Research Articles (Biotechnology)

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Glucoselipid biosurfactant biosynthesis operon of rouxiella badensis DSM 100043T: screening, identification, and heterologous expression in escherichia coli
(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Van Zyl Leonardo; Williams Wesley; Burger Anita; Harahap Andre
Rouxiella badensis DSM 100043T had been previously proven to produce a novel glucoselipid biosurfactant which has a very low critical micelle concentration (CMC) as well as very good stability against a wide range of pH, temperature, and salinity. In this study, we performed a function-based library screening from a R. badensis DSM 100043T genome library to identify responsible genes for biosynthesis of this glucoselipid. The identified open reading frames (ORFs) were cloned into several constructs in Escherichia coli for gene permutation analysis and the individual products were analyzed using high-performance thin-layer chromatography (HPTLC). Products of interest from positive expression strains were purified and analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and nuclear magnetic resonance (NMR) for further structure elucidation. Function-based screening of 5400 clones led to the identification of an operon containing three ORFs encoding acetyltransferase GlcA (ORF1), acyltransferase GlcB (ORF2), and phosphatase/HAD GlcC (ORF3). E. coli pCAT2, with all three ORFs, resulted in the production of identical R. badensis DSM 100043T glucosedilipid with Glu-C10:0-C12:1 as the main congener. ORF2-deletion strain E. coli pAFP1 primarily produced glucosemonolipids, with Glu-C10:0,3OH and Glu-C12:0 as the major congeners, predominantly esterified at the C-2 position of the glucose moiety. Furthermore, fed-batch bioreactor cultivation of E. coli pCAT2 using glucose as the carbon source yielded a maximum glucosedilipid titer of 2.34 g/L after 25 h of fermentation, which is 55-fold higher than that produced by batch cultivation of R. badensis DSM 100043T in the previous study.
Delphinidin as an antineoplastic agent targeting androgen receptors
(Wiley, 2025) Fadaka Adewale; Sibuyi Nicole; Alves Leandro
Researchers globally have discovered that both red and green peppers are extremely rich in bioactive phytoconstituents with pharmacological properties. These metabolites are associated with critical physiological functions, including anticancer and health-promoting effects. However, due to insufficient clinical evidence or lack of standardized studies, there are no recommendations regarding their use and dosage. We investigated the potential therapeutic effects of Capsicum chinense flesh as an inhibitor of the androgen receptor through computational studies. To explore potential novel antitumor markers from Capsicum chinense flesh, we employed in silico docking, molecular dynamics simulations, and principal component analysis. Our results consistently demonstrated significant binding across all the receptor models tested, with the potential candidate (Delphinidin) emerged as a promising candidate. This study offers valuable insights into a robust pharmacological approach that could aid in identifying targets with investigative roles in tumor development and provide potential therapeutic options for managing tumors and associated challenges.
The influence of season and land use on the occurrence of Metarhizium spp. in the Cape Peninsula region, South Africa
(Taylor and Francis Ltd, 2025) Keyster, Marshall; Rhoda, Ilyaas; Prins, Alaric
To investigate the environmental relationships between the occurrence of Metarhizium spp., season and land use in the Cape Peninsula region, soil samples were collected from randomly selected sampling sites within nature reserves and agricultural farms. Soil samples from the same sites were collected in different seasons (winter and summer), and Metarhizium spp. were isolated from the soil samples by insect baiting and plating soil, and identified. Soil pH, texture, and nutrient contents of air-dried composite soil samples were analysed, and the seasonal rainfall data were recorded. The associations between the number of Metarhizium isolates with soil nutrient contents and seasonal rainfall were assessed. Farm sites had a significantly higher number of Metarhizium isolates (36 of 40 isolates collected) and higher concentrations of soil macronutrients, P, Ca and N (NO3), than in soil samples from the reserves, while higher average monthly rainfall in winter correlated with higher occurrences of Metarhizium isolates. In conclusion, wet, cold winters and vegetable farming favoured the higher occurrence of Metarhizium spp. in the Cape Peninsula region.
