Biology subjects

Perez, L.

Publications and source records attributed to Perez, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Distinct mechanisms of neutralization by antibodies targeting a conserved pneumovirus F epitope

Pneumoviruses cause seasonal outbreaks leading to hospitalizations of vulnerable populations such as infants and the elderly. Cross-neutralizing antibodies targeting viral fusion have been isolated from infected individuals, but their elicitation and mechanisms of action remain understudied. Here, we describe two vaccine-elicited antibody classes, LOR24 and LOR69, that bind an overlapping epitope, and identify the somatic mutations that endow their breadth and potency, respectively. Cryo-electron microscopy structures of both antibodies bound to the HRSV fusion (F) protein show binding modes distinct from each other and from the previously described cross-neutralizing antibody MPE8, yet they all use similar motifs for binding. Complementary in vitro and electron microscopy experiments show that these antibodies either lock prefusion F as a trimer, arrest F in a monomeric or intermediate state, or promote the transition to the postfusion conformation. This work sheds light on mechanisms of pneumovirus neutralization and the elicitation of cross-neutralizing antibody responses.

immunology↗

bioRxiv2026

Oxidative inhibition of PTEN links ROS signaling to regeneration and homeostasis

Reactive oxygen species (ROS) are early signals of tissue damage, but how they engage growth-promoting pathways in vivo is unclear. Here we show that ROS promote regeneration by inhibiting PTEN, thereby activating PI3K-Akt signaling in Drosophila melanogaster. We identify cysteine 79 as an essential residue for redox regulation of PTEN, demonstrating that a ROS-insensitive PTEN mutant uncouples Akt activation from oxidative stress. This disruption impairs regenerative growth in wing imaginal epithelia and stem cell proliferation in the adult gut. Mechanistically, Akt activation links ROS signaling to p38 MAPK-dependent regeneration responses. Together, our findings define a conserved ROS-PTEN-Akt signaling axis that integrates oxidative damage with regenerative growth, establishing PTEN as a key redox-sensitive regulator of tissue repair.

developmental biology↗

bioRxiv2026

Environmental Regulation and Gene-by-Environment Interaction Influence RAP1 Activity and its Impact on Gene Expression

Gene-by-environment (GxE) interactions play a major role in shaping both phenotypic and molecular variation, with important implications for human health and disease. In this study, we used the Doxycycline (Dox) regulated, tetracycline-responsive (Tet-Off) promoter system to sequentially reduce or titrate gene expression levels of the essential yeast transcription factor Repressor Activator Protein 1 (RAP1) similar to a hypomorph allele series, across three distinct environments: Yeast Peptone Dextrose (YPD) media, YPD media with Heat Shock (HS), and Yeast Peptone Acetate (YPAC) media. We then performed RNA sequencing (RNA Seq) to assess global transcriptional responses to RAP1 reduction in these different growth environments. Our analysis first focused on the independent effects of varying RAP1 expression levels within and across environments. We then explored GxE interactions, revealing a subset of genes with significant consequences of reduced levels of RAP1 and environment-specific expression patterns. Notably, many genes exhibited opposite effects of RAP1 titration on gene expression when yeast were grown in YPAC media compared to YPD media and/or HS, suggesting environment-dependent regulatory architecture. This design reveals how cells integrate internal transcriptional and regulatory changes with external environmental cues, providing a deeper view of GxE architecture. Using Weighted Gene Co-expression Network Analysis (WGCNA), we identified co-regulated gene modules, and by combining this with transcription factor motif enrichment tests, our study identified candidate regulators driving their dynamics. Our findings demonstrate that gene regulatory networks can vary dramatically depending on the environmental context an organism experiences, which can then influence the specific phenotypes produced by a particular genetic perturbation. This illustrates the complexity of genotype-environment interactions and the importance of studying gene function in multiple environments to gain a truly comprehensive understanding of a genes sometimes numerous and diverse functions.

genomics↗

bioRxiv2026

A conserved enhancer cluster regulates efnb2 expression in the vertebrate dorsal retina

