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

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

Browse

Now showing 1 - 20 of 747

The effect of semiorganic iodine-containing compounds on the antibiotic susceptibility of pathogenic microorganisms
(MDPI, 2025-08) Kenesheva, Sabina T.; Turganbay, Seitzhan; Jumagaziyeva, Ardak B.; Askhatkyzy, Gaukhar; Askarova, Dana A.; Azembayev, Amir A.; Ilin, Alexandr I.; Reva, Oleg N.; Karpenyuk, Tatyana A.; oleg.reva@up.ac.za
OBJECTIVES : The global rise in multidrug resistance underscores the urgent need for the development of novel and effective antimicrobial agents. Semi-organic iodine-containing complexes, owing to their unique properties, low likelihood of resistance development, and stability under various conditions, represent a promising avenue for the design of new therapeutic strategies. This study describes the synthesis of semi-organic iodine-containing complexes and the in vitro evaluation of their impact on antibiotic susceptibility modulation in the multidrug-resistant pathogenic microorganisms S. aureus and E. coli. METHODS: The physicochemical properties of the semiorganic compounds were characterized using UV-Vis spectroscopy, potentiometric, and titrimetric methods. Evaluation of antimicrobial activity was obtained according to CLSI protocols. The impact of semiorganic compounds on the in vitro susceptibility of MDR strains was evaluated by the disk diffusion method. RESULTS : This study evaluated the effects of iodine-containing complexes KC-270 and KC-271 on the antibiotic susceptibility of Staphylococcus aureus BAA-39 and Escherichia coli BAA-196. The most pronounced effect was observed with KC-270 applied during the lag phase, which enhanced the activity of several antibiotics and, in some cases, restored susceptibility. KC-271 exhibited a weaker and more limited impact. The findings suggest that KC-270 has potential as a modulator of antibiotic susceptibility, particularly when administered at early stages of bacterial growth. CONCLUSIONS : The results support the ability of amino acid-based iodine coordination compounds to influence the antibiotic susceptibility of pathogenic bacteria, highlighting their potential as adjuvant agents to improve the effectiveness of current antimicrobial therapies. However, although changes in susceptibility were detected, neither compound fully eliminated resistance in the multidrug-resistant strains, indicating the necessity for further research into their mechanisms of action and possible synergistic interactions with antibiotics.
In vitro photoprotective and skin aging-related enzyme in-hibitory activities of Cylindrospermum alatosporum (NR125682) and Loriellopsis cavernicola (NR117881) extracts
(MDPI, 2025-09) Sithole, Siphesihle Z.; Ikhane, Albert O.; Osunsanmi, Foluso Oluwagbemiga; Mosa, Rebamang Anthony; Opoku, Andrew Rowland; rebamang.mosa@up.ac.za
The use of cyanobacteria has gained considerable interest in many industries, including the cosmetic industry, due to its rich array of bioactive metabolites. This study evaluates the in vitro photoprotective properties and the effect of Cylindrospermum alatosporum (NR125682) and Loriellopsis cavernicola (NR117881) extracts on slowing down the enzymes associated with skin aging. Various crude extracts were prepared using hexane, dichloromethane, and ethanol solvents. The resulting crude extract solvents were completely distilled to obtain their bioactive compounds, based on selected polarities. The sulfhydryl content of the crude extracts was determined and the aging-associated enzymes’ activity (collagenase, elastase, hyaluronidase, and tyrosinase) in the crude extracts was investigated. Furthermore, the in vitro photoprotective activity of the extracts was assessed by measuring UVA and UVB photoprotection. Most of the extracts contained varying amounts of sulfhydryl compounds (10.88–78.15 mg/g). All of the extracts demonstrated in vitro inhibitory activity against tyrosinase, hyaluronidase (IC50 6 µg/mL), and collagenase (IC50 50–70 µg/mL); weak elastase inhibitory activities were also observed. The crude extracts also showed appreciable UVA and UVB photoprotective activity. Meanwhile, L. cavernicola extracts demonstrated the highest UVB photoprotective activity (SPF 14.67–78.96). It is noteworthy that the crude extracts possessed anti-skin-aging potency with notable photoprotective capability.
