Research Articles (Biochemistry, Genetics and Microbiology (BGM))

Permanent URI for this collectionhttp://hdl.handle.net/2263/87805

Browse

Now showing 1 - 20 of 786

Low genotypic diversity and first reports of clinical Sporothrix from retrospective samples in South Africa
Fuchs, Taygen; Vismer, Hester F.; Visagie, Cobus M.; Wingfield, Brenda D.; Wingfield, Michael J. (Oxford University Press, 2025-11)
Sporotrichosis is a fungal infection caused by Sporothrix species. Some of the largest outbreaks of this disease have been recorded in South Africa, and the country is considered an endemic region for the pathogen. Previous work in the 1990s considered the etiological agents of the disease, with strains stored in various culture collections. In this study, we reconsidered the identity of these strains by polymerase chain reaction amplification and sequencing of three gene regions (ITS, BenA, and CaM) and assessed their genetic diversity by microsatellite typing. The results showed that the population included four species, S. schenckii (n = 69), S. globosa (n = 1), S. pallida (n = 1), and an uncharacterised taxon (n = 2). The mating type distribution of the S. schenckii population was predominantly of the MAT1-2 idiomorph (92%). Microsatellite markers revealed only four multi-locus genotypes, of which a single genotype represented 85% of the isolates. The results provide evidence for asexual proliferation of S. schenckii lineages in South Africa, and raise questions as to how they have been dispersed. Furthermore, the results highlight uncertainties regarding the relative significance of the other species reported here. PLAIN LANGUAGE SUMMARY : Sporotrichosis is a mammalian cutaneous traumatic infection caused by pathogenic Sporothrix fungi. Using genetic markers, we report several Sporothrix species in South Africa for the first time, and reveal the wide distribution of a closely related genetic lineage in the country.
Mycotoxins : an ongoing challenge to food safety and security
Yilmaz, Neriman; Verheecke-Vaessen, Carol; Ezekiel, Chibundu N. (Public Library of Science, 2025-11-10)
Mycotoxins have influenced human and animal health for centuries, often with serious and sometimes deadly consequences. The earliest known cases are outbreaks of ergotism in medieval Europe, caused by alkaloids from Claviceps purpurea growing on rye. These epidemics, called “St Anthony’s fire”, produced convulsions, gangrene and death. Ergot-infected grain has also been suggested as a possible factor behind the symptoms recorded during the Salem witch trials in 1692. During the Second World War, people in Russia consumed overwintered grain infected by trichothecene-producing Fusarium species. This led to the alimentary toxic aleukia epidemic, one of the best-documented examples of human mycotoxicosis. Such outbreaks demonstrate the longstanding impact of mycotoxins on societies.
Smallholder farmers’ knowledge, perception and management of Spodoptera frugiperda (Lepidoptera: Noctuidae) on Zea mays at irrigation schemes in Limpopo province, South Africa
Nethononda, Phophi D.; Hurley, Brett Phillip; Slippers, Bernard; Makhura, Moraka Nakedi (Elsevier, 2026-03)
The fall armyworm (Spodoptera frugiperda) was first detected in Limpopo province, South Africa, during the 2016/2017 cropping season and continues to cause significant damage to maize production in the region. Despite the significant damage caused by S. frugiperda to maize, there is a lack of documented information on smallholder farmers' responses and control practices in South Africa. This study investigated smallholder farmers' knowledge, perceptions, and management practices of S. frugiperda at the Dzindi and the Tshiombo irrigation schemes in Limpopo province, South Africa. In this study, an irrigation scheme refers to a communal water distribution system that channels water from a river to multiple plots under smallholder cultivation through furrows or canals. Data were collected through 16 focus group discussions with farmers from the two irrigation schemes. A total of 118 farmers participated in the interviews. Each was assigned a unique identifier, which allowed for the recording and analysis of individual responses where applicable. Thematic analysis was used to identify and summarize common themes from participants’ responses, while descriptive analysis using frequencies and percentages was employed to present the responses quantitively. Farmers perceived S. frugiperda as the most destructive insect pest, yet lacked knowledge of its biology, being unable to identify its eggs, pupae, or adult moths. Control was largely through insecticide use. At the Dzindi irrigation scheme, farmers adopted Bt maize but did not comply with resistance management practices. The findings underscore the urgent need for farmer education on insect biology, responsible pesticide use, and proper implementation of Bt maize. The study also highlights the importance of collective rather than individual efforts in managing S. frugiperda, as the consequences of mismanagement can affect all farmers. These findings reveal major gaps in Integrated Pest Management (IPM) practices among smallholder farmers in Limpopo province, South Africa. HIGHLIGHTS • First detection of Spodoptera frugiperda in Limpopo Province, South Africa, occurred during the 2016/2017 cropping season. • Smallholder farmers lack knowledge of the pest's biology, relying on insecticides for its management. • Concurrent use of insecticides and Bt maize raises concerns over the potential evolution of S. frugiperda resistance in the region.
Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans
Timilsina, Sujan; Iruegas-Bocardo, Fernanda; Jibrin, Mustafa O.; Sharma, Anuj; Subedi, Aastha; Kaur, Amandeep; Minsavage, Gerald V.; Huguet-Tapia, Jose C.; Klein-Gordon, Jeannie; Adhikari, Pragya; Adhikari, Tika B.; Cirvilleri, Gabriella; Tapia de la Barrera, Laura Belen; Bernal, Eduardo; Creswell, Tom C.; Doan, Tien Thi Kieu; Coutinho, Teresa A.; Egel, Daniel S.; Félix-Gastélum, Rubén; Francis, David M.; Kebede, Misrak; Ivey, Melanie Lewis; Louws, Frank J.; Luo, Laixin; Maynard, Elizabeth T.; Miller, Sally A.; Nguyen, Nga Thi Thu; Osdaghi, Ebrahim; Quezado-Duval, Alice M.; Roach, Rebecca; Rotondo, Francesca; Ruhl, Gail E.; Shutt, Vou M.; Thummabenjapone, Petcharat; Trueman, Cheryl; Roberts, Pamela D.; Jones, Jeffrey B.; Vallad, Gary E.; Goss, Erica M. (Public Library of Science, 2025-04-09)
Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.
Decoding Cryptococcus : from African biodiversity to worldwide prevalence
Coelho, Marco A.; David-Palma, Ma´rcia; Aylward, Janneke; Pham, Nam Q.; Visagie, Cobus M.; Fuchs, Taygen; Yilmaz, Neriman; Roets, Francois; Sun, Sheng; Taylor, John W.; Wingfield, Brenda D.; Fisher, Matthew C.; Wingfield, Michael J.; Heitman, Joseph (Public Library of Science, 2025-02-03)
Fungal pathogens cause millions of infections and deaths annually, while also contributing to global food insecurity [1]. Among them, basidiomycete Cryptococcus species—particularly C. neoformans (Cn; previously C. neoformans var. grubii, serotype A; lineages VNI, VNII, VNBI, and VNBII), C. deneoformans (Cd; previously C. neoformans var. neoformans, serotype D; lineage VNIV), and the C. gattii (Cg) species complex (Fig 1A)—are significant opportunistic and primary pathogens, especially in sub-Saharan Africa [2,3]. These pathogens primarily cause cryptococcosis, manifesting as severe pulmonary infections or life-threatening meningoencephalitis in both immunocompromised and apparently immunocompetent individuals. Exposures are typically thought to occur by inhalation of desiccated yeast cells or spores from the environment [4]. While Cryptococcus species vary in their occurrence worldwide, mounting evidence suggests an evolutionary origin in Africa for most of the pathogenic Cryptococcus species, where they occupy diverse ecological niches such as trees, pigeon guano, and mammalian middens (Fig 1B). While Cn, Cd, and Cg are pathogenic, nonpathogenic species within the genus (such as C. amylolentus, C. wingfieldii, and C. floricola; Fig 1A) occur either as African microendemic species or are known thus far from only a single isolate in the Canary Islands (C. floricola) [5,6]. This review explores the likely African origins of Cryptococcus, its ecological diversity, and how pathogenic species spread globally, transitioning from environmental microbes to human pathogens.
The hidden cost of open access : artificial intelligence, paywalls and the risk of knowledge inequity
Wingfield, Brenda D.; Wingfield, Beverly Jane (Academy of Science of South Africa, 2025-11)
SIGNIFICANCE : This Commentary underscores the urgency of rethinking how artificial intelligence systems and publishing models intersect. Rather than focusing solely on efficiency or access, we call attention to structural inequities that shape who is visible in the scholarly record. By highlighting the systemic risks of exclusion, we argue for proactive collaboration between policymakers, publishers and technologists to design frameworks that safeguard equity and inclusivity in the future of academic research.
Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria
Van Goethem, Marc W.; Vikram, Surendra; Cowan, Don A.; Makhalanyane, Thulani P. (BioMed Central, 2025-11-05)
BACKGROUND : Terrestrial polar cyanobacteria persist at the cold limits of life, enduring a suite of extreme stressors including sub-zero temperatures, frequent freeze–thaw cycles, oligotrophic soils, variable light regimes with long periods of darkness, and desiccation. To survive, cyanobacteria have evolved diverse physiological strategies. A key adaptation among Antarctic terrestrial cyanobacteria is niche colonization: inhabiting the undersides of translucent quartz rocks (hypoliths) and the interior spaces of porous rocks (endoliths), which buffer environmental extremes and sustains the potential for photoautotrophic carbon fixation. However, the full genomic repertoire facilitating their resilience is incomplete. RESULTS : We cultivated cyanobacteria from endolithic and hypolithic niches in Victoria Valley, Eastern Antarctica, and recovered four near-complete genomes (100% completeness, < 1% contamination). Three hypolithic genomes showed near-identical sequence similarity (whole genome average nucleotide identity = 99.98%) and phylogenomic proximity to the genus Coleofasciculus, yet represent a novel species, Coleofasciculus caryii H7-2. The fourth genome, derived from an endolith, showed moderate similarity to Aliterella antarctica (whole genome average nucleotide identity = 79.1%), and is proposed as a new species, Aliterella bergstromii E5.1. C. caryii H7-2 possessed a larger genome (~ 6.1 Mbp) than A. bergstromii E5.1 (~ 5.4 Mbp). Both genomes encoded complete pathways for carbon fixation via oxygenic photosynthesis (RuBisCO and phosphoribulokinase), extensive phycobilisomes, and multiple photoprotective mechanisms. Predicted optimal growth temperatures were 21.7 °C and 23.2 °C, respectively. Shared stress-mitigation genes included those for osmotic, thermal and oxidative (superoxide dismutase) stress response. All genomes contained biosynthetic gene clusters associated with stressadaptive secondary metabolites, including heterocyst glycolipids, siderophores, phenazines, compounds related to nostopeptolide and merocyclophane. The C. caryii H7-2 genome encoded multiple CRISPR-Cas systems, suggesting adaptive immunity and historical phage exposure. In contrast, A. bergstromii E5.1 harboured a single prophage and an array of 24 plasmids. CONCLUSIONS : These finding reveal that the newly-described cyanobacteria possess a rich genomic repertoire of adaptations to withstand Antarctic extremes, emphasizing the resilience and ecological importance of lithobiontic cyanobacteria in polar deserts.
Assessing Gonipterus defoliation levels using multispectral unmanned aerial vehicle (UAV) data in Eucalyptus plantations
Nzuza, Phumlani; Schröder, Michelle L.; Heim, Rene J.; Daniels, Louis; Slippers, Bernard; Hurley, Brett Phillip; Germishuizen, IIaria; Sivparsad, Benice; Roux, Jolanda; Maes, Wouter H. (Elsevier, 2025-12)
Invasive insect pest Gonipterus sp. n. 2 (Coleoptera: Curculionidae) threatens Eucalyptus species, causing defoliation and yield loss through adult and larval feeding. Early detection is important for early intervention to prevent pest outbreaks. As conventional insect pest monitoring methods are time-consuming and spatially restrictive, this study assessed the potential of UAV monitoring. Multispectral imagery was obtained with Unmanned Aerial Vehicles (UAVs) across six different stands of young Eucalyptus dunnii with varying levels of Gonipterus sp. n. 2 infestations. Some stands were revisited, a total of 9 datasets were covered. Reference damage levels were obtained through visual assessments of (n = 89–100) trees at each site. Across sites, a decrease in canopy reflectance in both the visual and the near-infrared domains with increasing damage levels was consistently observed. Several vegetation indices showed consistent patterns, but none showed site independence. XGBoost, Support Vector Machine and Random Forest (RF) were used to predict damage levels using five input spectral data types. XGBoost performed best, closely followed by RF. Both models consistently selected very similar features. The best-performing models included reflectance, vegetation indices and grey-level co-occurrence matrix data. When data from 10 different wavelengths were used, the highest classification accuracy was 92 % across all sites in classifying defoliation levels. With a classical 5-band multispectral camera, accuracy was 88 %, but distinguishing medium damage from low remained challenging. However, the method was less reliable when trained and validated on separate fields. This study highlights the potential of multi-site datasets in increasing the model's generalization, using UAV based multispectral imagery to assess Gonipterus sp. n. 2 damage and demonstrating reliable upscaling from individual tree assessments to stand scale. However, it also recognises the difficulty of generating a robust model that performs well on untrained sites. HIGHLIGHTS • Canopy damage from Gonipterus sp. n. 2 was assessed across stands using UAV imagery, capturing defoliation, chlorophyll reduction. • The 5-band imagery perfomed comparable to the 10-band but was less effective at detecting subtle low vs no damage defoliation. • Similar pattern was observed across sites but absolute reflectance and vegetation indices are site specific.
