Browsing by Author "Bakare, Olalekan Olanrewaju"

Now showing 1 - 12 of 12
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    Analytical studies of antimicrobial peptides as diagnostic biomarkers for the detection of bacterial and viral Pneumonia
    (MDPI, 2022) Bakare, Olalekan Olanrewaju; Gokul, Arun; Keyster, Marshall
    Pneumonia remains one of the leading causes of infectious mortality and significant economic losses among our growing population. The lack of specific biomarkers for correct and timely diagnosis to detect patients’ status is a bane towards initiating a proper treatment plan for the disease; thus, current biomarkers cannot distinguish between pneumonia and other associated conditions such as atherosclerotic plaques and human immunodeficiency virus (HIV). Antimicrobial peptides (AMPs) are potential candidates for detecting numerous illnesses due to their compensatory roles as theranostic molecules. This research sought to generate specific data for parental AMPs to identify viral and bacterial pneumonia pathogens using in silico technology.
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    Biocontrol Potential of Bacillus subtilis and Bacillus tequilensis against Four Fusarium Species
    (MDPI, 2023) Baard, Vejonepher; Bakare, Olalekan Olanrewaju; Daniel, Augustine Innalegwu; Nkomo, Mbukeni; Gokul, Arun
    The use of biological control agents as opposed to synthetic agrochemicals to control plant pathogens has gained momentum, considering their numerous advantages. The aim of this study is to investigate the biocontrol potential of plant bacterial isolates against Fusarium oxysporum, Fusarium proliferatum, Fusarium culmorum, and Fusarium verticillioides. Isolation, identification, characterization, and in vitro biocontrol antagonistic assays of these isolates against Fusarium species were carried out following standard protocols. The bacterial endophytes were isolated from Glycine max. L leaves (B1), Brassica napus. L seeds (B2), Vigna unguiculata seeds (B3), and Glycine max. L seeds (B4). The bacterial isolates were identified using 16S rRNA PCR sequencing. A phylogenetic analysis shows that the bacterial isolates are closely related to Bacillus subtilis (B1) and Bacillus tequilensis (B2–B4), with an identity score above 98%. All the bacterial isolates produced a significant amount (p < 0.05) of indole acetic acid (IAA), siderophores, and protease activity. In vitro antagonistic assays of these isolates show a significant (p < 0.05) growth inhibition of the fungal mycelia in the following order: F. proliferatum > F. culmorum > F. verticillioides > F. oxysporum, compared to the control. The results suggest that these bacterial isolates are good biocontrol candidates against the selected Fusarium species
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    Building HMM and molecular docking analysis for the sensitive detection of anti-viral pneumonia antimicrobial peptides (AMPs)
    (Nature Research, 2021) Bakare, Olalekan Olanrewaju; Keyster, Marshall; Pretorius, Ashley
    Pneumonia is the main reason for mortality among children under five years, causing 1.6 million deaths every year; late research has exhibited that mortality is increasing in the elderly. A few biomarkers used for its diagnosis need specificity and precision, as they are related to different infections, for example, pulmonary tuberculosis and Human Immunodeficiency Virus. There is a quest for new biomarkers worldwide to diagnose the disease to defeat these previously mentioned constraints. Antimicrobial peptides (AMPs) are promising indicative specialists against infection. This research work used AMPs as biomarkers to detect viral pneumonia pathogens, for example, Respiratory syncytial virus, Influenza A and B viruses utilizing in silico technologies, such as Hidden Markov Model (HMMER). HMMER was used to distinguish putative anti-viral pneumonia AMPs against the recognized receptor proteins of Respiratory syncytial virus, Influenza A, and B viruses. The physicochemical parameters of these putative AMPs were analyzed, and their 3-D structures were determined utilizing I-TASSER. Molecular docking interaction of these AMPs against the recognized viral pneumonia proteins was carried out using the PATCHDOCK and HDock servers. The results demonstrated 27 anti-viral AMPs ranked based on their E values with significant physicochemical parameters in similarity with known experimentally approved AMPs. The AMPs additionally had a high anticipated binding potential to the pneumonia receptors of these microorganisms sensitively. The tendency of the putative anti-viral AMPs to bind pneumonia proteins showed that they would be promising applicant biomarkers to identify these viral microorganisms in the point-of-care (POC) pneumonia diagnostics. The high precision observed for the AMPs legitimizes HMM’s utilization in the disease diagnostics’ discovery process
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    Diagnostic approaches of pneumonia for commercial-scale biomedical applications: An overview
    (Taylor & Francis, 2020) Bakare, Olalekan Olanrewaju; Fadaka, Adewale Oluwaseun; Klein, Ashwil
    Pneumonia remains the leading infectious cause of death among children under five years of age, and the elderly. Several biomarkers, which have been identified for its diagnosis lack specificity, as they could not differentiate viral from bacterial pathogens of the disease; these biomarkers also fail to establish a distinction between pneumonia and other associated diseases such as pulmonary tuberculosis and Human Immunodeficiency Virus (HIV). This review outlined the menace of pneumonia disease from the statistical prevalence, clinical and immunological view, challenges with the methods used in diagnosis, and more useful information about methods of diagnosis of pneumonia with their limitations as well. Additionally, the use of aptamers and antimicrobial peptides (AMPs) rather than antibodies to bind and recognize receptors for diagnostics, offers several advantages over other biomarkers shortcomings such as non-specificity.