Enhanced lactic acid production from potato peel waste via MnO2 nanoparticle-assisted simultaneous saccharification and fermentation: Process optimization and kinetic studies
(Elsevier, 2025) Mambili-Mamboundou Hermane; Naidu Talia; Sanusi Isaac A.
This study focused on optimizing lactic acid production from potato peel waste facilitated by MnO2 nanoparticle (NP). Also, kinetic analysis was conducted, utilizing the growth constant (Kg), logistic function, and modified Gompertz model to evaluate the process dynamics under optimized conditions and the control experiment (without NP). Under optimized conditions (0.034 wt% MnO2 NP, 6.02 pH, 34 ◦C temperature, and 14.90 wt% solid loading), notable increases in biomass and lactic acid concentrations of 2.85 g/L and 41.26 g/L were achieved representing a 1.16 and 1.42-fold increments respectively. In addition, the inclusion of MnO2 NP increased the maximum potential lactic acid concentration (Pm) and production rate, reaching 32.89 g/L and 1.51 g/L/h, respectively, compared to the control’s values of 29.80 g/L and 1.43 g/L/h. This study underscores the potential of MnO2 NP in boosting lactic acid bioprocessing and yield towards enhanced bioconversion of agricultural waste to useful products.
UYSD: a novel data repository accessible via public website for worldwide population frequencies of Y-SNP haplogroups
(Springer Nature, 2025) D’Amato, Maria E; Ralf, Arwin; Zandstra, Dion
For decades, there has been scientific interest in the variation and geographic distribution of paternal lineages associated with the human Y chromosome. However, the relevant data have been dispersed across numerous publications, making it difficult to consolidate. Additionally, understanding the relationships between different variants, and the tools used to analyze them, have evolved over time, further complicating efforts to harmonize this information. The Universal Y-SNP Database (UYSD) marks a substantial advancement by providing a comprehensive and accessible platform for Y-SNP and haplogroup data from populations around the world. UYSD harmonizes diverse datasets into a unified repository, facilitating the exploration of global Y-chromosomal variation. The platform handles data generated with both high- and low-throughput technology and is compatible with the automated analysis software tool, Yleaf v3. Key functionalities include the ability to: i) visualize haplogroup distributions on an interactive world map, ii) estimate haplogroup frequencies in geographic regions with sparse data through interpolation, and iii) display detailed phylogenetic trees of Y-chromosomal haplogroups. Currently, UYSD encompasses data from over 6,600 males across 27 populations. This dataset largely aligns with known global Y-haplogroup patterns, but also reveals unexplored finer-scale geographic variations. While the present dataset is largely European-centered, UYSD is designed for ongoing expansion by the scientific community, aiming to include more global data and higher-resolution population sequencing data. The platform thus offers valuable insights into human genetic diversity and migration patterns, serving several fields of research such as: human population genetics, genetic anthropology, ancient DNA analysis and forensic genetics.
Fimsbactin siderophores from a South African marine sponge symbiont, marinomonas sp. PE14-40
(John Wiley and Sons Ltd, 2025) Ikegwuoha, Nompumelelo Philile Praiseworth; Hanekom, Thea; Booysen, Elzaan; Jason, Corbyn; van Zyl, Leonardo Joaquim; Trindade, Marla
Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1–6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.
Effects of acidic and alkaline electrolyzed water treatments on the volatilomics and proteomics changes in fresh-cut apple during storage
(Royal Society of Chemistry, 2025) Mohamed, Gadija; Caleb, Oluwafemi James; Belay, Zinash A.
