Biology subjects

Mateos, M.

Publications and source records attributed to Mateos, M..

10 recordsLinked to original sources

bioRxiv2026

Environmental DNA analysis to search for an endangered desert fish

1.We conducted field surveys over two consecutive years (2022 and 2023) of freshwater habitats in the Rio De La Concepcion (several tributaries and sites) and one site in the Rio Santa Cruz (tributary of the Gila River) in the state of Sonora, Mexico. Our primary goal was to detect the presence of the Rio Concepcion Topminnow (Poeciliopsis jackschultzi), an endangered microendemic livebearing desert fish whose external morphology is indistinguishable from several sympatric congeners. Using an environmental DNA (eDNA) metabarcoding approach ("MiFish" locus), we failed to detect evidence of P. jackschultzi, implying that it is extinct or present at abundances below our detection ability. Applying a collective evidence approach including visual/eDNA surveys and past records, we discuss the strengths and limitations of the eDNA metabarcoding approach. In the Rio De La Concepcion, we confirm the presence of the other known native and previously reported introduced teleosts, and reveal more recent introductions. In the Rio Santa Cruz site, we detect three putative non-natives (Asexual Hybrid Topminnow, Yaqui Sucker, and Mexican Roundtail Chub). We recommend further monitoring of habitats and fish taxa, and implementation of practices that improve groundwater recharge and the quality and quantity of treated wastewater in the study area.

ecology↗

bioRxiv2024

Diverse toxin repertoire but limited metabolic capacities inferred from the draft genome assemblies of three Spiroplasma (Citri clade) strains associated with Drosophila

Spiroplasma (Class Mollicutes) is a diverse wall-less bacterial genus whose members are strictly dependent on eukaryotic hosts (mostly arthropods and plants), with which they engage in pathogenic to mutualistic interactions. Spiroplasma are generally fastidious to culture in vitro, especially those that are vertically transmitted by their hosts, which include flies in the genus Drosophila. Drosophila has been invaded by at least three independent clades of Spiroplasma: Poulsonii (the best studied; contains reproductive manipulators and defensive mutualists associated two major clades of Drosophila; and has among the highest substitution rates within bacteria); Citri (restricted to the repleta group of Drosophila); and Ixodetis. We report the first genome drafts of Drosophila-associated Citri Clade Spiroplasma: strain sMoj from D. mojavensis; strain sAld-Tx from D. aldrichi from Texas (newly discovered; also associated with D. mulleri); and strain sHy2 from D. hydei (the only Drosophila species known to naturally also harbor a Poulsonii clade strain, thereby providing an arena for horizontal gene transfer). Compared to their Poulsonii clade counterparts, we infer that the three Citri clade strains have: (1) equal or worse DNA repair abilities; (b) more limited metabolic capacities, which may underlie their comparatively lower titers and transmission efficiency; and (c) similar content of toxin domains, including at least one ribosome inactivating protein (RIP), which are implicated in the Poulsonii-conferred defense against natural enemies. As a byproduct of our phylogenomic analyses and exhaustive search for certain toxin domains in public databases, we document the toxin repertoire in close relatives of Drosophila-associated Spiroplasma, and in a very divergent newly discovered lineage (i.e., "clade X"). Phylogenies of toxin-encoding genes or domains imply substantial exchanges between closely and distantly related strains. Surprisingly, despite encoding several toxin genes and achieving relatively high prevalences in certain natural populations (sAld-Tx in this study; sMoj in prior work), fitness assays of sMoj (this study) and sAld-Tx (prior work) in the context of wasp parasitism fail to detect a beneficial effect to their hosts. Thus, how Citri clade strains persist in their Drosophila host populations remains elusive. Data summaryAll novel sequencing data are available through National Center for Biotechnology Information (NCBI) repositories. Illumina raw reads, assemblies, and NCBI annotations are available under BioProject Nos. PRJNA506493 for sHy2, PRJNA506491 for sAld-Tx, and PRJNA355307 for sMoj. Oxford Nanopore (MinIon) reads for sHy2 are under SRA Accession Number SRR12348752. Supporting Material is available under the DOI 10.6084/m9.figshare.c.7437997 or as accompanying supporting documents in the corresponding preprint server or scientific journal. Impact statementSymbiotic associations between arthropods and inherited microbes are pervasive, taxonomically and mechanistically diverse, and strongly influential. Research into the mechanisms and processes governing such heritable interactions is hindered by our inability to culture most inherited symbionts outside of their hosts. We studied three heritable strains of Spiroplasma (Citri clade) that naturally associate with Drosophila flies, and that reach relatively high prevalence in certain host populations, but appear to lack traits that would enable them to persist in host populations (e.g. such as high vertical transmission efficiency, reproductive manipulation, or fitness benefits). We compared their genomes to those of a separate Spiroplasma clade (Poulsonii) that associates with Drosophila, which does exhibit some of the traits that contribute to persistence, including protection against natural enemies of their hosts, and also has among the highest DNA substitution rates recorded for bacteria. Compared to Poulsonii, the three Citri clade strains have smaller genomes and fewer genes, leading us to predict they have similarly high DNA substitution rates, but more limited metabolic capacities, which may explain the comparatively lower densities they achieve within individual hosts, and their frequent loss in lab colonies of their hosts. However, the toxin repertoire of Citri clade was comparatively diverse, and the result of horizontal gene exchange among close and distant strains, and within-genome shuffling. We hypothesize that Citri clade strains persist via unknown fitness benefits conferred to their hosts, possibly mediated by toxins, or by substantial horizontal transmission. Our results, which also capitalized on publicly available assemblies, expand the range of Spiroplasma lineages that encode a particular combination of toxin types, and revealed the existence of a highly divergent lineage of Spiroplasma that associates with insects.

