A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.

BACKGROUND: 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.

Aspergillus fumigatus secretes a protease(s) that displays in silico binding affinity towards the SARS-CoV-2 spike protein and mediates SARS-CoV-2 pseudovirion entry into HEK-293T cells.

BACKGROUND: The novel coronavirus disease of 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Data from the COVID-19 clinical control case studies showed that this disease could also manifest in patients with underlying microbial infections such as aspergillosis. The current study aimed to determine if the Aspergillus (A.) fumigatus culture media (i.e., supernatant) possessed protease activity that was sufficient to activate the SARS-CoV-2 spike protein. METHODS: The supernatant was first analysed for protease activity. Thereafter, it was assessed to determine if it possessed proteolytic activity to cleave a fluorogenic mimetic peptide of the SARS-CoV-2 spike protein that contained the S1/S2 site and a full-length spike protein contained in a SARS-CoV-2 pseudovirion. To complement this, a computer-based tool, HADDOCK, was used to predict if A. fumigatus alkaline protease 1 could bind to the SARS-CoV-2 spike protein. RESULTS: We show that the supernatant possessed proteolytic activity, and analyses of the molecular docking parameters revealed that A. fumigatus alkaline protease 1 could bind to the spike protein. To confirm the in silico data, it was imperative to provide experimental evidence for enzymatic activity. Here, it was noted that the A. fumigatus supernatant cleaved the mimetic peptide as well as transduced the HEK-293T cells with SARS-CoV-2 pseudovirions. CONCLUSION: These results suggest that A. fumigatus secretes a protease(s) that activates the SARS-CoV-2 spike protein. Importantly, should these two infectious agents co-occur, there is the potential for A. fumigatus to activate the SARS-CoV-2 spike protein, thus aggravating COVID-19 development.

Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Reactive oxygen species as potential antiviral targets.

Reactive oxygen species (ROS) are by-products of cellular metabolism and can be either beneficial, at low levels, or deleterious, at high levels, to the cell. It is known that several viral infections can increase oxidative stress, which is mainly facilitated by viral-induced imbalances in the antioxidant defence mechanisms of the cell. While the exact role of ROS in certain viral infections (adenovirus and dengue virus) remains unknown, other viruses can use ROS for enhancement of pathogenesis (SARS coronavirus and rabies virus) or replication (rhinovirus, West Nile virus and vesicular stomatitis virus) or both (hepatitis C virus, human immunodeficiency virus and influenza virus). While several viral proteins (mainly for hepatitis C and human immunodeficiency virus) have been identified to play a role in ROS formation, most mediators of viral ROS modulation are yet to be elucidated. Treatment of viral infections, including hepatitis C virus, human immunodeficiency virus and influenza virus, with ROS inhibitors has shown a decrease in both pathogenesis and viral replication both in vitro and in animal models. Clinical studies indicating the potential for targeting ROS-producing pathways as possible broad-spectrum antiviral targets should be evaluated in randomized controlled trials.

Computational Insights and In Vitro Validation of Antibacterial Potential of Shikimate Pathway-Derived Phenolic Acids as NorA Efflux Pump Inhibitors.

The expression of the efflux pump systems is the most important mechanism of antibiotic resistance in bacteria, as it contributes to reduced concentration and the subsequent inactivity of administered antibiotics. NorA is one of the most studied antibacterial targets used as a model for efflux-mediated resistance. The present study evaluated shikimate pathway-derived phenolic acids against NorA (PDB ID: 1PW4) as a druggable target in antibacterial therapy using in silico modelling and in vitro methods. Of the 22 compounds evaluated, sinapic acid (-9.0 kcal/mol) and p-coumaric acid (-6.3 kcal/mol) had the best and most prominent affinity for NorA relative to ciprofloxacin, a reference standard (-4.9 kcal/mol). A further probe into the structural stability and flexibility of the resulting NorA-phenolic acids complexes through molecular dynamic simulations over a 100 ns period revealed p-coumaric acid as the best inhibitor of NorA relative to the reference standard. In addition, both phenolic acids formed H-bonds with TYR 76, a crucial residue implicated in NorA efflux pump inhibition. Furthermore, the phenolic acids demonstrated favourable drug likeliness and conformed to Lipinski's rule of five for ADME properties. For the in vitro evaluation, the phenolic acids had MIC values in the range 31.2 to 62.5 µg/mL against S. aureus, and E. coli, and there was an overall reduction in MIC following their combination with ciprofloxacin. Taken together, the findings from both the in silico and in vitro evaluations in this study have demonstrated high affinity of p-coumaric acid towards NorA and could be suggestive of its exploration as a novel NorA efflux pump inhibitor.