Electrolyzed water (EW) has shown potential to decontaminate and maintain the quality of fresh-cut apple; however, the underlying response of the product to this treatment remains unclear. Thus, this study aims to identify the possible quality regulation mechanisms of acidic electrolyzed water (AEW) and alkaline electrolyzed water (ALEW) treatments on fresh-cut ‘Granny Smith’ apples via volatile organic compound (VOC) and qualitative proteomics analysis during storage at 2 °C for 10 days. The results identified 43 VOCs, including 10 esters, 9 alcohols, 9 alkanes, 8 carboxylic acids, 6 ketones, and 1 aldehyde. The distribution of VOCs was significantly affected by the pretreatment conditions; fresh-cut apple treated with AEW was characterised by the highest number of esters, alcohols, and carboxylic acids, whereas samples treated with ALEW exhibited predominantly carboxylic acids, alcohols, and alkanes in comparison to control (untreated) samples. Ethyl dodecanoate, which was identified only in the ALEW samples on each sampling day, had the highest concentration among all the individual VOCs. The proteomics results showed that a total of 3434, 3401, and 3313 proteins were identified on day 3, 6, and 10, respectively, across all samples. Until day 6 of storage, no significant differences were observed among the samples. Notably, on day 6, “M16C_associated domain-containing protein” was shown to be unique to the control samples. KH type-2 domain-containing protein, methylenetetrahydrofolate reductase (MTHFR), and 1,4-alpha-glucan branching enzyme were unique proteins identified after AEW treatment at day 6 and 10 of storage. No unique protein was identified for the ALEW samples. These results provide the first report of the proteomic and volatilomic changes associated with EW-treated fresh-cut apple during storage.
Sex and environment shape cochlear sensitivity in human populations worldwide
(Elsevier B.V, 2025) Croze, Myriam; Balaresque, Patricia; Delmotte, Sébastien
Hearing remains an underexplored aspect of human evolution. While the growing prevalence of hearing issues worldwide highlights the need to investigate factors beyond age, ototoxic substances, and recreational noise— factors affecting only a subset of the population —the role of environmental influences remains relatively unaddressed. In contrast, hearing and vocalizations have been extensively studied in many vertebrates through the Acoustic Adaptation Hypothesis, which suggests that acoustic communication adapts to the structure of the immediate environment. To explore how the environment shapes the ear’s ability to process sound, studying the cochlea is essential since it is responsible for capturing, amplifying, and converting sound waves into electrical signals. Cochlear sensitivity can be measured using Transient-Evoked Otoacoustic Emissions (TEOAE), which assess the cochlea’s ability to produce and transmit an acoustic response after sound stimulation. By analyzing TEOAE profiles, we gain valuable insights into how the cochlea responds to external auditory stimuli. We evaluated the influence of both endogenous (age, sex, ear side) and exogenous factors (ethnicity, environment, language) on cochlear sensitivity by collecting TEOAE data from 448 healthy individuals across 13 global populations in Ecuador, England, Gabon, South Africa, and Uzbekistan, living in diverse environments. For each individual, we derived six acoustic metrics from these TEOAE profiles to characterize the amplitude and frequency spectrum of cochlear sensitivity. Our results show that amplitude is primarily influenced by sex (up to 2 dB) and environment (up to 3.6 dB), followed by age and ear side. The frequency spectrum is determined exclusively by exogenous factors, with environment— particularly altitude, and urban versus rural settings —being the most significant. These findings challenge existing assumptions and highlight the need to consider both biological and environmental factors when studying auditory processes.