Enhancing plantation forest sustainability : a review of Eucalyptus defence mechanisms to foliar fungal pathogens
Solis, Myriam; Hammerbacher, Almuth; Wingfield, Michael J.; Naidoo, Saloshnee (Springer, 2025-02)
PURPOSE OF THE REVIEW : In this review, we synthesize knowledge generated over many decades on the main defence responses of Eucalyptus to fungal leaf pathogens with the aim of identifying targets for breeding disease tolerant trees. We highlight physiological and molecular traits associated with host defence in relation to pathogen life-style. Overall, the purpose of this review is to identify resistance mechanisms that offer improved resilience of Eucalyptus plantations in the face of increasing threats by foliar fungal pathogens. The broad aim is to promote sustainable forestry through appropriate selection of resistance traits in trees that are widely planted for commercial timber production. RECENT FINDINGS : Eucalyptus is among the most important tree genera planted for commercial timber production worldwide. Numerous foliar pathogens have been reported on these trees in the last 30 years with numbers of recent reports increasing exponentially. The majority of these diseases affect the leaves and shoots of the trees. Knowledge on resistance traits in Eucalyptus to fungal foliar pathogens is limited. This is in part due to the high intra- and inter-species variation in molecular and physiological responses of the host and variation in responses to different pathogens, especially those with different trophic modes. A well-founded understanding of such host responses will provide valuable knowledge required to maintain healthy, sustainable Eucalyptus plantations, especially in the face of changing environmental conditions, where new diseases are caused by fungi previously not considered relevant. SUMMARY : Foliar diseases are among the most important challenges for Eucalyptus plantations globally. The effects of climate change and new or more serious outbreaks present an important threat to the sustainability of Eucalyptus plantations worldwide. Due to restrictions on the use of chemicals, more feasible solutions for disease management lie in selecting planting material with resistance traits. To achieve that goal, it is essential to understand the most important physiological and molecular responses of Eucalyptus to infection by pathogens that infect their foliar tissues. In this review we summarise the available knowledge of the main physiological defence barriers and genetic traits that play key roles in the broad defence against foliar fungal pathogens. Furthermore, we consider defence pathways that are specifically related to the lifestyle and trophic mode of the pathogens. In order to ensure the future sustainability of Eucalyptus plantations, it will be necessary to understand how disease resistance is affected by climate change, as well as the adaptability of the hosts and pathogens to newly emerging environmental conditions.
The pine pathogen Diplodia sapinea : expanding frontiers
Wingfield, Michael J.; Slippers, Bernard; Barnes, Irene; Duong, Tuan A.; Wingfield, Brenda D. (Springer, 2025)
PURPOSE OF REVIEW : This review offers a thorough examination of the pine pathogen Diplodia sapinea, tracing its historical significance from its initial impact on South African non-native Pinus plantations to its recent emergence as a major threat to forests, particularly in Europe. It also highlights recent findings regarding its taxonomic position, genetic studies, and shifts from being perceived as a wound-infecting pathogen to an endophyte in healthy Pinus species that causes disease after stress. RECENT FINDINGS : Recent years have witnessed a dramatic increase in the damage caused by D. sapinea in natural and planted forests. This escalation is apparently strongly linked to climate change. The pathogen’s previously confused taxonomic position has been clearly resolved in the Botryosphaeriaceae, alongside several sibling species. Diplodia sapinea is now well-understood as an endophyte in healthy trees, which has significant implications for studies aimed at understanding its biology. Importantly, robust techniques including those utilizing genome sequences, are now available for rapid identification and population genetic studies of the pathogen and the factors that drive disease outbreaks. SUMMARY : Over the past century, D. sapinea has transitioned from a localized problem in South African non-native plantations to a global threat to both natural and planted forests, particularly in Europe. This review underscores the importance of historical context in understanding the evolution of the pathogen’s impact. It also lays the foundation for future research endeavours, leveraging modern technologies to address key questions surrounding its biology and ecology.
