Biology subjects

Torres, M.

Publications and source records attributed to Torres, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Bacterial fitness for plant colonization is influenced by plant growth substrate

O_LIBacteria colonize plants and contribute to their health. Despite advances in our understanding of bacterial plant colonization, the extent to which growth substrate influences the molecular mechanisms enabling bacteria to efficiently colonize plants remains poorly understood. C_LIO_LITo evaluate if genes important for plant colonization are influenced by substrate, we used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Paraburkholderia graminis OAS925, an efficient rhizosphere colonizer, and Brachypodium distachyon plants grown in six different substrates. C_LIO_LIOf the 382 rhizosphere colonization genes that we identified in strain OAS925, 348 genes (91.1%) are dependent on the growth substrate evaluated, and 34 genes (8.9%) are shared across all the substrates. To further characterize the plant colonization fitness genes, we compared our data to growth in 110 distinct in vitro conditions. To validate our results, we used individual mutants of selected genes and tested them in different growth substrates. We also show the influence of substrate on colonization by P. phytofirmans PsJN, Variovorax sp. OAS795 and Rhizobium sp. OAE497. C_LIO_LIOur data confirms that bacterial fitness for plant colonization is strongly influenced by plant growth substrate type, and highlights the importance of taking this parameter into consideration when engineering bacterial strains for improved host colonization. C_LI

microbiology↗

bioRxiv2025

Identification and Functional Characterization of Regulatory Variants in DPP9 Associated with COVID-19 Severity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to a wide-range of clinical outcomes, which have been extensively studied through genome-wide association studies (GWAS). Starting from lead genetic variants associated with COVID-19 infection and severity, we identified a subset of non-coding candidate variants with potential regulatory functions. Using bioinformatics analysis and functional screening in three cell lines, we prioritized two DPP9 variants within a haplotype that increases the risk of severe COVID-19. This haplotype exhibited increased regulatory activity and altered transcription factor binding, suggesting its role in influencing COVID-19 severity through modulation of DPP9 expression in immune and lung cell types. The interest of our study lies in the functional characterization of regulatory variants responsible for the higher levels of DPP9 and lung damage observed in patients with severe COVID-19. These findings advance our understanding of genetic risk factors for COVID-19 and highlight functional SNPs that may guide future therapeutic research.

genetics↗

bioRxiv2024

Metabolism fine tuning and cardiokines secretion represent adaptative responses of the heart to High Fat and High Sugar Diets in flies

Cardiopathies are one of the leading causes of death in obese diabetics. Diabetic cardiomyopathies are notably characterized by contractile dysfunctions. Using the Drosophila model for cardiac function in pathophysiological context, we identified a set of candidate genes whose cardiac expression is modulated by High Sugar and High Fat regimes. Genes encoding core components of key homeostatic pathways - such as 1C-metabolism homeostasis, the Galactose metabolism pathway and metabolites transporters - were identified and characterized as adaptative factors of cardiac function under nutritional stresses. In addition, putative secreted proteins were found dysregulated, highlighting the heart as a secretory organ in hyperglycemia and hyperlipidemia. In particular, we characterized the Fit satiety hormone as a new fly cardiokine, which autonomously modulates the cardiac function and remotely affects feeding behavior. Overall, our study uncovered autonomous and systemic adjustable responses of the heart to nutritional stresses.

physiology↗

bioRxiv2024

Purkinje Cell-specific Deficiency in SEL1L-HRD1 Endoplasmic Reticulum-Associated Degradation Causes Progressive Cerebellar Ataxia in Mice

Recent studies have identified multiple genetic variants of SEL1L-HRD1 ER-associated degradation (ERAD) in humans with neurodevelopmental disorders and locomotor dysfunctions, including ataxia. However, the relevance and importance of SEL1L-HRD1 ERAD in the pathogenesis of ataxia remain unexplored. Here we show that SEL1L deficiency in Purkinje cells leads to early-onset progressive cerebellar ataxia with progressive loss of Purkinje cells with age. Mice with Purkinje cell-specific deletion of SEL1L (Sel1LPcp2Cre) exhibit motor dysfunction beginning around 9 weeks of age. Transmission electron microscopy (TEM) analysis reveals dilated ER and fragmented nuclei in Purkinje cells of adult Sel1LPcp2Cre mice, indicative of altered ER homeostasis and cell death. Lastly, loss of Purkinje cells is associated with a secondary neurodegeneration of granular cells, as well as robust activation of astrocytes and proliferation of microglia, in the cerebellum of Sel1LPcp2Cre mice. These data demonstrate the pathophysiological importance of SEL1L-HRD1 ERAD in Purkinje cells in the pathogenesis of cerebellar ataxia. One-sentence summarySEL1L-HRD1 ERAD is indispensable for Purkinje cell function and cerebellar ataxia pathogenesis in mice.

