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Item Open Access Optimizing models for the prediction of one step ahead extreme flows to wastewater treatment plants using different synthetic sampling methods(Journal of Environmental Management, 2025-09) Musaazi, Isaac G; Liu, Lu; Shaw, Andrew; Zaniolo, Marta; Stadler, Lauren B; Delgado Vela, JesethItem Open Access Visual Features in Stereo-Electroencephalography to Predict Surgical Outcome: A Multicenter Study.(Annals of neurology, 2025-06) Abdallah, Chifaou; Thomas, John; Aron, Olivier; Avigdor, Tamir; Jaber, Kassem; Doležalová, Irena; Mansilla, Daniel; Nevalainen, Päivi; Parikh, Prachi; Singh, Jaysingh; Beniczky, Sandor; Kahane, Philippe; Minotti, Lorella; Chabardes, Stephan; Colnat-Coulbois, Sophie; Maillard, Louis; Hall, Jeff; Dubeau, Francois; Gotman, Jean; Grova, Christophe; Frauscher, BirgitObjective
Epilepsy surgery needs predictive features that are easily implemented in clinical practice. Previous studies are limited by small sample sizes, lack of external validation, and complex computational approaches. We aimed to identify and validate visually stereo-electroencephalography (SEEG) features with the highest predictive value for surgical outcome, and assess the reliability of their visual extraction.Methods
We included 177 patients with drug-resistant epilepsy who underwent SEEG-guided surgery at 4 epilepsy centers. We assessed the predictive performance of 10 SEEG features from various SEEG periods for surgical outcome, using the area under the receiver operating characteristic curve, and considering resected channels and surgical outcome as the gold standard. Findings were validated externally using balanced accuracy. Six experts, blinded to outcome, evaluated the visual reliability of the optimal feature using interrater reliability, percentage agreement (standard deviation ± SD) and Gwet's kappa (κ ± SD).Results
The derivation cohort comprised 100 consecutive patients, each with at least 1-year of postoperative follow up (40% temporal lobe epilepsy; 42% Engel Ia). Spatial co-occurrence of gamma spikes and preictal spikes emerged as the optimal predictive feature of surgical outcome (area under the receiver operating characteristic curve 0.82). Applying the optimized threshold from the derivation cohort, external validation in 2 datasets showed similar performances (balanced accuracy 69.2% and 73.2%). Expert interrater reliability for gamma spikes (percentage agreement, 96% ± 2%; κ, 0.63 ± 0.16) and preictal spikes (percentage agreement, 92% ± 2%; κ, 0.65 ± 0.18) were substantial.Interpretation
Spatial co-occurrence of gamma spikes and preictal spikes predicts surgical outcome. These visually identifiable features may reduce the burden of SEEG analysis by reducing analysis time, and improve outcome by guiding surgical resection margins. ANN NEUROL 2025.Item Open Access The association of seizure control with neuropathology in dementia.(Brain : a journal of neurology, 2025-07) Zawar, Ifrah; Luniewski, Aleksander; Gundlapalli, Rithvik; Manning, Carol; Parikh, Prachi; Kapur, Jaideep; Quigg, MarkSeizures in people with dementia (PWD) are associated with faster cognitive decline and worse clinical outcomes. However, the relationship between ongoing seizure activity and post-mortem neuropathology in PWD remains unexplored. We compared post-mortem findings in PWD with active, remote and no seizures using multicentre data from 39 Alzheimer's Disease Research Centres from 2005 to 2021. PWD were grouped by seizure status into active (seizures over the preceding 1 year), remote (prior seizures but none in the preceding 1 year) and no seizures (controls). Baseline demographics, cognition, mortality and post-mortem findings of primary and contributing (co-pathologies) Alzheimer's disease (AD), frontotemporal lobar degeneration, Lewy body, vascular pathologies and neurodegeneration were compared among the groups using Pearson's χ2 test, Fisher's exact test, t-test and ANOVA. Of 10 474 deceased PWD, active seizure participants suffered the highest mortality among the groups (proportion deceased among the groups: active = 56%, remote = 35%, controls = 34%, P < 0.001). Among 6085 (58.1% of deceased) who underwent autopsy, 294 had active, 151 had remote and 5640 had no seizures. PWD and active seizures died at a younger age (active = 75.8, remote = 77.9, controls = 80.8 years, P < 0.001) and had more severe dementia (Clinical Dementia Rating score: active = 2.36, remote = 