Biology subjects

Mardones, W.

Publications and source records attributed to Mardones, W..

3 recordsLinked to original sources

bioRxiv2025

OmniBio: An Easy-to-Use Web App for Kinetic Growth Parameter Calculation from Microplate Reader Data

OmniBio is a user-friendly web application designed to streamline the analysis of microbial growth curves from microplate reader data, eliminating the need for coding skills or cumbersome file preprocessing. Built in R, using the gcplyr package and Shiny framework, OmniBio supports data outputs from both Gen5 and iControl software, handling multiple sheets within a single file. Users can upload raw data along with experimental metadata to the platform, compute kinetic parameters such as maximum growth rate, lag time, ODmax, and area under the curve, and promptly visualize the results in real-time. The app produces plots for each parameter and a global heatmap analysis for comparing microbial performance across strains and culture media. Importantly, all the primary and processed data can be readily downloaded in a summarized Excel report. In contrast to existing tools, OmniBio optimizes the analysis process by automating repetitive computations and offering an intuitive, step-by-step workflow that does not require bioinformatics training. OmniBio is freely accessible at https://sdehnhardt.shinyapps.io/OmniBio/, and can be modified from open-source code on GitHub (https://github.com/sidehnhardt/OmniBio). The tool enables researchers to conduct high-throughput kinetic analysis in an efficient and user-friendly manner, optimizing both time and resource utilization.

bioinformatics↗

bioRxiv2020

Rapid selection response to ethanol in S. eubayanus emulates the domestication process under brewing conditions

Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood. Domesticated yeasts for brewing, where short generation times and large phenotypic and genomic plasticity were attained in a few generations under selection, are prime examples. To experimentally emulate the lager yeast domestication process, we created a genetically complex (panmictic) artificial population of multiple Saccharomyces eubayanus genotypes, one of the parents of lager yeast. Then we imposed a constant selection regime under a high ethanol concentration in 10 replicated populations during 260 generations (six months) and compared them with evolved controls exposed solely to glucose. Evolved populations exhibited a selection differential of 60% in growth rate in ethanol, mostly explained by the proliferation of a single lineage (CL248.1) that competitively displaced all other clones. Interestingly, the outcome does not require the entire time course of adaptation, as four lineages monopolized the culture at generation 120. Sequencing demonstrated that de novo genetic variants were produced in all evolved lines, including SNPs, aneuploidies, INDELs, and translocations. In addition, the evolved populations showed correlated responses resembling the domestication syndrome: genomic rearrangements, faster fermentation rates, lower production of phenolic-off flavors and lower volatile compound complexity. Expression profiling in beer wort revealed altered expression levels of genes related to methionine metabolism, flocculation, stress tolerance and diauxic shift, likely contributing to higher ethanol and fermentation stress tolerance in the evolved populations. Our study shows that experimental evolution can rebuild the brewing domestication process in "fast motion" in wild yeast, and also provides a powerful tool for studying the genetics of the adaptation process in complex populations.

genetics↗

bioRxiv2017

The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes

The high lignocellulolytic activity displayed by the soft-rot fungus P. purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and CEGMA analysis reveals that our assembly covers most if not all all protein-coding genes. RNASeq was performed and 93.1% of the reads aligned within the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.

genomics↗