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    Dietary effects of antimicrobial peptides in therapeutics
    (Taylor & Francis, 2020-02-17) Bakare, Olalekan Olanrewaju; Fadaka, Adewale Oluwaseun; Klein, Ashwil; Pretorius, Ashley
    The notable increase in drug-resistant infections and the failure of the most potent antibiotics to establish their curative effect without side effect have presented a serious need for the discovery of new therapeutic agent and the study of dietary implications on the mode of entry of these therapeutic agents in the human system. This review provides insight into the forms and modes of action, and roles of beneficial but limited and underutilized antimicrobial peptides for use in dietary formulations, with particular focus on the technologies employed for their discovery as well as their dietary efficacy. The wide spectrum of activities of these peptides will allow the opportunity to explore their benefits as dietary supplements and additives.
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    Gene expression alterations and molecular analysis of CHEK1 in solid tumors
    (MDPI, 2020) Fadaka, Adewale Oluwaseun; Bakare, Olalekan Olanrewaju; Sibuyi, Nicole Remaliah Samantha
    Alterations in the Checkpoint kinase (CHEK1) gene, its regulation, and the possible clinical outcomes in human solid tumors have not been previously examined. Therefore, the present study was carried out to evaluate the expression of CHEK1 in solid tumors as well as the mechanism by which it can be regulated through non-coding RNAs. The expression of CHEK1 was investigated using Oncomine analysis. cBioPortal, Kaplan–Meier Plotter, and PrognoScan were performed to identify the prognostic roles of this gene in solid tumors. The copy number alteration, mutation, interactive analysis, and visualization of the altered networks were performed by cBioPortal. The molecular binding analysis was carried out by Schrodinger suite, PATCHDOCK, and discovery studio visualizer. The study demonstrated that the CHEK1 gene was differentially expressed in four different cancers, and that reduced CHEK1 mRNA expression is an unfavorable prognostic factor for patients with gastric and colorectal cancer. The molecular docking results showed that the CHEK1 gene can be regulated by microRNAs (miR-195-5p) due to the number of stable hydrogen atoms observed within the distance of 2.0 Å and the favorable amino acids (Ala221, Ile353, Ile365, Ile756, Val797, Val70, Val154, Ile159, Val347, Tyr804, Phe811, Tyr815, and Phe156) identified in the binding pocket of the argonaute protein.
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    Identification and Molecular validation of Biomarkers for the accurate and sensitive diagnosis of bacterial and viral Pneumonia
    (University of Western Cape, 2019) Bakare, Olalekan Olanrewaju; Pretorius, Ashley; Keyster, Marshall
    Pneumonia remains the major cause of death in children and the elderly and several efforts have been intensified to reduce the rate of pneumonia infection. The major breakthrough has been the discovery of certain biomarkers for the diagnosis of pneumonia through immunogenic techniques.
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    Identification of biomarkers for the accurate and sensitive diagnosis of three bacterial pneumonia pathogens using in silico approaches
    (Springer Nature, 2020) Bakare, Olalekan Olanrewaju; Keyster, Marshall; Pretorius, Ashley
    : Pneumonia ranks as one of the main infectious sources of mortality among kids under 5 years of age, killing 2500 a day; late research has additionally demonstrated that mortality is higher in the elderly. A few biomarkers, which up to this point have been distinguished for its determination lack specificity, as these biomarkers fail to build up a differentiation between pneumonia and other related diseases, for example, pulmonary tuberculosis and Human Immunodeficiency Infection (HIV). There is an inclusive global consensus of an improved comprehension of the utilization of new biomarkers, which are delivered in light of pneumonia infection for precision identification to defeat these previously mentioned constraints. Antimicrobial peptides (AMPs) have been demonstrated to be promising remedial specialists against numerous illnesses. This research work sought to identify AMPs as biomarkers for three bacterial pneumonia pathogens such as Streptococcus pneumoniae, Klebsiella pneumoniae, Acinetobacter baumannii using in silico technology. Hidden Markov Models (HMMER) was used to identify putative anti-bacterial pneumonia AMPs against the identified receptor proteins of Streptococcus pneumoniae, Klebsiella pneumoniae, and Acinetobacter baumannii. The physicochemical parameters of these putative AMPs were computed and their 3-D structures were predicted using I-TASSER. These AMPs were subsequently subjected to docking interaction analysis against the identified bacterial pneumonia pathogen proteins using PATCHDOCK.