neuroscience↗

bioRxiv2024

Contribution of neurons that express fruitless and Clock transcription factors to behavioral rhythms and courtship

Animals need to integrate information across neuronal networks that direct reproductive behaviors and circadian rhythms. In Drosophila, the master regulatory transcription factors that direct courtship behaviors and circadian rhythms are co-expressed in a small set of neurons. In this study we investigate the role of these neurons in both males and females. We find sex-differences in the number of these fruitless and Clock -expressing neurons (fru {cap} Clk neurons) that is regulated by male-specific Fru. We assign the fru {cap} Clk neurons to the electron microscopy connectome that provides high resolution structural information. We also discover sex-differences in the number of fru-expressing neurons that are post-synaptic targets of Clk-expressing neurons, with more post-synaptic targets in males. When fru {cap} Clk neurons are activated or silenced, males have a shorter period length. Activation of fru {cap} Clk neurons also changes the rate a courtship behavior is performed. We find that activation and silencing fru {cap} Clk neurons impacts the molecular clock in the sLNv master pacemaker neurons, in a cell-nonautonomous manner. These results reveal how neurons that subserve the two processes, reproduction and circadian rhythms, can impact behavioral outcomes in a sex-specific manner.

neuroscience↗

bioRxiv2024

Proteomic Insights into Circadian Transcription Regulation: Novel E-box Interactors Revealed by Proximity Labeling

Circadian clocks ([~]24h) are responsible for daily physiological, metabolic and behavioral changes. Central to these oscillations is the regulation of gene transcription. Previous research has identified clock protein complexes that interact with the transcriptional machinery to orchestrate circadian transcription, but technological constraints have limited the identification of de novo proteins. Here we use a novel genomic locus-specific quantitative proteomics approach to provide a new perspective on time-of-day-dependent protein binding at a critical chromatin locus involved in circadian transcription - the E-box. Using proximity labeling proteomics at the E-box of the clock-controlled Dbp gene in mouse fibroblasts, we identified 69 proteins at this locus at the time of BMAL1 binding. This method successfully enriched BMAL1 as well as HDAC3 and HISTONE H2A.V/Z, known circadian regulators. New E-box proteins include the MINK1 kinase and the XPO7 transporter, whose depletion in human U-2 OS cells results in disrupted circadian rhythms suggesting a role in the circadian transcriptional machinery. Overall, our approach uncovers novel circadian modulators and provides a new strategy to obtain a complete temporal picture of circadian transcriptional regulation.

molecular biology↗

bioRxiv2024

Elasmobranchs Exhibit Species-Specific Epidermal Microbiomes Guided by Denticle Topography

Elasmobranch epidermal microbiomes are species-specific, yet microbial assembly and retainment drivers are mainly unknown. The contribution of host-derived factors in recruiting an associated microbiome is essential for understanding host-microbe interactions. Here, we focus on the physical aspect of the host skin in structuring microbial communities. Each species of elasmobranch exhibits unique denticle morphology, and we investigate whether microbial communities and functional pathways are correlated with the morphological features or follow the phylogeny of the three species. We extracted and sequenced the DNA from the epidermal microbial communities of three captive shark species: Horn (Heterodontus francisci), Leopard (Triakis semifasciata), and Swell shark (Cephaloscyllium ventriosum) and use electron microscopy to measure the dermal denticle features of each species. Our results outline species-specific microbial communities, as microbiome compositions vary at the phyla level; C. ventriosum hosted a higher relative abundance of Pseudomonadota and Bacillota, while H. francisci were associated with a higher prevalence of Euryarchaeota and Aquificae, and Bacteroidota and Crenarchaeota were ubiquitous with T. semifasciata. Functional pathways performed by each species respective microbiome were species-specific metabolic. Microbial genes associated with aminosugars and electron-accepting reactions were correlated with the distance between dermal denticles, whereas desiccation stress genes were only present when the dermal denticle overlapped. Microbial genes associated with Pyrimidines, chemotaxis and virulence followed the phylogeny of the sharks. Several microbial genera display associations that resemble host evolutionary lineage, while others had linear relationships with interdenticle distance. Therefore, denticle morphology was a selective influence for some microbes and functions in the microbiome contributing to the phylosymbiosis. ImportanceMicrobial communities form species-specific relationships with vertebrate hosts, but the drivers of these relationships remain an outstanding question. We explore the relationship between a physical feature of the host and the microbial community. A distinguishing feature of the subclass Elasmobranchii (sharks, rays, and skates), is the presence of dermal denticles on the skin. These structures protrude through the epidermis providing increased swimming efficiency for the host and an artificial model skin affect microbial recruitment and establishment of cultured microbes but has not been tested on natural microbiomes. Here, we show some naturally occurring microbial genera and functional attributes were correlated with dermal denticle features, suggesting they are one, but not only contributing factor in microbiome structure on benthic sharks.

