Biology subjects

Hernaez-Sanchez, M. L.

Publications and source records attributed to Hernaez-Sanchez, M. L..

3 recordsLinked to original sources

bioRxiv2024

Candida albicans a comprehensive view of the proteome

We describe a new release of the Candida albicans PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The C. albicans PeptideAtlas summary web page provides "Build overview", "PTM coverage", "Experiment contribution", and "Dataset contribution" information. The protein and peptide information can also be accessed via the Candida Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments identifying each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyse PTM results is provided in the PeptideAtlas of this important pathogen. Candida albicans PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578

microbiology↗

bioRxiv2024

From high protection to lethal effect: diverse outcomes of immunization against invasive candidiasis with different Candida albicans extracellular vesicles

Extracellular vesicles (EVs) from Candida albicans can elicit immune responses, positioning them as promising acellular vaccine candidates. We characterized EVs from an avirulent C. albicans cell wall mutant (ecm33{Delta}) and evaluated their protective potential against invasive candidiasis. EVs from the yeast (YEVs) and hyphal (HEVs) forms of the SC5314 wild-type strain were also tested, yielding high survival rates with SC5314 YEVs (91%) and ecm33 YEVs immunization (64%). Surprisingly, HEV immunization showed a dual effect, resulting in 36% protection but also causing premature death in some mice. Proteomic analyses revealed distinct profiles among the top 100 proteins in the different EVs which may explain these effects: a shared core of 50 immunogenic proteins such as Pgk1, Cdc19, and Fba1; unique, relevant immunogenic proteins in SC5314 YEVs, and proteins linked to pathogenesis, like Ece1 in SC5314 HEVs. Sera from SC5314 YEVs-immunized mice showed the highest IgG2a titers and moderate IL-17, IFN-{gamma}, and TNF- levels, indicating the importance of both humoral and cellular responses for protection. These findings highlight the distinct immunogenic properties of C. albicans EVs, suggesting their potential in acellular vaccine development while emphasizing the need to carefully evaluate pathogenic risks associated with certain EVs.

microbiology↗

bioRxiv2022

Statistical evaluation of metaproteomics and 16s rRNA amplicon sequencing techniques for the study of the gut microbiota establishment of infants with cystic fibrosis

The newborn screening for cystic fibrosis (CF) can identify affected but still asymptomatic infants. The selection of omic technique for gut microbiota study is therefore crucial due to both the small amount of feces available and the low microorganism load. Our aim was to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis including McNemar (taxa presence) test and Bland-Altman (taxa abundance) data plotting for studying the sequential establishment of the gut microbiota during the first year of life in 8 infants with CF (28 fecal samples). The taxonomic assignation was similar by the two techniques, whereas certain discrepancies were observed in the abundance detection, mostly the underrepresentation of Bifidobacterium and the overestimation of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by poor alpha diversity, a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Our study provides an extended comparative analysis with robust statistical support that could optimize the use of both approaches for gut microbiota research. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes. Both techniques detected an aberrant microbiota in infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment.

microbiology↗