Biology subjects

Perez, I.

Publications and source records attributed to Perez, I..

15 recordsLinked to original sources

bioRxiv2026

Constraining Palaeogeography and Palaeotides for the Cambrian using cnidarian medusae

The ocean tides influence key Earth system processes at a range of spatial and temporal scales. It is known that the geometry of ocean basins is the leading controller of tidal energetics, so well-constrained palaeogeographic reconstructions and tidal properties for Earths past are imperative when investigating other Earth system processes. Here, we present a novel way to constrain both deep-time tidal model results and reconstructions, by combining palaeoecology with sedimentology. We compare new palaeo-tidal model simulations for the Cambrian period, significant for the early origin and radiation of major animal fauna, to tidal proxies. One of the most abundant soft-bodied organisms preserved during this time are cnidarian medusae (jellyfish). A total of 17 cnidarian medusae localities were obtained through the literature, which had an adequate global distribution and occurred at regular intervals throughout the period of study. In some locations there were also estimates of palaeo-tidal range. Our results show a good agreement between the simulations and proxy data. In the few locations where there is disagreement, it is proposed that the palaeogeographic reconstructions are missing details, e.g., island chains, and our results allow for the palaeogeographic reconstructions to be improved. The proxy method presented is promising and can be applied to other time-periods with different marine fossils, particularly at evolutionary and extinction periods where the marginal marine environment is of importance.

paleontology↗

bioRxiv2026

Identification of a new mycobacterial peptide that controls the activity of the iron-dependent regulator, IdeR.

Mycobacterium tuberculosis (Mtb) must regulate intracellular iron to survive in the host and cause disease. IdeR (Iron-dependent Regulator) is an essential Mtb protein that governs intracellular iron levels by regulating the expression of genes involved in iron metabolism. IdeR expression, however, is iron independent, and the mechanisms that regulate IdeRs function are not fully understood. Here, we report the discovery of a previously unrecognized Mtb peptide (PRI) that regulates IdeR activity. PRI is induced under iron limitation; it binds to IdeR and restricts its activity. In addition, we demonstrate that altering the balance between PRI and IdeR impairs iron homeostasis and intracellular replication of Mtb in macrophages. The findings reveal a new paradigm in mycobacterial iron regulation and open new avenues for targeting iron homeostatic mechanisms in Mtb, which are crucial for virulence and antibiotic resistance.

microbiology↗

bioRxiv2026

Linking immunity and nutrition: Vital DNA extracellular trap formation in Dictyostelium discoideum reveals an ancestral strategy for microbial management

Extracellular traps (ETs) were originally described in neutrophils as DNA-based structures that immobilize microbes and contribute to innate immunity. Subsequent studies revealed that ET formation occurs across diverse immune cell types and can proceed through non-lytic mechanisms involving mitochondrial DNA release. Whether ETosis also operates outside classical immune contexts and what its ancestral functions may be remain incompletely understood. Here, we show that vegetative, phagocytic cells of the social amoeba Dictyostelium discoideum, a professional bacterial predator with phagocytic mechanisms conserved with those of mammalian innate immune cells, deploy extracellular DNA traps in response to bacterial cues. ET formation is selectively induced by specific lipopolysaccharide variants, is not triggered by canonical neutrophil NET inducers, and occurs through a vital ETosis mechanism that preserves membrane integrity and feeding capacity. Ultrastructural analyses provide the first visualization of extracellular traps in Amoebozoa, revealing extracellular filamentous networks that physically capture bacteria. Molecular characterization demonstrates that amoeboid ETs are enriched in mitochondrial DNA and harbor a dynamic proteomic repertoire dominated by mitochondrial components, DNA-associated proteins, and multiple antibacterial effectors. Notably, ET composition varies with the bacterial stimulus, indicating that ETs are not static structures but rather responsive extracellular assemblies. Together, these findings establish ET formation as a regulated response in a unicellular phagocyte and suggest that extracellular traps may have originally functioned in microbial management during feeding, prior to their elaboration as immune effectors in multicellular organisms. HighlightsO_LIVegetative Dictyostelium discoideum cells deploy mitochondrial DNA-based extracellular traps in response to bacterial cues. C_LIO_LIET formation occurs through a vital, non-lytic mechanism that preserves membrane integrity and feeding capacity. C_LIO_LIExtracellular traps exhibit stimulus-dependent composition and are enriched in mitochondrial and antimicrobial proteins. C_LIO_LIETosis functions as an ancestral strategy for microbial containment and management beyond canonical immune contexts. C_LI

microbiology↗

bioRxiv2026

Inorganic polyphosphate and pyoverdine synthesis are essential for the virulence of Pseudomonas aeruginosa PAO1 in zebrafish larvae

