Biology subjects

Alvarez, P.

Publications and source records attributed to Alvarez, P..

9 recordsLinked to original sources

bioRxiv2026

Network-Level Characterization of Spontaneous Calcium Activity in an In-Vitro Alzheimer's Disease Model

The neurodegenerative disorder Alzheimers disease (AD) is widely known for biomarkers such as amyloid beta plaques and tauopathy, as well as functional differences in memory and cognitive ability. Despite this devastating functional impact, a large body of work only focuses on molecular biomarkers of AD. In this study, we investigate collective neural dynamics in vitro and assess how network-level properties differ between a well-established model of familial AD (FAD) and a newly developed in vitro accelerated model (acAD). The new model system reliably develops the key structural characteristics of AD in three weeks, but its calcium dynamics had not been characterized previously. Spontaneous network dynamics influences information processing as part of the internal network state. Here we measure this spontaneous activity of a network of hundreds of cells in each field of view. We find that the FAD model has a larger fraction of hyperactive cells, while the acAD model displays similar characteristics to healthy cells. Additionally, the FAD model has altered cooperation between cells, losing a proportion of highly correlated cellular activities, both for fast and slow coupling among cells. The acAD model is again consistent with healthy networks. Since the acAD model does not show the same spontaneous network dysfunction seen in FAD, it can enable measurements of changes in learning and memory associated with the plasticity, rather than the structure of the internal network state.

biophysics↗

bioRxiv2026

Mesenchymal predominance in olfactory epithelium-derived cultures limits modeling of neurodevelopmental brain disorders

The human olfactory epithelium (OE) represents a lifelong source of neural progenitor cells and has been proposed as an accessible model to investigate molecular alterations associated with neurodevelopmental disorders in postnatal individuals. Globose basal cells are considered the immediate neuronal progenitors within the OE, and several studies have attempted to culture these cells from nasal exfoliates. However, the actual contribution of neurogenic lineages in these cultures remains largely unquantified. Here, we cultured human nasal explants using an established protocol and characterized the resulting cell populations by immunohistochemistry and single-cell RNA sequencing. Integration with primary in vivo OE datasets revealed that these cultures are predominantly composed of mesenchymal-like cells, with limited representation of globose basal cells and neurons, and low expression of canonical neuronal markers. Using curated gene sets associated with neurodevelopmental disorders and malformations of cortical development, we assessed the extent to which disease-relevant transcriptional programs are captured in OE-derived cultures. While disease-associated genes are enriched in neurogenic lineages in vivo, their representation in mesenchymal cells is reduced. Together, our results challenge the assumption that standard OE culture systems faithfully model neurogenic compartments and suggest that current approaches may need refinement to recover neurogenic lineages.

neuroscience↗

bioRxiv2026

A metabolic model based on a pangenome core unveils new biochemical features of the phytopathogen Xylella fastidiosa

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium responsible for severe diseases in many economically important crops. Despite its impact, its metabolism remains poorly characterized due to fastidious growth and the limited availability of defined culture media. Here, we reconstruct the first pangenome-based genome-scale metabolic model for X. fastidiosa, integrating conserved metabolic functions from 18 strains across five subspecies. The resulting core model, iXfcore, is manually curated and used to explore the species metabolic capabilities. Model simulations predict minimal nutritional requirements that guided us in the formulation of defined media supporting biofilm formation in vitro, providing validation of the models predictive capacity. Network analysis also identifies a previously undescribed pathway enabling growth on acetate as a sole carbon source. In addition, the model predicts the overproduction of polyamines, compounds linked to virulence in other phytopathogens. Experimental analyses confirm the production and secretion of polyamines in multiple X. fastidiosa strains, providing the first evidence of this capability. These results suggest that polyamine biosynthesis may represent an uncharacterized virulence factor for X. fastidiosa, potentially contributing to protection against host-induced oxidative stress. Overall, iXfcore provides a systems-level framework to investigate X. fastidiosa metabolism, generate testable hypotheses on its physiology and virulence, and support future strain-specific models and studies of host-pathogen metabolic interactions.

systems biology↗

bioRxiv2025

Flux modelling analysis reveals the metabolic impact of cryptic plasmids and environmental conditions in probiotic Escherichia coli Nissle 1917