The vertebrate retina is patterned along its dorsal-ventral (DV) axis by conserved signaling centers, yet the cis-regulatory architecture maintaining these territories remains unclear. Using the four-eyed fish Anableps anableps, which enables physical separation of dorsal and ventral retina, we integrated RNA-seq, ATAC-seq and Hi-C to map DV regulatory landscapes. We identify a 29-kb dorsal-enriched enhancer cluster within a gene poor region between efnb2a and gtpbp8, embedded in a conserved topologically associating domain spanning efnb2a-gtpbp8-slc10a2. Dorsal-biased chromatin contacts link this cluster to the efnb2a promoter. The orthologous human region contains a genome-wide significant association with retinal thickness (rs2575134; P = 2e-14). Leveraging the compact genome of Tetraodon nigroviridis, we cloned the orthologous interval and show that it drives dorsal retina-specific reporter expression in zebrafish and mouse. Together, these results identify an evolutionarily conserved regulatory domain controlling retinal axial identity and linking enhancer architecture to human ocular variation. Funding, National Science Foundation.

evolutionary biology↗

bioRxiv2026

Systems analysis of ribosomal CAR-site dynamics

Developing approaches to link structure and function is an ongoing challenge in computational and structural biology. Using a systems-level framework, we present here an analysis pipeline in a Python package, mdsa-tools, that constructs network representations of structures in a time series of trajectory frames from molecular dynamics (MD) simulations. Here, we demonstrate its use on a ribosomal subsystem. The subsystem is centered on the CAR interaction surface, a "brake pad" adjacent to the aminoacyl (A-site) decoding center that tunes protein translation rates. We leverage unsupervised learning algorithms to explore the conformational landscape of behaviors visited by two versions of the subsystem (brake-on and brake-off) that differ at the codon 3 adjacent to the A-site codon. Our network representations of MD frames embody H-bond interactions between all pairwise combinations of residues in the system. By utilizing per-frame vector representations of network edges, we can apply standard clustering and dimensionality reduction methods to explore behavioral differences between the brake-on and brake-off versions of the system. K-means clustering of frame vectors revealed a striking separation of the two system versions, consistent with principal components analysis (PCA) embeddings and Uniform Manifold Approximation and Projection (UMAP) embeddings. Dissection of K-means centroids and PCA loadings highlighted H-bond interactions between residue pairs in the ribosomes peptidyl site (P site), suggesting potential allosteric signaling across the subsystem. Author summaryWith the impressive development of computational algorithms to successfully simulate the dynamics of biological molecules over time, the exploration and incorporation of systems modes of analysis is a natural next step to begin to understand the molecular dynamics behaviors that emerge from these experiments. Following the approaches of classical molecular genetics, we used a "computational genetics" paradigm where we introduced changes (mutations) in potentially important residues, changing their identities or modifying their chemical properties, and asked how the dynamic system responded to these changes, viewing the simulations as a series of movie frames of the dynamic structure over time. Starting with network representations of each frames structure, where the nodes are residues, and the edges denote H-bond interactions between the residues, we used several unsupervised machine learning algorithms to uncover behavioral changes in the different mutated versions of the system. Applied to our ribosome neighborhood, this revealed unexpected changes in behavior at the ribosome peptidyl site (P site) in response to mutating mRNA residues on the other side of the aminoacyl site (A site) codon, suggesting long-range allosteric interactions across the neighborhood.

systems biology↗

bioRxiv2026

Canonical mTOR signaling supports complete fin regeneration

The mechanistic target of rapamycin (mTOR) pathway is a deeply conserved regulator of cellular growth, metabolism, and tissue repair. In vertebrates, mTOR activity is broadly required for wound healing and regeneration. Recent work in salamanders identified unique amino acid expansions within the mTOR protein. These expansions are thought to confer hypersensitive kinase activity, which was proposed to support rapid translational activation and exceptional limb regeneration capacity. This has raised the possibility that canonical, mammalian-like mTOR signaling may be insufficient to support regeneration of complex appendages. Here, we test this hypothesis by investigating fin regeneration in the Senegal bichir (Polypterus senegalus), a ray-finned fish capable of fully regenerating fins containing bone, cartilage, muscle, and connective tissue with cellular complexity comparable to tetrapod limbs. We show that fin amputation triggers rapid activation of canonical mTOR signaling, and pharmacological inhibition of mTOR with rapamycin abolishes fin regeneration despite successful wound closure. Single-nucleus RNA sequencing (snRNA-seq) across multiple regenerative stages reveals that mTOR pathway components are selectively upregulated in proliferative epidermal and connective tissue cells, and myeloid cell populations. Rather than causing a global shutdown of gene expression, mTOR inhibition specifically dampened the induction of translational machinery and glycolytic programs, two canonical downstream outputs of mTOR signaling. In addition, myeloid cells exhibited pronounced sensitivity to mTOR inhibition, showing attenuated immune-competent and pro-regenerative programs such as interferon-associated signaling, antigen processing, and innate immune coordination. We propose that salamander-specific mTOR hypersensitivity represents an evolutionary acceleration of an ancestral regenerative program, rather than a prerequisite for limb regeneration. Significance StatementThe ability to regenerate complex appendages varies widely among vertebrates, yet the molecular basis of this variation remains poorly understood. Salamanders harbor a uniquely hypersensitive form of mTOR that has been proposed to be essential for limb regeneration. Using Polypterus fin regeneration as a model system, we demonstrate that a canonical vertebrate mTOR protein is compatible with regeneration of a complex, limb-like appendage. Our results show that mTOR acts through selective metabolic, translational, and immune programs. These findings suggest that salamander-specific mTOR hypersensitivity represents a derived enhancement rather than a condition for appendage regeneration and provide insight into the evolutionary foundations of regenerative competence.

