Biology subjects

Gonzales, J.

Publications and source records attributed to Gonzales, J..

9 recordsLinked to original sources

bioRxiv2026

Experimental reproduction numbers disentangle vaccine effects on susceptibility and infectiousness during H5N1 transmission in geese

Vaccination against high pathogenicity avian influenza virus (HPAIV) is increasingly used to protect poultry, but vaccine performance is commonly inferred from clinical protection and virus shedding rather than measured transmission. We asked whether reproduction numbers from controlled transmission experiments can quantify how vaccination changes susceptibility and infectiousness. Domestic geese were prime-boost vaccinated with an H5 clade 2.3.4.4b RNA-replicon vaccine and challenged with homologous HPAIV H5N1. Replicated seeder-sentinel groups represented transmission among unvaccinated animals, to vaccinated contacts, and from vaccinated breakthrough-infected animals. Vaccinated directly challenged geese remained clinically protected although all became RT-qPCR-positive. Estimated reproduction numbers were R0=4.7 (95% CI, 2.8-8.0) among unvaccinated geese, Rs=2.6 (1.6-4.5) for transmission to vaccinated contacts, Ri=3.7 (2.0-6.8) for transmission from vaccinated infected geese, and Rvacc=2.0 (0.8-4.9) for a fully vaccinated population. Vaccination reduced transmission but did not reduce the point estimate for Rvacc below one under these intensive exposure conditions. Vaccinated infected geese also shed substantially less viral RNA, whereas the estimated reduction in infectiousness was more modest, indicating that RNA shedding alone may not reliably predict transmission reduction. Experimental reproduction numbers therefore provide a direct population-level complement to conventional vaccine endpoints and separate effects on susceptibility from effects on onward transmission.

microbiology↗

bioRxiv2026

STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics

Sequencing-based spatial transcriptomics technologies, including Visium HD and Stereo-seq, now enable transcriptome-wide profiling at subcellular resolution. However, these platforms generate measurements over spatially barcoded units rather than biologically segmented cells, creating a fundamental bottleneck for cell-centric analysis and interpretation. Robust recon-struction of coherent single-cell transcriptomes from high-density spatial bins remains an unresolved computational challenge. Here we present STCS (Spatial Transcriptomics Cell Segmentation), a platform-agnostic framework that reconstructs cell-level gene expression profiles by integrating nuclei segmentation with a joint transcriptomic-spatial distance model. STCS is governed by two interpretable parameters and incorporates a reference-free parameter selection strategy based on internal stability and spatial coherence metrics, enabling adaptable deployment across tissue types and technologies without requiring matched ground-truth annotations. We benchmark STCS on a Visium HD human lung cancer dataset with matched Xenium-derived cell segmentation, enabling direct cell-level validation, and on high-resolution Stereo-seq mouse brain data to assess cross-platform generalizability. Across multiple evaluation dimensions--including cell-type agreement, spatial organization, gene-expression fidelity, and compositional accuracy--STCS achieves consistent improvements over existing methods while preserving biologically coherent spatial structure. As sequencing-based spatial transcriptomics is rapidly adopted across biomedical research, STCS provides a broadly applicable and open-source solution for reconstructing cell-resolved transcriptomes, facilitating more reliable downstream analyses and cross-platform integration.

bioinformatics↗

bioRxiv2024

Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of influenza A virus

Viral proteins frequently mutate to evade or antagonize host innate immune responses, yet the impact of these mutations on the molecular energy landscape remains unclear. Epistasis, the intramolecular communications between mutations, often renders the combined mutational effects unpredictable. Nonstructural protein 1 (NS1) is a major virulence factor of the influenza A virus (IAV) that activates host PI3K by binding to its p85{beta} subunit. Here, we present the deep analysis for the impact of evolutionary mutations in NS1 that emerged between the 1918 pandemic IAV strain and its descendant PR8 strain. Our analysis reveal how the mutations rewired inter-residue communications which underlies long-range allosteric and epistatic networks in NS1. Our findings show that PR8 NS1 binds to p85{beta} with approximately 10-fold greater affinity than 1918 NS1 due to allosteric mutational effects. Notably, these mutations also exhibited long-range epistatic effects. NMR chemical shift perturbation and methyl-axis order parameter analyses revealed that the mutations induced long-range structural and dynamic changes in PR8 NS1, enhancing its affinity to p85{beta}. Complementary MD simulations and graph-based network analysis uncover how these mutations rewire dynamic residue interaction networks, which underlies the long-range epistasis and allosteric effects on p85{beta}-binding affinity. Significantly, we find that conformational dynamics of residues with high betweenness centrality play a crucial role in communications between network communities and are highly conserved across influenza A virus evolution. These findings advance our mechanistic understanding of the allosteric and epistatic communications between distant residues and provides insight into their role in the molecular evolution of NS1.