Diversity of environmental Escherichia coli in subtropical freshwater systems of South Africa
Seale, Tarren; Brözel, Volker Siegfried; Potgieter, Sarah Catherine; Rupp, Oliver; Blom, Jochen; Steenkamp, Emma Theodora; Venter, S.N. (Stephanus Nicolaas) (Springer, 2025-07)
Escherichia coli is widely used as an indicator of faecal contamination, as it is assumed that faeces from warm-blooded animals is the primary source of E. coli in the environment. However, various studies have shown that E. coli can survive and multiply in environmental niches, including soil, sand and sediment. E. coli can be assigned to eight main phylogroups but environmental E. coli are associated primarily with phylogroups A and B1. In this study, 410 E. coli were isolated from different niches within two peri-urban catchments in the Gauteng province of South Africa. To represent the E. coli circulating within the human population, E. coli was also isolated from sewage before treatment and released into these reservoirs. To capture the diversity of E. coli among these isolates, the β-D-glucuronidase (uidA) and mismatch repair (mutS) genes were sequenced. While isolates linked to phylogroup B1 dominated as was expected, the recovery of many isolates linked to phylogroup B2, the second most dominant group, was unanticipated. To further investigate this observation, the genomes of representative phylogroup B2 isolates were sequenced and subjected to phylogenetic and functional analyses. The results showed that phylogroup B2 isolates formed a distinct phylogenetic cluster, apparently independent of niche or geographic origin. Our findings also showed that while isolates seem to be associated with environmental samples, they could have the ability to colonize the gut and cause disease as they harboured several virulence factors associated with extraintestinal E. coli.
Extracting protoplasts from filamentous fungi using extralyse, an enzyme used in the wine industry
Wilson, Andi M.; Van Dijk, Alida; Marx, Bianke; Du Plessis, Deanne; Terblanche, Grant; Bornman, Simoné; Wilken, Pieter Markus; Duong, Tuan A.; De Fine Licht, Henrik H.; Wingfield, Brenda D. (Wiley, 2025-03)
The ability to extract protoplasts has contributed significantly to the study of fungi and plants. Protoplasts have historically been used to determine chromosome number via pulsed-field electrophoresis and for the functional characterization of genes via protoplast transformation. More recently, protoplasts have been used to extract the high-molecular-weight DNA required for long-read sequencing projects. The availability of efficient protoplast extraction protocols is thus integral to the study and experimental manipulation of model and non-model fungi. One major hurdle to the development of such protocols has been the discontinuation of enzymes and enzyme cocktails used to digest the fungal cell wall. Here, we provide five protoplast extraction protocols for use in various filamentous ascomycete species spanning the genera Ceratocystis, Fusarium, Metarhizium, Ophiostoma, and Sclerotinia. These protocols all use an inexpensive, readily available enzyme cocktail called Extralyse, a commercially available product commonly used in the wine making industry. Using this enzyme cocktail overcomes reliance on the laboratory-grade enzymes that have frequently been discontinued and are often cost prohibitive at the concentrations required. The protocols described here will allow further research, including genome editing, to be conducted in these fungal genera. Importantly, these protocols also provide a starting point for the development of protoplast extraction techniques in other filamentous fungi. This resource can therefore be used to expand the molecular toolkits available for fungi beyond the species described here, including those with relevance in both medical and biotechnological industries. Basic Protocol 1: Protoplast extractions from Ceratocystis eucalypticola and Ceratocystis fimbriata. Basic Protocol 2: Protoplast extractions from Fusarium circinatum. Basic Protocol 3: Protoplast extractions from Metarhizium acridum, Metarhizium brunneum, and Metarhizium guizhouense. Basic Protocol 4: Protoplast extractions from Ophiostoma novo-ulmi. Basic Protocol 5: Protoplast extractions from Sclerotinia sclerotiorum.