developmental biology↗

bioRxiv2025

Evolutionary remodeling of the ventral retina enables aerial vision in the four-eyed fish Anableps anableps

The emergence of evolutionary novelties remains a central challenge in biology, particularly for complex organs such as the vertebrate eye. While visual systems have repeatedly undergone degeneration or loss, examples of innovation are rare and poorly understood. Mechanistic insight into such gains requires tractable systems in which novel visual functions have evolved. Here we leverage the four-eyed fish Anableps anableps to uncover the cellular and molecular basis of adaptation to simultaneous aerial and aquatic light. Combining single-nucleus and spatial transcriptomics, we show that the Anableps ventral retina has been developmentally and functionally reconfigured for aerial vision. In fully aquatic teleosts such as zebrafish, ventral photoreceptors are tuned to red-shifted, downwelling light. In contrast, we show that Anableps exhibits an expanded and diversified ventral cone population encompassing ultraviolet-, blue-, green-, and red-sensitive types, enabling broad-spectrum, high-intensity vision from above water. To estimate Anableps opsin spectral properties, we employed OPTICS, a machine-learning model of opsin spectral tuning, which predicts that the ventrally expressed opn1mw2 opsin is red-shifted relative to typical green-sensitive pigments. Analysis of dorsal-ventral patterning markers reveals an overrepresentation of ventral retinal cell types. Consistent with this, comparative spatial transcriptomic profiling of developing and adult Anableps and the killifish (Fundulus heteroclitus) indicates a dorsal displacement of the dorsal-ventral boundary in Anableps, resulting in a proportionally larger ventral retinal domain. Collectively, our results reveal that Anableps achieved its unique dual visual capacity by developmentally expanding and functionally reprogramming the ventral retina for aerial light detection, an evolutionary innovation that redefines how retinal domains can adapt to radically different visual environments.

evolutionary biology↗

bioRxiv2025

Cryoprotectants-assisted plunge freezing of thick brain tissue specimens for targeted physiologically relevant cryo-imaging in situ

In situ cryoET (cryoelectron tomography) and cryo-FIB/SEM (cryo-focused ion beam/scanning electron microscopy) volume-EM (electron microscopy) imaging provide spatiotemporal snapshots of biological systems in their near-native aqueous environment. Freezing and subsequent thinning of thick biological specimens prior to cryo-imaging is a time-consuming and challenging task that requires state-of-art methodology. As a result, cryo-imaging reports obtained from non-trivial specimens including mammalian brain tissues are scarce and their physiological relevance remains to be determined. Here, we benchmarked plunge freezing with a variety of cryoprotectants that allow for mouse brain tissue vitrification of up to about 100 microns thick and across several brain regions while keeping the tissue functional. By utilizing the knock-in (KI) mouse model with fluorescent astrocytes we have performed targeted cryo-FIB/SEM volume-EM imaging as well as targeted high-resolution cryoET imaging. Prior to cryoET, we have successfully generated lamellae in a semi-automated fashion on both LMIS (liquid metal ion source)- and plasma-based cryo-FIB/SEM instrumentation thus expanding applicability of our pipeline. We visualized the NVU (neurovascular unit) and astrocytes processes and validated the physiological relevance of our outputs based on the morphology of the corresponding cellular and subcellular features. The pipeline utilizes common vitrification setups and can be potentially extended toward alternative tissue specimens. Ultimately, we expect our approach to become an important step towards democratization of physiologically relevant in situ cryo-imaging studies.

biophysics↗

bioRxiv2025

Targeting PD-1+ T-cells with Chimeric Antigen Receptors to reduce the HIV Reservoir