Phenolics Profiling of Carpobrotus edulis (L.) N.E.Br. and Insights into Molecular Dynamics of Their Significance in Type 2 Diabetes Therapy and Its Retinopathy Complication.

Adverse effects associated with synthetic drugs in diabetes therapy has prompted the search for novel natural lead compounds with little or no side effects. Effects of phenolic compounds from Carpobrotus edulis on carbohydrate-metabolizing enzymes through in vitro and in silico methods were assessed. Based on the half-maximal inhibitory concentrations (IC50), the phenolic extract of the plant had significant (p < 0.05) in vitro inhibitory effect on the specific activity of alpha-amylase (0.51 mg/mL), alpha-glucosidase (0.062 mg/mL) and aldose reductase (0.75 mg/mL), compared with the reference standards (0.55, 0.72 and 7.05 mg/mL, respectively). Molecular interactions established between the 11 phenolic compounds identifiable from the HPLC chromatogram of the extract and active site residues of the enzymes revealed higher binding affinity and more structural compactness with procyanidin (-69.834 ± 6.574 kcal/mol) and 1,3-dicaffeoxyl quinic acid (-42.630 ± 4.076 kcal/mol) as potential inhibitors of alpha-amylase and alpha-glucosidase, respectively, while isorhamnetin-3-O-rutinoside (-45.398 ± 4.568 kcal/mol) and luteolin-7-O-beta-d-glucoside (-45.102 ± 4.024 kcal/mol) for aldose reductase relative to respective reference standards. Put together, the findings are suggestive of the compounds as potential constituents of C. edulis phenolic extract responsible for the significant hypoglycemic effect in vitro; hence, they could be exploited in the development of novel therapeutic agents for type-2 diabetes and its retinopathy complication.

Characterization of Blighia sapida synthesized-copper nanoparticle and its application in periodic pharmaceutical effluent treatment.

With the rapid increase in pharmaceutical wastewater treatment for diverse applications and to contribute to the understanding of suitability of nanoparticles (NPs) in pharmaceutical effluent treatment, this study was conceptualized. Here, we profiled the concentration of selected heavy metals (Cd, Cr, Pb, Cu and Ni) in pharmaceutical effluent samples over three sampling periods using atomic absorption spectroscopy and evaluated the effectiveness of B. sapida synthesized copper nanoparticles (Cu NPs) in pharmaceutical effluent treatment. The results showed that there was no significant (p > 0.05) difference in the heavy metals concentration of the pharmaceutical effluents across the three sampling periods. This observation could be attributed to the low environmental concentration of the metals that prevented significant leaching into the company's water source through rainfall or the highly effective water treatment pathways that successfully reduced the metals concentration. Despite the observed increase in Cu ions in the treated samples due to the synthesized NPs, its concentration still conforms to the internationally accepted admissible limit in drinkable water. Studies seeking to understand the suitability and toxicological implications of use of the NP-treated effluents are highly encouraged and efforts are underway in this direction.

An Appraisal of Antidotes' Effectiveness: Evidence of the Use of Phyto-Antidotes and Biotechnological Advancements.

Poisoning is the greatest source of avoidable death in the world and can result from industrial exhausts, incessant bush burning, drug overdose, accidental toxication or snake envenomation. Since the advent of Albert Calmette's cobra venom antidote, efforts have been geared towards antidotes development for various poisons to date. While there are resources and facilities to tackle poisoning in urban areas, rural areas and developing countries are challenged with poisoning management due to either the absence of or inadequate facilities and this has paved the way for phyto-antidotes, some of which have been scientifically validated. This review presents the scope of antidotes' effectiveness in different experimental models and biotechnological advancements in antidote research for future applications. While pockets of evidence of the effectiveness of antidotes exist in vitro and in vivo with ample biotechnological developments, the utilization of analytic assays on existing and newly developed antidotes that have surpassed the proof of concept stage, as well as the inclusion of antidote's short and long-term risk assessment report, will help in providing the required scientific evidence(s) prior to regulatory authorities' approval.

