Biology subjects

Ksiezopolska, E.

Publications and source records attributed to Ksiezopolska, E..

5 recordsLinked to original sources

bioRxiv2026

Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery

Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are distributed across coral cell types during stress and recovery remains unclear. Here, we generate a temporal single-cell transcriptomic atlas of the reef-building coral Stylophora pistillata, profiling 20,000 cells during seven days at 32 {degrees}C and after 45 days of recovery. Heat stress reduced symbiont abundance and photosynthetic efficiency, followed by partial restoration. Early oxidative-stress, detoxification, and proteostasis programmes gave way to mitochondrial, cytoskeletal, and vesicular remodelling. These shared responses accompanied cell type-specific changes: epidermal cells activated tissue-renewal programmes, calicoblasts repressed calcification genes, and alga-hosting cells progressively lost transport, lipid-biosynthesis, and nutrient-exchange functions. Targeted profiling of sorted alga-positive cells revealed rare transcriptional states, including a population consistent with symbiont engulfment. Our results reveal how bleaching and recovery are coordinated across coral tissues and symbiotic cell states.

genomics↗

bioRxiv2025

High genomic and phenotypic diversity among Candida dubliniensis isolates from the oral cavity of persons living with HIV

The opportunistic yeast pathogen Candida dubliniensis is frequently misidentified as its closest relative Candida albicans, due to their high phenotypic similarity. Although Candida dubliniensis is an important cause of fungal infections, especially in the oral cavities of immunocompromised patients, its phenotypic and genomic variability remains poorly understood. We addressed this knowledge gap by performing a comprehensive phenotypic and genomic characterization of 33 C. dubliniensis oral isolates from people living with HIV in Argentina. Our results uncovered significant phenotypic heterogeneity--observed both inter- and intra-patient--impacting clinically relevant traits such as drug susceptibility, stress sensitivity, filamentation, and hypoxic growth. Our isolates expanded the previously known MLST-based genetic diversity of the species. Leveraging whole-genome sequencing, we resolved intricate evolutionary relationships, proposed a more robust MLST scheme for future typing, and identified potential antifungal resistance-causing variants. Collectively, this work represents the most comprehensive population genomics characterization of C. dubliniensis to date, establishing a foundation for improved surveillance and diagnostic strategies to fully define its role in both oral and systemic infections. Author SummaryIn this study we uncover hidden genetic and morphological diversity in Candida dubliniensis, a poorly known opportunistic yeast pathogen related to Candida albicans, by characterising a collection of oral isolates from persons living with HIV in Argentina. Our findings provide the most detailed genetic and phenotypic snapshot of this pathogen to date, providing a much-needed foundation to develop better diagnostic tools and effective surveillance strategies to address infections caused by this overlooked threat.

microbiology↗

bioRxiv2020

The transcriptional aftermath in two independently formed hybrids of the opportunistic pathogen Candida orthopsilosis

Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new pathogenic species. Candida orthopsilosis is an emerging opportunistic pathogen for which most clinical isolates are hybrids, each derived from one of at least four independent crosses between the same two parental lineages. To gain insight on the transcriptomic aftermath of hybridization in these pathogens, we analyzed allele-specific gene expression in two independently formed hybrid strains, and in a homozygous strain representative of one parental lineage. Our results show that the effect of hybridization on overall gene expression is rather limited, affecting ~4% of the studied genes. However, we identified a larger effect in terms of imbalanced allelic expression, affecting ~9.5% of the heterozygous genes in the hybrids. Some of these altered genes have functions related to pathogenicity, including zinc transport and superoxide dismutase activities. Additionally, the number of shared genes with imbalanced expression in the two independently formed hybrids was higher than random expectation, suggesting selective retention. While it remains unclear whether the observed imbalanced genes play a role in virulence, our results suggest that differences in allele-specific expression may add an additional layer of phenotypic plasticity to traits related to virulence in C. orthopsilosis hybrids. ImportanceHow new pathogens emerge is an important question that remains largely unanswered. Some emerging yeast pathogens are hybrids originated through the crossing of two different species, but how hybridization contributes to a higher virulence is unclear. Here we show that hybrids selectively retain gene regulation plasticity inherited from the two parents, and that this plasticity affects genes involved in virulence.

genomics↗

bioRxiv2018

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs.

evolutionary biology↗

bioRxiv2017

Patterns of genomic variation in the opportunistic pathogen Candida glabrata suggest the existence of mating and a secondary association to the human host

Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae than to other Candida pathogens, and hence its ability to infect humans is thought to have emerged independently. Morover, C. glabrata has all the necessary genes to undergo a sexual cycle, but it is considered an asexual organism due to the lack of direct evidence of sexual reproduction. Here, we assessed genomic and phenotypic variation across 33 globally-distributed C. glabrata isolates. We cataloged extensive copy number variation, which particularly affects genes encoding cell-wall associated proteins, including adhesins. The observed level of genetic variation in C. glabrata is significantly larger than that found in Candida albicans. This variation is structured in seven deeply divergent clades, which show recent geographical dispersion and large within-clade genomic and phenotypic differences. We show compelling evidence of recent admixture between differentiated lineages, and of purifying selection on mating genes, which provide fist evidence for the existence of a sexual cycle in this yeast. Altogether, our data point to a recent global spread of previously genetically isolated populations and suggest that humans are only a secondary niche for this yeast.

microbiology↗