Understanding how bacterial metabolism shapes virulence requires infection models that are both biologically informative and experimentally accessible. Here, we used zebrafish (Danio rerio) larvae infection by static immersion as a simple and robust vertebrate model to study Pseudomonas aeruginosa host-pathogen interactions and virulence regulation. Using this approach, we show that disruption of polyphosphate (polyP) synthesis by loss of ppk1 gene ({tau}1ppk1) leads to marked attenuation of virulence, whereas interrupting ppk2 gene ({tau}1ppk2) results in a hypervirulent phenotype. Phenotypic assays and quantitative proteomics revealed that loss of polyP selectively impairs pyoverdine production, with minimal effects on other canonical virulence factors. Consistently, a pyoverdine-deficient mutant ({tau}1pvdF) exhibited reduced virulence in zebrafish, validating the capacity of the zebrafish model to functionally resolve key virulence factors. Together, our results highlight polyphosphate metabolism as a central regulator of P. aeruginosa virulence and position zebrafish immersion assays as an efficient and ethically aligned alternative to mammalian models for studying bacterial pathogenesis.

microbiology↗

bioRxiv2026

Intrinsic class C extended-spectrum β-lactamases mediate resistance to oxyimino-cephalosporins in Antarctic Pseudomonas fluorescens complex bacteria

From a One Health perspective, identifying environmental reservoirs of antibiotic resistance determinants with potential clinical relevance is increasingly important. Among resistance mechanisms, {beta}-lactamases are of particular concern because they compromise the efficacy of {beta}-lactam antibiotics, the most widely used class in clinical practice. Antarctic soils harbor thousands of putative {beta}-lactamase genes, yet the functional properties and resistance contributions of these enzymes remain largely unexplored. Here, we investigated the distribution, diversity, and functional impact of intrinsic class C {beta}-lactamases (AmpC-type) in Antarctic members of the Pseudomonas fluorescens species complex, a lineage widely distributed in Antarctic soils and increasingly recognized as an opportunistic pathogen of humans, animals, and plants. Genome-scale analyses revealed that class C {beta}-lactamases are intrinsic, widespread, and highly diverse within this lineage. Phenotypic assays demonstrated that Antarctic isolates exhibit elevated resistance to {beta}-lactam antibiotics, particularly oxyimino-cephalosporins such as cefotaxime and ceftazidime, and that this phenotype is largely attenuated by {beta}-lactamase inhibition. Heterologous expression of selected Antarctic AmpC variants in a susceptible Escherichia coli host confirmed their ability to increase minimum inhibitory concentrations to oxyimino-cephalosporins. Notably, several Antarctic {beta}-lactamases harbor amino acid substitutions previously associated with extended-spectrum AmpC (ESAC) variants, including M174L and N346I, while others display broader substrate profiles despite lacking known ESAC-associated signatures. Comparative analyses further showed that the sequence diversity of Antarctic class C {beta}-lactamases exceeds that reported for clinical PDC variants from Pseudomonas aeruginosa. Together, these findings provide functional evidence that pristine Antarctic environments constitute reservoirs of naturally occurring class C {beta}-lactamases with extended-spectrum potential. Our results highlight the evolutionary depth and functional diversity of environmental {beta}-lactamases and underscore the importance of incorporating remote ecosystems into One Health-oriented antimicrobial resistance surveillance frameworks.

microbiology↗

bioRxiv2025

Expanding the toolbox for hypervirulent Klebsiella pneumoniae using the social amoeba Dictyostelium discoideum as a virulence biosensor

Hypervirulent Klebsiella pneumoniae (hvKp) represents a critical global threat due to its capacity to cause severe, community-acquired infections in healthy individuals and its convergence with multidrug resistance. However, current methods to evaluate hvKp virulence are limited by their reliance on mammalian models, which are costly, ethically constrained, and unsuitable for high-throughput applications. Here, we introduce a biosensing approach using the social amoeba Dictyostelium discoideum as a living phenotypic sensor for hvKp virulence. Through a suite of quantitative assays integrating predation resistance, social development, and real-time single-cell motility tracking, we show that D. discoideum can discriminate avirulent, virulent, and hypervirulent K. pneumoniae strains. Using the model hvKp strain SGH10 and its capsule-null mutant {Delta}wcaJ, we demonstrate that capsule production is strongly associated with phagocytosis resistance, developmental arrest, and amoebae paralysis, all quantifiable through imaging and motility-based readouts. Multivariate data integration revealed a clear segregation of virulence phenotypes, validating D. discoideum as a sensitive, scalable, and genetically tractable biosensor for functional virulence detection. This work establishes a conceptual and methodological framework for developing cell-based biosensors that report virulence levels through measurable host behavioral responses and outlines a calibration path to vertebrate endpoints. These systems provide a low-cost alternative to mammalian systems, especially for early-stage evaluation, and a potential foundation for automated high-throughput screening and surveillance of virulence in critical priority bacterial pathogens.