Escherichia coli Nissle 1917 (EcN) is a well-characterized Gram-negative probiotic distinguished by its unique, strain-specific physiology. Genome-scale metabolic models (GEMs) are powerful tools for elucidating metabolic traits and predicting genotype-phenotype relationships. Although several EcN GEMs have been published, none have explicitly represented its probiotic physiology. Here, we present a manually curated GEM of EcN that, for the first time, incorporates the energetic costs associated with its cryptic plasmids. Inclusion of a plasmid-specific module improved biomass yield predictions and overall model accuracy, providing a more physiologically realistic representation of EcN metabolism. Using COBRA methodologies and possibilistic metabolic flux analysis, this model and previous EcN reconstructions were systematically compared to evaluate the trade-off between model complexity and predictive performance. The analysis revealed that increased structural detail does not necessarily enhance quantitative accuracy and that predictive reliability depends on both computational methodology and model context. Metabolomic profiling under gut-like anaerobic conditions further showed that EcN exhibits a distinctive metabolic phenotype, characterized by elevated amino acid consumption and enhanced short-chain fatty acid production. These findings highlight the unique probiotic physiology of EcN and demonstrate the utility of metabolic modeling for reproducing and exploring such traits. Overall, this study provides a quantitatively reliable and physiologically relevant framework for modeling E. coli Nissle 1917 and related commensal bacteria, supporting advances in probiotic engineering, synthetic biology, and bioprocess design. Graphical Abstract SummaryThis study presents a manually curated genome-scale model of Escherichia coli Nissle 1917 that accounts for the metabolic cost of its cryptic plasmids. Through systematic comparison with previous reconstructions and validation against fluxomics datasets, the models improved accuracy in predicting growth and fluxes. Simulations and experiments under gut-like conditions provide new insights into EcNs unique probiotic traits. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/688048v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@6c8c98org.highwire.dtl.DTLVardef@8263e3org.highwire.dtl.DTLVardef@6c04c3org.highwire.dtl.DTLVardef@1acb811_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2025

Analgesic actions of Intrathecal NaV 1.7 antisense in rats: loss of antagonist channel binding, message depletion, and neuraxial distribution of oligonucleotide

BackgroundGenome targeting strategies to address NaV 1.7 mediated signaling in nociceptive afferents produce highly selective and persistent analgesic outcomes. Here, we analyze the concentration-dependent effects of the reduction of primary afferent NaV 1.7 channel expression by intrathecal delivery of an antisense oligonucleotide on pain behaviors and the covariance of Scn9a knock-down on NaV 1.7 message expression and channel binding. MethodsMale Sprague-Dawley rats were implanted with lumbar intrathecal catheters and dosed with different NaV 1.7 ASO concentrations (100 to 3000 g;10 L). Pain behavior assays were conducted 0-28 days after ASO injections. Brain, spinal cords (SC) and dorsal root ganglia (DRGs) were collected. Quantification of ASO knock-down was assessed through RT-qPCR. NaV 1.7 expression was assessed by binding of NaV 1.7 fluorescent labeled antagonist (ATTO488PTx-II). Distribution studies were performed using anti-ASO antibody staining in brain, SCs and DRGs. ResultsNaV 1.7 message was detected in nerve, DRG and SC. Intrathecal ASO induced a concentration dependent gradient of knock down in DRGs (lumbar to cervical) of Scn9a mRNA and ATTO488PTx-II binding in small DRG neurons, and in spinal parenchyma, and a suppression of pain behaviors initiated by mechanical compression, inflammation and following intraplantar NaV1.7 agonist (OD1) or formalin. At 1000 {micro}g, there was a 47% reduction in phase 2 flinching, a 60% reduction in DRG mRNA and a 36% reduction in ATTO488PTx-II DRG binding in comparison with mismatch controls. Although marked changes were seen at the sensory ganglia level and spinal dorsal horn, no changes in NaV 1.7 binding or mRNA were detected in sciatic nerves. Reduction in DRG message displayed a rostrocaudal gradient that corresponded with ASO distribution. ConclusionsThe study presents how NaV 1.7 ASOs reduce primary afferent channel binding through an effective knock-down on Scn9a mRNA, and channel binding leading to a covariate reduction in pain behavior.

neuroscience↗

bioRxiv2024

From raw microalgae to bioplastics: conversion of Chlorella vulgaris starch granules into thermoplastic starch

Microalgae are emerging as a promising feedstock for bioplastics, with Chlorella vulgaris yielding significant amounts of starch. This polysaccharide is convertible into thermoplastic starch (TPS), a biodegradable plastic of industrial relevance. In this study, we developed a pilot-scale protocol for extracting and purifying starch from starch-enriched Chlorella vulgaris biomass. From 430.3 {+/-} 0.5 g (dry weight - DW) of microalgae biomass containing 42.2 {+/-} 3.4 % of starch, we successfully extracted 205.8 {+/-} 1.2 gDW of purified starch extract containing 86.9 {+/-} 3.0 % of starch, resulting in a final recovery yield of 98.5%. We have characterized this extracted starch and processed it into TPS using twin-screw extrusion and injection molding. Microalgal starch showed similar properties to those of native plant starch, but with smaller granules. We compared the mechanical properties of microalgal TPS with two controls, namely a commercial TPS and a TPS prepared from commercial potato starch granules. TPS prepared from microalgal starch showed a softer and more ductile behavior compared to the reference materials. This study demonstrates the feasibility of recovering high-purity microalgal starch on a pilot scale with high yields, and highlights the potential of microalgal starch for the production of TPS using industrially relevant processes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/589749v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@f2f7fcorg.highwire.dtl.DTLVardef@176dc8corg.highwire.dtl.DTLVardef@8989d3org.highwire.dtl.DTLVardef@1b7b978_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2022

