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Research Publications (Applied Sciences)

Permanent URI for this collectionhttp://ir-dev.dut.ac.za/handle/10321/213

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Author: search.filters.author.Pillay, CharleneHas files: Yes

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    A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.
    (Springer Science and Business Media LLC, 2024-06) Nwokorogu, Vivian C.; Pillai, Santhosh; San, James E.; Pillay, Charlene; Nyaga, Martin M.; Sabiu, Saheed
    Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.

    Methods

    The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.

    Results

    The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).

    Conclusion

    The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
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    Cheminformatics identification and validation of dipeptidyl peptidase-IV modulators from Shikimate pathway-derived phenolic acids towards interventive type-2 diabetes therapy
    (MDPI AG, 2022-10) Balogun, Fatai Oladunni; Naidoo, Kaylene; Aribisala, Jamiu Olaseni; Pillay, Charlene; Sabiu, Saheed
    Recently, dipeptidyl peptidase-IV (DPP-IV) has become an effective target in the management of type-2 diabetes mellitus (T2D). The study aimed to determine the efficacy of shikimate pathway-derived phenolic acids as potential DPP-IV modulators in the management of T2D. The study explored in silico (molecular docking and dynamics simulations) and in vitro (DPP-IV inhibitory and kinetics assays) approaches. Molecular docking findings revealed chlorogenic acid (CA) among the examined 22 phenolic acids with the highest negative binding energy (-9.0 kcal/mol) showing a greater affinity for DPP-IV relative to the standard, Diprotin A (-6.6 kcal/mol). The result was corroborated by MD simulation where it had a higher affinity (-27.58 kcal/mol) forming a more stable complex with DPP-IV than Diprotin A (-12.68 kcal/mol). These findings were consistent with in vitro investigation where it uncompetitively inhibited DPP-IV having a lower IC50 (0.3 mg/mL) compared to Diprotin A (0.5 mg/mL). While CA showed promising results as a DPP-IV inhibitor, the findings from the study highlighted the significance of medicinal plants particularly shikimate-derived phenolic compounds as potential alternatives to synthetic drugs in the effective management of T2DM. Further studies, such as derivatisation for enhanced activity and in vivo evaluation are suggested to realize its full potential in T2D therapy.
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    Bioaugmentation efficiency of diesel degradation by Bacillus pumilus JLB and Acinetobacter calcoaceticus LT1 in contaminated soils
    (2010-10-11) Pillay, Charlene; Lin, Johnson
    The abilities of diesel-degrading Bacillus pumilus JLB and Acinetobacter calcoaceticus LT1 were tested in contaminated soils. The effect of nutrient supplementation on bioaugmented samples was also examined. The results show that bio-augmentation and biostimulation accelerated significantly (p < 0.05) the diesel degradation in the contaminated loam soil and sea sand. Supplementing fertilizers to the augmented loam samples did not result in a significantly higher degradation rate. Furthermore, A. calcoaceticus LT1 alone failed to stimulate higher degradation rates in sea sand unless further supplementation of fertilizer. The results from environmental scanning electron microscopy demonstrate the population increases, then decreases in augmented samples corresponding to the level of diesel degradation. Fungi-like microorganisms became dominant in contaminated loam soil at the end of the study but not in sea sand. The study shows that it is critical not only to understand the physiology of the inoculum but also how it affects microbial community structure and function before the microorganism being introduced in the contaminated soil.
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    Identification of flavonoid C-glycosides as promising antidiabetics targeting protein tyrosine phosphatase 1B
    (Hindawi Limited, 2022-06-24) Rampadarath, Athika; Balogun, Fatai Oladunni; Pillay, Charlene; Sabiu, Saheed
    Protein tyrosine phosphatase 1B (PTP1B), a negative regulator of the insulin signaling pathway, has gained attention as a validated druggable target in the management of type 2 diabetes mellitus (T2DM). The lack of clinically approved PTP1B inhibitors has continued to prompt research in plant-derived therapeutics possibly due to their relatively lesser toxicity profiles. Flavonoid C-glycosides are one of the plant-derived metabolites gaining increased relevance as antidiabetic agents, but their possible mechanism of action remains largely unknown. This study investigates the antidiabetic potential of flavonoid C-glycosides against PTP1B in silico and in vitro. Of the seven flavonoid C-glycosides docked against the enzyme, three compounds (apigenin, vitexin, and orientin) had the best affinity for the enzyme with a binding score of -7.3 kcal/mol each, relative to -7.4 kcal/mol for the reference standard, ursolic acid. A further probe (in terms of stability, flexibility, and compactness) of the complexes over a molecular dynamics time study of 100 ns for the three compounds suggested orientin as the most outstanding inhibitor of PTP1B owing to its overall -34.47 kcal/mol binding energy score compared to ursolic acid (-19.24 kcal/mol). This observation was in accordance with the in vitro evaluation result, where orientin had a half maximal inhibitory concentration (IC50) of 0.18 mg/ml relative to 0.13 mg/ml for the reference standard. The kinetics of inhibition of PTP1B by orientin was mixed-type with V max and K m values of 0.004 μM/s and 0.515 μM. Put together, the results suggest orientin as a potential PTP1B inhibitor and could therefore be further explored in the management T2DM as a promising therapeutic agent.
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    Poultry gut health : microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies
    (Springer Science and Business Media LLC, 2021-12-02) Aruwa, Christiana Eleojo; Pillay, Charlene; Nyaga, Martin M.; Sabiu, Saheed
    The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.