Toxicological implications and laxative potential of ethanol root extract of Morella serrata in loperamide-induced constipated Wistar rats.

CONTEXT: Morella serrata L. (Myricaceae) is commonly used in South Africa to treat several diseases including constipation. OBJECTIVES: This study investigated toxicological implications and laxative potential of the ethanol root extract of the plant. MATERIALS AND METHODS: While normal control animals were placed on sterile placebo, the loperamide-constipated rats were treated with the extract at 75, 150 and 300 mg/kg doses for 7 days, and their feeding patterns and faecal properties were monitored. Gastrointestinal transit ratio and the toxicity profile of the tested doses were thereafter evaluated. RESULTS: The significantly increased faecal volume (192.08%), feed (63.63%), water intake (55.97%) and improved intestinal motility (95.05%) in the constipated rats following treatment with the extract (at 300 mg/kg) suggested laxative potential of the extract. The 1.5-2.0-fold normalization of the platelets, erythrocytes and leukocytes counts in the extract-treated constipated rats suggests its non-haematotoxic tendency. Furthermore, the extract (at the highest investigated dose) reversed the attenuation in the concentrations of the electrolytes (0.5-2-fold), total protein (62.12%) and albumin (55.88%) in the constipated animals as well as attenuated activities of hepatic enzymes (0.5-3.0-fold) and levels of urea (126.67%), creatinine (40.32%), cholesterol (3-fold) and triglycerides (9-fold). These further support its non-toxic and therapeutic attributes against constipation. CONCLUSION: Overall, the effect exhibited by M. serrata in this study competed well with Senokot (standard drug) and proved that it may be relatively safe and with excellent laxative potential, thus, supporting its pharmacological applications in South Africa.

Indomethacin-induced gastric ulceration in rats: Ameliorative roles of Spondias mombin and Ficus exasperata.

CONTEXT: Spondias mombin Linn (Anacardiaceae) and Ficus exasperata Valh (Moraceae) are botanicals with known phytotherapeutic potentials in the traditional system of medicine in the world. OBJECTIVE: The objective of this study is to investigate the quantitative polyphenolic constituents and gastroprotective effects of aqueous leaf extracts of Spondias mombin and Ficus exasperata against indomethacin-induced gastric ulcer in rats. MATERIALS AND METHODS: Ulceration was induced by a single oral administration of indomethacin (30 mg/kg body weight (b.w.)). Ulcerated rats were orally administered with esomeprazole (a reference drug) at a dose of 20 mg/kg body weight, and Spondias mombin and Ficus exasperata at a dose of 100 and 200 mg/kg b.w. once daily for 21 d after ulcer induction. Gastric secretions and antioxidant parameters were thereafter evaluated. RESULTS: The significantly increased (p < 0.05) ulcer index, gastric volume, malondialdehyde level, and pepsin activity by indomethacin were effectively reduced by 65.40, 36.47, 45.71, and 53.79%, respectively, following treatment with F. exasperata at 200 mg/kg b.w. S. mombin at this regimen also attenuated these parameters by 71.70, 46.62, 50.16, and 55.73%. Moreover, the extracts significantly increase the reduced activity of superoxide dismutase as well as pH and mucin content in the ulcerated rats. DISCUSSION AND CONCLUSION: These findings are indicative of gastroprotective and antioxidative potentials of the extracts which is also evident in the degree of % inhibition against ulceration. The available data in this study suggest that the extracts proved to be capable of ameliorating indomethacin-induced gastric ulceration and the probable mechanisms are via antioxidative and proton pump inhibition.

Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy.