Understanding the genetics of sex determination in insects and its relevance to genetic pest management
(Wiley, 2025-06) Ashmore, Jade Sabrina; Slippers, Bernard; Duong, Tuan A.; Dittrich-Schroder, Gudrun; gudrun.dittrich@fabi.up.ac.za
Sex determination pathways regulate male and female-specific development and differentiation and offer potential targets for genetic pest management methods. Insect sex determination pathways are comprised of primary signals, relay genes and terminal genes. Primary signals of coleopteran, dipteran, hymenopteran and lepidopteran species are highly diverse and regulate the sex-specific splicing of relay genes based on the primary signal dosage, amino acid composition or the interaction with paternally inherited genes. In coleopterans, hymenopterans and some dipterans, relay genes are Transformer orthologs from the serine-arginine protein family that regulate sex-specific splicing of the terminal genes. Alternative genes regulate the splicing of the terminal genes in dipterans that lack Transformer orthologs and lepidopterans. Doublesex and Fruitless orthologs are the terminal genes. Doublesex and Fruitless orthologs are highly conserved zinc-finger proteins that regulate the expression of downstream proteins influencing physical traits and courtship behaviours in a sex-specific manner. Genetic pest management methods can use different mechanisms to exploit or disrupt female-specific regions of different sex determination genes. Female-specific regions of sex determination genes can be exploited to produce a lethal gene only in females or disrupted to impede female development or fertility. Reducing the number of fertile females in pest populations creates a male-biased sex ratio and eventually leads to the local elimination of the pest population. Knowledge on the genetic basis of sex determination is important to enable these sex determination pathways to be exploited for genetic pest management.
Ferrocenyl quinoline-benzimidazole hybrids : a multistage strategy to combat drug-resistant malaria
(American Chemical Society, 2025-07) Golding, Taryn M.; Garnie, Larnelle F.; Rabie, Tayla Anne; Reader, Janette; Birkholtz, Lyn-Marie; Wicht, Kathryn J.; Smith, Gregory S.
Molecular hybridization and metal incorporation are widely employed strategies for drug development aimed at enhancing pharmacological efficacy while mitigating the emergence of drug resistance. The effectiveness of these approaches is supported by numerous studies demonstrating their success against a range of diseases. Despite the deployment of malaria vaccines, effective treatment remains hindered by the persistent emergence of drug-resistant Plasmodium falciparum strains, contributing to an alarming global disease burden. Inspired by the antimalarial candidate ferroquine, this study focused on the design and synthesis of ferrocenyl-based quinoline-benzimidazole molecular hybrids. The hybrids were evaluated for their in vitro blood-stage antiplasmodial activity against drug-sensitive NF54 and multidrug-resistant K1 P. falciparum strains, exhibiting potent submicromolar activity. Notably, incorporating an N,N-dimethylaminomethyl side chain significantly enhanced activity against both strains. Further assays revealed a compound with multistage antiplasmodial activity, targeting both immature and mature gametocytes. Mechanistic studies implicated the inhibition of hemozoin formation as a key mode of action, supported by in vitro cellular heme fractionation analysis. Additionally, fluorescence assays indicated the generation of reactive oxygen species under oxidative conditions, suggesting a complementary pathway contributing to the compounds’ antiplasmodial activity. These findings highlight the potential of ferrocenyl-based molecular hybrids as promising candidates in antiplasmodial drug development.
Genetic variants associated with suspected neonatal hypoxic ischaemic Encephalopathy : a study in a South African context
(MDPI, 2025-03) Foden, Caroline J.; Durant, Kevin; Mellet, Juanita; Joubert, Fourie; Van Rensburg, Jeanne; Masemola, Mogomane Yvonne Khomotso; Velaphi, Sithembiso C.; Nakwa, Firdose L.; Horn, Alan R.; Pillay, Shakti; Kali, Gugu; Coetzee, Melantha; Ballot, Daynia E.; Kalua, Thumbiko; Babbo, Carina; Pepper, Michael Sean; NESHIE Working Group; michael.pepper@up.ac.za
Neonatal encephalopathy suspected to be due to hypoxic ischaemic encephalopathy (NESHIE) carries the risk of death or severe disability (cognitive defects and cerebral palsy). Previous genetic studies on NESHIE have predominantly focused on exomes or targeted genes. The objective of this study was to identify genetic variants associated with moderate–severe NESHIE through whole-genome, unbiased analysis. Variant filtering and prioritization were performed, followed by association testing both on a case–control basis and to compare the grades of severity and/or progression. Association testing on neonates with NESHIE (N = 172) and ancestry-matched controls (N = 288) produced 71 significant genetic variants (false discovery rate corrected p-value < 6.2 × 10−4), all located in non-coding regions and not previously implicated in NESHIE. Disease-associated variants in non-coding regions are considered to affect regulatory functions, possibly by modifying gene expression, promoters, enhancers, or DNA structure. The most significant variant was at position 6:162010973 in the Parkin RBR E3 ubiquitin protein ligase (PRKN) intron. Intronic variants were also identified in genes involved in inflammatory processes (SLCO3A1), DNA repair (ZGRF1), synaptogenesis (CNTN5), haematopoiesis (ASXL2), and the transcriptional response to hypoxia (PADI4). Ten variants were associated with a higher severity or lack of improvement in NESHIE, including one in ADAMTS3, which encodes a procollagen amino protease with a role in angiogenesis and lymphangiogenesis. This analysis represents one of the first efforts to analyze whole-genome data to investigate the genetic complexity of NESHIE in diverse ethnolinguistic groups of African origin and provides direction for further study.