Enhancing Fusarium oxysporum tolerance in Phaseolus vulgaris: Isolation and characterization of bacterial endophytes
(Elsevier B.V., 2025) Holman, Darin Edward; Keyster, Marshall; Klein, Ashwil; Daniel, Augustine Innalegwu
Research surrounding microbial biocontrol has garnered considerable attention in the last few years due to the numerous advantages as opposed to synthetic agrochemicals. Phaseolus vulgaris is an important legume that is cultivated worldwide, especially in third-world countries. The growth and yield of this crop are often severely limited by the pathogen Fusarium oxysporum. The aim of the study is to investigate the biological control potential of six plant bacterial isolates against F. oxysporum, both in vitro and in vivo. Six bacterial endophytes were isolated from Ledebouria ovatifolia leaves (E1), Solanum dulcamara leaves (E2), Cortalaria retusa leaves (E3), Euphorbia prostrata roots (R1), Solanum nigrum roots (R2), and Helichrysum splendidum roots (R3). These isolates were characterized for any biocontrol activity they might have against F. oxysporum PPR1. Isolation, characterization, identification, and biocontrol antagonistic assays were carried out in vitro against F. oxysporum, following standard protocols. The isolates were identified using 16S rRNA gene PCR sequencing. A phylogenetic analysis indicated that the leaf isolates displayed a close relationship with Bacillus altitudinis (E1), Streptomyces bikiensis strain SBM (E2), and Pseudomonas rhodesiae (E3). Root isolates displayed a close relationship with Enterobacter kobei (R1), Enterobacter sp. (R2), and Pseudomonas sp. strain (R3). Five out of the six isolates exhibited catalase activity and zinc solubilization activity, whereas all isolates exhibited siderophore production activity. Most of the tested isolates were able to produce the extracellular hydrolytic enzymes protease and amylase. The isolates exhibiting the highest hydrolytic enzyme activities were able to significantly inhibit F. oxysporum growth in vitro. E. kobei exhibited the most promising plant growth-promoting activity, hydrolytic enzyme activity, F. oxysporum antagonism, and increased seedling growth of P. vulgaris. These results suggest that E. kobei represents a good biocontrol candidate against F. oxysporum. The ability of this bacterial isolate to colonize and its promising biological activities suggest it has enormous potential to be used as both a biopesticide and plant growth stimulator.
Interference of a phytoconstituent from Nymphaea lotus-derived ligand N-acetyl glucosamine with signaling receptors in diabetes mellitus development: a targeted computational analysis
(Elsevier B.V., 2025) Fadaka, Adewale Oluwaseun; Onikanni, Sunday Amos; Dao, Tran Nhat-Phong
Diabetes mellitus is a world-wide health concern with several millions affected in all ages. Computer-aided drug design (CADD) is a powerful tool that has revolutionized the process of discovering and developing new drugs. It provides innovative methods that can speed up drug discovery and lower costs thereby results to increase enthusiasm at developing instinctive antidiabetic agents as alternatives for managing diabetes. Nymphaea lotus, a plant with medicinal properties known for its anti-diabetic effects, contains bioactive components like N-acetyl glucosamine. An in silico study was conducted to investigate its potential in targeting proteins related to diabetes. Molecular docking studies, toxicity prediction, examination of drug depiction, and Molecular Dynamics Simulation (MDs) of the ligands with the identified receptor target were conducted using the Schrödinger platform. The receptor-ligand complex of Nymphaea lotus was compared with known inhibitors. Molecular dynamics simulation, principal component analysis, and free energy landscape analysis showed that the binding affinity of the Nymphaea lotus complex was higher than that of reference ligands. This suggests that Nymphaea lotus and its bioactive compounds have promising medicinal value for managing type 2 diabetes, warranting further research into their therapeutic potential
Potential matrix metalloproteinase 2 and 9 inhibitors identified from Ehretia species for the treatment of chronic wounds - Computational drug discovery
(Elsevier Ltd, 2025) Oselusi, Samson; Martin, Darius; Meyer, Mervin; Madiehe, Abram; Sibuyi, Nicole
Matrix metalloproteinases (MMPs) serve as prognostic factors in several pathophysiological conditions, including chronic wounds. Therefore, they are considered important therapeutic targets in the intervention and treatment of these conditions. In this study, computational tools such as molecular docking and molecular dynamics simulations were used to gain insight into protein‒ligand interactions and determine the free binding energy between Ehretia species phytoconstituents and gelatinases (MMP2 and MMP9). A total of 74 phytoconstituents from Ehretia species were compiled from the literature, and 46 of these compounds were identified as potential inhibitors of at least one type of MMP. Molecular docking revealed that lithospermic acid B, rosmarinic acid, and danshensu had stronger binding affinities against the two enzymes than the reference ligands. Furthermore, (9S, 10E, 12Z, 15Z)-9-hydroxy-10,12,15-octadecatrienoic (∗-octadecatrienoic) had a higher binding energy for MMP2, whereas caffeic anhydride and caffeic acid established stronger binding energy with MMP9 than the reference ligand. These complexes also demonstrated relatively stable, favourable, and comparable conformational changes with those of unbound proteins at 500 ns. The free energy decomposition results further provide detailed insights into the contributions of active site residues and different types of interactions to the overall binding free energy. Finally, most of the hit phytoconstituents (rosmarinic acid, caffeic anhydride, caffeic acid, and danshensu) had good physicochemical, drug-likeness, and pharmacokinetic properties. Collectively, our findings showed that phytoconstituents from Ehretia species could be beneficial in the search for novel MMP inhibitors as therapeutic agents for the treatment of chronic wounds.