High-resolution climate downscaling using terrain features and global circulation models : applications for species suitability in the management of plantation forestry
Van der Merwe, Jaco Pierre; Van Heerden, Elane; Germishuizen, Ilaria; Christie, Nanette; Kok, James; Ncongwane, Thandekile H.; Spencer, Katharine; Melane, Mandlakazi; Mansfield, Shawn D.; Ernst, Yolandi (Springer, 2026)
The forestry landscape is being climatically redefined due to global warming. Limited knowledge is available on whether introduced pine species will be viable for plantation forestry in South Africa. Existing global circulation models were scaled down to a finer resolution by incorporating historical climate data, global positioning, and terrain conditions (terrain scaling). Terrain scaling of mean annual maximum temperature (MAT-max), minimum temperature (MAT-min), and median annual precipitation rainfall (MAP-median) was statistically significant, achieving R2 values of 0.70, 0.78 and 0.90, respectively. Decadal climate change was analyzed for the period ranging from 2020 to 2060. Future decadal temperatures were found to increase and were generally greater in high-altitude regions compared to low-altitude regions. MAT-max increased by up to 1.7 °C and MAT-min by 0.4 °C by 2060. MAP-median decreased by up to 10% by 2060, with high-rainfall areas in low-altitude regions being more greatly impacted. Climate suitability was determined for Pinus elliottii, P. taeda, P. patula and the hybrid P. patula × P. tecunumanii by harnessing existing species-specific climate threshold models for the region. Current and future conditions were found to be most suitable for P. patula × P. tecunumanii plantations. Isolated climate niches with warmer, drier conditions were best suited for P. patula plantations, while warm, humid conditions favoured P. elliottii plantations. None of the current and future climatic conditions were suitable for P. taeda plantations. A similar approach can be applied to forestry regions globally to enable pre-emptive tree breeding and the introduction of new forest species due to climate change.
Short communication: Elevated testosterone correlates with enhanced innate immune function in a cooperatively breeding rodent
Wallace, Kyra Mary Elizabeth; Venter, S.N. (Stephanus Nicolaas); Bennett, Nigel Charles; Hart, Daniel William (Elsevier, 2025-10)
In many vertebrates, elevated testosterone is believed to compromise the immune function, reflecting a trade-off between reproduction and survival. However, such trade-offs may potentially be relaxed in cooperative breeders, where social conflict and sexual selection are reduced. We investigated the relationship between testosterone, cortisol, and innate immunity in captive male Damaraland mole-rats (Fukomys damarensis), a eusocial rodent with minimal aggression-driven reproductive competition. Using microbial killing assays (MKAs) and white blood cell counts as proxies of immune function, we found that urinary testosterone concentration was positively correlated with immune strength. Males with higher urinary testosterone concentrations exhibited significantly greater antimicrobial capacity and elevated total white blood cell counts. However, urinary testosterone was unrelated to independent immune cell differentials. While, reproductive status, age, body mass, and urinary cortisol concentrations had a limited effect on any immune metric. These findings, while correlative, challenge traditional endocrine-immune trade-off models and infer that, in this species, testosterone may signal condition rather than impose immunosuppressive costs.
Electro-impedimetric detection of human anti-mycolate antibody biomarkers of TB before, during, and after treatment
Baumeister, Carl Robert; Verschoor, Jan Adrianus; Ueckermann, Veronica; Molatseli, Mosa; Sesing, Thoriso; Khuboni, Nomthandazo; Fourie, Bernard P. (Taylor and Francis, 2025)
Efficient TB management requires rapid and accurate diagnosis of active pulmonary and extrapulmonary TB at the point-of-care. Blood-based antibody biomarker assays may be ideal if unaffected by HIV co-infection and antibody memory from prior TB or vaccination. AIM : This study assessed electro-impedimetric detection (EIS-MARTI) of anti-mycolate antibodies (AMAb) in TB patients before, during, and after treatment, compared to sputum culture (MGIT) as the gold standard. METHODS : A prospective pilot study enrolled 15 confirmed TB patients and 73 healthy controls at a Pretoria hospital (2016–2017). A prospective monitoring study followed 25 confirmed TB patients over 6 months of treatment at a Pretoria clinic (2019–2020) to evaluate biomarker behavior. Outcomes were analyzed using descriptive statistics, wherein diagnostic accuracy and predictive values were assessed by ROC curve analysis. RESULTS : EIS-MARTI detected 14/15 true TB-positive cases independent of HIV co-infection and 68/73 true TB-negatives in the pilot study. In the monitoring study, EIS-MARTI correlated with culture in 7/8 cases at treatment end, but not during the first 2 months. CONCLUSION : AMAbs arise independently of HIV co-infection in active TB, recede during treatment, and are rapidly detected by a hand-held EIS-MARTI device. While suitability for treatment monitoring remains uncertain, EIS-MARTI shows promise for rapid, accurate TB diagnosis and confirming cure. PLAIN LANGUAGE SUMMARY : The purpose of this work was to investigate anti-mycolate antibodies as a suitable biomarker for diagnosing tuberculosis, monitoring treatment, and screening people at risk for TB.