1.90, controls = 1.69, P < 0.001). In post hoc analyses, those with primary post-mortem diagnosis of AD with active seizures had more severe and later stages of AD pathology and ATN (amyloid, tau and neurodegeneration), as evidenced by Braak stage for neurofibrillary (tau) degeneration and Consortium to Establish a Registry for Alzheimer's Disease (CERAD) score density of neuritic (amyloid) plaques, than remote seizure participants and controls. Active seizure participants had more neurodegeneration, evidenced by cerebral atrophy, hippocampal atrophy and locus coeruleus hypopigmentation, than controls. Among participants with primary post-mortem diagnosis of non-AD, in post hoc analyses, active seizure participants had worse AD co-pathology, evidenced by higher Braak stages than remote seizures and controls and a higher Thal phase of beta-amyloid plaques than remote seizure participants. Neurodegeneration (cerebral/hippocampal atrophy) and locus coeruleus hypopigmentation were comparable among the groups. In both primary post-mortem AD and non-AD diagnoses, frontotemporal lobar degeneration (co)pathology was less prevalent among active seizure participants than controls, while vascular pathology, Circle of Willis atherosclerosis, Lewy body pathology, lobar atrophy and substantia nigra hypopigmentation were comparable among the three groups. This study shows that active seizures, compared with remote seizures, are associated with earlier death and post-mortem evidence of more severe ATN pathology. Active seizures are associated with more advanced AD pathology in AD and worse AD co-pathology in non-AD dementias. Therefore, clinicians should be vigilant in detecting ongoing seizures, because this could reflect a worse prognosis in PWD.Item Open Access Prognostic value of the 5-SENSE Score to predict focality of the seizure-onset zone as assessed by stereoelectroencephalography: a prospective international multicentre validation study.(BMJ neurology open, 2024-01) Astner-Rohracher, Alexandra; Ho, Alyssa; Archer, John; Bartolomei, Fabrice; Brazdil, Milan; Cacic Hribljan, Melita; Castellano, James; Dolezalova, Irena; Fabricius, Martin Ejler; Garcés-Sanchez, Mercedes; Hammam, Kahina; Ikeda, Akio; Ikeda, Kristin; Kahane, Philippe; Kalamangalam, Giridhar; Kalss, Gudrun; Khweileh, Mays; Kobayashi, Katsuya; Kwan, Patrick; Laing, Joshua Andrew; Leitinger, Markus; Lhatoo, Samden; Makhalova, Julia; McGonigal, Aileen; Mindruta, Iona; Mizera, Mary Margaret; Neal, Andrew; Oane, Irina; Parikh, Prachi; Perucca, Piero; Pizzo, Francesca; Rocamora, Rodrigo; Ryvlin, Philippe; San Antonio Arce, Victoria; Schuele, Stephan; Schulze-Bonhage, Andreas; Suller Marti, Ana; Urban, Alexandra; Villanueva, Vincente; Vilella Bertran, Laura; Whatley, Benjamin; Beniczky, Sandor; Trinka, Eugen; Zimmermann, Georg; Frauscher, BirgitIntroduction
Epilepsy surgery is the only curative treatment for patients with drug-resistant focal epilepsy. Stereoelectroencephalography (SEEG) is the gold standard to delineate the seizure-onset zone (SOZ). However, up to 40% of patients are subsequently not operated as no focal non-eloquent SOZ can be identified. The 5-SENSE Score is a 5-point score to predict whether a focal SOZ is likely to be identified by SEEG. This study aims to validate the 5-SENSE Score, improve score performance by incorporating auxiliary diagnostic methods and evaluate its concordance with expert decisions.Methods and analysis
Non-interventional, observational, multicentre, prospective study including 200 patients with drug-resistant epilepsy aged ≥15 years undergoing SEEG for identification of a focal SOZ and 200 controls at 22 epilepsy surgery centres worldwide. The primary objective is to assess the diagnostic accuracy and generalisability of the 5-SENSE in predicting focality in SEEG in a prospective cohort. Secondary objectives are to optimise score performance by incorporating auxiliary diagnostic methods and to analyse concordance of the 5-SENSE Score with the expert decisions made in the multidisciplinary team discussion.Ethics and dissemination
Prospective multicentre validation of the 5-SENSE score may lead to its implementation into clinical practice to assist clinicians in the difficult decision of whether to proceed with implantation. This study will be conducted in accordance with the Tri-Council Policy Statement: Ethical Conduct for Research Involving Humans (2014). We plan to publish the study results in a peer-reviewed full-length original article and present its findings at scientific conferences.Trial registration number