Nano-based co-valorization, detoxification, and fermentation of potato waste and black liquor for bioethanol production
(Springer Science and Business Media Deutschland GmbH, 2025) Sewsynker-Sukai, Yeshona; Zondi, Amanda; Sanusi, Isaac
Black liquor from paper and pulp mills is an underutilized waste resource. Black liquor can be valorized due to its useful chemical fractions and water component that can be employed for the pretreatment and biochemical conversion of starchy potato waste (SPW) into bioethanol. Hence, in this study, the simultaneous co-valorization, detoxification, and fermentation of SPW and black liquor (without the addition of freshwater and chemicals) were optimized for bioethanol production. The scanning electron microscopy (SEM) and the Fourier-transform infrared (FTIR) clearly confirmed the distortion of SPW inherent structure for the recovery of useful carbohydrates. A significant reduction in process inhibitors (furfural = 1.26-fold, hydroxymethylfurfural (HMF) = 5.68-fold, and phenols = 1.03-fold) was observed with CuO NP inclusion. The response surface methodology (RSM) model of the bioethanol production showed a high coefficient of determination (R2) value of 0.98. The optimized process with CuO NP inclusion displayed a biomass and bioethanol concentrations of 2.12 g/L and 21.37 g/L corresponding to 1.74- and 1.68-fold improvement over the control respectively. In addition, the kinetic data showed that the incorporation of CuO nanoparticle (NP) significantly improved (1.86-fold) the potential maximum bioethanol concentration (Pm) (20.21 g/L) compared to the control experiment (10.86 g/L). The study demonstrates a 100% freshwater conservation approach for improved sugar recovery, remarkable inhibitor removal, and bioethanol production from pretreated SPW towards reduced biofuel production cost, waste management, and green environment sustainability.
Effects of acidic and alkaline electrolyzed water treatments on the volatilomics and proteomics changes in fresh-cut apple during storage
(Royal Society of Chemistry, 2025) Caleb, Oluwafemi James; Belay, Zinash A.; Nkomo, Mbukeni
Electrolyzed water (EW) has shown potential to decontaminate and maintain the quality of fresh-cut apple; however, the underlying response of the product to this treatment remains unclear. Thus, this study aims to identify the possible quality regulation mechanisms of acidic electrolyzed water (AEW) and alkaline electrolyzed water (ALEW) treatments on fresh-cut ‘Granny Smith’ apples via volatile organic compound (VOC) and qualitative proteomics analysis during storage at 2 °C for 10 days. The results identified 43 VOCs, including 10 esters, 9 alcohols, 9 alkanes, 8 carboxylic acids, 6 ketones, and 1 aldehyde. The distribution of VOCs was significantly affected by the pretreatment conditions; fresh-cut apple treated with AEW was characterised by the highest number of esters, alcohols, and carboxylic acids, whereas samples treated with ALEW exhibited predominantly carboxylic acids, alcohols, and alkanes in comparison to control (untreated) samples. Ethyl dodecanoate, which was identified only in the ALEW samples on each sampling day, had the highest concentration among all the individual VOCs. The proteomics results showed that a total of 3434, 3401, and 3313 proteins were identified on day 3, 6, and 10, respectively, across all samples. Until day 6 of storage, no significant differences were observed among the samples. Notably, on day 6, “M16C_associated domain-containing protein” was shown to be unique to the control samples. KH type-2 domain-containing protein, methylenetetrahydrofolate reductase (MTHFR), and 1,4-alpha-glucan branching enzyme were unique proteins identified after AEW treatment at day 6 and 10 of storage. No unique protein was identified for the ALEW samples. These results provide the first report of the proteomic and volatilomic changes associated with EW-treated fresh-cut apple during storage. Data are available via ProteomeXchange with identifier PXD056621. © 2025 RSC.
