in the scRNA samples. Cell composition analysis demonstrated significant differences in cell type abundance between DCM and healthy tissues, including an increased ratio of fibroblasts in DCM and a decrease in cardiomyocytes. DE analysis identified several significant differentially expressed genes (DEGs), MYH6. DEGs were shown to overlap with well-known DCM genes from the PannelApp list. GSEA validated the enrichment of our genes in DCM-associated pathways; moreover, a strong trend of downregulation of many critical pathways was found across many cell types, including metabolic and energy pathways. Conclusion: Despite some limitations of single-cell technology in preserving certain cardiac cell types, the analysis revealed significant differences in cell type abundance and DE profile between healthy and DCM samples. This discovery of distinct gene expression patterns in DCM samples compared to healthy individuals presents potential diagnostic and therapeutic targets, offering hope for improved patient outcomes.6 0Item Restricted Comparative genomic analysis and evolutionary study of repetitive DNA for estimating variation and mobility(University of Leicester, 2024-09) Alwadani, Khawla; Heslop-Harrison, PatRepetitive DNA sequences, motifs repeated hundreds, thousands of times in the nuclear genome, represent typically half of the DNA and are some of the most rapidly evolving sequences. The objective of this study was to see how repetitive sequences differ and evolve between and within the wider Polygonaceae family and Malus domestica species. High volume DNA sequence reads from 12 Polygonaceae species were analysed using individual graphbased repeat clustering, revealing substantial differences in amount and composition of TEs. Many genus-specific repetitive elements were found in the comparative clustering of 21 samples, notwithstanding the close relationship of the genera. The repetitive sequence landscape was characterised among three apple cultivars. Repetitive DNA represents some 45 % of the apple genome. Graph-based sequence-read clustering showed the amount and genome composition of TEs with genome-wide dispersal was similar in various apple cultivars. LTR-retrotransposons were the most abundant, and similar Ty1-copia and Ty3-gypsy proportions. Analysis of in situ hybridisation to chromosomes was used for localisation of the various repetitive elements (including the 5S and 45S rDNA loci) and comparing abundance and organisation with published genome assemblies and unassembled raw sequence reads. In apple fruit, sectors of different colours are occasionally observed, just in the skin (peel) of the apple. The colour sectors arise from movement of TEs around the MYB transcription factor, giving rise to different expression of anthocyanin genes and hence pigmentation. Genomic DNA (c. 12-fold genome coverage) from the skin sectors was analysed. Notably, Gala is heterozygous for a key MYB gene. Insertional polymorphisms were identified in or around the MYB genes between the sectors and rest of the fruit, showing that DNA sequence movement was likely to cause the colour differences.44 0Item Restricted A Comprehensive Bioinformatics Analysis of the Proteomic Landscape and Therapeutic Potential of EDIL3-Enriched Extracellular Vesicles Derived from Y201 Mesenchymal Stromal Cells(University of York, 2024) Almelabi, Rahaf; Genever, PaulMesenchymal stromal cells (MSCs) are recognised for their regenerative capabilities, but their clinical application is often limited by cellular heterogeneity. Recent research highlights the therapeutic potential of extracellular vesicles (EVs) as key mediators of MSC function, facilitating intercellular communication and modulating various biological processes. This research investigates the proteomic landscape of EVs derived from Y201 MSCs, focusing on EDIL3, a prominent protein implicated in the pathogenesis of osteoarthritis. To achieve this, we employed a comprehensive bioinformatics pipeline that included pathway enrichment analysis, network construction, Matrisome protein classification, and functional enrichment. Our findings revealed significant enrichment in focal adhesion (FA) pathways, emphasising the critical roles of integrins and their interactions with proteins such as EDIL3. A core protein module consisting of EDIL3, MFGE8, and ITGB5 was identified, with functional annotation confirming the enrichment of the coagulation factor 5/8 C-terminal domain within this core module. Additionally, the potential role of Y201 EVs in OA pathogenesis was explored, particularly through EDIL3's involvement in pathways related to collagen-containing extracellular matrix and coagulation processes. This research enhances our understanding of EV heterogeneity and the specific contributions of individual proteins in mediating the therapeutic effects of Y201 MSCs. In conclusion, by linking the properties of Y201 MSC EVs, particularly the presence of EDIL3, integrins, and collagen proteins, we established a more comprehensive theoretical framework for further investigation into the therapeutic potential of Y201 MSC EVs by targeting specific pathways involved in OA progression.8 0Item Restricted The Detection of transmembrane domains of Nucleocytoplasmic Large DNA Viruses(University of Exeter, 2024-08) Almutairi, Adel; Monier, AdamIt is estimated that transmembrane proteins (TMPs) represent 20-30% of all proteins encoded by a given genome, and they constitute 60% of current drug targets. These proteins participate in cell signaling, forming the integrity of the cellular membrane, and transporting substances across the cell membrane. In addition, TMPs have exhibited high conservation levels within distantly related members of the tree of life, making them valuable for tracing ancestral history. Not alone the most abundant entities, viruses also rely on TMPs in many pivotal functions, including viral fusion and entry, replication, along with maintaining their envelopes (if present). Nucleocytoplasmic Double stranded DNA Viruses (NCLDVs) have large virion sizes and extensive genome lengths compared to other viruses, which prompted scientists to