Biology subjects

Ayala, M.

Publications and source records attributed to Ayala, M..

4 recordsLinked to original sources

bioRxiv2026

Uncovering Conceptual Biases in DNA Stabilization: A Student-Led Investigation

Deoxyribonucleic acid (DNA) stands as one of the most foundational concepts in life sciences, essential for students to master. However, when surveyed about the forces that stabilize the double-stranded DNA structure, many students exhibited a conceptual bias-- favoring base pairing as the primary stabilizing force, while overlooking the equally critical role of base stacking interactions. To investigate the origins of this misconception, students conducted a comprehensive analysis of 35 widely used textbooks. Their findings revealed that one-third of these texts explicitly emphasized base pairing as the sole stabilizing force in their written content. Furthermore, two-thirds of the textbook contained illustrations that reinforced this bias, visually highlighting base pairing while neglecting base stacking. Recognizing this bias, students embarked on a literature review to gain a more accurate and nuanced understanding of DNA stabilization. Through this research, we identified three concept areas--DNA structure and function, environmental effects on DNA, and DNA-protein interactions--to illustrate how base pairing and base stacking work in concert to stabilize the antiparallel double helical structure of DNA. This interplay between base pairing and base stacking is crucial not only for the structural integrity of DNA, but also for its biological functionality. By addressing this conceptual bias, we aim to promote a more balanced and scientifically accurate representation of DNA stabilization in educational materials.

scientific communication and education↗

bioRxiv2026

Anti-psychotic drugs act synergistically in combination with antifungal drugs to inhibit drug-resistant Cryptococcus and Candida species

Systemic antifungal infections cause an estimated 3.8 million deaths annually, approximately 10% of which are caused by drug-resistant infections. With only five classes of antifungal drugs, treatment options are limited. Here we explore synergistic drug combinations - when the efficacy of two drugs combined is greater than expected based on the sum of each individual drugs efficacy - to improve treatment of drug-resistant Cryptococcus neoformans and Candida species. Chlorpromazine acts synergistically with both amphotericin B and fluconazole against multiple fungal species, including azole-resistant C. neoformans and C. auris. We then performed a genome-wide knockout mutant screen and found that ESCRT pathway mutants are resistant to chlorpromazine and knockout mutants of genes involved in fatty acid biosynthesis are sensitive. Based on these data, we investigated sterols and fatty acids in chlorpromazine-treated cells and found only minor increases in sterol precursors but a substantial increase in lipid droplet size and decrease lipid droplet number. We conclude that chlorpromazine acts by potentially sequesters lipids, preventing lipolysis and lipid mobilization in response to stress. Together, these data suggest that chlorpromazine and its analogs are potentially promising treatments for systemic fungal infections that act via lipid homeostasis and stress response.

microbiology↗

bioRxiv2025

End-to-end evaluation of white matter microstructure of the visual pathway in asymmetric glaucoma

Diffusion magnetic resonance imaging is a non-invasive neuroimaging technique that enables in vivo evaluation of white matter microstructure, providing sensitivity to tissue abnormalities caused by disease. Glaucoma, the second leading cause of blindness worldwide, is characterized by progressive loss of retinal ganglion cells and axonal damage in the optic nerve, leading to degeneration along the entire visual pathway. This degeneration includes secondary effects on fiber crossings within the optic chiasm, which are challenging to characterize with conventional diffusion models. In this study, we evaluated 31 patients with asymmetric glaucoma and 31 healthy controls using advanced diffusion magnetic resonance imaging methods, including Diffusion Tensor Imaging, Constrained Spherical Deconvolution, multi-tensor fit via Multi-Resolution Discrete Search method, and Fixel-Based Analysis. We found significant differences of diffusion metrics in white matter tracts of the visual system, including the optic nerve, optic chiasm, optic tracts, and optic radiations. Moreover, diffusion metrics correlated with clinical ophthalmological parameters such as cup-to-disc ratio, visual field mean deviation, and retinal nerve fiber layer thickness. These findings support the use of advanced diffusion magnetic resonance imaging models as sensitive tools for detecting Wallerian degeneration and resolving complex white matter architecture in the human visual pathway, and demonstrate their utility to study other fiber-crossing regions throughout the brain.

neuroscience↗

bioRxiv2021

In-solution buffer-free digestion for the analysis of SARS-CoV-2 RBD proteins allows a full sequence coverage and detection of post-translational modifications in a single ESI-MS spectrum

Subunit vaccines based on the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2, are among the most promising strategies to fight the COVID-19 pandemic. The detailed characterization of the protein primary structure by mass spectrometry (MS) is mandatory, as described in ICHQ6B guidelines. In this work, several recombinant RBD proteins produced in five expression systems were characterized using a non-conventional protocol known as in-solution buffer-free digestion (BFD). In a single ESI-MS spectrum, BFD allowed very high sequence coverage ([≥] 99 %) and the detection of highly hydrophilic regions, including very short and hydrophilic peptides (2-8 amino acids), the His6-tagged C-terminal peptide carrying several post-translational modifications at Cys538 such as cysteinylation, glutathionylation, cyanilation, among others. The analysis using the conventional digestion protocol allowed lower sequence coverage (80-90 %) and did not detect peptides carrying some of the above-mentioned post-translational modifications. The two C-terminal peptides of a dimer [RBD(319-541)-(His)6]2 linked by an intermolecular disulfide bond (Cys538-Cys538) with twelve histidine residues were only detected by BFD. This protocol allows the detection of the four disulfide bonds present in the native RBD and the low-abundance scrambling variants, free cysteine residues, O-glycoforms and incomplete processing of the N-terminal end, if present. Artifacts that might be generated by the in-solution BFD protocol were also characterized. BFD can be easily implemented and we foresee that it can be also helpful to the characterization of mutated RBD.

biochemistry↗