Identification of a Papain-Like Protease Inhibitor with Potential for Repurposing in Combination with an Mpro Protease Inhibitor for Treatment of SARS-CoV-2

SARS-CoV-2 requires two cysteine proteases for viral polypeptide processing to allow maturation and replication: the 3C-like protease also known as the Main protease (Mpro) and the papain-like protease (PLpro). In addition to its critical role in viral replication, PLpro removes post-translational modifications like ubiquitin and interferon-stimulated gene product 15 (ISG15) from host proteins through its deubiquitinase domain, leading to host immunosuppression and increased ability of the virus to evade the host antiviral immune response. Through screening of a custom clinical compound library, we identified eltrombopag (DDL-701), a thrombopoietin receptor agonist, as having PLpro inhibitory activity that is sustained in the presence of the Mpro inhibitor nirmatrelvir. DDL-701 also suppressed both the deubiquitinase and ISG15 cleavage activities of PLpro. In addition, DDL-701 partially restored interferon-{beta} induction - an element of the host immune response - in an in vitro model system. Further, modeling and docking studies suggest DDL-701 interacts with the active site region of the PLpro enzyme and pilot pharmacokinetic studies indicate it is brain permeable. DDL-701 is already approved for treatment of thrombocytopenia and has previously been shown to achieve human plasma levels after oral dosing that is above the IC50 needed for it to exert its PLpro inhibitory activity in vivo. In addition, it has also been reported to have antiviral efficacy against SARS-CoV-2. DDL-701 thus represents a drug that can immediately be repurposed and undergo clinical evaluation as a PLpro inhibitor that may be most effectively used in a protease inhibitor cocktail with an Mpro inhibitor such as nirmatrelvir (Paxlovid) for the treatment of COVID-19.

microbiology↗

bioRxiv2021

The transcription factor IscR promotes Yersinia type III secretion system activity by antagonizing the repressive H-NS-YmoA histone-like protein complex

The type III secretion system (T3SS) is a appendage used by many bacterial pathogens, such as pathogenic Yersinia, to subvert host defenses. However, because the T3SS is energetically costly and immunogenic, it must be tightly regulated in response to environmental cues to enable survival in the host. Here we show that expression of the Yersinia Ysc T3SS master regulator, LcrF, is orchestrated by the opposing activities of the repressive YmoA/H-NS histone-like protein complex and induction by the iron and oxygen-regulated IscR transcription factor. Although IscR has been shown to bind the lcrF promoter and is required for in vivo expression of lcrF, in this study we show IscR alone fails to enhance lcrF transcription in vitro. Rather, we find that in a ymoA mutant, IscR is no longer required for LcrF expression or T3SS activity. Additionally, a mutation in YmoA that prevents H-NS binding (ymoAD43N) rescues the T3SS defect of a {Delta}iscR mutant, suggesting that a YmoA/H-NS complex is needed for this repressive activity. Furthermore, chromatin immunoprecipitation analysis revealed that H-NS is enriched at the lcrF promoter at environmental temperatures, while IscR is enriched at this promoter at mammalian body temperature under aerobic conditions. Importantly, CRISPRi knockdown of H-NS leads to increased lcrF transcription. Collectively, our data suggest that as IscR levels rise with iron limitation and oxidative stress, conditions Yersinia experiences during extraintestinal infection, IscR antagonizes YmoA/H-NS-mediated repression of lcrF transcription to drive T3SS activity and manipulate host defense mechanisms. Author SummaryFacultative pathogens must silence virulence gene expression during growth in the environment, while retaining the ability to upregulate these genes upon infection of a host. H-NS is an architectural DNA binding protein proposed to silence horizontally acquired genes, regulating virulence genes in a number of pathogens. Indeed, H-NS was predicted to regulate plasmid-encoded virulence genes in pathogenic Yersinia. However, Yersinia H-NS is reported to be essential, complicating testing of this model. We used chromatin immunoprecipitation and inducible CRISPRi knockdown to show that H-NS binds to the promoter of a critical plasmid-encoded virulence gene, silencing its expression. Importantly, under conditions that mimic Yersinia infection of a mammalian host, the transcriptional regulator IscR displaces H-NS to drive virulence factor expression.

microbiology↗

bioRxiv2019

Quantifying topography-guided actin dynamics across scales using optical flow

Periodic surface topographies with feature sizes comparable to those of in vivo collagen fibers are used to measure and compare actin dynamics for two representative cell types that have markedly different migratory modes and physiological purposes: slowly migrating epithelial MCF10A cells and polarizing, fast migrating, neutrophil-like HL60 cells. Both cell types exhibit reproducible guidance of actin waves (esotaxis) on these topographies, enabling quantitative comparisons of actin dynamics. We adapt a computer-vision algorithm, optical flow, to measure the directions of actin waves at the submicron scale. Clustering the optical flow into regions that move in similar directions enables micron-scale measurements of actin-wave speed and direction. Although the speed and morphology of actin waves differ between MCF10A and HL60 cells, the underlying actin guidance by nanotopography is similar in both cell types at the micron and sub-micron scales.

biophysics↗