Antibacterial resistance to ß-lactams in microorganisms has been attributed majorly to alterations in penicillin-binding proteins (PBPs) coupled with ß-lactams' inactivation by ß-lactamase. Consequently, the identification of a novel class of therapeutics with improved modulatory action on the PBPs is imperative and plant secondary metabolites, including phenolics, have found relevance in this regard. For the first time in this study, the over 10,000 phenolics currently known were computationally evaluated against PBP3 of Pseudomonas aeruginosa, a superbug implicated in several nosocomial infections. In doing this, a library of phenolics with an affinity for PBP3 of P. aeruginosa was screened using structure-activity relationship-based pharmacophore and molecular docking approaches. Subsequent thermodynamic screening of the top five phenolics with higher docking scores, more drug-likeness attributes, and feasible synthetic accessibility was achieved through a 120 ns molecular dynamic (MD) simulation. Four of the top five hits had higher binding free energy than cefotaxime (-18.72 kcal/mol), with catechin-3-rhamside having the highest affinity (-28.99 kcal/mol). All the hits were stable at the active site of the PBP3, with catechin-3-rhamside being the most stable (2.14 Å), and established important interactions with Ser294, implicated in the catalytic activity of PBP3. Also, PBP3 became more compact with less fluctuation of the active site amino acid residues following the binding of the hits. These observations are indicative of the potential of the test compounds as PBP3 inhibitors, with catechin-3-rhamside being the most prominent of the compounds that could be further improved for enhanced druggability against PBP3 in vitro and in vivo.Communicated by Ramaswamy H. Sarma.

Adipose tissue inflammation linked to obesity: A review of current understanding, therapies and relevance of phyto-therapeutics.

Obesity is a current global challenge affecting all ages and is characterized by the up-regulated secretion of bioactive factors/pathways which result in adipose tissue inflammation (ATI). Current obesity therapies are mainly focused on lifestyle (diet/nutrition) changes. This is because many chemosynthetic anti-obesogenic medications cause adverse effects like diarrhoea, dyspepsia, and faecal incontinence, among others. As such, it is necessary to appraise the efficacies and mechanisms of action of safer, natural alternatives like plant-sourced compounds, extracts [extractable phenol (EP) and macromolecular antioxidant (MA) extracts], and anti-inflammatory peptides, among others, with a view to providing a unique approach to obesity care. These natural alternatives may constitute potent therapies for ATI linked to obesity. The potential of MA compounds (analysed for the first time in this review) and extracts in ATI and obesity management is elucidated upon, while also highlighting research gaps and future prospects. Furthermore, immune cells, signalling pathways, genes, and adipocyte cytokines play key roles in ATI responses and are targeted in certain therapies. As a result, this review gives an in-depth appraisal of ATI linked to obesity, its causes, mechanisms, and effects of past, present, and future therapies for reversal and alleviation of ATI. Achieving a significant decrease in morbidity and mortality rates attributed to ATI linked to obesity and related comorbidities is possible as research improves our understanding over time.

Fatty acid-modified chitosan and nanoencapsulation of essential oils: A snapshot of applications.

Chitosan (CS) and its modification with fatty acid (FA) in addition to the nanoencapsulation with essential oils (EOs) have emerged as promising approaches with diverse applications, particularly in food and fruit preservation. This review aims to curate data on the prospects of CS modified with FA as nanostructures, serving as carriers for EOs and its application in the preservation of fruits. A narrative review with no restricted period was used for the general overview of CS and strategies for its modification with FA. Report on CS modified with FA and nanoencapsulation with EO and their applications were appraised. The prospects of CS modified with FA and EO nanoencapsulation in food and fruit preservation were outlined. Most chitosan-fatty acid (CS-FA) studies have found relevance in water, medical and pharmaceutical industries, with few studies on food preservation. CS-FA formulation with EOs shows substantial potential in preserving fruits and will significantly impact the food industry in the future by extending the shelf life of fruits and reducing food waste.

In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae.

Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.

Cryptococcal proteases exhibit the potential to activate the latent SARS-CoV-2 spike protein.