NCT06138808.Item Open Access Responsive neurostimulation detections: "Recognizing the unseen".(Epileptic disorders : international epilepsy journal with videotape, 2025-05) Haskell-Mendoza, Aden P; Ramani, Praveen; Dhoot, Roshni; Parikh, Prachi; Frauscher, Birgit; Sinha, Saurabh R; Muh, Carrie R; Southwell, Derek; Husain, Aatif; Agashe, ShrutiBackground
Closed-loop responsive neurostimulation (RNS) is an established non-resective neuromodulatory therapy for individuals with drug-resistant epilepsy (DRE). RNS systems are typically programmed to detect and respond to predefined seizure onset patterns, with detector settings often remaining unchanged for extended periods.Aims
To describe the delayed recognition of a novel seizure onset pattern in the acute and chronic clinical settings.Methods
The case of a 35-year-old female with history of drug-refractory temporal lobe epilepsy who presented with increasing seizure frequency and headaches was reviewed.Results
We demonstrate emergence of a new seizure onset pattern in a 35-year-old female with DRE who had undergone RNS implantation 5.5 years prior to presentation. Guided primarily by strong clinical suspicion, with live electrocorticography (ECoG) serving as a confirmatory tool, we identified a previously unrecognized seizure onset pattern linked to a rare, delayed intraparenchymal hemorrhage associated with an RNS lead. Longitudinal ECoG analysis in this patient, who experienced over a 95% reduction in seizures since implantation, revealed evolving seizure patterns over several years that contributed to delayed detections.Conclusion
This case underscores the risk of misdiagnosis when acute changes in seizure patterns occur, in the context of detections programmed to identify specific patterns. Longitudinal analysis of ECoG in the same patient showed changes in seizure patterns over several years that were detected with delay, highlighting importance of vigilant detection monitoring.Item Open Access Empower GBM: A pilot study of a patient–caregiver supportive intervention for patients with glioblastoma(Palliative and Supportive Care, 2025-06-19) Leo, Karena; Porter, Laura S; Lisenbee, Jodie; Ramos, KatherineItem Open Access Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe.(Molecular ecology, 2014-02) David-Palma, Márcia; Libkind, Diego; Sampaio, José PauloMicrobes establish very diverse but still poorly understood associations with other microscopic or macroscopic organisms that do not follow the more conventional modes of competition or mutualism. Phaffia rhodozyma, an orange-coloured yeast that produces the biotechnologically relevant carotenoid astaxanthin, exhibits a Holarctic association with birch trees in temperate forests that contrasts with the more recent finding of a South American population associated with Nothofagus (southern beech) and with stromata of its biotrophic fungal parasite Cyttaria spp. We investigated whether the association of Phaffia with Nothofagus-Cyttaria could be expanded to Australasia, the other region of the world where Nothofagus are endemic, studied the genetic structure of populations representing the known worldwide distribution of Phaffia and analysed the evolution of the association with tree hosts. The phylogenetic analysis revealed that Phaffia diversity in Australasia is much higher than in other regions of the globe and that two endemic and markedly divergent lineages seem to represent new species. The observed genetic diversity correlates with host tree genera rather than with geography, which suggests that adaptation to the different niches is driving population structure in this yeast. The high genetic diversity and endemism in Australasia indicate that the genus evolved in this region and that the association with Nothofagus is the ancestral tree association. Estimates of the divergence times of Phaffia lineages point to splits that are much more recent than the break-up of Gondwana, supporting that long-distance dispersal rather than vicariance is responsible for observed distribution of P. rhodozyma.Item Open Access Genetic Dissection of Sexual Reproduction in a Primary Homothallic Basidiomycete.