genomics↗

bioRxiv2022

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer

Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. We combined immunohistochemistry (IHC) and molecular profiling to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME in high-risk paediatric tumours. Using this novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

cancer biology↗

bioRxiv2021

Preliminary Characterization of Phage-like Particles from the Male-Killing Mollicute Spiroplasma poulsonii (an Endosymbiont of Drosophila)

Bacteriophages are vastly abundant, diverse, and influential, but with few exceptions (e.g. the Proteobacteria genera Wolbachia and Hamiltonella), the role of phages in heritable bacteria-arthropod interactions, which are ubiquitous and diverse, remains largely unexplored. Despite prior studies documenting phage-like particles in the mollicute Spiroplasma associated with Drosophila flies, genomic sequences of such phage are lacking, and their effects on the Spiroplasma-Drosophila interaction have not been comprehensively characterized. We used a density step gradient to isolate phage-like particles from the male-killing bacterium Spiroplasma poulsonii (strains NSRO and MSRO-Br) harbored by Drosophila melanogaster. Isolated particles were subjected to DNA sequencing, assembly, and annotation. Several lines of evidence suggest that we recovered phage-like particles of similar features (shape, size, DNA content) to those previously reported in Drosophila-associated Spiroplasma strains. We recovered three [~]19 kb phage-like contigs (two in NSRO and one in MSRO-Br) containing 21-24 open reading frames, a read-alignment pattern consistent with circular permutation, and terminal redundancy (at least in NSRO). Although our results do not allow us to distinguish whether these phage-like contigs represent infective phage-like particles capable of transmitting their DNA to new hosts, their encoding of several typical phage genes suggests that they are at least remnants of functional phage. We also recovered two smaller non-phage-like contigs encoding a known Spiroplasma toxin (Ribosome Inactivating Protein; RIP), and an insertion element, suggesting that they are packaged into particles. Substantial homology of our particle-derived contigs was found in the genome assemblies of members of the Spiroplasma poulsonii clade.