Resolving the population structure and demographic history of the European anchovy in the Northeast Atlantic : tracking historical and contemporary environmental changes
Pujolar, Jose Martin; Gardiner, Courtney E.C.; Von Der Heyden, Sophie; Robalo, Joana I.; Castilho, Rita; Cunha, Regina; Henriques, Romina; Nielsen, Einar E. (Wiley, 2025-07)
The spatial distribution of the European anchovy has expanded in the northern part of its range in the Northeast Atlantic in recent decades. However, whether this results from a northward range shift of southern conspecifics or the expansion of a local northern population is unknown. Using for the first time whole-genome sequencing, we explore current patterns of genetic diversity and population sub-structuring of European anchovy in the Northeast Atlantic, with special focus on recently expanded North Sea areas. Genomic data suggested three distinct groups: Northern (North Sea and Kattegat), Southern (Ireland and Central Portugal) and Cadis (South Portugal). Despite most of the genome being homogenised by high levels of gene flow characteristic of small pelagic fish, several large regions of high genetic differentiation were observed. This suggests that genomic population boundaries might be maintained by local adaptation within chromosome structural variants (inversions). Admixture analysis indicates that the ongoing northern range shift involves both migrants of southern origin and expansion of the local North Sea population. Historical demographic inference suggests that anchovies survived the last glacial period with small population sizes, followed by a split into the current Northern and Southern groups at the end of the last glacial maximum. The Southern group then expanded into the North Sea as the ice sheets retreated, in an expansion involving a large number of individuals, which is consistent with the retention of most of the genetic diversity. In comparison with other small pelagic fish, the genetic patterns found in anchovies (deeply divergent groups, no loss of genetic diversity during expansion, mixing between groups) align well with those found in European sprat, while sardines fit the pattern of expansion of a leading-edge population, with reduced genetic diversity and much shallower divergence between populations. This study contributes to a better understanding of population structure, range shifts and local adaptation in small pelagic fish under climate change, informing conservation and management efforts.
Resolving the stasis-dynamism paradox : genome evolution in tree ferns
Wei, Zuoying; Chen, Hengchi; Feng, Chao; Xia, Zengqiang; Van de Peer, Yves; Kang, Ming; Wang, Jing (Oxford University Press, 2025-10)
The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental fluctuations—remains unresolved in evolutionary biology. Here, we present chromosome-scale genomes for three ecologically divergent species (including both arborescent and nonarborescent growth forms) within Cyatheaceae, an ancient tree fern family characterized by morphological conservation dating back to the Jurassic era. Our results revealed substantial yet cryptically regulated genomic dynamism. A shared Jurassic whole-genome duplication (∼154 Ma) conferred dual adaptive advantages: initially buffering tree ferns against Late Jurassic climatic extremes through retention of stress-response genes, and subsequently facilitating niche diversification and phenotypic innovation via lineage-specific repurposing of duplicate genes. Arborescent lineages preferentially retained duplicates involved in cell wall biogenesis, essential for structural reinforcement and lignification, while nonarborescent forms conserved paralogs linked to metabolic resilience and defense. Alongside slow substitution rates, we detected cryptic genome dynamism mediated primarily by bursts of transposable elements, leading to genome size variations, chromosomal rearrangements, and localized innovation hotspots with elevated evolutionary rates. The concerted expansion and expression of lignification-related genes, coordinated with light signaling components, suggest a potential evolutionary mechanism integrating light perception with shade adaptation and lignification, facilitating arborescent adaptation in angiosperm-dominated understories. Our findings redefine evolutionary stasis as a dynamic equilibrium, sustained by regulatory plasticity and localized genomic innovation within a conserved morphological framework. This study offers a novel genomic perspective on the long-term persistence and evolution of ancient plant lineages, demonstrating how regulated genomic dynamism enables adaptive diversification while sustaining morphological conservatism.