The unique ability of chimeric antigen receptor (CAR) T-cells to infiltrate tissues is revolutionizing our perspectives for tackling severe-refractory and otherwise untreatable diseases. In HIV, CAR-T-cells have been designed to target viral biomarkers, with limited success so far. Here, we investigated the possibility of redirecting CAR-T-cells against a cellular biomarker of the HIV reservoir, PD-1. We designed two second-generation 4-1BB-CARs using the scFv of either a blocking (bPD1-CAR) or a nonblocking (nbPD1-CAR) anti-PD-1 monoclonal antibody. The CAR avidity modulated T-cell sensitivity, trogocytosis, and effector functions, independently of the PD-1 signalling domain. Both anti-PD-1 CAR T-cells could persist for 70 days in HIV-infected humanized mice, correlating with viral protection and a disruption of the lymphoid architecture in the white pulp of the spleen. Altogether, our results open new strategic avenues for reducing the HIV reservoir as we demonstrate the feasibility of depleting specific T-cell subpopulations. SummaryT cells can be redirected against cellular rather than viral-specific biomarkers to reduce the HIV reservoir.

immunology↗

bioRxiv2025

Exodermis lignification impacts lateral root emergence in Brachypodium distachyon

RationaleThe mechanisms controlling lateral root emergence in monocots, particularly the role of the exodermis, are poorly understood. We investigated how natural variation in the Brachypodium distachyon stress response shapes root system architecture by modulating cell wall dynamics. MethodsWe used root tip excision to synchronize lateral root development across natural accessions. The resulting phenotypes were analysed using comparative transcriptomics, biochemical lignin quantification, confocal Raman spectroscopy, and chemical inhibition of lignin biosynthesis. Key ResultsTwo distinct root system architectures, pine tree and fishbone, were identified. The fishbone phenotype results from an emergence-specific defect caused by the premature and intense lignification of the exodermis. This was driven by the transcriptional upregulation of lignin biosynthesis genes and was rescued by a lignin inhibitor. Main ConclusionStress-induced exodermal lignification acts as a mechanical brake on lateral root emergence. This positions the exodermis as a key regulatory hub that integrates environmental cues with developmental programs to control RSA plasticity in grasses.

plant biology↗

bioRxiv2025

A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies

Microbes live in environments that fluctuate faster than they can adjust their cellular machinery. To survive these fluctuations, they must dynamically regulate protein synthesis--a resource-intensive process that is often slower than environmental changes. Here, we develop a mechanistic model coupling antibiotic kinetics with dynamic proteome allocation to understand how limitations in translational capacity shape acclimation strategies. Using translation-inhibiting antibiotics and resistance proteins, we show that the temporal mismatch between environmental perturbations (seconds) and protein synthesis responses (hours) creates a growth advantage for anticipatory strategies where cells pre-synthesize resistance proteins before antibiotic exposure. Further, we find that the largest benefits of anticipation and the largest protein fractions reserved for anticipation are realized in environments with multiple antibiotics, suggesting that anticipation is most important in complex environments. This work establishes a framework for quantifying the costs and benefits of various acclimation strategies in dynamical environments based on the fundamental constraints of protein synthesis, with implications for microbial ecology, antibiotic resistance, and biotechnology applications.

microbiology↗

bioRxiv2025

Integrative multi-omics analysis of Polypterus fin regeneration reveals shared and derived fin and limb regeneration mechanisms

Comparative studies of salamander limbs and fish fins may reveal shared components of an ancestral vertebrate appendage regeneration toolkit. However, traditional fish models, such as zebrafish, regenerate only dermal fin rays, which are neither homologous to limbs nor as cellularly complex. To address this, we employed a multi-omics approach leveraging the regenerative capacity of Polypterus senegalus, a fish species capable of full fin regeneration. Single-nucleus RNA-sequencing revealed extensive erythrocyte and myeloid cell infiltration during Polypterus fin regeneration. Spatial transcriptomics identified key cellular contributors to the blastema, while cross-species comparisons with axolotl limbs uncovered both common and divergent expression patterns of wound epidermis and blastema markers. Fin amputation triggered a conserved injury response, including sequential activation of pro- and anti-inflammatory programs and DNA damage repair in cycling cells. Hypoxia responses involved hif1a modulation, consistent with other regenerative models, but uniquely included the expression of hif4a in erythrocytes and the upregulation of a myoglobin gene in the wound epidermis. Furthermore, genome-wide chromatin profiling identified candidate regeneration-responsive elements. Together, these findings establish Polypterus as a powerful comparative model for identifying shared and derived mechanisms of limb and fin regeneration.