microbiology↗

bioRxiv2024

Unraveling a novel dual-function regulatory element showing epistatic interaction with a variant that escapes genome-wide association studies.

Regulation of gene expression has recently been complexified by the identification of Epromoters, a subset of promoters with enhancer function. Here, we uncovered the first dual cis-regulatory element, "ESpromoter," exhibiting both enhancer and silencer function, as a regulator of the nearby genes ATP2B4 and LAX1 in single human T cells. Through integrative approach, we pinpointed functional rs11240391, a severe malaria risk variant that escapes detection in genome-wide association studies, challenging conventional strategies for identifying causal variants. CRISPR-modified cells demonstrated the regulatory effect of ESpromoter and rs11240391 on LAX1 expression and T cell activation. Furthermore, our findings revealed an epistatic interaction between ESpromoter SNPs and rs11240391, impacting severe malaria susceptibility by further reducing LAX1 expression. This groundbreaking discovery challenges the conventional enhancer-silencer dichotomy. It highlights the sophistication of transcriptional regulation and argues for an integrated approach combining genetics, epigenetics, and genomics to identify new therapeutic targets for complex diseases. HIGHLIGHTSO_LINovel dual enhancer-silencer element (ESpromoter) in a single human cell type C_LIO_LIFunctional SNP for severe malaria risk that escapes genome-wide association studies C_LIO_LIGenome editing at the SNP demonstrates a regulatory effect on LAX1 and T cell activation C_LIO_LIEpistatic interaction between SNPs increases the risk of severe malaria C_LI In briefEpistatic interaction between common variants within a novel dual enhancer-silencer regulatory element and the LAX1 promoter variant is responsible for severe malaria susceptibility through T-cell activation.

genomics↗

bioRxiv2024

Epigenetic priming of embryonic lineages in the mammalian epiblast

Understanding the diversification of mammalian cell lineages is an essential to embryonic development, organ regeneration and tissue engineering. Shortly after implantation in the uterus, the pluripotent cells of the mammalian epiblast generate the three germ layers: ectoderm, mesoderm and endoderm1. Although clonal analyses suggest early specification of epiblast cells towards particular cell lineages2-4, single-cell transcriptomes do not identify lineage-specific markers in the epiblast5-11 and thus, the molecular regulation of such specification remains unknow. Here, we studied the epigenetic landscape of single epiblast cells, which revealed lineage priming towards endoderm, ectoderm or mesoderm. Unexpectedly, epiblast cells with mesodermal priming show a strong signature for the endothelial/endocardial fate, suggesting early specification of this lineage aside from other mesoderm. Through clonal analysis and live imaging, we show that endothelial precursors show early lineage divergence from the rest of mesodermal derivatives. In particular, cardiomyocytes and endocardial cells show limited lineage relationship, despite being temporally and spatially co-recruited during gastrulation. Furthermore, analysing the live tracks of single cells through unsupervised classification of cell migratory activity, we found early behavioral divergence of endothelial precursors shortly after the onset of mesoderm migration towards the cardiogenic area. These results provide a new model for the phenotypically silent specification of mammalian cell lineages in pluripotent cells of the epiblast and modify current knowledge on the sequence and timing of cardiovascular lineages diversification12,13.

developmental biology↗

bioRxiv2023

A reference genome for the Andean cavefish Trichomycterus rosablanca (Siluriformes, Trichomycteridae): building genomic resources to study evolution in cave environments