biophysics↗

bioRxiv2024

Immune-profiling of T helper 1 (Th1), Th2 and Th17 signatures in murine splenocytes by targeting intracellular cytokines

Functional cytokines shape both innate and adaptive immune responses in the host after infection or immunization. Deep immunophenotyping of the key functional cytokine signatures associated with T cells in murine lymphoid tissue, especially in the spleen, is challenging. Using spectral flow cytometry, we developed a 17-parameter panel to profile major immune cell subsets along with T cells, memory phenotypes and functional cytokines in murine splenocytes in steady state as well as in stimulated conditions. This panel dissects the memory T cell compartment via CD62L and CD44 expression after mitogen stimulation. To profile T helper (Th) cells distribution after mitogen stimulation, established Th1 markers IFN{gamma}, TNF and IL-2; Th2 markers IL-4/5 and the Th17 marker, IL-17, are included. This optimized multicolor spectral flow panel allows a detailed immune profiling of functional cytokines in the murine T cell compartment and might be useful for exploratory analysis of how these functional cytokines shape host immunity after infection or vaccination. Our panel could be easily modified, if researchers wish to tailor the panel to their specific needs.

immunology↗

bioRxiv2024

NaV1.7 targeted fluorescence imaging agents for nerve identification during intraoperative procedures

Surgeries and trauma result in traumatic and iatrogenic nerve damage that can result in a debilitating condition that approximately affects 189 million individuals worldwide. The risk of nerve injury during oncologic surgery is increased due to tumors displacing normal nerve location, blood turbidity, and past surgical procedures, which complicate even an experienced surgeons ability to precisely locate vital nerves. Unfortunately, there is a glaring absence of contrast agents to assist surgeons in safeguarding vital nerves. To address this unmet clinical need, we leveraged the abundant expression of the voltage-gated sodium channel 1.7 (NaV1.7) as an intraoperative marker to access peripheral nerves in vivo, and visualized nerves for surgical guidance using a fluorescently-tagged version of a potent NaV1.7-targeted peptide, Tsp1a, derived from a Peruvian tarantula. We characterized the expression of NaV1.7 in sensory and motor peripheral nerves across mouse, primate, and human specimens and demonstrated universal expression. We synthesized and characterized a total of 10 fluorescently labeled Tsp1a-peptide conjugates to delineate nerves. We tested the ability of these peptide-conjugates to specifically accumulate in mouse nerves with a high signal-to-noise ratio in vivo. Using the best-performing candidate, Tsp1a-IR800, we performed thyroidectomies in non-human primates and demonstrated successful demarcation of the recurrent laryngeal and vagus nerves, which are commonly subjected to irreversible damage. The ability of Tsp1a to enhance nerve contrast during surgery provides opportunities to minimize nerve damage and revolutionize standards of care across various surgical specialties.

biochemistry↗

bioRxiv2021

Bees can be trained to identify SARS-CoV-2 infected samples.

The COVID-19 pandemic has illustrated the need for the development of fast and reliable testing methods for novel, zoonotic, viral diseases in both humans and animals. Pathologies lead to detectable changes in the Volatile Organic Compound (VOC) profile of animals, which can be monitored, thus allowing the development of a rapid VOC-based test. In the current study, we successfully trained honeybees (Apis mellifera) to identify SARS-CoV-2 infected minks (Neovison vison) thanks to Pavlovian conditioning protocols. The bees can be quickly conditioned to respond specifically to infected minks odours and could therefore be part of a wider SARS-CoV-2 diagnostic system. We tested two different training protocols to evaluate their performance in terms of learning rate, accuracy and memory retention. We designed a non-invasive rapid test in which multiple bees are tested in parallel on the same samples. This provided reliable results regarding a subjects health status. Using the data from the training experiments, we simulated a diagnostic evaluation trial to predict the potential efficacy of our diagnostic test, which yielded a diagnostic sensitivity of 92% and specificity of 86%. We suggest that a honeybee-based diagnostics can offer a reliable and rapid test that provides a readily available, low-input addition to the currently available testing methods. A honeybee-based diagnostic test might be particularly relevant for remote and developing communities that lack the resources and infrastructure required for mainstream testing methods.