evolutionary biology↗

bioRxiv2025

The response of mitochondrial position to glucose stimulation in a model system of the pancreatic beta cell

The compartmentalization of eukaryotic cells into membrane-bound organelles with specific subcellular positioning enables precise spatial and temporal control of cellular functions. While functionally significant mitochondrial localization has been demonstrated in cells such as neurons, it remains unclear how general these cell principles are. Here, we examine the spatial organization of mitochondria within MIN6 pancreatic beta cells under variable glucose conditions. We observe glucose-dependent redistributions of mitochondria, favoring peripheral localization at elevated glucose levels when insulin secretion is also elevated. Our results, formalized into a stochastic model of mitochondrial trafficking, suggest that active mitochondrial transport along microtubules and calcium activity, but not ATP synthesis, are critical regulators of this redistribution. These results suggest that mitochondrial positioning may contribute to optimizing energy delivery in response to local demand, potentially representing a general regulatory mechanism across various cell types.

cell biology↗

bioRxiv2024

Comprehensive characterization of mitochondrial bioenergetics at different larval stages reveals novel insights about the developmental metabolism of Caenorhabditis elegans

Mitochondrial bioenergetic processes are fundamental to development, stress responses, and health. Caenorhabditis elegans is widely used to study developmental biology, mitochondrial disease, and mitochondrial toxicity. Oxidative phosphorylation generally increases during development in many species, and genetic and environmental factors may alter this normal trajectory. Altered mitochondrial function during development can lead to both drastic, short-term responses including arrested development and death, and subtle consequences that may persist throughout life and into subsequent generations. Understanding normal and altered developmental mitochondrial biology in C. elegans is currently constrained by incomplete and conflicting reports on how mitochondrial bioenergetic parameters change during development in this species. We used a Seahorse XFe24 Extracellular Flux (XF) Analyzer to carry out a comprehensive analysis of mitochondrial and non-mitochondrial oxygen consumption rates (OCR) throughout larval development in C. elegans. We optimized and describe conditions for analysis of basal OCR, basal mitochondrial OCR, ATP-linked OCR, spare and maximal respiratory capacity, proton leak, and non-mitochondrial OCR. A key consideration is normalization, and we present and discuss results as normalized per individual worm, protein content, worm volume, mitochondrial DNA (mtDNA) count, nuclear DNA (ncDNA) count, and mtDNA:ncDNA ratio. Which normalization process is best depends on the question being asked, and differences in normalization explain some of the discrepancies in previously reported developmental changes in OCR in C. elegans. Broadly, when normalized to worm number, our results agree with previous reports in showing dramatic increases in OCR throughout development. However, when normalized to total protein, worm volume, or ncDNA or mtDNA count, after a significant 2-3-fold increase from L1 to L2 stages, we found small or no changes in most OCR parameters from the L2 to the L4 stage, other than a marginal increase at L3 in spare and maximal respiratory capacity. Overall, our results indicate an earlier cellular shift to oxidative metabolism than suggested in most previous literature.

developmental biology↗

bioRxiv2024

GNN codon adjacency regulates protein translation

The central dogma treats the ribosome as a molecular machine that reads one mRNA codon at a time as it adds each amino acid to its growing peptide chain. However, this and previous studies suggest that ribosomes actually perceive pairs of adjacent codons as they take three-nucleotide steps along the mRNA. We examined GNN codons which we find are surprisingly overrepresented in eukaryote protein-coding open reading frames (ORFs), especially immediately after NNU codons. Ribosome profiling experiments in yeast revealed that ribosomes with NNU at their aminoacyl (A) site have particularly elevated densities when NNU is immediately followed (3) by a GNN codon, indicating slower mRNA threading of the NNU codon from the ribosomes A to peptidyl (P) sites. Moreover, if the assessment was limited to ribosomes that have only recently arrived at the next codon, by examining 21-nucleotide ribosome footprints (21-nt RFPs), elevated densities were observed for multiple codon classes when followed by GNN. This striking translation slowdown at adjacent 5-NNN GNN codon pairs is likely mediated in part by the ribosomes CAR surface which acts as an extension of the A-site tRNA anticodon during ribosome translocation and interacts through hydrogen bonding and pi stacking with the GNN codon. The functional consequences of 5-NNN GNN codon adjacency are expected to influence the evolution of protein coding sequences. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/583757v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@d29087org.highwire.dtl.DTLVardef@e8f7dorg.highwire.dtl.DTLVardef@1ee5792org.highwire.dtl.DTLVardef@b750fb_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

molecular biology↗

bioRxiv2024

Thermostable in vitro transcription-translation for enzyme screening in microdroplets