Animals living in caves are of broad relevance to evolutionary biologists interested in understanding the mechanisms underpinning convergent evolution. In the Eastern Andes of Colombia, populations from at least two distinct clades of Trichomycterus catfishes (Siluriformes) independently colonized cave environments and converged in phenotype by losing their eyes and pigmentation. We are pursuing several research questions using genomics to understand the evolutionary forces and molecular mechanisms responsible for repeated morphological changes in this system. As a foundation for such studies, here we describe a diploid, chromosome-scale, long-read reference genome for Trichomycterus rosablanca, a blind, depigmented species endemic to the karstic system of the department of Santander. The nuclear genome comprises 1Gb in 27 chromosomes, with a 40.0x HiFi long-read genome coverage having a N50 scaffold of 40.4 Mb and N50 contig of 13.1 Mb, with 96.9% (Eukaryota) and 95.4% (Actinopterygii) universal single-copy orthologs (BUSCO). This assembly provides the first reference genome for the speciose genus Trichomycterus, which will serve as a key resource for research on the genomics of phenotypic evolution.

genomics↗

bioRxiv2023

SpatialDDLS: An R package to deconvolute spatial transcriptomics data using neural networks

SummarySpatial transcriptomics has changed our way to study tissue structure and cellular organization. However, there are still limitations in its resolution, and most available plaXorms do not reach a single cell resolution. To address this issue, we introduce SpatialDDLS, a fast neural network-based algorithm for cell type deconvolution of spatial transcriptomics data. SpatialDDLS leverages single-cell RNA sequencing (scRNA-seq) data to simulate mixed transcriptional profiles with predefined cellular composition, which are subsequently used to train a fully-connected neural network to uncover cell type diversity within each spot. By comparing it with two state-of-the-art spatial deconvolution methods, we demonstrate that SpatialDDLS is an accurate and faster alternative to the available state-of-the art tools. Availability and implementationThe R package SpatialDDLS is available via CRAN-The Comprehensive R Archive Network: https://CRAN.R-project.org/package=SpatialDDLS. A detailed manual of the main functionalities implemented in the package can be found at https://diegommcc.github.io/SpatialDDLS. Contactfscabo@cnic.es Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

plant biology↗

bioRxiv2023

P53 and BCL-2 family proteins PUMA and NOXA define competitive fitness in Pluripotent Cells

Cell Competition is a process by which neighboring cells compare their fitness. As a result, viable but suboptimal cells are selectively eliminated in the presence of fitter cells. In the early mammalian embryo, epiblast pluripotent cells undergo extensive Cell Competition, which prevents suboptimal cells from contributing to the newly forming organism. While competitive ability is regulated by MYC in the epiblast, the mechanisms that contribute to competitive fitness in this context are largely unknown. Here, we report that P53 and its pro-apoptotic targets PUMA and NOXA regulate apoptosis susceptibility and competitive fitness in pluripotent cells. PUMA is widely expressed specifically in pluripotent cells in vitro and in vivo. We show that the p53-PUMA/NOXA pathway regulates mitochondrial membrane potential and oxidative status. We found that P53 regulates MYC levels in pluripotent cells, which connects these two Cell competition pathways, however, MYC and PUMA/NOXA levels are independently regulated by P53. We propose a model that integrates a bifurcated P53 pathway regulating both MYC and PUMA/NOXA levels and determines competitive fitness through regulation of mitochondrial activity.

developmental biology↗

bioRxiv2023

SEL1L-HRD1 ER-associated degradation is a new ataxia gene

The SEL1L-HRD1 protein complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD); however, definitive evidence for the importance of SEL1L in HRD1 ERAD is lacking. Here we report that attenuation of the interaction between SEL1L and HRD1 impairs HRD1 ERAD function and has pathological consequences in mice. Our data show that SEL1L variant p.Ser658Pro (SEL1LS658P) previously identified in Finnish Hound suffering cerebellar ataxia is a recessive hypomorphic mutation, causing partial embryonic lethality, developmental delay, and early-onset cerebellar ataxia in homozygous mice carrying the bi-allelic variant. Mechanistically, SEL1LS658P variant attenuates the SEL1L-HRD1 interaction and causes HRD1 dysfunction by generating electrostatic repulsion between SEL1L F668 and HRD1 Y30 residues. Proteomic screens of SEL1L and HRD1 interactomes revealed that the SEL1L-HRD1 interaction is prerequisite for the formation of a functional HRD1 ERAD complex, as SEL1L recruits not only the lectins OS9 and ERLEC1, but the E2 UBE2J1 and retrotranslocon DERLIN, to HRD1. These data underscore the pathophysiological importance and disease relevance of the SEL1L-HRD1 complex, and identify a key step in organizing the HRD1 ERAD complex.