Survey and Identification of Fusarium Head Blight Pathogens of Wheat in the Western Cape Region of South Africa
(Multidisciplinary Digital Publishing Institute (MDPI), 2025) Ali, Al-Hashimi,; Augustine Innalegwu, Daniel; Omolola, Aina
Fusarium head blight (FHB) is a major disease affecting wheat production worldwide, caused by multiple Fusarium species. In this study, seven Fusarium strains were isolated from wheat fields across the Western Cape region of South Africa and identified through phylogenetic analysis. The strains were classified into three species complexes: the Fusarium graminearum species complex (FGSC), Fusarium incarnatum-equiseti species complex (FIESC), and Fusarium tricinctum species complex (FTSC). Disease severity was highest in the South coast regions of Swellendam (42.73%) and Caledon (38.00%), with the dough stage of wheat development showing the highest disease rate (0.3 in Swellendam and Caledon). The phylogenetic analysis showed distinct clustering of these isolates with known species from the NCBI database, confirming their classification. F. ipomoeae was uniquely found in Swellendam and Caledon, while F. tricinctum occurred only in Klipheuwel and Caledon, highlighting geographical variation in species distribution. Mycotoxin profiling revealed that F. culmorum and F. pseudograminearum produced zearalenone, F. culmorum and F. tricinctum produced 15-acetyl-deoxynivalenol (15-ADON), while F. pseudograminearum produced nivalenol (NIV). These findings provide significant insights into the distribution of Fusarium species and their associated trichothecene chemotypes in the Western Cape, which is crucial for developing effective FHB management strategies and ensuring food security and safety. © 2025 by the authors.
Effects of ZnO nanoparticles concentration on the morphology and textural properties of ZnO/NiFe2O4 nanocomposite
(Elsevier B.V., 2025) Daniel, Augustine Innalegwu; Keyster, Marshall; Tijani, Jimoh Oladejo
The aim of this study is to synthesize and characterize ZnO and NiFe2O4 nanoparticles via green route and co-precipitation of ZnO/NiFe2O4. X-ray diffraction (XRD) data show no extra diffraction peaks belonging to other phases except wurtzite. High resolution transmission electron microscopy (HRTEM) images showed that the average interplanar distance of wurtzite phase at 3, 5, and 7 % dopant concentration were about 0.28, 0.44 and 0.33 nm respectively. X-ray photoelectron spectroscopy (XPS) results show difference in binding energies of the elements present in different concentration of the dopants. Electron Energy Loss Spectroscopy (EELS) spectra show similarities in the shape of Zn, Fe and Ni from zero loss, low loss and core loss region with a little shift in energy. All the elements exhibit multiple oxidation state; +2 and +3 for Fe and +1 and +2 for Zn and Ni. Brunauer-Emmett-Teller (BET) plot shows that ZnO belongs to the type II isotherm curve while NiFe2O4 and 3, 5 and 7 % ZnO/NiFe2O4 all belong to type IV isotherm curve indicating ZnO as macroporous while NiFe2O4 and different dopant concentration of ZnO/NiFe2O4 are mesoporous. The study shows the complete synthesis of ternary ZnO/NiFe2O4 nanocomposites using green synthesis and sol-gel approach. • Green synthesis of ZnO and NiFe2O4 using leaf extract of Anacardium occidentale • Co-precipitation method at different concentration of ZnO and NiFe2O4 for the synthesis of ZnO/NiFe2O4. • Nanocomposites was characterized using different analytical tools
Repurposing of apoptotic inducer drugs against mycobacterium tuberculosis
(Nature Research, 2025) Klein, Ashwil; Keyster, Marshall; Nyambo, Kudakwashe
