Biology subjects

Hurtado, J.

Publications and source records attributed to Hurtado, J..

At least 19 recordsLinked to original sources

bioRxiv2026

End-to-end plaque counting and virus titration from laboratory plate images with deep learning

Plaque assays are the gold standard for quantifying infectious virus, yet plaque enumeration is still routinely performed manually, making virus titration labor-intensive, subjective, and difficult to standardize across analysts and laboratories. Existing automated methods primarily address individual tasks, such as plaque segmentation or counting, but do not provide an integrated workflow from plate images to biological quantification. In this paper we present Titra, an end-to-end workflow for automated cytopathic effect (CPE)-based virus titration from standard photographs of plaque assay plates. The workflow combines automatic well detection, plaque segmentation, post-processing for instance separation, plaque counting, and plaque-forming units per millilitre (PFU/mL) estimation within a single web-based platform that also enables experiment management and expert review. The approach was evaluated using images from three viral species (Mayaro virus, Coxsackievirus B3, and vaccinia virus), two plate formats (6- and 12-well), and heterogeneous image acquisition conditions, including both a newly curated dataset and the public VACVPlaque dataset. Automated plaque counts showed strong agreement with manual annotations (Pearson correlation coefficients of 0.98 for MAYV/CVB3 and 0.88 for VACV), while PFU/mL estimates closely matched manual calculations for the MAYV/CVB3 dataset (Pearson r=0.975). Comparative experiments against U-Net, StarDist, HSD-WBR, and PyPlaque demonstrated competitive segmentation and counting performance, with the proposed approach achieving the highest Dice and mAP on the public VACVPlaque dataset.

bioinformatics↗

bioRxiv2026

Evaluating Expert Specialization in Mixture-of-Experts Antibody Language Models

AO_SCPLOWBSTRACTC_SCPLOWAntibody language models (AbLMs) show an impressive aptitude for learning antibody features, but tend to struggle learning the highly diverse, non-templated regions of antibodies. Existing AbLMs use dense architectures, where all model parameters attend to each amino acid token. We hypothesized that the modular nature of antibodies could benefit from a sparse mixture-of-experts (MoE) architecture, allowing specific parameters (referred to as experts) to specialize in distinct antibody features. While MoE architectures are widely adopted and optimized in natural language processing domains, they are less common in biological modeling. To this end, we assess existing MoE routing strategies and find that token-choice routing strategies outperform expert-choice routing, presumably due to their specialization in CDRH3 residues. We further optimized the token-choice router for AbLMs, by minimizing the routing of padding tokens to enable pre-training with varying sequence lengths. Finally, we show that a large-scale baseline antibody language model with a Top-2 MoE architecture (BALM-MoE), trained on a mixture of unpaired and paired antibody sequences, outperforms its dense counterpart with the same number of active parameters.

immunology↗

bioRxiv2026

Potent broad-spectrum antiviral activity of the marine natural product Plitidepsin

Viruses pose a critical global health threat, yet therapeutic options remain limited. Finding drugs with broad-spectrum antiviral activity is essential to confront this threat. Here, we investigated whether plitidepsin, a marine-derived anticancer drug targeting the host eukaryotic elongation factor 1A (eEF1A), has such broad-spectrum activity. Using in vitro infection models and complementary assays (MTT, plaque-forming assays, RT-qPCR, Western blot, flow cytometry), we demonstrated that plitidepsin exhibits potent dose-dependent antiviral activity against Mayaro virus (MAYV) and Chikungunya virus (CHIKV). The compound achieved 4-6 log10 reduction in viral titers at nanomolar concentrations across multiple cell lines and viral strains. Plitidepsin protected human dermal fibroblasts from viral cytopathic effects and disrupted both entry and post-entry replication stages by suppressing viral protein expression (E1, nsP1) and RNA synthesis. The compound also demonstrated antiviral activity against other medically important arboviruses, including Una, Punta Toro, Zika, and Oropouche viruses, as well as RNA and DNA viruses such as influenza A virus, vesicular stomatitis virus, and human cytomegalovirus. These findings establish plitidepsin as a potent host-directed antiviral agent with reduced likelihood of resistance development and therapeutic potential against multiple viral families.

microbiology↗

bioRxiv2026

Heterologous betacoronavirus spike immunization in nonhuman primates elicits cross-reactive antibodies that neutralize both sarbeco- and merbecoviruses