microbiology↗

bioRxiv2025

Intestinal Stem Cells Retain an Epigenetic Memory of Prior Inflammation

Intestinal epithelial damage and impaired repair are hallmarks of ulcerative colitis (UC), even after inflammation resolves. Intestinal stem cells (ISCs) can retain stable epigenetic changes after inflammation, highlighting the potential for long-lived epithelial memory in the gut. Inflammatory injury in barrier tissues induces epigenetic memory in epithelial stem cells, and the tendency of UC to relapse at previously inflamed sites led us to hypothesize that ISCs from IBD patients acquire lasting memory of prior inflammation. To test this, we derived colonic organoids from inflamed and uninflamed regions of the same UC patients and propagated in long-term culture. Chromatin profiling revealed 2,252 accessible regions unique to prior-inflamed (PI) organoids, associated with stress response, repair, and inflammatory genes. Although these regions remained accessible, [~]95% of associated genes were not upregulated in PI organoids, indicating a primed state. Upon inflammatory or injury re-challenge, PI organoids exhibited heightened transcriptional responses and accelerated wound closure, despite reduced clonogenicity and impaired barrier function, indicating a retained inflammatory memory program. Our findings demonstrate that human ISCs retain a chromatin-based memory of inflammation that persists in the absence of immune cues and shapes future responses to injury. While this may support epithelial adaptation to secondary insults, it may predispose tissue to relapse in patients with UC.

molecular biology↗

bioRxiv2024

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert

The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Despite the highly restrictive conditions, microbial life has been found in these environments, although with limited information on their genetic properties and functional capabilities. Moreover, the accelerated melting of the Antarctic permafrost, the increasing exposure of soils, and the growing human transit pose the question of whether these environments could be a source of microbes or genes that could emerge and cause global health problems. In this line, although a high bacterial diversity and autochthonous multidrug-resistant bacteria have been found in soils of the Antarctic Peninsula, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a high-latitude cold desert in West Antarctica. Despite the low organic matter content, diverse bacterial lineages were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. We recovered more than 80 species-level representative genomes (SRGs) of predominant bacterial taxa and the archaeon Nitrosocosmicus sp. Diverse putative resistance and virulence genes were predicted among the SRGs, metagenomic reads, and contigs. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarcticas soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in the white continent. HIGHLIGHTS-Union Glacier soils host a microbial community dominated by bacteria, mainly from the phylum Actinomycetota. -Archaea from the Nitrosocosmicus genus (family Nitrosphaeraceae) were ubiquitously detected. -Although extreme and remote, these soils host multidrug-resistant and potentially pathogenic bacteria. Some were cultured and tested in vitro. -Metagenomes and species-level representative genomes revealed diverse putative resistance and virulence genes. -Part of the putative antimicrobial resistance genes and virulence factors could be associated with mobile elements in bacterial genomes.

microbiology↗

bioRxiv2024

Single NV in nanodiamond for quantum sensing of protein dynamics in an ABEL trap

Enzymes are cellular protein machines using a variety of conformational changes to power fast biochemical catalysis. Our goal is to exploit the single-spin properties of the luminescent NV (nitrogen-vacancy) center in nanodiamonds to reveal the dynamics of an active enzyme complex at physiological conditions with the highest spatio-temporal resolution. Specifically attached to the membrane enzyme FoF1-ATP synthase, the NV sensor will report the adenosine triphosphate (ATP)-driven full rotation of Fo motor subunits in ten consecutive 36{degrees} steps. Conformational dynamics are monitored using either a double electron-electron resonance scheme or NV- magnetometry with optical readout or using NV- relaxometry with a superparamagnetic nanoparticle as the second marker attached to the same enzyme. First, we show how all photophysical parameters like individual size, charge, brightness, spectral range of fluorescence and fluorescence lifetime can be determined for the NV- center in a single nanodiamond held in aqueous solution by a confocal anti-Brownian electrokinetic trap (ABEL trap). Stable photon count rates of individual nanodiamonds and the absence of blinking allow for observation times of single nanodiamonds in solution exceeding hundreds of seconds. For the proposed quantum sensing of nanometer-sized distance changes within an active enzyme, we show that local magnetic field fluctuations can be detected all-optically by analyzing fluorescence lifetime changes of the NV- center in each nanodiamond in solution.