Computational approaches complement traditional in-vitro or in-vivo assays, significantly accelerating the drug discovery process by increasing the probability of identifying promising lead compounds. In this study, the apoptotic compounds were assessed for antimycobacterial activity and immunomodulatory potential in infected THP-1 macrophage cells. The antimycobacterial activity of the apoptotic compounds was evaluated using the minimum inhibitory concentration (MIC) assay. The immunomodulatory potential of the apoptotic compounds was determined on mycobacterial-infected THP-1 and non-infected THP-1 macrophage cells. The potential binding dynamics of the compounds against InhA were predicted using molecular docking, molecular dynamics, and MM-GBSA binding free energies. The in-vitro MIC assay showed that cepharanthine (CEP) had the highest antimycobacterial activity against Mycobacterium smegmatis mc2155 and Mycobacterium tuberculosis H37Rv, with MICs of 3.1 and 1.5 µg/mL, respectively, followed by CP-31398 dihydrochloride hydrate (DIH) (MICs = 6.2 and 3.1 µg/mL, respectively), marinopyrrole A (MAR) (MICs = 25 and 12.5 µg/mL, respectively), and nutlin-3a (NUT) (MICs = 50 and 25 µg/mL, respectively). MICs for the rest of the drugs were > 200 µg/mL against both M. smegmatis mc2155 and M. tuberculosis H37Rv. Furthermore, the growth of M. smegmatis mc2155 in infected THP-1 macrophage cells treated with DIH, CEP, carboxyatractyloside potassium salt (CAR), and NUT was inhibited by the mentioned drugs. Cytokine profiling showed that DIH optimally regulated the secretion of IL-1β and TNF-α which potentially enhanced the clearance of the intracellular pathogen. Molecular dynamics simulations showed that NUT, MAR, 17-(allylamino)-17-demethoxygeldanamycin (17-AAG), and BV02 strongly bind to InhA. However, 17-AAG and BV02 did not show significant activity in-vitro. This study highlights the importance of probing already existing chemical scaffolds as a starting point for discovery of therapeutic agents against M. tuberculosis H37Rv using both pathogen and host directed approaches. The integration of molecular dynamics simulations provides valuable insights into potential scaffold modifications to enhance the affinity.
High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida)
(Nature Research, 2025) Trindade Marla; Di Costanzo F; Di Marsico M
Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.
Genome-wide characterization of DREB transcription factors in Medicago truncatula: Insights into their roles in development and abiotic stress response
(Elsevier Inc, 2025) Ndiko, Ludidi; Haddoudi, Loua; Ayadi, Mariem
Dehydration-responsive-element binding (DREB) proteins play a crucial role in drought, salt, and environmental stress tolerance. In this study, we identified and annotated fifty-four DREB genes from the Medicago truncatula genome. These genes were analyzed at the molecular level, focusing on gene classification, genomic organization, phylogeny, synteny, structural features, and expression profiles. Phylogenetic analysis revealed that MtDREB proteins are categorized into six subgroups (A1–A6), with highly conserved motif compositions among them. Expression profiling showed that MtDREB genes are differentially expressed in various plant organs and under abiotic stresses (cold, salinity, and dehydration), with 30 % exhibiting high expression during flowering and development. Data from RNA-seq and microarrays demonstrated that 76 % of MtDREB genes are differentially expressed under at least one stress condition, indicating their involvement in various signaling pathways activated by abiotic stresses. Notably, MtDREB05, primarily induced under osmotic stress, appears to be a promising candidate for improving abiotic stress tolerance. These findings will enhance our understanding of the DREB family and aid in functional validation of DREBgenes in M. truncatula and related forage species.