In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques with SARS-CoV-2 spike (S)-protein, then boosted with heterologous {beta}-CoV S-proteins to focus responses to common conserved S2 bnAb epitopes. Initial SARS-CoV-2 priming elicited receptor-binding domain (RBD)-focused responses, while MERS-CoV boosting redirected responses toward the S2 region, including the stem-helix bnAb site. Although S2-directed serum cross-neutralization was undetectable and most isolated cross-reactive monoclonal antibodies (mAbs) targeted non-neutralizing epitopes, two S2 stem-helix mAbs were identified from memory B cells. These bnAbs neutralized diverse sarbeco- and merbecoviruses, including MERS-CoV, and conferred robust in vivo protection against SARS-CoV-2 challenge. Structural studies revealed that these macaque bnAbs closely mimic human S2-stem bnAbs induced by infection. These findings provide proof-of-principle for vaccination strategies that elicit broadly protective {beta}-coronavirus responses and highlight non-human primates as a translational model for evaluating S2-targeted immunogens.

immunology↗

bioRxiv2026

Extended tissue tropism and vertical transmission in a murine model of Mayaro virus infection

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus associated with acute febrile illness and persistent arthralgia, with increasing reports in Latin America and potential for geographic expansion. However, its dissemination dynamics, tissue tropism and transmission routes remain incompletely defined. Here, we developed a murine model to characterize systemic viral dissemination, tissue tropism and the impact of gestational stage on maternal-fetal outcomes. A nanoluciferase-expressing MAYV reporter enabled non-invasive in vivo imaging, revealing rapid and widespread systemic dissemination under controlled conditions. Complementary infection with wild-type (WT) virus confirmed broad tropism across lymphoid, musculoskeletal and reproductive tissues. At 24 hours post-infection (hpi), viral distribution was relatively homogeneous across tissues, whereas at 48 hpi, tissue-specific differences emerged, with increased viral loads in selected organs, including the spleen and male reproductive tissues. Transient sex-dependent differences were observed at 24 hpi but were not sustained at later time points. Hematological and biochemical analyses revealed early systemic alterations consistent with changes in leukocyte distribution during acute infection. Infectious viral particles were detected in reproductive tissues of both sexes, including in sperm, supporting the biological plausibility of non-vector transmission, although detection in exposed animals was limited. Gestational stage influenced infection outcomes: early gestation (infected at 7.5-8.5 dpc; analyzed at 9.5-10.5 dpc) was associated with detection of infectious virus in fetal tissues, whereas mid-gestation (infected at 13.5-14.5 dpc; analyzed at 15.5-16.5 dpc) showed no detectable infectious virus in fetuses despite evidence of viral antigen persistence and sustained infectious viral presence in maternal and placental compartments. Together, these findings provide a preclinical framework for investigating MAYV pathogenesis and underscore the role of tissue tropism and gestational context in shaping infection dynamics and maternal-fetal involvement. Author summaryMayaro virus (MAYV) is an emerging mosquito-borne virus that causes fever and long-lasting joint pain, with increasing reports in Latin America and potential for wider geographic spread. Despite its growing relevance, key aspects of MAYV pathogenesis remain to be fully defined, including the mechanisms underlying systemic dissemination and tissue tropism, as well as its potential to affect pregnancy or be transmitted through non-vector routes. Here, we used a mouse model with a luminescent reporter virus to track MAYV dissemination in vivo, revealing rapid and widespread distribution across multiple tissues. In studies using wild-type virus, infectious virus was detected not only in muscle and immune-related organs but also in reproductive tissues of both females and males. Importantly, gestational stage influenced viral distribution. When infection occurred early in gestation, infectious viral particles were detected in fetal tissues. In contrast, at later stages of pregnancy, infectious virus was no longer detectable in fetuses, despite evidence of viral antigen persistence and sustained infectious viral presence in maternal and placental tissues. Together, these findings advance our understanding of MAYV infection, highlight gestational timing as a factor associated with fetal exposure and suggest the possibility of transmission through routes other than mosquitoes, providing a framework for future studies on this emerging virus.