microbiology↗

bioRxiv2021

Discrimination of species within the Enterobacter cloacae complex using MALDI-TOF Mass Spectrometry and Fourier-Transform Infrared Spectroscopy coupled with Machine Learning tools

The Enterobacter cloacae complex (ECC) encompasses heterogeneous clusters of species that have been associated with nosocomial outbreaks. These species may host different acquired antimicrobial resistance and virulence mechanisms and their identification are challenging. This study aims to develop predictive models based on MALDI-TOF MS spectral profiles and machine learning for species-level identification. A total of 198 ECC and 116 K. aerogenes clinical isolates from the University Hospital Ramon y Cajal (Spain) and the University Hospital Basel (Switzerland) were included. The capability of the proposed method to differentiate the most common ECC species (E. asburiae, E. kobei, E. hormaechei, E. roggenkampii, E. ludwigii, E. bugandensis) and K. aerogenes was demonstrated by applying unsupervised hierarchical clustering with PCA pre-processing. We observed a distinctive clustering of E. hormaechei and K. aerogenes and a clear trend for the rest of the ECC species to be differentiated over the development dataset. Thus, we developed supervised, non-linear predictive models (Support Vector Machine with Radial Basis Function and Random Forest). The external validation of these models with protein spectra from the two participating hospitals yielded 100% correct species-level assignment for E. asburiae, E. kobei, and E. roggenkampii and between 91.2% and 98.0% for the remaining ECC species. Similar results were obtained with the MSI database developed recently (https://msi.happy-dev.fr/) except in the case of E. hormaechei, which was more accurately identified by Random Forest. In short, MALDI-TOF MS combined with machine learning demonstrated to be a rapid and accurate method for the differentiation of ECC species.

microbiology↗

bioRxiv2021

DROP: Molecular voucher database for identification of Drosophila parasitoids

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP (http://doi.org/10.5281/zenodo.4519656), genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and 6 proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyze research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

genomics↗

bioRxiv2020

Transcriptomic response during wasp parasitism in the Drosophila-Spiroplasma interaction

Several facultative bacterial symbionts of insects protect their hosts against natural enemies. Spiroplasma poulsonii strain sMel, a male-killing heritable symbiont of Drosophila melanogaster, confers protection against some species of parasitic wasps. Several lines of evidence suggest that Spiroplasma-encoded ribosome inactivating proteins (RIPs) are involved in the protection mechanism, but the potential contribution of the fly-encoded functions has not been deeply explored. Here we used RNA-seq to evaluate the response of D. melanogaster to infection by Spiroplasma and parasitism by the Spiroplasma-susceptible wasp Leptopilina heterotoma, and the Spiroplasma-resistant wasp Ganaspis hookeri. In the absence of Spiroplasma infection, we found evidence of Drosophila immune activation by G. hookeri, but not by L. heterotoma, which in turn negatively influenced functions associated with male gonad development. As expected for a symbiont that kills males, we detected extensive downregulation in the Spiroplasma-infected treatments of genes known to have male-biased expression. We detected very few genes whose expression was influenced by the Spiroplasma-L. heterotoma interaction, and they do not appear to be related to immune response. For most of them, parasitism by L. heterotoma (in the absence of Spiroplasma) caused an expression change that was at least partly reversed when Spiroplasma was also present. It is unclear whether such genes are involved in the Spiroplasma-mediated mechanism that leads to wasp death or fly rescue. Nonetheless, the expression pattern of some of these genes, which reportedly undergo expression shifts during the larva-to-pupa transition, is suggestive of an influence of Spiroplasma on the development time of L. heterotoma-parasitized flies. In addition, we used the RNAseq data and quantitative (q)PCR to evaluate the transcript levels of the Spiroplasma-encoded RIP genes. One of the five RIP genes (RIP2) was consistently highly expressed independently of wasp parasitism, in two substrains of sMel. Finally, the RNAseq data revealed evidence consistent with RIP-induced damage in the ribosomal (r)RNA of the Spiroplasma-susceptible, but not the Spiroplasma-resistant, wasp. We conclude that immune priming is unlikely to contribute to the Spiroplasma-mediated protection against wasps, and that the mechanism by which G. hookeri resists/tolerates Spiroplasma does not involve inhibition of RIP transcription.