BACKGROUND: The COVID-19 pandemic has affected more than 650 million people and resulted in over 6.8 million deaths. Notably, the disease could co-manifest with microbial infections, like cryptococcosis, which also presents as a primary lung infection. OBJECTIVE: In this contribution, we sought to determine if cryptococcal supernatant (which contains secreted furin-like proteases) could activate the SARS-CoV-2 spike protein. METHODS: Molecular docking of the crystal structures of the SARS-CoV-2 spike protein (target) and selected cryptococcal proteases (ligands) was executed using the high ambiguity driven protein-protein docking (HADDOCK) server, with the furin protease serving as a reference ligand. The furin protease is found in human cells and typically activates the SARS-CoV-2 spike protein. Importantly, in order to provide experimental evidence for enzymatic activity, we also assessed the biochemical efficiency of cryptococcal proteases to initiate viral entry into HEK-293 T cells by SARS-CoV-2 spike pseudotyped Lentivirus. RESULTS: We show that the selected cryptococcal proteases could interact with the spike protein, and some had a better or comparable binding affinity for the spike protein than furin protease following an in silico comparative analysis of the molecular docking parameters. Furthermore, it was noted that the biochemical efficiency of the cryptococcal supernatant to transduce HEK-293 T cells with SARS-CoV-2 pseudovirions was comparable (p > 0.05) to that of recombinant furin. CONCLUSIONS: Taken together, these data show that cryptococcal proteases could activate the SARS-CoV-2 spike protein. In practice, it may be critical to determine if patients have an underlying cryptococcal infection, as this microbe could secrete proteases that may further activate the SARS-CoV-2 viral particles, thus undermining COVID-19 intervention measures.

Cheminformatics Bioprospection of Sunflower Seeds' Oils against Quorum Sensing System of Pseudomonas aeruginosa.

Clinically significant pathogens such as Pseudomonas aeruginosa evade the effects of antibiotics using quorum sensing (QS) systems, making antimicrobial resistance (AMR) a persistent and potentially fatal global health issue. Hence, QS has been identified as a novel therapeutic target for identifying novel drug candidates against P. aeruginosa, and plant-derived products, including essential oils, have been demonstrated as effective QS modulators. This study assessed the antipathogenic efficacy of essential oils from two sunflower cultivars (AGSUN 5102 CLP and AGSUN 5106 CLP) against P. aeruginosa ATCC 27853 in vitro and in silico. At the sub-inhibitory concentrations, both AGSUN 5102 CLP (62.61%) and AGSUN 5106 CLP (59.23%) competed favorably with cinnamaldehyde (60.74%) and azithromycin (65.15%) in suppressing the expression of QS-controlled virulence phenotypes and biofilm formation in P. aeruginosa. A further probe into the mechanism of anti-QS action of the oils over a 100-ns simulation period against Las QS system revealed that phylloquinone (-66.42 ± 4.63 kcal/mol), linoleic acid (-53.14 ± 3.53 kcal/mol), and oleic acid (-52.02 ± 3.91 kcal/mol) had the best affinity and structural compactness as potential modulators of LasR compared to cinnamaldehyde (-16.95 ± 1.75 kcal/mol) and azithromycin (-32.08 ± 10.54 kcal/mol). These results suggest that the identified compounds, especially phylloquinone, could be a possible LasR modulator and may represent a novel therapeutic alternative against infections caused by P. aeruginosa. As a result, phylloquinone could be further studied as a QS modulator and perhaps find utility in developing new therapeutics.

Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.

Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.

A review of indigenous knowledge and ethnopharmacological significance of African Copaiba Balsam Tree, Daniellia oliveri (Fabaceae).