biophysics↗

bioRxiv2023

Mechanism of ADP-inhibited ATP hydrolysis in single proton-pumping FoF1-ATP synthase trapped in solution

FoF1-ATP synthases in mitochondria, in chloroplasts and in most bacteria are the proton-driven membrane enzymes supplying the cells with ATP made from ADP and phosphate. To monitor and prevent the reverse chemical reaction of fast wasteful ATP hydrolysis by the enzymes, different control mechanisms exist including mechanical or redox-based blockade of catalysis and ADP inhibition. In general product inhibition is expected to slow down the mean catalytic turnover. However, biochemical assays are ensemble measurements and cannot discriminate between a mechanism affecting all enzymes equally or individually. For example, all enzymes could work slower at a decreasing substrate/product ratio, or more and more individual enzymes are blocked completely. Here, we examined how increasing amounts of ADP affected ATP hydrolysis of single Escherichia coli FoF1-ATP synthases in liposomes. We observed individual catalytic turnover of the enzymes one after another by monitoring the internal subunit rotation using single-molecule Forster resonance energy transfer (smFRET). Observation times of single FRET-labeled FoF1-ATP synthase in solution were increased up to seconds using a confocal Anti-Brownian electrokinetic trap (ABEL trap). By counting active versus inhibited enzymes we revealed that ADP inhibition did not decrease the catalytic turnover of all FoF1-ATP synthases equally. Instead, increasing ADP in the ADP/ATP mixture reduced the number of the remaining active enzymes which were operating at similar catalytic rates for varying substrate/product ratios.

biophysics↗

bioRxiv2023

Monitoring oligomerization dynamics of individual human neurotensin receptors 1 in living cells and in SMALP nanodiscs

The human neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor. The receptor is activated by a small peptide ligand neurotensin. NTSR1 can be expressed in HEK cells by stable transfection. Previously we used the fluorescent protein markers mRuby3 or mNeonGreen fused to NTSR1 for EMCCD-based structured illumination microscopy (SIM) in living HEK cells. Ligand binding induced conformational changes in NTSR1 which triggered the intracellular signaling processes. Recent single-molecule studies revealed a dynamic monomer/dimer equilibrium of this receptor in artificial lipid bilayers. Here we report on the oligomerization state of human NTSR1 from living cells by trapping them into lipid nanodiscs. Briefly, SMALPs (styrene-maleic acid copolymer lipid nanoparticles) were produced directly from the plasma membranes of living HEK293T FlpIn cells. SMALPs with a diameter of 15 nm were soluble and stable. NTSR1 in SMALPs were analyzed by single-molecule intensity measurements one membrane patch at a time using a custom-built confocal anti-Brownian electrokinetic trap (ABEL trap) microscope. We found oligomerization changes before and after stimulation of the receptor with its ligand neurotensin.

biophysics↗

bioRxiv2023

Mutation of gabra1 is associated with hypermotility and abnormal expression of proteins critical for ion homeostasis and synaptic vesicle transport.

Mutation of the GABRA1 gene is associated with neurodevelopmental defects and epilepsy. GABRA1 encodes for the 1 subunit of the gamma-aminobutyric acid type A receptor (GABAAR), which regulates the fast inhibitory impulses of the nervous system. Multiple model systems have previously been developed to understand the function of GABRA1 during development, but these models have produced complex and at times incongruent data. Thus, additional model systems are required to validate and substantiate previously published results. We investigated the behavioral swim patterns associated with a nonsense mutation of the zebrafish gabra1 (sa43718 allele) gene. The sa43718 allele causes a decrease in gabra1 mRNA expression, which is associated with light induced hypermotility, one phenotype associated with seizure like behavior in zebrafish. Mutation of gabra1 was accompanied by decreased mRNA expression of gabra2, gabra3, and gabra5, indicating a reduction in the expression of additional alpha sub-units of the GABAAR. Although multiple sub-units were decreased in total expression, larvae continued to respond to pentylenetetrazole (PTZ) indicating that a residual GABAAR exists in the sa43718 allele. Proteomics analysis demonstrated that nonsense mutation of gabra1 is associated with abnormal expression of proteins that regulate proton transport, ion homeostasis, vesicle transport, and mitochondrial protein complexes. These data support previous studies performed in a zebrafish nonsense allele created by CRISPR/Cas9 and validate that loss of function mutations in the gabra1 gene result in seizure like phenotypes with abnormal function of inhibitory synapses.

developmental biology↗

bioRxiv2023

Abnormal chondrocyte intercalation in a zebrafish model of cblC syndrome restored by an MMACHC cobalamin binding mutant.