cell biology↗

bioRxiv2023

Control of coronary lymphangiogenesis by epicardial VEGFC/D

The contractile ability of the mammalian heart critically relies on blood coronary circulation, essential to provide oxygen and nutrients to myocardial cells. In addition, the lymphatic vasculature is essential for the myocardial immune response, extracellular fluid homeostasis and response to injury. Recent studies identified different origins of coronary lymphatic endothelial cells, however, the cues that govern coronary lymphangiogenesis remain unknown. Here we show that the coronary lymphatic vasculature develops in intimate contact with the epicardium and with epicardial-derived cells. The epicardium expresses the lymphangiogenic cytokine VEGFC and its conditional elimination from the epicardium abrogates coronary lymphatic vasculature development. Interestingly, VEGFD is also expressed in the epicardium and cooperates with VEGFC in coronary lymphangiogenesis, but it does so only in females, uncovering an unsuspected sex-specific role for this cytokine. These results identify a role for the epicardium/subepicardium as a signalling niche required for coronary lymphangiogenesis and VEGFC/D as essential mediators of this role.

developmental biology↗

bioRxiv2023

Spatial enhancer activation determines inhibitory neuron identity

The mammalian telencephalon contains a tremendous diversity of GABAergic projection neuron and interneuron types, that originate in a germinal zone of the embryonic basal ganglia. How genetic information in this transient structure is transformed into different cell types is not yet fully understood. Using a combination of in vivo CRISPR perturbation, lineage tracing, and ChIP-seq in mice, we found that the transcription factor MEIS2 favors the development of projection neurons through genomic binding sites in regulatory enhancers of projection neuron specific genes. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity towards these sites. In interneuron precursors, the activation of projection neuron specific enhancers by MEIS2 and DLX5 is repressed by the transcription factor LHX6. When MEIS2 carries a mutation associated with intellectual disability in humans, it is less effective at activating enhancers involved in projection neuron development. This suggests that GABAergic differentiation may be impaired in patients carrying this mutation. Our research supports a model ("Differential Binding ) where the spatial specific composition of transcription factors at cis-regulatory elements determines differential gene expression and cell fate decisions in the ganglionic eminence.

developmental biology↗

bioRxiv2022

Genomic accordions may hold the key to Monkeypox Clade IIb's increased transmissibility

The currently expanding monkeypox epidemic is caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. In contrast to monkeypox cases caused by clade I and subclade IIa MPXV, the prognosis of current cases is generally favorable, but person-to-person transmission is much more efficient. MPXV evolution is driven by selective pressure from hosts and loss of virus-host interacting genes. However, there is no satisfactory genetic explanation using single-nucleotide polymorphisms (SNPs) for the observed increased MPXV transmissibility. We hypothesized that key genomic changes may occur in the genomes low-complexity regions (LCRs), which are highly challenging to sequence and have been dismissed as uninformative. Using a combination of highly sensitive techniques, we determined a first high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This effort revealed significant variation in short-tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of SNPs and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs) 153, 204, and 208 could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. Consequently, we posit that genomic studies focusing on phenotypic MPXV clade-/subclade-/lineage-/strain differences should change their focus to the study of LCR variability instead of SNP variability.

genomics↗

bioRxiv2022

Identification of Circular Dorsal Ruffles as Signal Platforms for the AKT pathways in Glomerular Podocytes

Circular dorsal ruffles (CDRs) are rounded membrane ruffles induced by growth factors to function as precursors of the large-scale endocytosis called macropinocytosis. In cell line systems, CDR/macropinocytosis regulate the AKT-mTORC1 pathway, a canonical growth factor signaling. However, it is not known if this mechanism occurs in tissues. Here, utilizing ultra-high-resolution scanning electron microscopy, we report that CDRs are expressed in glomerular podocytes ex vivo and in vivo. Biochemical and imaging analysis revealed that AKT phosphorylation is localized to CDRs upstream of mTORC1 activation in podocyte cell line and isolated glomeruli, indicating that CDRs function as signal platforms for AKT-mTORC1 pathway in podocytes to maintain the kidney function. Because mTORC1 has critical roles in the podocyte metabolism and the aberrant activation of mTORC1 triggers podocytopathies, these results suggest that targeting CDR formation would be a potential therapeutic approach for the diseases.

cell biology↗