Biology subjects

Ochoa, E.

Publications and source records attributed to Ochoa, E..

4 recordsLinked to original sources

bioRxiv2025

Activity of Geranium macrorrhizum extracts, essential oils and their main components against three relevant flagellated protozoa

Plant-derived natural products are structurally diverse secondary metabolites that play essential ecological roles and have long been recognized for their therapeutic potential. Geranium macrorrhizum is known to produce bioactive extracts and essential oils rich in monoterpenoids and sesquiterpenes. While various Geranium species have demonstrated antiprotozoal activity, the potential of G. macrorrhizum against protozoan parasites remains unexplored. Given the increasing resistance of protozoan pathogens to conventional treatments, there is a pressing need to identify alternative therapeutic agents from natural sources. Plant material was grown in greenhouse and aeroponic systems. Extracts were obtained via hydrodistillation and Soxhlet, and analyzed by GC-MS. In vitro assays were performed to evaluate antiparasitic activity and cytotoxicity. Morphological changes induced by germacrone were analyzed using light microscopy. The study evaluated the antiparasitic potential of essential oils, extracts, and compounds from Geranium macrorrhizum, cultivated under controlled conditions, against Giardia duodenalis, Trichomonas gallinae, and Leishmania infantum. Results showed broad-spectrum activity, particularly from non-polar extracts and EOs, suggesting that lipophilic compounds, especially germacrone, are key contributors to the observed effects. Germacrone exhibited strong activity and selective toxicity. Structural analogues of germacrone showed reduced efficacy, highlighting the importance of its specific chemical structure. Morphological analyses revealed parasite-specific responses to germacrone, contrasting with the more destructive effects of metronidazole and amphotericin B. The findings support G. macrorrhizum as a promising source of natural antiprotozoal agents and justify further investigation into its bioactive compounds and mechanisms of action.

microbiology↗

bioRxiv2024

Transcriptomic atlas of the morphologic development of the fungal pathogen Coccidioides reveals key phase-enriched transcripts

Coccidioides spp. are highly understudied but significant dimorphic fungal pathogens that can infect both immunocompetent and immunocompromised people. In the environment, they grow as multicellular filaments (hyphae) that produce vegetative spores called arthroconidia. Upon inhalation by mammals, arthroconidia undergo a process called spherulation. They enlarge and undergo numerous nuclear divisions to form a spherical structure, and then internally segment until the spherule is filled with multiple cells called endospores. Mature spherules rupture and release endospores, each of which can form another spherule, in a process thought to facilitate dissemination. Spherulation is unique to Coccidioides and its molecular determinants remain largely unknown. Here, we report the first high-density transcriptomic analyses of Coccidioides development, defining morphology-dependent transcripts and those whose expression is regulated by Ryp1, a major regulator required for spherulation and virulence. Of approximately 9000 predicted transcripts, we discovered 273 transcripts with consistent spherule-associated expression, 82 of which are RYP1-dependent, a set likely to be critical for Coccidioides virulence. ChIP-Seq revealed 2 distinct regulons of Ryp1, one shared between hyphae and spherules and the other unique to spherules. Spherulation regulation was elaborate, with the majority of 227 predicted transcription factors in Coccidioides displaying spherule-enriched expression. We identified provocative targets, including 20 transcripts whose expression is endospore-enriched and 14 putative secreted effectors whose expression is spherule-enriched, of which 6 are secreted proteases. To highlight the utility of these data, we selected a cluster of RYP1-dependent, arthroconidia-associated transcripts and found that they play a role in arthroconidia cell wall biology, demonstrating the power of this resource in illuminating Coccidioides biology and virulence.

microbiology↗

bioRxiv2024

Optimizing in vitro spherulation cues in the fungal pathogen Coccidioides

Coccidioides spp. are part of a group of thermally dimorphic fungal pathogens, which grow as filamentous cells (hyphae) in the soil and transform to a different morphology upon inhalation into the host. The Coccidioides host form, the spherule, is unique and highly under characterized due to both technical and biocontainment challenges. Each spherule arises from an environmental spore (arthroconidium), matures, and develops hundreds of internal endospores, which are released from the spherule upon rupture. Each endospore can then go on to form another spherule in a cycle called spherulation. One of the foremost technical challenges has been reliably growing spherules in culture without the formation of contaminating hyphae, and consistently inducing endospore release from spherules. Here, we present optimization of in vitro spherule growth and endospore release, by closely controlling starting cell density in the culture, using freshly-harvested arthroconidia, and decreasing the concentration of multiple salts in spherulation media. We developed a minimal media to test spherule growth on various carbon and nitrogen sources. We defined a critical role for the dispersant Tamol in both early spherule formation and prevention of the accumulation of a visible film around spherules. Finally, we examined how the conditions under which arthroconidia are generated influence their transcriptome and subsequent development into spherules, demonstrating that this is an important variable to control when designing spherulation experiments. Together, our data reveal multiple strategies to optimize in vitro spherulation growth, enabling characterization of this virulence-relevant morphology.

microbiology↗

bioRxiv2019

MethylCal: Bayesian calibration of methylation levels

Bisulfite amplicon sequencing has become the primary choice for single-base methylation quantification of multiple targets in parallel. The main limitation of this technology is a preferential amplification of an allele and strand in the PCR due to methylation state. This effect, known as \"PCR bias\", causes inaccurate estimation of the methylation levels and calibration methods based on standard controls have been proposed to correct for it. Here, we present a Bayesian calibration tool, MethylCal, which can analyse jointly all CpGs within a DMR or CpG island, avoiding \"one-at-a-time\" CpG calibration. This enables more precise modeling of the methylation levels observed in the standard controls. It also provides accurate predictions of the methylation levels not considered in the controlled experiment, a feature that is paramount in the derivation of the corrected methylation degree. We tested the proposed method on eight independent assays (two CpG islands and six imprinting DMRs) and demonstrated its benefits, including the ability to detect outliers. We also evaluated MethylCals calibration in two practical cases, a clinical diagnostic test on 18 patients potentially affected by Beckwith-Wiedemann syndrome, and 17 individuals with celiac disease. The calibration of the methylation levels obtained by MethylCal allows a clearer identification of patients undergoing loss or gain of methylation in borderline cases and could influence further clinical or treatment decisions. MethylCal is availability as an R package on https://github.com/lb664/MethylCal.

bioinformatics↗