Combination of citrus peel-derived essential oils with acarbose to inhibit amylolytic enzymes – a potential type II diabetes treatment approach
(Elsevier, 2025-05) Tshiyoyo, Kadima Samuel; Rabbad, Ali; Yusuf, Abdullahi Ahmed; Malgas, Samkelo; samkelo.malgas@up.ac.za
Type 2 diabetes (T2D) can be managed by inhibiting amylolytic enzymes, α-amylase and α-glucosidase, reducing the impact of dietary carbohydrates on blood glucose elevation. Acarbose, a current α-glucose inhibitor (AGI), has excessive α-amylase inhibition, resulting in side effects associated with large amounts of undigested starch being fermented in the colon. This study evaluated the AGI efficacy of citrus peel-derived essential oils, where they were first tested in silico against the target amylolytic enzymes, and then their AGI activity was tested in vitro. The synergistic effects of the essential oils with acarbose against amylolytic enzymes were also determined. In silico and in vitro data of the efficacy of the essential oils as AGIs correlated positively; lower Ki values correlated with more negative binding affinity. Furthermore, molecular dynamic simulations of the most potent compounds were evaluated and indicated relative flexibility and stability induced upon ligand interactions with the protein. The standard AGI drug, acarbose, had the lowest Ki (0.10 ± 0.01 mg/mL) and more negative binding affinity (−7.5 kcal/mol) than the essential oils for α-glucosidase; however, the essential oils only showed potent inhibition against α-glucosidase, with the most potent essential oils being valencene (Ki = 0.33 ± 0.04 mg/mL), carveol (Ki = 0.53 ± 0.02 mg/mL) and geraniol (Ki = 0.56 ± 0.02 mg/mL). The essential oils and acarbose displayed competitive inhibition of α-glucosidase. Furthermore, a combination of acarbose with carveol or geraniol at a ratio of 12.5 μg/mL: 2 mg/mL exhibited antagonistic (CI > 10) and synergistic (CI < 0.7) effects on α-amylase and α-glucosidase inhibition, respectively. Carveol or geraniol can be considered as potentially therapeutic in managing T2D, as it may display lowered AGI-associated side effects. HIGHLIGHTS • Terpenes were identified from Citrus peel-derived essential oils. • Some individual essential oils tolerably inhibited amylolytic enzymes. • Synergism of essential oils with acarbose against amylolytic enzymes was established. • Essential oils inhibited glucose release with reduced starch residues.
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
(Nature Research, 2024-04-15) Salojärvi, Jarkko; Rambani, Aditi; Yu, Zhe; Guyot , Romain; Strickler, Susan; Lepelley, Maud; Wang, Cui; Rajaraman, Sitaram; Rastas , Pasi; Zheng, Chunfang; Muñoz, Daniella Santos; Meidanis , João; Paschoal , Alexandre Rossi; Krabbenhoft, Trevor J.; Bawin, Yves; Wang, Zhen Qin; Fleck , Steven J.; Aussel, Rudy; Bellanger, Laurence; Charpagne, Aline; Fournier, Coralie; Kassam, Mohamed; Lefebvre, Gregory; Métairon , Sylviane; Moine, Déborah; Rigoreau, Michel; Stolte, Jens; Hamon, Perla; Couturon, Emmanuel; Tranchant-Dubreuil, Christine; Mukherjee , Minakshi; Lan, Tianying; Engelhardt , Jan; Stadler, Peter; Correia De Lemos, Samara Mireza; Suzuki , Suzana Ivamoto; Sumirat, Ucu; Wai , Ching Man; Dauchot , Nicolas; Orozco-Arias, Simon; Garavito , Andrea; Kiwuka, Catherine; Musoli, Pascal; Nalukenge, Anne; Guichoux, Erwan; Reinout, Havinga; Smit, Martin; Carretero-Paulet, Lorenzo; Filho, Oliveiro Guerreiro; Braghini, Masako Toma; Padilha, Lilian; Sera, Gustavo Hiroshi; Ruttink, Tom; Henry, Robert; Marraccini, Pierre; Van de Peer, Yves ; Andrade, Alan; Domingues , Douglas; Giuliano , Giovanni; Mueller, Lukas; Pereira, Luiz Filipe; Plaisance, Stephane; Poncet , Valerie; Rombauts , Stephane; Sankoff, David; Albert, Victor A.; Crouzillat , Dominique; De Kochko , Alexandre; Descombes, Patrick
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000–610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
Monitoring of species’ genetic diversity in Europe varies greatly and overlooks potential climate change impacts
(Nature Research, 2024-01-15) Pearman, Peter B.; Broennimann , Olivier; Aavik, Tsipe; Albayrak, Tamer; Alves, Paulo C.; Aravanopoulos, F.A.; Bertola , Laura D.; Biedrzycka, Aleksandra; Buzan , Elena; Cubric-Curik , Vlatka; Djan , Mihajla; Fedorca, Ancuta; Fuentes-Pardo, Angela P.; Fussi , Barbara; Godoy , José A.; Gugerli , Felix; Hoban , Sean; Holderegger, Rolf; Hvilsom, Christina; Iacolina , Laura; Stroil , Belma Kalamujic; Klinga , Peter; Konopiński, Maciej K.; Kopatz, Alexander; Laikre , Linda; Lopes-Fernandes, Margarida; McMahon, Barry John; Mergeay, Joachim; Neophytou , Charalambos; Pálsson, Snæbjörn; Paz-Vinas , Ivan; Posledovich, Diana; Primmer, Craig R.; Raeymaekers , Joost A.M.; Rinkevich, Baruch; Rolečková , Barbora; Ruņģis, Dainis; Schuerz , Laura; Segelbacher , Gernot; Sonnenschein , Katja Kavčič; Stefanovic , Milomir; Thurfjell , Henrik; Träger, Sabrina; Tsvetkov, Ivaylo N.; Velickovic, Nevena; Vergeer , Philippine; Vernesi, Cristiano; Vilà , Carles; Westergren , Marjana; Zachos, Frank E.; Guisan, Antoine; Bruford, Michael W.