microbiology↗

bioRxiv2025

Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques

Germline-targeting-(GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a germline-targeting trimer immunogen Q23-APEX-GT2 that primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated V2-apex-specific B cells in humanized knock-in mice and consistently elicited immunofocused antibody responses in rhesus macaques, priming multiple long CDRH3-loop bnAb-B cell lineages. Monoclonal antibodies from immunized macaques exhibited broad heterologous HIV trimer binding and cross-neutralization. Atomic-level structural studies confirmed precise epitope targeting and revealed CDRH3-paratope configurations that mirrored those of human V2-apex bnAbs. This study provides proof-of-principle for successful priming and maturation of authentic V2-apex bnAb precursors in outbred macaques, underscoring the potential of V2-apex-targeted vaccines. HIGHLIGHTSO_LIEngineered Q23-APEX-GT2 trimer to stimulate diverse V2-apex bnAb B cell precursors C_LIO_LIQ23-APEX-GT2 primed rare V2-apex bnAb B cells in mice and outbred rhesus macaques C_LIO_LIQ23-APEX-GT2 elicited immunofocused antibody responses and diverse V2-apex B cell lineages with desirable long-CDRH3 paratope properties C_LIO_LIQ23-APEX-GT2 alone induced V2-apex antibodies with broad HIV trimer binding and modest neutralization breadth C_LIO_LIStructural analysis confirmed bnAb site targeting, mirroring human and rhesus V2-apex bnAbs C_LI

immunology↗

bioRxiv2025

A Single-Cell Atlas of Transcriptional and Immunoglobulin Repertoire Evolution in Early B Cell Development

The development of human B cells in the bone marrow can be separated into functionally and transcriptionally distinct subsets, which while canonically described have yet to be profiled deeply and individually and with NGS and bioinformatic techniques. In this study, single-cell RNA sequencing was performed on 65,110 B cells from six healthy donors to observe the foundation of the diversity observed in mature immune repertoires. Following the established narrative of development, committed B cells undergo heavy and light chain recombination, which together form the functional BCR. However, a granular per-subset phenotypic analysis reveals proliferative bursts following each recombination event, an aspect of BCR recombination previously undescribed in the pro-B phase of development. Heavy and light chain pairing becomes more similar to that of mature, circulating B cells with progress through lymphopoiesis, deleting features associated with autoreactivity. Prominent among these repertoire alterations is a substantial shortening of heavy chain CDR3s, and changes in V, D, and J gene usage. This study provides a detailed snapshot of the transcriptomic and repertoire genetics landscape of developing B cells, providing a deeper understanding of the repertoire-shaping influence of early selection processes, and introducing new avenues for repertoire development research.

immunology↗

bioRxiv2025

Data-optimal scaling of paired antibody language models

Scaling laws for large language models in natural language domains are typically derived under the assumption that performance is primarily compute-constrained. In contrast, antibody language models (AbLMs) trained on paired sequences are primarily data-limited, thus requiring different considerations. To explore how model size and data scale affect AbLM performance, we trained 15 AbLMs across all pairwise combinations of five model sizes and three training data sizes. From these experiments, we derive an AbLM-specific scaling law and estimate that training a data-optimal AbLM equivalent of the highly performant 650M-parameter ESM-2 protein language model would require [~]5.5 million paired antibody sequences. Evaluation on multiple downstream classification tasks revealed that significant performance gains emerged only with sufficiently large model size, suggesting that in data-limited domains, improved performance depends jointly on both model scale and data volume.

immunology↗

bioRxiv2025

Mechanical strain modulates Min patterning and division in E. coli filaments

Bacteria often encounter physico-chemical stresses that disrupt division, leading to filamentation, where cells elongate without dividing. While this adaptive response enhances survival, it also exposes filaments to significant mechanical strain, raising questions about the mechanochemical feedback in bacterial systems. In this study, we investigate how mechanical strain influences the Min oscillatory system, a reaction-diffusion network central to division in Escherichia coli. Through a multidisciplinary approach combining quantitative fluorescence microscopy, biophysical modeling, microfluidics, and patterned growth substrates, we demonstrate that filamentous E. coli undergoes growth-induced buckling instability. This phenomenon alters the diffusivity of membrane proteins and modulates the spatiotemporal patterning of the Min system. Moreover, we show that this mechanochemical interplay determines division site positioning after stress relief, effectively creating a mechanical "memory" for cytokinesis. Our findings underscore the critical role of mechanical forces in bacterial filamentation and provide new insights into the functional implications of mechanobiology in microbial systems.