ecology↗

bioRxiv2020

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

Spiroplasma are a group of Mollicutes whose members include plant pathogens, insect pathogens, and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5% sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.

evolutionary biology↗

bioRxiv2019

Effect of heritable symbionts on maternally-derived embryo transcripts

Maternally-transmitted endosymbiotic bacteria are ubiquitous in insects. Among other influential phenotypes, many heritable symbionts of arthropods are notorious for manipulating host reproduction through one of four reproductive syndromes, which are generally exerted during early developmental stages of the host: male feminization; parthenogenesis induction; male killing; and cytoplasmic incompatibility (CI). Major advances have been achieved in understanding mechanisms and identifying symbiont factors involved in reproductive manipulation, particularly male killing and cytoplasmic incompatibility. Nonetheless, whether cytoplasmically-transmitted bacteria influence the maternally-loaded components of the egg or early embryo has not been examined. In the present study, we investigated whether heritable endosymbionts that cause different reproductive phenotypes in Drosophila melanogaster influence the mRNA transcriptome of early embryos. We used mRNA-seq to evaluate differential expression in Drosophila embryos lacking endosymbionts (control) to those harbouring the male-killing Spiroplasma poulsonii strain MSRO-Br, the CI-inducing Wolbachia strain wMel, or Spiroplasma poulsonii strain Hyd1; a strain that lacks a reproductive phenotype and is naturally associated with Drosophila hydei. We found no consistent evidence of influence of symbiont on mRNA composition of early embryos, suggesting that the reproductive manipulation mechanism does not involve alteration of maternally-loaded transcripts. In addition, we capitalized on several available mRNA-seq datasets derived from Spiroplasma-infected Drosophila melanogaster embryos, to search for signals of depurination of rRNA, consistent with the activity of Ribosome Inactivating Proteins (RIPs) encoded by Spiroplasma poulsonii. We found small but statistically significant signals of depurination of Drosophila rRNA in the Spiroplasma treatments (both strains), but not in the symbiont-free control or Wolbachia treatment, consistent with the action of RIPs. The depurination signal was slightly stronger in the treatment with the male-killing strain. This result supports a recent report that RIP-induced damage contributes to male embryo death.

genomics↗

bioRxiv2018

Wolbachia pipientis associated to tephritid fruit fly pests: from basic research to applications

Members of the true fruit flies (family Tephritidae) are among the most serious agricultural pests worldwide, whose control and management demands large and costly international efforts. The need for cost-effective and environmentally-friendly integrated pest management (IPM) has led to the development and implementation of autocidal control strategies. Autocidal approaches include the widely used sterile insect technique (SIT) and the incompatible insect technique (IIT). IIT relies on maternally transmitted bacteria (namely Wolbachia), to cause a conditional sterility in crosses between released mass-reared Wolbachia-infected males and wild females, which are either uninfected or infected with a different Wolbachia strain (i.e., cytoplasmic incompatibility; CI). Herein, we review the current state of knowledge on Wolbachia-tephritid interactions including infection prevalence in wild populations, phenotypic consequences, and their impact on life history traits. Numerous pest tephritid species are reported to harbor Wolbachia infections, with a subset exhibiting high prevalence. The phenotypic effects of Wolbachia have been assessed in very few tephritid species, due in part to the difficulty of manipulating Wolbachia infection (removal or transinfection). Based on recent methodological advances (high-throughput DNA sequencing) and a breakthrough concerning the mechanistic basis of CI, we suggest research avenues that could accelerate generation of necessary knowledge for the potential use of Wolbachia-based IIT in area-wide integrated pest management (AW-IPM) strategies for the population control of tephritid pests.

ecology↗