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    Plant antimicrobial peptides (pamps): Features, applications, production, expression and challenges
    (MDPI, 2022) Bakare, Olalekan Olanrewaju; Gokul, Arun; Fadaka, Adewale Oluwaseun
    The quest for an extraordinary array of defense strategies is imperative to reduce the challenges of microbial attacks on plants and animals. Plant antimicrobial peptides (PAMPs) are a subset of antimicrobial peptides (AMPs). PAMPs elicit defense against microbial attacks and prevent drug resistance of pathogens given their wide spectrum activity, excellent structural stability, and diverse mechanism of action. This review aimed to identify the applications, features, production, expression, and challenges of PAMPs using its structure–activity relationship. The discovery techniques used to identify these peptides were also explored to provide insight into their significance in genomics, transcriptomics, proteomics, and their expression against disease-causing pathogens.
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    PR-1-Like Protein as a Potential Target for the Identification of Fusarium oxysporum: An In Silico Approach
    (BioTech, 2021-07) Bakare, Olalekan Olanrewaju; Gokul, Arun; Keyser, Marshall
    Fusarium oxysporum remains one of the leading causes of economic losses and poor crop yields; its detection is strained due to its presentation in various morphological and physiological forms. This research work sought to identify novel biomarkers for the detection of Fusarium oxys porum using in silico approaches. Experimentally validated anti-Fusarium oxysporum antimicrobial peptides (AMPs) were used to construct a profile against Fusarium oxysporum. The performance and physicochemical parameters of these peptides were predicted. The gene for the Fusarium oxysporum receptor protein PR-1-like Protein, Fpr1, was identified and translated. The resulting protein model from the translation was then validated. The anti Fusarium oxysporum AMPs and Fusarium oxysporum receptor protein 3-D structures were characterized, and their docking interaction analyses were carried out. The HMMER in silico tool identified novel anti-Fusarium oxysporum antimicrobial peptides with good performance in terms of accuracy, sensitivity, and specificity. These AMPs also displayed good physicochemical properties and bound with greater affinity to Fusarium oxysporum protein receptor PR-1-like Protein. The tendency of these AMPs to precisely detect Fusarium oxysporum PR-1-like Protein, Fpr1, would justify their use for the identification of the fungus. This study would enhance and facilitate the identification of Fusarium oxysporum to reduce problems associated with poor crop yield, economic losses, and decreased nutritional values of plants to keep up with the growing population.
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    The Relationship between Cadmium Toxicity and the Modulation of Epigenetic Traits in Plants
    (International Journal of Molecular Sciences, 2021-06) Niekerk, Lee- Ann; Bakare, Olalekan Olanrewaju; Carelse, Mogamat Fahiem; Keyser, Marshall; Mavumengwana, Vuyo; Gokul, Arun
    Elevated concentrations of heavy metals such as cadmium (Cd) have a negative impact on staple crop production due to their ability to elicit cytotoxic and genotoxic effects on plants. In order to understand the relationship between Cd stress and plants in an effort to improve Cd tolerance, studies have identified genetic mechanisms which could be important for conferring stress tolerance. In recent years epigenetic studies have garnered much attention and hold great potential in both improving the understanding of Cd stress in plants as well as revealing candidate mechanisms for future work. This review describes some of the main epigenetic mechanisms involved in Cd stress responses. We summarize recent literature and data pertaining to chromatin remodeling, DNA methylation, histone acetylation and miRNAs in order to understand the role these epigenetic traits play in cadmium tolerance. The review aims to provide the framework for future studies where these epigenetic traits may be used in plant breeding and molecular studies in order to improve Cd tolerance.
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    Structural and molecular docking analytical studies of the predicted ligand binding sites of cadherin-1 in cancer prognostics
    (Dove Medical Press, 2020) Bakare, Olalekan Olanrewaju; Keyster, Marshall; Fadaka, Adewale Oluwaseun
    Several studies have explored the design of antimicrobial peptides (AMPs) for the development of therapeutic and diagnostic molecules for the treatment and identification of pathogenic diseases as well as cancer. Human cadherin-1 protein has been identified to be involved in adhesion-mediated signalling pathways in normal cells and its loss through genetic and epigenetic alterations can result in an enhanced invasion and metastasis of malignancy in tumours. Therefore, the identification of cadherin during treatment of cancer can be used as prognostic biomarker to establish the responsiveness of patients to treatment regimen. Antimicrobial peptides (AMPs) offer several compensatory advantages in biomedical applications and have been used for treatment of diseases, dietary supplements and diagnosis of diseases. The aim of this research work was to use in silico approaches to analyse retrieved human cadherin-1 as prognostic targets in cancer treatments using modelled putative anticancer AMPs.