biophysics↗

bioRxiv2024

Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques

SummaryDuring infection, the fusion peptide (FP) of HIV envelope glycoprotein (Env) serves a central role in viral fusion with the host cell. As such, the FP is highly conserved and therefore an attractive epitope for vaccine design. Here, we describe a vaccination study in non-human primates (NHPs) where glycan deletions were made on soluble HIV Env to increase FP epitope exposure. When delivered via implantable osmotic pumps, this immunogen primed immune responses against the FP, which were then boosted with heterologous trimers resulting in a focused immune response targeting the conserved FP epitope. Although autologous immunizations did not elicit high affinity FP-targeting antibodies, the conserved FP epitope on a heterologous trimer further matured the lower affinity, FP-targeting B cells. This study suggests using epitope conservation strategies on distinct Env trimer immunogens can focus humoral responses on desired neutralizing epitopes and suppress immune-distracting antibody responses against non-neutralizing epitopes.

immunology↗

bioRxiv2024

Conformational ensemble-based framework enables rapid development of Lassa virus vaccine candidates

Lassa virus (LASV), an arenavirus endemic to West Africa, poses a significant public health threat due to its high pathogenicity and expanding geographic risk zone. LASV glycoprotein complex (GPC) is the only known target of neutralizing antibodies, but its inherent metastability and conformational flexibility have hindered the development of GPC-based vaccines. We employed a variant of AlphaFold2 (AF2), called subsampled AF2, to generate diverse structures of LASV GPC that capture an array of potential conformational states using MSA subsampling and dropout layers. Conformational ensembles identified several metamorphic domains--areas of significant conformational flexibility--that could be targeted to stabilize the GPC in its immunogenic prefusion state. ProteinMPNN was then used to redesign GPC sequences to minimize the mobility of metamorphic domains. These redesigned sequences were further filtered using subsampled AF2, leading to the identification of promising GPC variants for further testing. A small library of redesigned GPC sequences was experimentally validated and showed significantly increased protein yields compared to controls. Antigenic profiles indicated these variants preserved essential epitopes for effective immune response, suggesting their potential for broad protective efficacy. Our results demonstrate that AI-driven approaches can predict the conformational landscape of complex pathogens. This knowledge can be used to stabilize viral proteins, such as LASV GPC, in their prefusion conformation, optimizing them for stability and expression, and offering a streamlined framework for vaccine design. Our deep learning / machine learning enabled framework contributes to global efforts to combat LASV and has broader implications for vaccine design and pandemic preparedness.

immunology↗

bioRxiv2023

No evidence for highly pathogenic avian influenza virus H5N1 (clade 2.3.4.4b) in the Antarctic region during the austral summer 2022/23

The current highly pathogenic avian influenza H5N1 panzootic has substantial impacts on wild birds and marine mammals. Although major outbreaks occurred in South America, incursion to Antarctica emerged late in the breeding season of 2023/2024 and was confined the wider region of the Antarctic Peninsula. To infer potential underlying processes, we compiled H5N1 surveillance from Antarctica and Sub-Antarctic Islands prior to the first confirmed cases.

microbiology↗

bioRxiv2023

Germline-targeting chimpanzee SIV Envelopes induce V2-apex broadly neutralizing-like B cell precursors in a rhesus macaque infection model

Eliciting broadly neutralizing antibodies-(bnAbs) remains a major goal of HIV-1 vaccine research. Previously, we showed that a soluble chimpanzee SIV Envelope-(Env) trimer, MT145K, bound several human V2-apex bnAb-precursors and stimulated an appropriate response in V2-apex bnAb precursor-expressing knock-in mice. Here, we tested the immunogenicity of three MT145 variants (MT145, MT145K, MT145K.dV5) expressed as chimeric simian-chimpanzee-immunodeficiency-viruses-(SCIVs) in rhesus macaques-(RMs). All three viruses established productive infections with high setpoint vRNA titers. RMs infected with the germline-targeting SCIV_MT145K and SCIV_MT145K.dV5 exhibited larger and more clonally expanded B cell lineages featuring long anionic heavy chain complementary-determining-regions-(HCDR3s) compared with wildtype SCIV_MT145. Moreover, antigen-specific B cell analysis revealed enrichment for long-CDHR3-bearing antibodies in SCIV_MT145K.dV5 infected animals with paratope features resembling prototypic V2-apex bnAbs and their precursors. Although none of the animals developed bnAbs, these results show that germline-targeting SCIVs can activate and preferentially expand B cells expressing V2-apex bnAb-like precursors, the first step in bnAb elicitation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/558743v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@17673c8org.highwire.dtl.DTLVardef@1ab61a8org.highwire.dtl.DTLVardef@98781forg.highwire.dtl.DTLVardef@1f63e9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