BackgroundIn vitro expression involves the utilization of the transcription and translation machinery derived from the cell to produce one or more proteins of interest and has found widespread application in the optimization of gene circuits or metabolic pathways in synthetic biology but also in pharmaceutical manufacturing. Most in vitro expression systems available are active at moderate temperatures but to screen large libraries of natural or artificial genetic diversity for highly thermostable enzymes or enzyme variants, it is instrumental to enable protein synthesis at high temperatures. Moreover, given the fact that the main barrier toward the general use of in vitro expression is its high price compared with host-based recombinant expression, there is a need to develop alternative in vitro expression systems operating at high temperatures and compatible with technologies that enable ultrahigh-throughput screening in reduced volumes, such as microfluidic water-in-oil (w/o) droplets. ResultsTo this end, we produced high-expression cell-free extracts from Thermus thermophilus for in vitro translation and supplemented them with thermostable enzymatic cascades for energy regeneration and a moderately thermostable RNA polymerase for transcription, which ultimately limited the temperature of protein synthesis. The yield was comparable to other thermostable in vitro expression systems, while the preparation procedure is simpler and can be suited to different Thermus thermophilus strains. Furthermore, these extracts have enabled in vitro expression in microfluidic droplets at high temperatures for the first time. Although the composition of these extracts showed a high background in carboxyl esterase assays, {beta}-glucosidase and cellobiose hydrolase activities could be measured with minimal background. ConclusionsCell-free extracts from Thermus thermophilus represent a simpler alternative to heavily optimized or pure component thermostable in vitro expression systems. Moreover, due to their compatibility with droplet microfluidics and enzyme assays at high temperatures, the reported system represents a convenient gateway for enzyme screening at higher temperatures with ultrahigh-throughput.

microbiology↗

bioRxiv2023

ACE2 mimetic antibody potently neutralizes all SARS-CoV-2 variants and fully protects in XBB.1.5 challenged monkeys

The rapid evolution of SARS-CoV-2 to variants with improved transmission efficiency and reduced sensitivity to vaccine-induced humoral immunity has abolished the protective effect of licensed therapeutic human monoclonal antibodies (mAbs). To fill this unmet medical need and protect vulnerable patient populations, we isolated the P4J15 mAb from a previously infected, vaccinated donor, with <20 ng/ml neutralizing activity against all Omicron variants including the latest XBB.2.3 and EG.1 sub-lineages. Structural studies of P4J15 in complex with Omicron XBB.1 Spike show that the P4J15 epitope shares [~]93% of its buried surface area with the ACE2 contact region, consistent with an ACE2 mimetic antibody. Although SARS-CoV-2 mutants escaping neutralization by P4J15 were selected in vitro, these displayed lower infectivity, poor binding to ACE2, and the corresponding escape mutations are accordingly rare in public sequence databases. Using a SARS-CoV-2 XBB.1.5 monkey challenge model, we show that P4J15 confers complete prophylactic protection. We conclude that the P4J15 mAb has potential as a broad-spectrum anti-SARS-CoV-2 drug.

microbiology↗

bioRxiv2023

Impact of magnetite nanowires orientation on morphology and activity of in vitro hippocampal neural networks

Nanomaterials design, synthesis and characterization are ever-expanding approaches towards developing biodevices or neural interfaces to treat neurological diseases. The ability of nanomaterials features, to tune neuronal networks morphology or functionality is still under study. In this work, we unveil how, when interfacing mammalian brain cultured neurons, iron oxide nanowires (NWs) orientation affects neuronal and glial densities, and network activity. Iron oxide NWs were synthesized by electrodeposition, fixing the diameter to 100 nm and the length to 1 m. Scanning electron microscopy, Raman and contact angle measurements were performed to characterize the NWs morphology, chemical composition and hydrophilicity. Hippocampal cultures were seeded on NWs devices and after 14 days the cell morphology was studied by immunocytochemistry and confocal microscopy. Live calcium imaging was performed to study neuronal activity. Using random (R-NWs) a higher neuronal and glial cell densities were obtained compared with the control and vertical (V-NWs), while using V-NWs more stellate glial cells were found. R-NWs produced a reduction in neuronal activity while V-NWs increased the neuronal network activity, possibly due to higher neuronal maturity and a lower number of GABAergic neurons, respectively. These results highlight the potential of NWs manipulations to design ad hoc regenerative interfaces.

bioengineering↗