Genetic monitoring of populations currently attracts interest in the context of the Convention on Biological Diversity but needs long-term planning and investments. However, genetic diversity has been largely neglected in biodiversity monitoring, and when addressed, it is treated separately, detached from other conservation issues, such as habitat alteration due to climate change. We report an accounting of efforts to monitor population genetic diversity in Europe (genetic monitoring effort, GME), the evaluation of which can help guide future capacity building and collaboration towards areas most in need of expanded monitoring. Overlaying GME with areas where the ranges of selected species of conservation interest approach current and future climate niche limits helps identify whether GME coincides with anticipated climate change effects on biodiversity. Our analysis suggests that country area, financial resources and conservation policy influence GME, high values of which only partially match species’ joint patterns of limits to suitable climatic conditions. Populations at trailing climatic niche margins probably hold genetic diversity that is important for adaptation to changing climate. Our results illuminate the need in Europe for expanded investment in genetic monitoring across climate gradients occupied by focal species, a need arguably greatest in southeastern European countries. This need could be met in part by expanding the European Union’s Birds and Habitats Directives to fully address the conservation and monitoring of genetic diversity.
Rapid establishment of species barriers in plants compared with that in animals
(American Association for the Advancement of Science, 2025-09) Monnet, Francois; Postel, Zoe; Touzet, Pascal; Fraisse, Christelle; Van de Peer, Yves; Vekemans, Xavier; Roux, Camille
Speciation, the process by which new reproductively isolated species emerge from ancestral populations, results from the gradual accumulation of barriers to gene flow within genomes. To date, the notion that interspecific genetic exchange (introgression) occurs more frequently between plant species than animals has gained a strong footing in scientific discourse. By examining the dynamics of gene flow across a continuum of divergence in both kingdoms, we observed the opposite relationship: Plants experience less introgression than animals at the same level of genetic divergence, suggesting that species barriers are established more rapidly in plants. This pattern raises questions about which differences in microevolutionary processes between plants and animals influence the dynamics of reproductive isolation establishment at the macroevolutionary scale.
Fungal Planet description sheets : 1697–1780
(Westerdijk Fungal Biodiversity Institute, 2024-12-06) Crous, Pedro W.; Wingfield, Michael J.; Jurjević, Ž.; Balashov, S.; Osieck, E.R.; Marin-Felix, Y.; Luangsa-ard, J.J.; Mejía, L.C.; Cappelli, A.; Parra, L.A.; Lucchini, G.; Chen, J.; Moreno, G.; Faraoni, M.; Zhao, R.L.; Weholt, Ø.; Borovička, J.; Jansen, G.M.; Shivas, R.G.; Tan, Y.P.; Akulov, A.; Alfenas, A.C.; Alfenas, R.F.; Altés, A.; Avchar, R.; Barreto, R.W.; Catcheside, D.E.A.; Chi, T.Y.; Esteve-Raventós, F.; Fryar, S.C.; Hanh, L.T.M.; Larsbrink, J.; Oberlies, N.H.; Olsson, L.; Pancorbo, F.; Raja, H.A.; Thanh, V.N.; Thuy, N.T.; Ajithkumar, K.; Akram, W.; Alvarado, P.; Angeletti, B.; Arumugam, E.; Atashi