Biology subjects

Mena, A.

Publications and source records attributed to Mena, A..

4 recordsLinked to original sources

bioRxiv2025

Chromosome-level genomics and historical museum collections reveal new insights into the population structure and chromosome evolution of waterbuck

Advances in the sequencing and assembly of chromosome-level genome assemblies has enabled the study of non-model animals, providing further insights into the evolution of genomes and chromosomes. Here, we present the waterbuck (Kobus ellipsiprymnus) as an emerging model antelope for studying population dynamics and chromosome evolution. Antelope evolutionary history has been shaped by Robertsonian (Rb) fusions, with waterbuck also showing variation in karyotype due to two polymorphic Rb fusions. These polymorphisms are variable between and within the two recognised subspecies, the common and defassa waterbuck. To provide new insights into waterbuck evolution, we firstly assembled a chromosome-level genome assembly for the defassa subspecies using PacBio HiFi and Hi-C sequencing. We then utilised museum collections to carry out whole genome sequencing (WGS) of 24 historical waterbuck skins from both subspecies. Combined with a previous WGS dataset (n = 119), this represents the largest study of waterbuck populations to date. We found novel population structure and gene flow between waterbuck populations and regions across the genome with high genomic differentiation between the two subspecies. Several of these regions were found around the centromeres of fixed and polymorphic Rb fusions, exhibiting signatures of low recombination and local population structure. Interestingly, these regions contain genes involved in development, fertility, and recombination. Our results highlight the importance of assembling genomes to the chromosome-level, the utility and value of historical collections in sampling a wide-ranging species to uncover fine-scale population structure, and the potential impacts of Rb fusions on genomic differentiation and the recombination landscape.

evolutionary biology↗

bioRxiv2021

Whole genome sequencing evidences higher rates of relapse in Clostridioides difficile infection caused by PCR ribotype 106

Increasing prevalence and widespread of Clostridioides difficile infection (CDI) caused by the epidemic DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or the higher resistance rates found in some strains. Previous studies have also attributed higher recurrence rates to RT106 as compared to others. This study describes the genetic analysis by whole genome sequencing (WGS) of primary and recurrent isolates of RT106 to determine if the higher rate of recurrence associated to RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. The whole-genome sequences of ten primaries and fourteen recurrent RT106 isolates from ten patients were obtained to determine MLST profiles, resistance mutations and phylogenetic relatedness between the different isolates by comparative single nucleotide variants (SNV) analysis using the C. difficile DH/NAP11/106/ST-42 genome as reference (GenBank accession: GCA_002234355.1). All isolates were classified as ST42 and SNVs comparative analysis showed that those belonging to the same patient were isogenic (differed by [≤]3 SNVs), with one exception (6 SNVs); while strains belonging to different patients were not (differing by 4 to 43 SNVs) with two exceptions of isogenic isolates from different patients, suggesting putative transmission events. Phylogenetic analysis suggested the presence of similar local epidemic lineages, except for one patient whose isolates clustered with different US isolates. All the isolates, except those clustering with the US lineage, were also associated to moxifloxacin resistant since all of them were resistant by agar diffusion (MIC >32) and contained the Thr82Ile mutation in gyrA. Our results evidence that recurrent Clostridioides difficile infections caused by RT06/ST42 are mainly due to relapses, caused by primary strains, showing the great capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes.

microbiology↗

bioRxiv2021

Hypusinated eIF5A is required for the translation of collagen

The evolutionary conserved elongation factor eIF5A is required for the translation of mRNAs that encode protein sequences with consecutive prolines or combined with glycine and charged amino acids. Mammalian collagens are enriched in putative eIF5A-dependent Pro-Gly-containing tripeptides. Here, we show that eIF5A is needed for heterologous expression of collagen in yeast, and using a dual luciferase reporter system we confirmed that eIF5A depletion interrupts translation at Pro-Gly-collagenic motifs. Using mouse fibroblasts, we showed that depletion of active eIF5A reduced collagen 1 (Col1a1) content, which became concentrated around the nuclei, in contrast to a stronger and all over the cell collagen signal in untreated cells. Active eIF5A-depleted mouse fibroblast showed upregulation of endoplasmic reticulum (ER) stress markers, suggesting retention of partially synthesized Col1a1 in the ER. A dramatically lower level of Col11 protein was also observed in functional eIF5A-depleted human hepatic stellate cells treated with the profibrotic cytokine TGF-{beta}1. Our results show that collagen expression requires eIF5A and imply its potential as a target for regulating collagen production in fibrotic diseases.

molecular biology↗

bioRxiv2018

Conditioned increase of locomotor activity induced by haloperidol

Dopamine antagonist drugs have profound effects on locomotor activity. In particular, the administration of the D2 antagonist haloperidol produces a state that is similar to catalepsy. In order to confirm whether the modulation of the dopaminergic activity produced by haloperidol can act as an unconditioned stimulus, we carried out two experiments in which the administration of haloperidol was repeatedly paired with the presence of distinctive contextual cues that served as a Conditioned Stimulus. Paradoxically, the results revealed a dose-dependent increase in locomotor activity following conditioning with dopamine antagonist (Experiments 1) that was susceptible of extinction when the conditioned stimulus was presented repeatedly by itself after conditioning (Experiment 2). These data are interpreted from an associative perspective, considering them as a result of a classical conditioning process.

animal behavior and cognition↗