(PLoS genetics, 2016-06) David-Palma, Márcia; Sampaio, José Paulo; Gonçalves, PaulaIn fungi belonging to the phylum Basidiomycota, sexual compatibility is usually determined by two genetically unlinked MAT loci, one of which encodes one or more pheromone receptors (P/R) and pheromone precursors, and the other comprehends at least one pair of divergently transcribed genes encoding homeodomain (HD) transcription factors. Most species are heterothallic, meaning that sexual reproduction requires mating between two sexually compatible individuals harboring different alleles at both MAT loci. However, some species are known to be homothallic, one individual being capable of completing the sexual cycle without mating with a genetically distinct partner. While the molecular underpinnings of the heterothallic life cycles of several basidiomycete model species have been dissected in great detail, much less is known concerning the molecular basis for homothallism. Following the discovery in available draft genomes of the homothallic basidiomycetous yeast Phaffia rhodozyma of P/R and HD genes, we employed available genetic tools to determine their role in sexual development. Two P/R clusters, each harboring one pheromone receptor and one pheromone precursor gene were found in close vicinity of each other and were shown to form two redundant P/R pairs, each receptor being activated by the pheromone encoded by the most distal pheromone precursor gene. The HD locus is apparently genetically unlinked to the P/R locus and encodes a single pair of divergently transcribed HD1 and HD2 transcription factors, both required for normal completion of the sexual cycle. Given the genetic makeup of P. rhodozyma MAT loci, we postulate that it is a primarily homothallic organism and we propose a model for the interplay of molecular interactions required for sexual development in this species. Phaffia rhodozyma is considered one of the most promising microbial source of the carotenoid astaxanthin. Further development of this yeast as an industrial organism will benefit from new insights regarding its sexual reproduction system.Item Open Access Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma.(BMC genomics, 2016-11) Bellora, Nicolás; Moliné, Martín; David-Palma, Márcia; Coelho, Marco A; Hittinger, Chris Todd; Sampaio, José P; Gonçalves, Paula; Libkind, DiegoBackground
The class Tremellomycete (Agaricomycotina) encompasses more than 380 fungi. Although there are a few edible Tremella spp., the only species with current biotechnological use is the astaxanthin-producing yeast Phaffia rhodozyma (Cystofilobasidiales). Besides astaxanthin, a carotenoid pigment with potent antioxidant activity and great value for aquaculture and pharmaceutical industries, P. rhodozyma possesses multiple exceptional traits of fundamental and applied interest. The aim of this study was to obtain, and analyze two new genome sequences of representative strains from the northern (CBS 7918T, the type strain) and southern hemispheres (CRUB 1149) and compre them to a previously published genome sequence (strain CBS 6938). Photoprotection and antioxidant related genes, as well as genes involved in sexual reproduction were analyzed.Results
Both genomes had ca. 19 Mb and 6000 protein coding genes, similar to CBS 6938. Compared to other fungal genomes P. rhodozyma strains and other Cystofilobasidiales have the highest number of intron-containing genes and highest number of introns per gene. The Patagonian strain showed 4.4 % of nucleotide sequence divergence compared to the European strains which differed from each other by only 0.073 %. All known genes related to the synthesis of astaxanthin were annotated. A hitherto unknown gene cluster potentially responsible for photoprotection (mycosporines) was found in the newly sequenced P. rhodozyma strains but was absent in the non-mycosporinogenic strain CBS 6938. A broad battery of enzymes that act as scavengers of free radical oxygen species were detected, including catalases and superoxide dismutases (SODs). Additionally, genes involved in sexual reproduction were found and annotated.Conclusions