SeqWord motif mapper : a tool for rapid statistical analysis and visualization of epigenetic modifications in bacterial genomes
Lefebvre, Christophe M.J.; Pierneef, Rian Ewald; Reva, Oleg N. (Elsevier, 2025-10)
Genomic methylation in bacteria plays a crucial role in gene regulation, chromosome replication, pathogenicity, and defense against phages. While single-molecule real-time (SMRT) sequencing technologies have advanced the detection of epigenetically modified bases, the statistical analysis of their distribution and the possible roles they play in bacterial cells remains challenging. To address this gap, we developed SeqWord Motif Mapper (SWMM), a computational tool designed for the statistical analysis and visualization of bacterial methylation patterns. SWMM utilizes PacBio sequencing data to identify sequence coverage, methylation motif distribution, and putative functional associations. Implemented in Python 3.9, the tool is platform-independent and requires minimal dependencies, making it accessible to a wide range of users. The SWMM command-line interface and a web-based version of the program facilitate the exploration of epigenetic modifications across bacterial genomes. Through case studies on different bacterial and archaeal taxa, we demonstrated that genome methylation in microorganisms extends beyond canonical sites and possibly influences gene expression, adaptation, and genome architecture. The tool enables detailed statistical evaluation of methylation motif distribution and provides insights into the potential regulatory roles of epigenetic modifications in bacterial genomes. SWMM is freely available at https://begp.bi.up.ac.za, with source code hosted on GitHub at https://github.com/chrilef/BactEpiGenPro. HIGHLIGHTS • Visualizes bacterial methylation using PacBio sequencing data. • Detects canonical and non-canonical methylation motif distributions. • Highlights strand-biased and replicon-specific methylation patterns. • Includes statistical analysis of motif bias in coding and non-coding regions. • Open-source and web-based tool for epigenetic data exploration.
Optimization and characterization of the antimalarial activity of N-aryl acetamides that are susceptible to mutations in ROM8 and CSC1
Nguyen, William; Boulet, Coralie; Dans, Madeline G.; Loi, Katie; Jarman, Kate E.; Barnes, Claudia B.G.; Yeo, Tomas; Sheth, Tanaya; Mukherjee, Partha; Chakraborty, Arnish; Famodimu, Mufuliat T.; Delves, Michael J.; Pollard, Harry; Sutherland, Colin J.; Coyle, Rachael; Sevilleno, Nicole; Boonyalai, Nonlawat; Lee, Marcus C.S.; Rabie, Tayla Anne; Birkholtz, Lyn-Marie; Baud, Delphine; Brand, Stephen; Chowdury, Mrittika; De Koning-Ward, Tania F.; Fidock, David A.; Gilson, Paul R.; Sleebs, Brad E. (American Chemical Society, 2025-07)
New antimalarials are needed due to the threat of emerging resistance against existing antimalarial therapies. A phenotypic screen uncovered the N-aryl acetamide class that inhibits the development of P. falciparum asexual ring-stage parasites. The structure–activity relationship of this class was investigated, and key modifications were introduced that produced WEHI-326 with potent antimalarial activity. Enhancing the metabolic stability of this class will be a future challenge to achieve efficacy in a malaria mouse model. WEHI-326 was found to have a moderate barrier to resistance and a moderate rate of asexual kill, potently inhibited gametocyte and gamete development, and in turn, blocked the transmission of parasites to the mosquito. Forward genetics and cross-resistance profiling determined that parasites resistant to N-aryl acetamides had mutations in rhomboid protease 8 (ROM8) and the putative cation channel, CSC1. WEHI-326 will be an important tool in unraveling the role of ROM8 and CSC1 in P. falciparum development.
Novel inhibitors of Plasmodium Phosphatidylinositol 4-kinase IIIβ with low propensity for resistance : life cycle stage activity and in vivo efficacy in a humanized mouse malaria infection model
Dziwornu, Godwin A.; Mmonwa, Mmakwena M.; Coertzen, Dina; Krugmann, Liezl; Salomane, Nicolaas; Leshabane, Meta; Thomas, Jean Argyle; Da Rocha, Shanté; Reader, Janette; Masike, Keabetswe; Njoroge, Mathew; Sevilleno, Nicole; Coyle, Rachael; Boonyalai, Nonlawat; Mayville, Emily; Lee, Marcus C.S.; Fidock, David A.; Coulson, Lauren B.; Woodland, John G.; Wicht, Kathryn J.; Ghorpade, Sandeep R.; Birkholtz, Lyn-Marie; Chibale, Kelly (American Chemical Society, 2025-08)
Please read abstract in the article.

Browse

Recent Submissions