National University Biomedical Research Institute (NUBRI)

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    Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan
    (PLOS COMPUTATIONAL BIOLOGY, 2021) Mohamed, Sofia B; Kambal, Sumaya; Ibrahim, Sabah A.E.; Abdalwhab, Esra; Munir, Abdalla; Ibrahim, Arwa; Ali, Qurashi Mohamed
    The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computa tional tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on spe cific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the devel opment of bioinformatics in the country.
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    Proteomics and Docking Study Targeting Penicillin Binding Protein and Penicillin-Binding Protein2a of Methicillin-Resistant Staphylococcus aureus Strain SO-1977 Isolated from Sudan
    (Evolutionary Bioinformatics, 2019) Mohamed, Sofia B; Adlan, Talal A; Khalafalla, Nagla A; Abdalla, Nusiba; Ali, Zainab SA; KA, Abdella Munir; Hassan, Mohamed M; Elnour, Mohammed-Ahmed B
    Whole genome sequencing of methicillin-resistant Staphylococcus aureus (MRSA) strain isolated from Sudan has led to a great deal of information, which allows the identification and characterization of some pivotal proteins. The objective of this study was to investigate the penicillin-binding proteins, PBP and PBP2a, of SO-1977 strain to have insights about their physicochemical properties and to assess and describe the interaction of some phytochemicals against them in silico. PBP and PBP2a from MRSA’s Sudan strain were found to be of great resemblance with some other strains. G246E single-nucleotide polymorphism was reported and identified in the allosteric binding site positioned in the non-penicillin-binding domain. The docked compounds demonstrated good binding energies and hydrogen bond interactions with residue Ser404 which plays crucial roles in β-lactam activity. This finding would contribute significantly to designing effective β-lactam drugs, to combat and treat β-lactam–resistant bacteria in the future.
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    Genomic analysis of methicillin-resistant Staphylococcus aureus strain SO-1977 from Sudan
    (BMC Microbiology, 2019) Ali,Mohamed S; Isa,Nurulfiza M; Abedelrhman,Faisal M; Alyas,Tahani B; Mohammed,Sara E; Ahmed,Abdallah E; Ahmed,Zainab S. A; Lau,Nyok-Sean; Garbi,Mohamed I; Amirul,Abdullah Al-Ashraf; Seed,Almeen O; Omer,Rihab A; Mohamed,Sofia B
    Background: Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA’s virulence and resistance mechanisms is a continuing concern toward controlling such burdens through using high throughput whole Genome Sequencing (WGS) and molecular diagnostic assays. The objective of the present study is to perform whole-genome sequencing of MRSA isolated from Sudan using Illumina Next Generation Sequencing (NGS) platform. Results: The genome of MRSA strain SO-1977 consists of 2,827,644 bp with 32.8% G + C, 59 RNAs and 2629 predicted coding sequences (CDSs). The genome has 26 systems, one of which is the major class in the disease virulence and defence. A total of 83 genes were annotated to virulence disease and defence category some of these genes coding as functional proteins. Based on genome analysis, it is speculated that the SO-1977 strain has resistant genes to Teicoplanin, Fluoroquinolones, Quinolone, Cephamycins, Tetracycline, Acriflavin and Carbapenems. The results revealed that the SO-1977, strain isolated from Sudan has a wide range of antibiotic resistance compared to related strains. Conclusion: The study reports for the first time the whole genome sequence of Sudan MRSA isolates. The release of the genome sequence of the strain SO-1977 will avail MRSA in public databases for further investigations on the evolution of resistant mechanism and dissemination of the -resistant genes of MRSA.

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