A draft genome sequence of the type strain of P. rhodozyma is now available, and comparison with that of the Patagonian population suggests the latter deserves to be assigned to a distinct variety. An unexpected genetic trait regarding high occurrence of introns in P. rhodozyma and other Cystofilobasidiales was revealed. New genomic insights into fungal homothallism were also provided. The genetic basis of several additional photoprotective and antioxidant strategies were described, indicating that P. rhodozyma is one of the fungi most well-equipped to cope with environmental oxidative stress, a factor that has probably contributed to shaping its genome.Item Open Access The Evolution of Sexual Reproduction and the Mating-Type Locus: Links to Pathogenesis of Cryptococcus Human Pathogenic Fungi.(Annual review of genetics, 2019-12) Sun, Sheng; Coelho, Marco A; David-Palma, Márcia; Priest, Shelby J; Heitman, JosephCryptococcus species utilize a variety of sexual reproduction mechanisms, which generate genetic diversity, purge deleterious mutations, and contribute to their ability to occupy myriad environmental niches and exhibit a range of pathogenic potential. The bisexual and unisexual cycles of pathogenic Cryptococcus species are stimulated by properties associated with their environmental niches and proceed through well-characterized signaling pathways and corresponding morphological changes. Genes governing mating are encoded by the mating-type (MAT) loci and influence pathogenesis, population dynamics, and lineage divergence in Cryptococcus. MAT has undergone significant evolutionary changes within the Cryptococcus genus, including transition from the ancestral tetrapolar state in nonpathogenic species to a bipolar mating system in pathogenic species, as well as several internal reconfigurations. Owing to the variety of established sexual reproduction mechanisms and the robust characterization of the evolution of mating and MAT in this genus, Cryptococcus species provide key insights into the evolution of sexual reproduction.Item Open Access Genetic and genomic evolution of sexual reproduction: echoes from LECA to the fungal kingdom.(Current opinion in genetics & development, 2019-10) Fu, Ci; Coelho, Marco A; David-Palma, Márcia; Priest, Shelby J; Heitman, JosephSexual reproduction is vastly diverse and yet highly conserved across the eukaryotic domain. This ubiquity suggests that the last eukaryotic common ancestor (LECA) was sexual. It is hypothesized that several critical processes in sexual reproduction, including cell fusion and meiosis, were acquired during the evolution from the first eukaryotic common ancestor (FECA) to the sexual LECA. However, it is challenging to delineate the exact origin and evolution of sexual reproduction given that both FECA and LECA are extinct. Studies of diverse eukaryotes have helped to shed light on this sexual evolutionary trajectory, revealing that a primordial sexual ploidy cycle likely involved endoreplication followed by concerted chromosome loss and that cell-cell fusion, meiosis, and sex determination later arose to shape modern sexual reproduction. Despite the general conservation of sexual reproduction processes throughout eukaryotes, modern sexual cycles are immensely diverse and complex. This diversity and complexity has become readily apparent in the fungal kingdom with the recent rapid expansion of whole-genome sequencing. This abundance of data, the variety of genetic tools available to manipulate and characterize fungi, and the thorough characterization of many fungal sexual cycles make the fungal kingdom an excellent forum, in which to study the conservation and diversification of sexual reproduction.Item Open Access The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov.(Microorganisms, 2020-10) David-Palma, Márcia; Libkind, Diego; Brito, Patrícia H; Silva, Margarida; Bellora, Nicolás; Coelho, Marco A; Coelho, Marco A; Heitman, Joseph; Gonçalves, Paula; Sampaio, José PauloPhaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark-the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.Item Open Access Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction.(bioRxiv, 2023-06-09) Coelho, Marco A; Ianiri, Giuseppe; David-Palma, Márcia; Theelen, Bart; Goyal, Rohit; Narayanan, Aswathy; Lorch, Jeffrey M; Sanyal, Kaustuv; Boekhout, Teun; Heitman, JosephUNLABELLED: Fungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining ( MAT ) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By incorporating newly generated chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere- flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight towards the discovery of a sexual cycle in Malassezia , with possible implications for pathogenicity. SIGNIFICANCE STATEMENT: Malassezia , the dominant fungal group of the mammalian skin microbiome, is associated with numerous skin disorders. Sexual development and yeast-to-hyphae transitions, governed by genes at two mating-type ( MAT ) loci, are thought to be important for fungal pathogenicity. However, Malassezia sexual