Ewa Ksiezopolska

Ewa Ksiezopolska
Centre for Genomic Regulation | CRG · Bioinformatics and Genomics

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50
Publications
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491
Citations
Citations since 2016
49 Research Items
489 Citations
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2016201720182019202020212022050100150
2016201720182019202020212022050100150
2016201720182019202020212022050100150
Introduction
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Publications

Publications (50)
Article
Full-text available
The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the composition of the oral microbiome is relevant beyond just oral health, impacting systemic processes acro...
Article
Full-text available
Background Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing this diversity limits our ability to accurately establish how chromosomal structure and gene content vary across strains. Results H...
Article
Full-text available
Each year, infections caused by fungal pathogens claim the lives of about 1.6 million people and affect the health of over a billion people worldwide. Among the most recently developed antifungal drugs are the echinocandins, which noncompetitively inhibit β-glucan synthase, a membrane-bound protein complex that catalyzes the formation of the main p...
Article
Full-text available
Fungal infections are a growing medical concern, in part due to increased resistance to one or multiple antifungal drugs. However, the evolutionary processes underpinning the acquisition of antifungal drug resistance are poorly understood. Here, we used experimental microevolution to study the adaptation of the yeast pathogen Candida glabrata to fl...
Article
Full-text available
Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act as a reservoir or as a barrier for infectious microorganisms that can colonize the lungs. However, the specific composition of the...
Article
Full-text available
Introduction: The oral cavity harbors an abundant and diverse microbial community (i.e. the microbiome), whose composition and roles in health and disease have been the focus of intense research. Down syndrome (DS) is associated with particular characteristics in the oral cavity, and with a lower incidence of caries and higher incidence of periodon...
Article
Full-text available
The formation of interspecific hybrids results in the coexistence of two diverged genomes within the same nucleus. It has been hypothesized that negative epistatic interactions and regulatory interferences between the two sub-genomes may elicit a so-called genomic shock involving, among other alterations, broad transcriptional changes. To assess th...
Article
Full-text available
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 de...
Preprint
Full-text available
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 de...
Article
Full-text available
Candida glabrata is an opportunistic fungal pathogen that currently ranks as the second most common cause of candidiasis. Although the mechanisms underlying virulence and drug resistance in C. glabrata are now starting to be elucidated, we still lack a good understanding of how this yeast adapts during the course of an infection. Outstanding questi...
Data
Detail of read mapping on the FKS1 gene region, visualized using IGV software (Thorvaldsdóttir et al., 2013) in the strains CMRL1, CMRL2, CMRL3, CMRL4, CMRL5, and CMRL6. Zoom-in square indicates private non-synonymous SNP S629P present only in CMRL1 (in blue).
Data
Correlation between genome-wide mutation density (SNPs/Kb) and days spanned between the first isolate and second isolate in serial isolates. As Figure 1B but strains are colored according to the presence of non-synonymous mutations in MSH2.
Data
Distribution of strains based on SNPs using a Multiple Correspondence Analysis (MCA). Each pair of strains used marked in different colors and names in plot. White circles in plot indicates strains used to provide a global comparison (Carreté et al., 2018).
Data
List of genes affected by private exonic INDELs. Columns indicates, in this order: pair of strains; INDEL position; systematic name; standard name; type of mutation; description of the gene affected.
Data
Single nucleotide polymorphisms (SNPs)/Kb value compared to reference genome CBS138. First column indicates list of C. glabrata isolates analyzed in this study. Second column indicates SNPs/Kb compared to reference genome (CBS138).
Data
List of genes affected by private non-synonymous mutations in clonal strains. Columns indicates: strain name; Systematic name of the gene affected by a private non-synonymous mutation; standard name of that gene; amino acid (AA) altered; description of the gene.
Data
List of genes deleted and duplicated in one of the two pair of isolates. First column indicates gene name; second column indicates description of the gene affected.
Data