Khalilabad, A.; Bandini, D.; Baroni, T.J.; Barreto, G.G.; Boertmann, D.; Akram, W.; Alvarado, P.; Angeletti, B.; Arumugam, E.; Atashi Khalilabad, A.; Bandini, D.; Baroni, T.J.; Barreto, G.G.; Boertmann, D.; Bose, Tanay; Castañeda Ruiz, R.F.; Couceiro, A.; Cykowska-Marzencka, B.; Dai, Y.C.; Darmostuk, V.; Da Silva, S.B.G.; Dearnaley, J.D.W.; De Azevedo Santiago, A.L.C.M.; Declercq, B.; De Freitas G. , L.W.S.; De la Peña-Lastra, S.; Delgado, G.; De Lima, C.L.F.; Dhotre, D.; Dirks, A.C.; Eisvand, P.; Erhard, A.; Ferro, L.O.; García, D.; García-Martín, A.; Garrido-Benavent, I.; Gené, J.; Ghobad-Nejhad, M.; Gore, G.; Gunaseelan, S.; Gusmão, L.F.P.; Hammerbacher, Almuth; Hernández-Perez, A.T.; Hernández-Restrepo, M.; Hofmann, T.A.; Hubka, V.; Jiya, N.; Kaliyaperumal, M.; Keerthana, K.S.; Ketabchi, M.; Kezo , K.; Knoppersen, Rosa; Kolarczyková, D.; Kumar, T.K.A.; Læssøe, T.; Langer, E.; Larsson, E.; Lodge, D.J.; Lynch, M.J.; Maciá-Vicente, J.G.; Mahadevakumar, S.; Mateos, A.; Mehrabi-Koushki, M.; Miglio, B.V.; Noor, A.; Oliveira, J.A.; Pereira, O.L.; Piątek, M.; Pinto, A.; Ramírez, G.H.; Raphael, B.; Rawat, G.; Renuka, M.; Reschke, K.; Ruiz Mateo, A.; Saar, I.; Saba, M.; Safi, A.; Sánchez, R.M.; Sandoval-Denis, M.; Savitha, A.S.; Sharma, A.; Shelke, D.; Sonawane, H.; Souza, M.G.A.P.; Stryjak-Bogacka, M.; Thines, M.; Thomas, A.; Torres-Garcia, D.; Traba, J.M.; Vauras, J.; Vermaas, M.; Villarreal, M.; Vu, D.; Whiteside, E.J.; Zafari, D.; Starink-Willemse, M.; Groenewald, J.Z.; Akram
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes
The VP7 protein of the African horse sickness virus core particle facilitates binding to Culicoides sonorensis cells in an RGD-independent manner
(Elsevier, 2025-11) Buyens, Ariel Renée Monique; Van Staden, Vida; Theron, Jacques; jacques.theron@up.ac.za
African horse sickness, caused by African horse sickness virus (AHSV) that is transmitted by midges of the Culicoides genus, leads to rapid mortality among horses. Proteases in the saliva of Culicoides midges cleave the VP2 outer capsid protein, resulting in infectious sub-virus particles that have increased infectivity for the Culicoides vector insect and Culicoides-derived cells (KC cells). The AHSV VP7 protein has an arginine-glycine-aspartate (RGD) motif, but the functional relevance of this protein and motif in facilitating binding to insect cells is unknown. To investigate, core-like particles (CLPs) were produced using the baculovirus expression system through the co-expression of VP3 and sVP7, which is a soluble version of the AHSV-4 VP7 protein. Insect cell binding assays indicated that the CLPs bind to KC cells, suggesting a role for VP7 in this interaction. Subsequently, recombinant baculoviruses expressing mutant sVP7 proteins were synthesized, in which the RGD motif was either deleted or mutated. All RGD-mutated sVP7 proteins, except for the deletion of the RGD motif, formed trimers and, when co-expressed with VP3, assembled into CLPs that retained the ability to bind to insect cells. These findings indicate that VP7 facilitates the binding of CLPs to insect cells through an RGD-independent mechanism. HIGHLIGHTS • VP7 is the outermost protein of AHSV core particles and possesses an RGD motif. • AHSV CLPs, formed by VP3 and VP7 proteins, bind to Culicoides-derived insect cells. • RGD-mutant CLPs retain the ability to bind to insect cells. • VP7 acts as an attachment protein for insect cells, independent of the RGD motif. • The findings provide new insights into early AHSV–insect vector interactions.
Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes
(Elsevier, 2026-01) Maake, Mabodiba Masutane; Beukes, Chrizelle Winsie; Van der Nest, Magrieta Aletta; Avontuur, Juanita R.; Muema, Esther K.; Stȩpkowski, Tomasz M.; Venter, Stephanus N.; Steenkamp, Emma Theodora; emma.steenkamp@up.ac.za
Given that several, mainly endemic South African Genisteae genera occupy basal positions in legume phylogenetic trees, this region of Africa is considered a primaeval centre of diversification of this legume tribe. Despite the importance of South Africa in Genisteae evolution, almost all studies have focused on rhizobia nodulating Genisteae in their centres of diversity in either the Mediterranean Basin or the Americas. Therefore, this study aimed to identify and characterize rhizobial strains associated with Argyrolobium species native to areas of the Grassland biome associated with the Great Escarpment, which dominates the subcontinent’s eastern landscape, and compare these to bradyrhizobia nodulating Genisteae in other centres of diversity. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB) separated the 18 Bradyrhizobium strains examined into five well-supported groups. Three of these were conspecific with B. arachidis, B. brasilense/B. australafricanum and B. ivorense, while the remaining two appeared to be new to science. After confirming their novelty using Average Nucleotide Identity, a metric for genome relatedness, and certain phenotypic traits, we recognized them as novel species for which we proposed the names B. spitzkopense sp. nov. (Arg816Ts) and B. mpumalangense sp. nov. (Arg237LTs). Phylogenetic analyses of nodA gene sequences showed that about half of the strains examined, irrespective of their species identity, harboured alleles known only from the Grassland biome along the Great Escarpment that were previously detected in Bradyrhizobium strains nodulating Crotalarieae endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique nodA alleles typically encode the nodH gene, the product of which adds a sulfate moiety to the Nod factor (the signalling molecule for establishing the nitrogen-fixing symbiosis). The remaining strains had nodA alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, the genomes of these other strains lacked nodH but encoded nodZ, the gene involved in the fucosylation of the Nod factor. Our findings, therefore, showed that the root nodules of Genisteae (and its sister tribe Crotalarieae) native to the Grassland biome along the Great Escarpment are often related Bradyrhizobium strains that are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas. HIGHLIGHTS • Diverse bradyrhizobia, including two novel species, nodulate Argyrolobium in the Grassland biome along the Great Escarpment of South Africa. • New species were named Bradyrhizobium spitzkopense and B. mpumalangense, using their genome data as nomenclatural types. • Argyrolobium-nodulating Bradyrhizobium species from this region have unusual sets of host-specific nodulation genes. • The reducing end of their Nod factor is likely sulfated and not fucosylated as is common for bradyrhizobia occurring elsewhere in the world.
A single centre audit of genetic testing in early-onset breast cancer
(Medpharm Publications, 2025-03) Pillay, C.A.; Ngwisanyi, W.; Benn, C.A.
BACKGROUND : This paper serves to audit the number of women who received genetic testing after diagnosis with breast cancer ≤ 35 years. Patients were diagnosed or sought treatment at the Breast Care Centre of Excellence (BCCE), a private accredited specialist breast unit in Johannesburg, South Africa. This study focuses specifically on genetic testing for pathogenic variants of the BRCA 1 and BRCA 2 genes. METHODS : Files of patients diagnosed ≤ 35 years were retrieved, and medical information was extracted. These patient files were then compared to records from the University of the Witwatersrand genetic service facility and the GC Network Pty (Ltd) genetic service facility, and genetic service data was recorded. All data was then compiled and analysed. RESULTS : Over 10 years, 196 patients were diagnosed with breast cancer ≤ 35 years, while only 5 received genetic testing. CONCLUSION : In order to understand the relationship between BRCA1/2 genetic diagnosis and cancer diagnosis, greater emphasis must be placed on the availability of genetic services and testing. Ensuring that these services are available, accessible, and funded by either the State or medical insurance will greatly enhance the understanding between BRCA diagnosis, breast cancer diagnosis, risk reduction procedures, and quality of life in many young women.
Bacterial fruit tree quarantine pathogens – a threat to biosecurity in South Africa
(Academy of Science of South Africa, 2025-09) Coutinho, Teresa A.; teresa.coutinho@up.ac.za
Quarantine bacterial plant pathogens present a serious threat to the biosecurity of South Africa’s fruit tree industry, posing significant risks to agricultural productivity, trade and biodiversity. Pathogens such as Candidatus Liberobacter asiaticus, Xanthomonas citri pv. citri, Erwinia amylovora and Xylella fastidiosa can cause widespread economic losses in fruit crops, including citrus, apples, pears, grapes and olives. Managing these pathogens is challenging due to their ability to spread rapidly, often by the movement of infected plant material and/or by insect vectors. Limited diagnostic capabilities, few chemical control options, and the emergence of pathogen resistance also hamper effective management. This review highlights the importance of an integrated approach should an incursion occur, which would initially involve eradication, improved surveillance and public awareness. Strengthening these biosecurity practices is essential in safeguarding the agricultural sector and ensuring continued fruit trade viability. SIGNIFICANCE : • This review highlights the significant threat posed by quarantine bacterial fruit tree pathogens to South Africa’s agricultural biosecurity. These pathogens endanger essential fruit crops, and an outbreak could lead to severe losses, trade restrictions, and socio-economic impacts. • The review also highlights the challenges that would likely be faced if an incursion should occur. It advocates for an integrated management approach including eradication, surveillance, public awareness, and robust phytosanitary measures, legislative support and inter-agency collaboration. This approach could ensure that we safeguard the agricultural sector and mitigate potential crises.