reproduction has never been observed. Here, we used chromosome-level assemblies and comparative genomics to uncover unforeseen transitions in MAT loci organization within Malassezia , possibly related with fragility of centromeric-associated regions. Additionally, by expressing different MAT alleles in the same cell, we show that Malassezia can undergo hyphal development and this phenotype is associated with increased expression of key mating genes along with other genes known to be virulence factors, providing a possible connection between hyphal development, sexual reproduction, and pathogenicity.Item Open Access Multiple Pathways to Homothallism in Closely Related Yeast Lineages in the Basidiomycota.(mBio, 2021-02) Cabrita, Alexandra; David-Palma, Márcia; Brito, Patrícia H; Heitman, Joseph; Coelho, Marco A; Gonçalves, PaulaSexual reproduction in fungi relies on proteins with well-known functions encoded by the mating type (MAT) loci. In the Basidiomycota, MAT loci are often bipartite, with the P/R locus encoding pheromone precursors and pheromone receptors and the HD locus encoding heterodimerizing homeodomain transcription factors (Hd1/Hd2). The interplay between different alleles of these genes within a single species usually generates at least two compatible mating types. However, a minority of species are homothallic, reproducing sexually without an obligate need for a compatible partner. Here, we examine the organization and function of the MAT loci of Cystofilobasidium capitatum, a species in the order Cystofilobasidiales, which is unusually rich in homothallic species. We determined MAT gene content and organization in C. capitatum and found that it resembles a mating type of the closely related heterothallic species Cystofilobasidium ferigula To explain the homothallic sexual reproduction observed in C. capitatum, we examined HD protein interactions in the two Cystofilobasidium species and determined C. capitatum MAT gene expression both in a natural setting and upon heterologous expression in Phaffia rhodozyma, a homothallic species belonging to a clade sister to that of Cystofilobasidium. We conclude that the molecular basis for homothallism in C. capitatum appears to be distinct from that previously established for P. rhodozyma Unlike in the latter species, homothallism in C. capitatum may involve constitutive activation or dispensability of the pheromone receptor and the functional replacement of the usual Hd1/Hd2 heterodimer by an Hd2 homodimer. Overall, our results suggest that homothallism evolved multiple times within the Cystofilobasidiales.IMPORTANCE Sexual reproduction is important for the biology of eukaryotes because it strongly impacts the dynamics of genetic variation. In fungi, although sexual reproduction is usually associated with the fusion between cells belonging to different individuals (heterothallism), sometimes a single individual is capable of completing the sexual cycle alone (homothallism). Homothallic species are unusually common in a fungal lineage named Cystofilobasidiales. Here, we studied the genetic bases of homothallism in one species in this lineage, Cystofilobasidium capitatum, and found it to be different in several aspects from those of another homothallic species, Phaffia rhodozyma, belonging to the genus most closely related to Cystofilobasidium Our results strongly suggest that homothallism evolved independently in Phaffia and Cystofilobasidium, lending support to the idea that transitions between heterothallism and homothallism are not as infrequent as previously thought. Our work also helps to establish the Cystofilobasidiales as a model lineage in which to study these transitions.Item Open Access Obligate sexual reproduction of a homothallic fungus closely related to the Cryptococcus pathogenic species complex.(eLife, 2022-06) Passer, Andrew Ryan; Clancey, Shelly Applen; Shea, Terrance; David-Palma, Márcia; Averette, Anna Floyd; Boekhout, Teun; Porcel, Betina M; Nowrousian, Minou; Cuomo, Christina A; Sun, Sheng; Heitman, Joseph; Coelho, Marco AeLife digest.Fungi are enigmatic organisms that flourish in soil, on decaying plants, or during infection of animals or plants. Growing in myriad forms, from single-celled yeast to multicellular molds and mushrooms, fungi have also evolved a variety of strategies to reproduce. Normally, fungi reproduce in one of two ways: either they reproduce asexually, with one individual producing a new individual identical to itself, or they reproduce