Values from phenotypic analysis. Columns indicate: sample; condition used for the phenotypic analysis; carrying capacity (k), population size at time 0 (time 0); growth rate (r); time when the population density reaches ½ K (½ K time); fastest possible generation time; area under the logistic curve measured by taking the integral logistic equation...
Data
MIC value (μg/ml) for the different strains analyzed. Columns indicates: name of the strains analyzed, isolation site, drugs tested (fluconazole, Voriconazole, Amphotericin B, Anidulafungin, Micafungin, Caspofungin, 5-fluorocystosine, Posaconazole, Itraconazole, Isavuconazole); method used; and source data.
Article
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...
Article
Full-text available
Background The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral micro...
Article
Full-text available
Candida parapsilosis is an opportunistic fungal pathogen with the ability to cause infections in immunocompromised patients. Echinocandins are the currently recommended first line of treatment for all Candida species. Resistance of Candida albicans to this drug type is well characterized. C. parapsilosis strains have the lowest in vitro susceptibil...
Article
Full-text available
Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug familie...
Preprint
Full-text available
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...
Data
Table S2. Synonymous versus Non-synonymous Variation per Gene, Related to Figure 5 The first column indicates the gene functional category (based on their function in S. cerevisiae). The following columns indicate gene ID, gene name (only for S. cerevisiae), and πN/πS for C. glabrata, C. albicans, and S. cerevisiae genes.
Data
Table S5. Levels of Nucleotide Variation per Strain and Mutations in MSH2, Related to Figure 6 Columns indicate, in this order: strain name; clade; non-synonymous variant; Saccharomycotina species presenting the same non-synonymous mutations (five-letter codes correspond to species mnemonic based on the UniProt taxonomy database [33]); reduced sen...
Data
Table S1. Information about the 32 Strains of C. albicans Re-analyzed in This Study, Related to Figure 5 Columns indicate, in this order: strain name or ID; host; isolation site; country of isolation; mating type (if any); experiment name in short read archive (SRA); number of SRA run.
Data
Columns indicate, in this order: condition used for the analysis; sample; clade; carrying capacity (K); population size at time 0 (n0); growth rate (r); time when the population density reaches ½K (t_mid); fastest possible generation time (t_gen); area under the logistic curve measured by taking the integral of the logistic equation (auc_l); empiri...
Data
Range of sensitivity levels (triplicate experiments) to amphotericin B (MIC90), 5-fluorocytosine, fluconazole, voriconazole, posaconazole, isavuconazole, micafungin, and caspofungin (all MIC50) and, where available (http://www.eucast.org/clinical_breakpoints), classification according to clinical breakpoints. S, sensitive; I, intermediate; R, resis...
Data
Columns indicate, in this order: duplication or deletion number in this study (corresponds to Figure 2); gene ID; gene name; name of S. cerevisiae one-to-one ortholog (if any); description.
Data
Data S2. Private Mutations per Strain, Non-synonymous SNPs and CNVs, Related to Figure 6 Columns of private non-synonymous SNPs indicate, in this order: strain ID; chromosome and position affected by the SNP; gene ID; amino acid substitution; gene name; description. The first column based on CNV indicates the strain analyzed. The following columns...
Article
Full-text available
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. Moreover, C....
Preprint
Full-text available
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....
Article
Full-text available
Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into the recent evolution of C. metapsilosis and the genetic basis of its virulence, we sequenced the genome of 11 clinical isolates from various locations, which we...

Questions

Questions (2)
Question
Is there a company that sells nice turbidostats?
There are numerous articles of how to build one but it gets harder when you simply would like to buy one.
Any suggestions?
Question
I have already seen different theories on the issue.
Yet, I would appreciate opinions from those who have on-hands experience on obtaining and/or preserving the RNA structures that are the closest to the real once.
Thanks in advance!
Ewa

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Project (1)
Project
Candida species constitute one of the most prevalent groups of fungal pathogens. From their phylogenetic relationships it is clear that virulence to humans has emerged in this clade several, independent times. The Candida parapsilosis complex is particularly suitable to investigate the emergence of virulence, with three closely-related species of varying degree of pathogenicity and of growing relevance: C. parapsilosis, C. orthopsilosis and C. metapsilosis.