microbiology↗

bioRxiv2021

Non-invasive Imaging of Sense of Smell by Tracking the Voltage-Gated Sodium Channel NaV1.7

The sense of smell (olfaction) is one of the most important senses for animals including humans. Despite significant advances in the understanding mechanism of olfaction, currently, there are no objective non-invasive methods that can identify loss of smell. Covid-19-related loss of smell has highlighted the need to develop methods that can identify loss of olfaction. Voltage-gated sodium channel 1.7 (NaV1.7) plays a critical role in olfaction by aiding the signal propagation to the olfactory bulb. We have identified several conditions such as chronic inflammation and viral infections such as Covid-19 that lead to loss of smell correlate with downregulation of NaV1.7 expression at transcript and protein levels in the olfactory epithelium. Leveraging this knowledge, we have developed a novel fluorescent probe Tsp1a-IR800 that targets NaV1.7. Using fluorescence imaging we can objectively measure the loss of sense of smell in live animals non-invasively. We also demonstrate that our non-invasive method is semiquantitative because the loss of fluorescence intensity correlates with the level of smell loss. Our results indicate, that our probe Tsp1a-IR800, can objectively diagnose anosmia in animal and human subjects using infrared fluorescence. We believe this method to non-invasively diagnose loss of smell objectively is a significant advancement in relation to current methods that rely on highly subjective behavioral studies and can aid in studying olfaction loss and the development of therapeutic interventions.

neuroscience↗

bioRxiv2021

Evolutionary dynamics of asexual hypermutators adapting to a novel environment

How microbes adapt to a novel environment is a central question in evolutionary biology. While adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects the effects of genetic draft under strong linkage. Despite these linkage effects, the evolved populations exhibit parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results generally negate the presumed relationship between high mutation rates and high adaptive speed of evolution, providing insight into how clonal adaptation occurs in novel environments. Significance statementWhile mutations are critical source for the adaptation in a new environment, whether or not the elevated mutation rates can empirically lead to the elevated adaptation rates remains unclear, especially when the environment is more heterogenous. To answer this question, we evolved E. coli populations with different starting mutation rates in a complex medium for 900 days and then examined their fitness and genome profiles. In the populations that have a higher starting mutation rate, despite faster genome evolution, their fitness improvement is not significantly faster. Our results reveal that the effect of elevated mutation rates is only very limited, and the mutations accumulated in hypermutators are largely due to linkage effect.

evolutionary biology↗

bioRxiv2020

Mfd affects global transcription and the physiology of stressed Bacillus subtilis cells

For several decades, Mfd has been studied as the bacterial transcription-coupled repair factor. However, recent observations indicate that this factor influences cell functions beyond DNA repair. Our lab recently described a role for Mfd in disulfide stress that was independent of its function in nucleotide excision repair and base excision repair. Because reports showed that Mfd influenced transcription of single genes, we investigated the global differences in transcription in wild-type and mfd mutant growth-limited cells in the presence and absence of diamide. Surprisingly, we found 1,997 genes differentially expressed in Mfd- cells in the absence of diamide. Using gene knockouts, we investigated the effect of genetic interactions between Mfd and the genes in its regulon on the response to disulfide stress. Interestingly, we found that Mfd interactions were complex and identified additive, epistatic, and suppressor effects in the response to disulfide stress. Pathway enrichment analysis of our RNASeq assay indicated that major biological functions, including translation, endospore formation, pyrimidine metabolism, and motility, were affected by the loss of Mfd. Further, our RNASeq findings correlated with phenotypic changes in growth in minimal media, motility, and sensitivity to antibiotics that target the cell envelope, transcription, and DNA replication. Our results suggest that Mfd has profound effects on the modulation of the transcriptome and on bacterial physiology, particularly in cells experiencing nutritional and oxidative stress.

microbiology↗