sexually, with two individuals of different 'mating types' contributing to produce a new individual. However, individuals of some species exhibit 'homothallism' or self-fertility: these individuals can produce reproductive cells that are universally compatible, and therefore can reproduce sexually with themselves or with any other cell in the population.Homothallism has evolved multiple times throughout the fungal kingdom, suggesting it confers advantage when population numbers are low or mates are hard to find. Yet some homothallic fungi been overlooked compared to heterothallic species, whose mating types have been well characterised. Understanding the genetic basis of homothallism and how it evolved in different species can provide insights into pathogenic species that cause fungal disease.With that in mind, Passer, Clancey et al. explored the genetic basis of homothallism in Cryptococcus depauperatus, a close relative of C. neoformans, a species that causes fungal infections in humans. A combination of genetic sequencing techniques and experiments were applied to analyse, compare, and manipulate C. depauperatus' genome to see how this species evolved self-fertility.Passer, Clancey et al. showed that C. depauperatus evolved the ability to reproduce sexually by itself via a unique evolutionary pathway. The result is a form of homothallism never reported in fungi before. C. depauperatus lost some of the genes that control mating in other species of fungi, and acquired genes from the opposing mating types of a heterothallic ancestor to become self-fertile.Passer, Clancey et al. also found that, unlike other Cryptococcus species that switch between asexual and sexual reproduction, C. depauperatus grows only as long, branching filaments called hyphae, a sexual form. The species reproduces sexually with itself throughout its life cycle and is unable to produce a yeast (asexual) form, in contrast to other closely related species.This work offers new insights into how different modes of sexual reproduction have evolved in fungi. It also provides another interesting case of how genome plasticity and evolutionary pressures can produce similar outcomes, homothallism, via different evolutionary paths. Lastly, assembling the complete genome of C. depauperatus will foster comparative studies between pathogenic and non-pathogenic Cryptococcus species.Item Open Access Frequent transitions in mating-type locus chromosomal organization in Malassezia and early steps in sexual reproduction.(Proceedings of the National Academy of Sciences of the United States of America, 2023-08) Coelho, Marco A; Ianiri, Giuseppe; David-Palma, Márcia; Theelen, Bart; Goyal, Rohit; Narayanan, Aswathy; Lorch, Jeffrey M; Sanyal, Kaustuv; Boekhout, Teun; Heitman, JosephFungi in the basidiomycete genus Malassezia are the most prevalent eukaryotic microbes resident on the skin of human and other warm-blooded animals and have been implicated in skin diseases and systemic disorders. Analysis of Malassezia genomes revealed that key adaptations to the skin microenvironment have a direct genomic basis, and the identification of mating/meiotic genes suggests a capacity to reproduce sexually, even though no sexual cycle has yet been observed. In contrast to other bipolar or tetrapolar basidiomycetes that have either two linked mating-type-determining (MAT) loci or two MAT loci on separate chromosomes, in Malassezia species studied thus far the two MAT loci are arranged in a pseudobipolar configuration (linked on the same chromosome but capable of recombining). By generating additional chromosome-level genome assemblies, and an improved Malassezia phylogeny, we infer that the pseudobipolar arrangement was the ancestral state of this group and revealed six independent transitions to tetrapolarity, seemingly driven by centromere fission or translocations in centromere-flanking regions. Additionally, in an approach to uncover a sexual cycle, Malassezia furfur strains were engineered to express different MAT alleles in the same cell. The resulting strains produce hyphae reminiscent of early steps in sexual development and display upregulation of genes associated with sexual development as well as others encoding lipases and a protease potentially relevant for pathogenesis of the fungus. Our study reveals a previously unseen genomic relocation of mating-type loci in fungi and provides insight toward the identification of a sexual cycle in Malassezia, with possible implications for pathogenicity.Item Open Access Fungal pathogens and symbionts: Living off the fat of the land.