Pathogenicity of Pythium myriotylum on Acacia crassicarpa and Acacia mangium x Acacia auriculiformis clones in Indonesia
(Taylor and Francis, 2025) Tarigan, Marthin; Wingfield, Michael J.; Jami, Fahimeh; Oliveira, Leonardo S.S.; Saha, Muhammad A.; Duran, Alvaro; Pham, Nam Q.; nam.pham@fabi.up.ac.za
The oomycete Pythium myriotylum is an important pathogen of several crops, causing wilt and damping-off during nursery propagation. The pathogen was recently reported as the causal agent of wilt and damping-off on Acacia crassicarpa plants in nurseries located in Riau, Indonesia. The aim of this study was to evaluate the relative pathogenicity of P. myriotylum on different clones of A. crassicarpa and Acacia mangium × Acacia auriculiformis hybrids. Based on the results, greater tolerance was found on the A. mangium × A. auriculiformis hybrid clones than on those of pure A. crassicarpa. The different Acacia clones also displayed different levels of tolerance of infection. Overall the results showed that screening for tolerance to infection by P. myriotylum will be important in the Acacia breeding programme and make it possible to produce sufficient nursery stock for plantation establishment.
Exploring meiotic recombination and its potential benefits in South African beef cattle : a review
(MDPI, 2025-07) Magagula, Nozipho A.; Ncube, Keabetswe T.; Zwane, Avhashoni Agnes; Mtileni, Bohani
Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems. SIMPLE SUMMARY By generating novel allele combinations during prophase I of meiosis, meiotic recombination is a fundamental evolutionary mechanism that enhances genetic diversity and supports the selection of desirable traits in livestock breeding. This process is crucial for improving the genetic potential of livestock through selective breeding. While recombination has been studied in commercial cattle breeds from Europe and North America, it remains unexplored and not understood in South African beef cattle, especially the Bonsmara and Nguni breeds. These indigenous breeds are highly valued for their adaptability to harsh, resource-limited environments, yet the genetic mechanisms underlying their resilience and productivity are not well characterised. This review explores how genome-wide technologies, especially those using high-density single nucleotide polymorphism (SNP) markers, can be used to map recombination patterns and identify genes involved in key traits. Applying these tools to South African cattle could enhance breeding strategies by improving the accuracy of selecting animals with a superior genetic merit. Understanding recombination in these breeds will also support their conservation and sustainable use. Ultimately, this knowledge has significant implications for advancing food security, promoting rural development, and ensuring the long-term adaptability of South African beef cattle under climate change.
The re-identification of Penicillium and Talaromyces (Eurotiales) catalogued in South African culture collections
(National Herbarium of the Netherlands, 2024-12) Visagie, Cobus M.; Houbraken, J.; Yilmaz, Neriman; cobus.visagie@fabi.up.ac.za
The taxonomy of Penicillium and Talaromyces has been modernized in the past decade, resulting in more robust and accurate identifications, while hundreds of new species were described from around the world. South Africa has emerged as somewhat of a biodiversity hotspot for these genera, with 48 new species being described in recent years. The aim of this current project was to re-identify Penicillium and Talaromyces strains held in South African culture collections, including the National Collections of Fungi (PPRI) and the Medical Research Council (MRC). A total of 295 PPRI and 56 MRC strains were revived and identified using β-tubulin (BenA) gene sequences. For new or rarely found species, we also sequenced the rDNA internal transcribed spacer regions (ITS), calmodulin (CaM), and RNA polymerase second largest subunit (RPB2) genes. The strains were identified to 99 Penicillium and 25 Talaromyces species, among them eight new Penicillium and three new Talaromyces species. Morphological comparisons with close relatives confirmed the novelty of these species, and they are formally described here as P. drakensteinense, P. kirstenboschense, P. limpopoense, P. lydenburgense, P. mbombelaense, P. potchefstroomense, P. roodeplaatense, P. silvertonense, T. gautengensis, T. macrodendroideus, and T. mzansiensis. This study provides a much-needed update on species diversity captured in South African culture collections and makes an important contribution to international knowledge on these important genera.
Biofilm characterisation of the maize rot-causing pathogen, Fusarium verticillioides
(Taylor and Francis, 2025) Peremore, Chizne; Van't Hof, Cairin; Nkosi, Cebo-LeNkosi; Tshiyoyo, Kadima Samuel; Ratsoma, Francinah M.; Kola, Wisely; Malgas, Samkelo; Santana, Quentin C.; Wingfield, Brenda D.; Steenkamp, Emma Theodora; Motaung, Thabiso Eric; thabiso.motaung@up.ac.za
Biofilm formation was investigated in a maize rot-causing pathogen, Fusarium verticillioides. This work revealed that in vitro cultures produce structured, adherent communities with a dense extracellular matrix (ECM) surrounding hyphae that makes up the biomass of a matured biofilm. Pellicle containing exopolysaccharide had a hydrodynamic diameter of 4.19 nm and a low viscosity (0.022 dl/g). The exopolysaccharide was composed of amino sugars and unordered, facilitating stability through complexation with the anionic eDNA. Biofilm formation varied over different pH and temperature values, emphasising its role in promoting adaption, survival, and persistence in F. verticillioides, potentially contributing to its pathogenicity in maize. Collectively, the results provide valuable insights into biofilm structure and stress resistance in this fungus, and will serve as a foundation for future studies incorporating in planta infection systems.
Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms : implications for pathogenesis in avocado sunblotch disease
(Springer, 2025-09) Joubert, Melissa; Van den Berg, Noelani; Theron, Jacques; Swart, Velushka; velushka.swart@fabi.up.ac.za
Avocado sunblotch viroid (ASBVd) is a structured RNA molecule responsible for sunblotch disease of avocado, characterised by distinct chloroses of fruit, leaves, and stems. Despite its impact on avocado, the mechanism by which ASBVd elicits sunblotch symptoms remains unknown. Previous studies on other avsunviroids have shown that viroid-derived small RNAs (vd-sRNAs) with specific sequence mutations can trigger leaf chlorosis via RNA silencing of host genes. Building on this knowledge, we aimed to shed light on the molecular basis of ASBVd pathogenesis by analysing ASBVd sequence variants and ASBVd-sRNAs from bleached and asymptomatic leaf tissues of sunblotch-affected avocado trees. Sequencing of ASBVd clones revealed that variants carrying the pathogenic determinant for bleaching were present in both green and yellow leaf tissues. Next-generation sequencing (NGS) identified ASBVd-sRNAs that varied in abundance between symptomatic and asymptomatic leaf tissues, correlating with viroid titre. We discovered 64 vd-sRNAs spanning the pathogenic region of the ASBVd genome, which were almost exclusively found in yellow tissues. The ASBVd-sRNAs containing the bleaching-associated mutation were predicted to target numerous avocado transcripts for degradation, with 25 of these transcripts significantly downregulated in bleached tissues. Notably, one of these genes, encoding a chloroplastic protein, demonstrated strong evidence of ASBVd-sRNA-guided RNA silencing, presenting a promising candidate for future research into the molecular trigger for ASBVd-induced bleaching symptoms. This study is the first to investigate ASBVd-sRNAs in bleached leaves using NGS. Our findings support the role of RNA silencing in sunblotch symptom development and reveal a unique silencing trigger compared to other avsunviroids.
Revisiting the description of Atractoscion macrolepis (Perciformes: Sciaenidae) : another argument for comprehensive taxonomy
(Magnolia Press, 2024-10-24) Gouws, Gavin; Kruger, Jerraleigh L.; Smale, Malcolm; Henriques, Romina; Potts, Warren M.; romina.henriques@up.ac.za
Atractoscion macrolepis was described as a species separate to A. aequidens, distinguished by a geographically-separated distribution, genetic evidence and a diagnostic meristic character: the number of pored lateral line scales. However, the distinction of these species and description of A. macrolepis were based on the examination of a limited number of specimens, some of which were incorrectly catalogued and possibly wrongly identified. Moreover, earlier data, demonstrating the overlap of the supposedly diagnostic character, were overlooked or not considered fully. The present study aimed to reconsider the distinction of these two species and to highlight characters for identification, using a more extensive representation of specimens, additional character sets and multivariate analyses. Seven meristic characters, 24 morphometric measurements and nine otolith variables were examined from up to 33 specimens of A. aequidens and 52 specimens of A. macrolepis. These were compared among the species and subjected to univariate and multivariate analyses, including Principal Component Analyses (PCAs) and Discriminant Function Analyses (DFAs). No meristic characters, including the number of lateral line scales, could distinguish the species, with modes being identical or with nodes differing, but ranges overlapping. While the PCA of size-transformed morphometric data revealed some separation of the two species, the DFA indicated significant and reliable discrimination. Considering the otolith variables, the PCA showed weak separation of the two species, while fair discrimination was observed in the DFA. ANOVAs indicated a number of significant differences for some transformed otolith measurements, but there were no clear trends with respect to proportions that would discriminate the species. Further exploration of those morphometric variables highlighted as contributing to separation in the PCA and DFA provided a number of variables that, when expressed as a proportion of SL and used in combination, discriminate A. aequidens and A. macrolepis: HL, MCL, PFL, AFL and PLFL. The present study does not contest the taxonomic status of A. macrolepis, the distinction of which has been demonstrated repeatedly, but does refute the characters regarded as diagnostic. In light of this, an updated key is provided for the five species of the genus. The study demonstrates the value of increased specimen representation and having data fully available rather than in summary.

Browse

Recent Submissions