Biology subjects

Villanueva-Canas, J. L.

Publications and source records attributed to Villanueva-Canas, J. L..

6 recordsLinked to original sources

bioRxiv2025

Rapid quantification of short-chain fatty acids by Fourier-transform infrared spectroscopy for microbiota quality assessment

Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of a healthy microbiota. Their quantification, however, is time-consuming, expensive and requires specialized personal and equipment. Thus, their use for quality assessment of stool samples in clinical contexts is limited. In this study we explored the use of Fourier-transform infrared (FT-IR) spectroscopy as an alternative method for metabolomic quality assessment of stool samples. FT-IR identifies the chemical bonds present in SCFAs and allows clear discrimination between healthy and dysbiotic stool samples (caused by Clostridioides difficile infection) through Principal Component Analysis (PCA). Overall, FT-IR provides a rapid, cost-effective and simple method for stool samples quality assessment. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential application for routine implementation in clinical laboratories.

microbiology↗

bioRxiv2022

Evolutionary insights reveal a new role of PADI2 in transcriptional elongation

Peptidyl arginine deiminases (PADIs) catalyze protein citrullination, a post-translational conversion of arginine to citrulline. The most widely expressed member of this family, PADI2, regulates cellular processes that impact several diseases. We hypothesized that we could gain new insights into PADI2 function through a systematic evolutionary and structural analysis. Here, we identify 20 positively selected PADI2 residues, 16 of which are structurally exposed and maintain PADI2 interactions with cognate proteins. Many of these selected residues reside in non-catalytic regions of PADI2. We validate the importance of a prominent loop in the middle domain that encompasses PADI2 L162, a residue under positive selection. This site is essential for interaction with the transcription elongation factor (P-TEFb) and mediates active transcription of the oncogenes c-MYC, and CCNB1, as well as impacting cellular proliferation. These insights could be key to understanding and addressing the role of the PADI2 c-MYC axis in cancer progression. Significance StatementHere we use a systematic evolutionary analysis to identify positively selected residues in the non-catalytic domain of PADI2 and link the positive selection of key residues to a role in transcription. Specifically, a structurally exposed loop in the PADI2 middle domain encompasses the positively selected residue L162 which is linked to transcription and cellular proliferation. This loop contributes to PADI2 interaction with the P-TEFb complex and cellular proliferation. Our results showcase the utility of combining evolutionary and experimental approaches to dissect the evolution of essential functional processes.

evolutionary biology↗

bioRxiv2020

ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR

Current global pandemic due to the SARS-CoV-2 has struggled and pushed the limits of global health systems. Supply chain disruptions and scarce availability of commercial laboratory reagents have motivated worldwide actors to search for alternative workflows to cope with the demand. We have used the OT-2 open-source liquid-handling robots (Opentrons, NY), RNA extraction and RT-qPCR reagents to set-up a reproducible workflow for RT-qPCR SARS-CoV-2 testing. We developed a framework with a template and several functions and classes that allow the creation of customized RT-qPCR automated circuits. As a proof of concept, we provide data obtained by a fully-functional tested code using the MagMax Pathogen RNA/DNA kit and the MagMax Viral/Pathogen II kit (Thermo Fisher Scientific, MA) on the Kingfisher Flex instrument (Thermo Fisher Scientific, MA). With these codes available is easy to create new stations or circuits from scratch, adapt existing ones to changes in the experimental protocol, or perform fine adjustments to fulfil special needs. The affordability of this platform makes it accessible for most laboratories and hospitals with a bioinformatician, democratising automated SARS-CoV-2 PCR testing and increasing, temporarily or not, the capacity of carrying out tests. It also confers flexibility, as this platform is not dependant on any particular commercial kit and can be quickly adapted to protocol changes or other special needs.

bioinformatics↗

bioRxiv2019

Frequent birth of de novo genes in the compact yeast genome

Evidence has accumulated that some genes originate directly from previously non-genic sequences, or de novo, rather than by the duplication or fusion of existing genes. However, how de novo genes emerge and eventually become functional is largely unknown. Here we perform the first study on de novo genes that uses transcriptomics data from eleven different yeast species, all grown identically in both rich media and in oxidative stress conditions. The genomes of these species are densely-packed with functional elements, leaving little room for the co-option of genomic sequences into new transcribed loci. Despite this, we find that at least 213 transcripts (~5%) have arisen de novo in the past 20 million years of evolution of bakers yeast-or approximately 10 new transcripts every million years. Nearly half of the total newly expressed sequences are generated from regions in which both DNA strands are used as templates for transcription, explaining the apparent contradiction between the limited empty genomic space and high rate of de novo gene birth. In addition, we find that 40% of these de novo transcripts are actively translated and that at least a fraction of the encoded proteins are likely to be under purifying selection. This study shows that even in very highly compact genomes, de novo transcripts are continuously generated and can give rise to new functional protein-coding genes.

evolutionary biology↗

bioRxiv2018

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Mapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations of Drosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Indeed, we, and others, found evidence of selective sweeps and/or population differentiation for 65 of them. The analysis of the genes located nearby these 65 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affect expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.

evolutionary biology↗

bioRxiv2016

New genes and functional innovation in mammals

The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected for. To address these questions we have obtained a large collection of mammalian-specific gene families that lack homologues in other eukaryotic groups. We have combined gene annotations and de novo transcript assemblies from 30 different mamalian species, obtaining about 6,000 gene families. In general, the proteins in mammalian-specific gene families tend to be short and depleted in aromatic and negatively charged residues. Proteins which arose early in mammalian evolution include milk and skin polypeptides, immune response components, and proteins involved in reproduction. In contrast, the functions of proteins which have a more recent origin remain largely unknown, despite the fact that these proteins also have extensive proteomics support. We identify several previously described cases of genes originated de novo from non-coding genomic regions, supporting the idea that this mechanism frequently underlies the evolution of new protein-coding genes in mammals. Finally, we show that most young mammalian genes are preferentially expressed in testis, suggesting that sexual selection plays an important role in the emergence of new functional genes.

evolutionary biology↗