Antioxidant and antimicrobial activities of green-synthesized silver nanoparticles using a cocktaila aqueous extract of capparis sepiaria root and tabernaemontana elegans bark
(Wiley, 2025) Mashilo, Cate M.; Sibuyi Nicole RS; Botha, Subelia; Meyer, Mervin; Madiehe, Abram M
The increasing incidence of antimicrobial resistance (AMR) poses a serious threat to public health, which necessitates the development of alternative countermeasures to combat it. Green nanotechnology, in particular the use of silver nanoparticles (AgNPs), shows promise in combating AMR. Although the synthesis of AgNPs using medicinal plant extracts has been explored, combining extracts from two medicinal plants to synthesize AgNPs with enhanced properties has received less attention. Therefore, this study addresses this gap by presenting the green synthesis of AgNPs using a cocktail of Capparis sepiaria–Tabernaemontana elegans (CsTe) aqueous extract as reducing, stabilizing, and capping agents. The focus is on assessing the antioxidant and antimicrobial activities of the synthesized CsTe-AgNPs. Various parameters, such as pH, temperature, extract and silver concentrations, reaction ratio, and synthesis time, were optimized to enhance the efficiency of CsTe-AgNPs synthesis. The CsTe- AgNPs were monodispersed and spherical, with an average core size of 14 ± 2.953 and 7 ± 3.849 nm, and hydrodynamic size of 23 ± 12.260 and 138 ± 2.086 nm for pH = 6 and pH = 11, respectively. The FTIR analysis revealed a shift in peaks of biomolecules present in the CsTe extracts that could be responsible for the reduction of Ag salt to form CsTe-AgNPs. Notably, CsTe-AgNPs_pH11 had potent antimicrobial activity, with a minimum inhibitory concentration (MIC) of 12.5 ± 0 μg/mL against K. pneumoniae and P. aeruginosa, and a slightly higher MIC for C. albicans of 25 ± 5.449 μg/mL. This study demonstrated the effectiveness of using a mixture of two extracts to synthesize AgNPs with enhanced antioxidant and antimicrobial activities, and therefore, could serve as a promising reagent to combat AMR.
Carbon dynamics in termite mounds: the effect of land use on microbial oxalotrophy
(Elsevier B.V., 2025) Trindade, Marla; Nel, Teneille; Clarke, Catherine E
The semi-arid western region of South Africa hosts extensive earthen mounds known as heuweltjies, which are inhabited by Microhodotermes viator termites and play a critical role in soil biogeochemical cycling. These mounds accumulate significant stores of soil organic and inorganic carbon (C), including pedogenic calcium carbonate, which may form through microbially induced calcite precipitation. In this study, the effects of land use change on C dynamics in heuweltjie soils were assessed by examining soil biogeochemistry and apparent respiratory quotient (ARQ, based on soil pore gas composition). We investigated the oxalate-carbonate pathway (OCP) as a potential mechanism of C sequestration. Topsoils were collected from one pristine and one cultivated termite mound in a semi-arid region of South Africa and incubated for one week. The carbon dioxide (CO2) and oxygen concentrations of soil pore gas as well as chemical properties of soils treated with termite frass (excrement) or calcium oxalate (CaOx) were monitored. Increases in pH and the calcite saturation index in both CaOx- and frass-treated soils suggested the potential occurrence of the OCP. The ARQ values did not reflect geochemical changes associated with OCP due to competing metabolic pathways, such as potential lignin degradation in frass-treated soils. Higher ARQ values in uncultivated versus cultivated CaOx-treated soils may indicate higher carbon use efficiency in uncultivated soils or destabilization of existing C in cultivated soils. Respiration in frass-treated soils was higher than control and CaOx-treated soils and resulted in production of bicarbonate (via dissociation of carbonic acid formed by dissolution of respired CO2 in water). This implies that termite-affected landscapes may sequester C in inorganic form. Increased total C in both cultivated and uncultivated soils treated with frass suggests that microbial CO2-fixation may occur in termite-affected landscapes, necessitating further investigation of pathways responsible for this process.

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