Daniellia oliveri has found its indigenous relevance in the management of diseases including but not limited to diabetes mellitus, tuberculosis, fever, ulcers, pain, worm manifestation, pneumonia, skin ailments, infectious diseases, sickle cell anaemia, hence, a review of its indigenous knowledge, ethnopharmacological and nutritional benefits was undertaken. Information used for the review was sourced from popular scientific databases (Google Scholar, PubMed, Science Direct, Web of Science, BioMed Central, JSTOR, African Plant, Global Biodiversity Information and others), conference proceedings, dissertations or theses, chapters in books, edited books, and journal collections. The materials obtained from 121 scientific documents targeting majorly between 1994 and 2023 established the presence of major secondary metabolites (such as polyphenols, flavonoids, saponins, alkaloids, etc.), minerals (e.g., sodium, potassium, phosphorus, selenium, calcium, magnesium, etc.), vitamins (beta-carotene, thiamine, riboflavin, niacin, ascorbic acid, etc.), and nutrients (crude protein, moisture, dry matter, ether, carbohydrates, and energy). Literature also lent credence to the preliminary safety profiles of the plant and its pharmacological potentials as analgesic, antinociceptive, antioxidant, antidiabetic, antidiarrhoeal, anthelmintic, anti-inflammatory, antimelanogenesis, antimicrobial, antiplasmodial, antisickling, cardiotoxic, cytotoxic, and neuroprotective agents. While the review is majorly limited to Africa particularly western countries (such as Nigeria, Burkina Faso, Mali, Ghana, Togo, and Benin) and the plant is found to be largely underutilized, it is evident that limited information exists on the in vivo pharmacological evaluation, bioactive compounds identification, and there is a lack of preclinical and clinical trials for possible drug development. Based on the aforementioned, it is hoped that further research studies geared toward providing insights into the established grey areas (such as traditional use investigation, targeted or assay-guided compounds identification, and preclinical and clinical studies) are necessary in order to fully explore the therapeutic, nutritional, and economic benefits of the plant.

Characterization of Microbial Diversity of Two Tomato Cultivars through Targeted Next-Generation Sequencing 16S rRNA and ITS Techniques.

Even though the nutritional and economic values of Solanum lycopersicum (tomato) are substantially impacted by microbial spoilage, the available data on its microbial community, particularly during spoilage, are limited and have primarily been characterized using conventional culture-dependent methods. This study employed a targeted high-throughput next-generation sequencing method to longitudinally characterize the microbial diversity of two South African tomato cultivars (jam and round) at varied storage intervals (1, 6, and 12 days). Throughout the storage period, the bacterial communities of the two cultivars were more diverse than the fungal communities. The microbial diversity of both bacteria and fungi was greater and comparable between the cultivars on day 1, but becomes distinct as the storage period increases, with round tomatoes being more diverse than jam tomato, though, on day 12, jam tomato develops greater diversity than round tomato. Overall, the most abundant phyla (though Proteobacteria was most dominant) were Proteobacteria, Firmicutes, and Bacteriodota in the bacterial communities, while Ascomycota and Basidiomycota formed most fungal communities with Ascomycota being dominant. At the genus level, Pantoea and Klebsiella (bacteria), Hanseniaspora, Stemphylium, and Alternaria (fungi) were prevalent. Taken together, this study casts light on a broad microbial diversity profile thus, confirms the cultivars' diversity and abundance differences.

Molecular Modeling Identification of Key Secondary Metabolites from Xylopia aethiopica as Promising Therapeutics Targeting Essential Measles Viral Proteins.

This study computationally screened three key compounds (vanillin (VAN), oxophoebine (OPB), and dihydrochalcone (DHC)) derived from Xylopia aethiopica (Guinea pepper), a medicinal plant with known antiviral activity, against key druggable measles virus (MV) proteins (fusion protein (FUP), haemagglutinin protein (HMG), and phosphoprotein (PSP)). Each molecular species was subjected to a 100 ns molecular dynamics (MD) simulation following docking, and a range of postdynamic parameters including free binding energy and pharmacokinetic properties were determined. The docking scores of the resulting OPB-FUP (-5.4 kcal/mol), OPB-HMG (-8.1 kcal/mol), and OPB-PSP (-8.0 kcal/mol) complexes were consistent with their respective binding energy values (-25.37, -28.74, and -40.68 kcal/mol), and higher than that of the reference standard, ribavirin (RBV) in each case. Furthermore, all the investigated compounds were thermodynamically compact and stable, especially HMG of MV, and this observation could be attributed to the resulting intermolecular interactions in each system. Overall, OPB may possess inhibitory properties against MV glycoproteins (FUP and HMG) and PSP that play important roles in the replication of MV and measles pathogenesis. While OPB could serve as a scaffold for the development of novel MV fusion and entry inhibitors, further in vitro and in vivo evaluation is highly recommended.