PERK-mediated antioxidant response is key for pathogen persistence in ticks

A crucial phase in the lifecycle of tick-borne pathogens is the time spent colonizing and persisting within the arthropod. Tick immunity is emerging as a key force shaping how transmissible pathogens interact with the vector. How pathogens remain in the tick despite immunological pressure remains unknown. In persistently infected Ixodes scapularis, we found that Borrelia burgdorferi (Lyme disease) and Anaplasma phagocytophilum (granulocytic anaplasmosis) activate a cellular stress pathway mediated by the endoplasmic reticulum receptor PERK and the central regulatory molecule, eIF2. Disabling the PERK pathway through pharmacological inhibition and RNAi significantly decreased microbial numbers. In vivo RNA interference of the PERK pathway not only reduced the number of A. phagocytophilum and B. burgdorferi colonizing larvae after a bloodmeal, but also significantly reduced the number of bacteria that survive the molt. An investigation into PERK pathway-regulated targets revealed that A. phagocytophilum and B. burgdorferi induce activity of the antioxidant response regulator, Nrf2. Tick cells deficient for nrf2 expression or PERK signaling showed accumulation of reactive oxygen and nitrogen species in addition to reduced microbial survival. Supplementation with antioxidants rescued the microbicidal phenotype caused by blocking the PERK pathway. Altogether, our study demonstrates that the Ixodes PERK pathway is activated by transmissible microbes and facilitates persistence in the arthropod by potentiating an Nrf2-regulated antioxidant environment.

microbiology↗

bioRxiv2023

Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple epitopes

Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. Current strategies for developing pan-coronavirus countermeasures have largely focused on the receptor binding domain (RBD) and S2 regions of the coronavirus Spike protein; it has been unclear whether the N-terminal domain (NTD) is a viable target for universal vaccines and broadly neutralizing antibodies (Abs). Additionally, many RBD-targeting Abs have proven susceptible to viral escape. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees using multiplexed panels of uniquely barcoded antigens in a high-throughput single cell workflow to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. We observed many instances of clonal coalescence between individuals, suggesting that Ab responses frequently converge independently on similar genetic solutions. Among the recovered antibodies was TXG-0078, a public neutralizing mAb that binds the NTD supersite region of the coronavirus Spike protein and recognizes a diverse collection of alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing mAb that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 provides protection against in vivo challenge with SARS-CoV-2, suggesting potential future use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.

immunology↗

bioRxiv2022

Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies

SummaryLassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences amongst LASV lineages. Despite the sequence diversity of GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VI, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of GPC in complex with GP1-A antibodies reveal their neutralization mechanisms. Finally, we present the isolation and characterization of a novel trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines. HighlightsO_LIStructural characterization of soluble glycoproteins from four Lassa virus lineages. C_LIO_LIMAb 12.1F, belonging to the GP1-A cluster, inhibits matriglycan and LAMP-1 binding. C_LIO_LIGP1-A mAbs show glycan-dependence with 19.7E demonstrating lineage-dependent binding. C_LIO_LIA novel trimer-preferring NAb S370.7 targets the GPC-B epitope. C_LI

immunology↗

bioRxiv2022

Efficient isolation of rare B cells using next-generation antigen barcoding

The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (mAbs) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.

immunology↗

bioRxiv2021

Propagation of seminal toxins through binary expression gene drives can suppress polyandrous populations

Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this restriction may be relaxed by using a double gene drive design to spread a split binary expression system. One drive carries a dominant lethal/toxic effector alone and the other a transactivator factor, without which the effector will not act. Only after the drives reach sufficiently high frequencies would individuals have the chance to inherit both system components and the effector be expressed. We explore through mathematical modeling the potential of this design to spread dominant lethal/toxic alleles and suppress populations. We show that this system could be implemented to spread engineered seminal proteins designed to kill females, making it highly effective against polyandrous populations.

bioinformatics↗