(PLoS pathogens, 2024-09) Nev, Olga A; David-Palma, Márcia; Heitman, Joseph; Brown, Alistair JP; Coelho, Marco AItem Open Access Decoding Cryptococcus: From African biodiversity to worldwide prevalence.(PLoS pathogens, 2025-02) Coelho, Marco A; David-Palma, Márcia; 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, JosephFungal 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.Item Open Access Fungal sexual reproduction and mating-type loci.(Current biology : CB, 2025-06) Sun, Sheng; Coelho, Marco A; David-Palma, Márcia; Huang, Jun; Bian, Zhuyun; Heitman, JosephSexual reproduction is a hallmark of eukaryotes, generating diversity and variation through recombination and allele segregation, thereby facilitating natural selection. Unlike animals and plants, fungi do not have conventional male and female sexes but instead rely on mating types, which are determined by allelic differences at a specialized chromosomal region called the mating-type locus (MAT). The MAT locus typically exhibits great diversity in both organization and gene content, partially driven by reduced meiotic recombination in these regions during sexual reproduction. While ascomycetes predominantly have a bipolar mating system with a single MAT locus determining the mating type of the cell, there are also species that possess silent MAT cassettes that enable mating-type switching during vegetative growth. This process generates cells with compatible mating types, allowing mating between mother and daughter cells and resulting in inbreeding. In basidiomycetes, the ancestral mating system is tetrapolar, with two independent MAT loci (P/R and HD) collectively determining the mating type of the cell. Some species, however, have a bipolar mating system in which the P/R and HD loci have become completely linked genetically or even fused together, while others exhibit a so-called pseudobipolar mating system in which only partial genetic linkage has been established between the P/R and HD loci. Additionally, fungi employ a vast array of sexual reproductive strategies, including classical mating between cells of opposite mating types, as well as noncanonical modes such as unisexual, pseudosexual, and parasexual reproduction. In this Primer, we aim to introduce this fascinating diversity in mating-type determination and modes of sexual reproduction in fungi, with a focus on Cryptococcus species as a model. We then discuss how recent advances in genomics research have facilitated studies on fungal MAT loci and mating systems, highlighting key outstanding questions in the field and potential ways to address them.Item Open Access Understanding scientific creativity: an exploratory creativity scale for organic chemistry(Frontiers in Education) Blue, Connor; Barr, Nathaniel; Ma, Baldwin; He, Helena; Cox, Charles T; Seli, PaulCreativity is pivotal for innovation across various domains, including science, technology, engineering, and mathematics (STEM). The present study explores domain-specific creativity in organic chemistry by introducing the Divergent Skeletal Formula Task (DSFT) as a novel measure. The DSFT requires participants to generate constitutional isomers of a given molecular formula, providing an objective quantification of creativity based on the rarity and originality of responses. We investigated the correlations between DSFT performance and established creativity indices—the Alternate Uses Task (AUT) and the Divergent Association Task (DAT)—while controlling for age, gender, and fluid intelligence through partial correlation analyses. The results revealed that correlations between DSFT performance and both AUT Creativity and DAT scores were not statistically significant. However, there was a significant positive correlation between DSFT performance and AUT Flexibility, suggesting that cognitive flexibility is a critical component of creativity in chemistry, even when statistically accounting for age, gender, and fluid intelligence. This finding supports the idea of domain-generality in creativity, indicating that cognitive processes underlying general creative thinking, particularly flexibility, are applicable to specific STEM domains like organic chemistry. Thus, insights from studies on general creativity may be valuable for understanding and fostering creativity in specialized fields, offering practical implications for educational and research settings.