National University Biomedical Research Institute (NUBRI)
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Item Extraction and Identification of Fungi from Different Sudanese Soil(Journal of Measurement Science & Applications, JMSA, 2024) Ibrahim, Nesreen A. A.; Saeed, Humodi A.; Saeed, Samar M.; Ibrahim, Sabah A. E.; Mohamed, Sofia B.; Ahmed, Mohamed E. N.The biosynthesis process utilizing fungi and other microorganisms is an essential sustainable method for the manufacture of nanomaterials, aligning with sustainable development goals. Consequently, the extraction and accurate identification of fungi from soil is strongly advised. In this study, various fungus species were collected from different Sudanese agricultural soil at various locations. Afterwards, the fungi were extracted and identified. The fungi have been isolated were then identified to the genus level and to the species according to the basis of macro morphological. Thus, the colonies were investigated for slow or for rapid growth, also based on topography and texture. Interestingly, the identification methods used for fungi isolated displayed that various fungi have been successfully identified. Thus, based on the culture method, there are fungal species of 121 species with 100% were recognized. However, based on the microscopic investigation there are 102 species of fungal species were identified. However, based on the molecular method the identified fungi were found to be 90 of the fungal species isolated.Item The impact of mutations on TP53 protein and MicroRNA expression in HNSCC: Novel insights for diagnostic and therapeutic strategies(PLOS One, 2025) Mahmoud, Ashraf Attia; Raih, Mohd Firdaus; Sage, Edison Eukun; Ali, Qurashi M.; Suliman, Omnia H.; Ibrahim, Sabah A. E.; Mohamed, Osama; Abdelrazeg, Samar; Mohamed, Sofia B.The tumor suppressor protein p53 (TP53) is frequently mutated in various types of human malignancies, including HNSCC, which affects tumor growth, prognosis, and treatment. Gaining insight into the impact of TP53 mutations in HNSCC is crucial for developing new diagnostic and therapeutic methods. In this study, we aimed to investi gate the influence of mutations on the structure and functions of the TP53 protein and miRNA expression using computational analysis. The genomic data of patients with HNSCC were obtained from TCGA, and the impact of mutations on the TP53 gene was investigated using different bioinformatics tools. Results: The findings showed that the TP53 mutations increased TP53 expression levels in HNSCC and were associated with a poor prognosis. Furthermore, hsa-mir-133b expression was reduced in TP53- mutated samples, significantly affecting patient survival in HNSCC. Six mutations, including R273C, G105C, G266E, Q136H/P, and R280G, were identified as delete rious, carcinogenic, driver, highly conserved, and exposed. These mutations were located in the P53 domain, and PTM analysis revealed that R280G and R273C are at a methylation site, and R273C, Q136H/P, and R280G are located in the protein pocket. The docking research indicated that these mutations decreased the binding affinity for DNA, with R273C, R280G, G266E, and G105C displaying the most significant differ ences. The molecular dynamics analysis indicates that R280G, Q136H, and G105C mutations confer a gain of function by stabilizing the TP53-substrate complex. Conclu sions: Based on the research findings, the mutations on TP53 were found to have an impact on protein and miRNA expression, development, survival, and progression of HNSCC patients, and has-mir-133b could be a promising novel biomarker for mon itoring the progression of HNSCC. It was discovered that G105C and Q136H/P, as novel mutations, affect the function and structure of proteins causing HNSCC, which indicates that they could be interesting subjects for further investigation, diagnostics, and therapeutic strategies. Furthermore, the precise positioning of R280G and R273C within the methylation site and Q136H/P in the binding site has been documented for the first time. Moreover, the G105C, Q136H, and R280G mutations that stabi lized TP53 structure and altered its interaction dynamics with substrates may serve as novel potential diagnostic biomarkers in cancer, guiding patient stratification and personalized treatment strategies. The molecular dynamics analysis provides insights into how specific TP53 mutations impact protein structure, stability, and function upon substrate binding, highlighting their role in cancer biology and potential implications for therapeutic interventions. This paper provides a novel understanding of the mecha nisms by which these mutations contribute to the development of cancer.Item Reverse vaccinology and immunoinformatics approaches for multi-epitope vaccine design against Klebsiella pneumoniae reveal a novel vaccine target protein(Journal of Genetic Engineering and Biotechnology, 2025) Elfadil, Mayada M.; Samhoon, Samah Omer A.; Saadaldin, Moaaz M.; Ibrahim, Sabah A.E.; Mohamed, Ahmed Abdelghyoum M.; Suliman, Omnia H.; Mohamed, Osama; Damiri, Nadzirah; Firdaus-Raih, Mohd; Mohamed, Sofia B.; Ali, Qurashi. M.Klebsiella pneumoniae (K. pneumoniae), a Gram-negative pathogen, is a leading cause of hospital-acquired in fections in Sudan and worldwide. The emergence of multidrug-resistant (MDR) strains has severely limited treatment options, underscoring the urgent need for an effective vaccine. In this study, we employed reverse vaccinology and immunoinformatics to design a novel multi-epitope vaccine targeting the hypervirulent NUBRI- K strain. Two conserved, non-host homologous iron acquisition proteins, IucA/IucC and FyuA, were prioritized as targets. The vaccine construct integrates six B-cell, six cytotoxic T lymphocyte (CTL), and six helper T lymphocyte (HTL) epitopes, linked by optimized spacers and fused to a β-defensin adjuvant. Computational analyses confirmed strong antigenicity (1.0429), non-allergenicity, and favorable solubility (0.477). Molecular docking revealed high-affinity binding to Toll-like receptor 4 (TLR4) ( 278.22 kcal/mol), stabilized by eight hydrogen bonds and two salt bridges. Structural validation showed that 91 % of residues were located in favored regions of the Ramachandran plot. Additionally, CABSflex 2.0 dynamics analysis confirmed stable vaccine–TLR4 interactions, with minimal residue-level fluctuations (RMSF <1.5 Å), indicating conformational stability of the complex. In silico immune simulations predicted potent humoral and cellular responses, including elevated IgG/ IgM titers, T-cell proliferation, and IFN-γ secretion. The construct was further optimized for mammalian expression, achieving an ideal GC content (48.27 %) and a codon adaptation index (CAI) of 1.0, facilitating efficient in silico cloning into the pcDNA3 vector. By targeting conserved iron acquisition systems, this vaccine candidate presents a promising strategy to combat antibiotic-resistant K. pneumoniae while minimizing selective pressure. Future in vitro and in vivo studies are warranted to validate its immunogenicity and protective efficacy