Variants in the MMACHC gene cause combined methylmalonic acidemia and homocystinuria cblC type, the most common inborn error of intracellular cobalamin (vitamin B12) metabolism. cblC is associated with neurodevelopmental, hematological, ocular, and biochemical abnormalities. In a subset of patients, mild craniofacial dysmorphia has also been described. Mouse models of Mmachc deletion are embryonic lethal but cause severe craniofacial phenotypes such as facial clefts. MMACHC encodes an enzyme required for cobalamin processing and variants in this gene result in the accumulation of two metabolites: methylmalonic acid (MMA) and homocysteine (HC). Interestingly, other inborn errors of cobalamin metabolism, such as cblX syndrome, are associated with mild facial phenotypes. However, the presence and severity of MMA and HC accumulation in cblX syndrome is not consistent with the presence or absence of facial phenotypes. Thus, the mechanisms by which mutation of MMACHC cause craniofacial defects have not been completely elucidated. Here we have characterized the craniofacial phenotypes in a zebrafish model of cblC (hg13) and performed restoration experiments with either wildtype or a cobalamin binding deficient MMACHC protein. Homozygous mutants did not display gross morphological defects in facial development, but did have abnormal chondrocyte intercalation, which was fully penetrant. Abnormal chondrocyte intercalation was not associated with defects in the expression/localization of neural crest specific markers, sox10 or barx1. Most importantly, chondrocyte organization was fully restored by wildtype MMACHC and a cobalamin binding deficient variant of MMACHC protein. Collectively, these data suggest that mutation of MMACHC causes mild to moderate craniofacial phenotypes that are independent of cobalamin binding.

developmental biology↗

bioRxiv2022

Mutational screens highlight glycosylation as a modulator of CSF3R activity

The colony-stimulating factor 3 receptor (CSF3R) controls the growth of neutrophils, the most abundant type of white blood cell. In healthy neutrophils, signaling is dependent on CSF3R binding to its ligand CSF3. A single amino acid mutation in CSF3R, T618I, instead allows for constitutive, ligand-independent cell growth and leads to a rare type of cancer called chronic neutrophilic leukemia (CNL). We investigated why this threonine to isoleucine substitution is the predominant mutation in CNL and how it leads to uncontrolled neutrophil growth. Using protein domain mapping, we demonstrated that the single CSF3R domain containing residue 618 is sufficient for ligand-independent activity. We then applied an unbiased mutational screening strategy focused on this domain and found that activating mutations are enriched at sites normally occupied by asparagine, threonine, and serine residues - the three amino acids which are commonly glycosylated. We confirmed glycosylation at multiple CSF3R residues by mass spectrometry, including the presence of GalNAc and Gal-GalNAc glycans at wild-type threonine 618. Using the same approach applied to other cell surface receptors, we identified an activating mutation, S489F, in the interleukin-31 receptor alpha chain (IL-31R). Combined, these results suggest a role for glycosylated hotspot residues in regulating receptor signaling, mutation of which can lead to ligand-independent, uncontrolled activity.

biochemistry↗

bioRxiv2019

The CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1

Circadian rhythms are generated by a transcription-translation feedback loop that establishes cell-autonomous biological timing of ~24-hours. A prevalent human variation in the core clock gene cryptochrome 1, Cry1{Delta}11, lengthens circadian period to cause Delayed Sleep Phase Disorder (DSPD). CRY1 has a 55 kDa photolyase homology region (PHR) followed by a ~100 residue tail that is intrinsically disordered; the {Delta}11 variant lacks a short segment encoded by Exon 11 within its tail. We show here that the disordered tail of CRY1 interacts directly with its PHR, and that Exon 11 is necessary and sufficient to disrupt the interaction between CRY1 and CLOCK, a subunit of the primary circadian transcription factor. Competition between PER2 and the tail for the CRY1 PHR suggests a regulatory role for the tail in the early morning, when CRY1 binds to CLOCK:BMAL1 on DNA independently of PER2. Discovery of this autoregulatory role for mammalian CRY1 highlights functional conservation with plant and insect cryptochromes, which also utilize PHR-tail interactions to reversibly control their activity.\n\nOne Sentence SummaryThe disordered tail of the CRY1 protein regulates interactions between CRY1 and other core circadian rhythm proteins.

biochemistry↗