reevaluate the concept of viruses and delve deeper into their evolutionary history. TMPs are one of the most critical fields in virology, which was invaluable in the recent pandemic of corona virus. Although the identification of TMPs through experimental approaches is highly accurate and precise, it is extremely time-consuming and costly. The development of computational power and tools facilitated studying proteomics, specifically TMP detection and evolution. In this study, we adapted a comprehensive workflow to catalog TMPs in NCLDVs, trace their evolution history, and annotate poorly annotated TM proteins with structural predictions.8 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08-30) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.13 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.29 0Item Restricted Characterisation of peroxisomes in the fission Yeast Schizosaccharomyces pombe and slime mold Dictyostelium discoideum(University of Sheffield, 2024-02-05) Alhammad, Yousef Mohammed A.; King, Jason; Hettema, Ewald; Watts, DonaldPeroxisome is a compartment that is found in most eukaryotic organisms' cells. It has several crucial roles, such as fatty acid beta (β) oxidation and hydrogen peroxide (H2O2) detoxification. It contains many essential enzymes, including oxidase and catalase, and has several metabolic and non-metabolic pathways, depending on the environment and the organisms within its cells. This study investigates the role of peroxisomes in two organisms, S. pombe and D. discoideum. Although S. pombe is a well-studied yeast, there is only one study of this yeast that has focused on peroxisomes. This study offers a few crucial observations, including that S. pombe contains peroxisomes, that GFP containing a well-characterized PTS1 (SKL) is efficiently imported, and that peroxisome numbers increase in cells grown on a fatty acid as the sole carbon source, suggesting a role for peroxisomes in fatty acid degradation. The starting point in my research was initially a bioinformatics screen. This screening recognized the enzymes imported into peroxisomes based on the presence of a potential peroxisomal targeting signal. A few proteins were found. However, the low number of proteins with a classical PTS might be the result of different targeting signals that are not recognized by our bioinformatics parameters. Indeed, in other organisms, there are proteins without PTS1 that still use Pex5 for import. The first example is S. cerevisiae Acyl-CoA oxidase. In a global yeast two-hybrid screen, S. pombe Pex5 was found to bind S. pombe Str3 and Lys3. Consequently, we think that there is conserved targeting of a peroxisomal protein lacking a PTS1 and PTS2 imported into the peroxisome by Pex5. One of these is the Str3 case. Interestingly, proteins involved in peroxisomal fatty acid β -oxidation are absent from the S. pombe genome, casting doubt on the conclusions from the previous study and explaining the low number of potential peroxisomal enzymes. In D. discoideum, this study investigates the dynamic regulation of peroxisome numbers in response to growth conditions and identifies peroxisomal import and contents through a proximity labeling approach (BioID). Overall, this study sheds light on the roles and regulation of peroxisomes in these two organisms.35 0Item Restricted Computational Analysis of Antibody Binding Mechanisms to the Omicron RBD of SARS-CoV-2 Spike Protein: Identification of Epitopes and Hotspots for De opes and Hotspots for Developing E eloping Effective Therapeutic apeutic Strategies.(2023-05) Alshahrani, Mohammed Rajeh; Verkhivker, GennadyThe advent of the Omicron strain of SARS-CoV-2 has elicited apprehension regarding its potential influence on the effectiveness of current vaccines and antibody treatments. The present investigation involved the implementation of mutational scanning analyses to examine the impact of Omicron mutations on the binding affinity of four categories of antibodies that target the Omicron receptor binding domain (RBD) of the Spike protein. The study demonstrates that the Omicron variant harbors 23 unique mutations across the RBD regions I, II, III, and IV. Of these mutations, seven are shared between RBD regions I and II, while three are shared among RBD regions I, II, and III. The findings suggest that the mutations exert a noteworthy influence on the antibodies' binding affinity, especially in Class II and Class III antibodies. Among the mutations, those located at positions R346, L452, and F490 appear to have a particularly notable impact. Multiple mutations were detected at positions F375, Y501, and H505 across all sub-variants of Omicron, indicating their potential significance in evading the immune system. The mutations could potentially bear significant ramifications with regards to immune evasion. The research underscores the significance of continuous observation and scrutiny of viral mutations in order to guide the creation of efficacious treatments for novel strains of SARS-CoV-2.12 0Item Restricted Computational Prediction of pH-Dependent Binding Energies in HPV Capsid Antibody Interactions(ProQuest, 2023-04-13) Alqarni, Amjad Mahdi; Joshua L. PhillipsHPV is the most common sexually transmitted infection in the world. In high-risk types, HPV infection is associated with virtually all cervical cancers and a significant proportion of anogenital and oropharyngeal cancers. Neutralizing antibodies can prevent HPV infection with their effectiveness depending on the way they interact with HPV capsid proteins. The ability of antibodies to attach to capsid proteins is influenced by pH variations, which can impact the characteristics and stability of both the viral capsid and the antibody. In this thesis, we apply a computational simulation pipeline to predict the pH- dependent binding energies in HPV capsid-antibody interactions. Our results predict that there is a strong preference for binding to antibody 28F10 for HPV subtypes 6, 16, 18, 33, and 58 while A12A3 shows a strong preference for HPV 35 and 59. The results also predict that both antibodies bind non-preferentially to the HPV 11 capsid.26 0