Biology subjects

Nunez, M.

Publications and source records attributed to Nunez, M..

12 recordsLinked to original sources

bioRxiv2026

Metric-driven Pre-acquisition Diagnostics for Automated Microscopy Ultraviolet Surface Excitation (MUSE)

Background Automated microscopy enables large-scale tiled imaging but remains sensitive to variations in alignment, illumination, focus, and sample coverage that may only be detected after acquisition. We present an adaptive pre-acquisition quality-control framework for microscopy ultraviolet surface excitation (MUSE) that uses sparse scout imaging and tile-level metrics to guide acquisition and selective rescanning. Methods The framework quantifies brightness, dynamic range, focus, tissue fraction, and exposure error across the field of view. For example, in a representative 10 x 10 acquisition (100 tiles, 20-megapixel imagery), the mean p99 brightness was 0.525 (CV 10.4%), the mean dynamic range was 0.331, the median focus score was 0.0333, and the median tissue fraction was 0.943. Furthermore, applying a conservative exposure-error threshold (|error| > 0.25) identified 25% of tiles as rescan candidates. Results These results show that compact tile-level metrics can be converted into actionable quality gates, enabling early detection of local acquisition errors and targeted rescanning to improve mosaic consistency while minimizing unnecessary acquisition.

bioinformatics↗

bioRxiv2026

Music-Inspired Acoustic-Piezoelectric Stimulation Accelerates Extracellular Vesicle Production and Programs Therapeutic Function

Macrophage small extracellular vesicles (sEVs) carry phenotype-linked cargo and bioactivity for immunomodulation and regeneration, but therapeutic translation is limited by low secretion and poor control of function. We introduce a music-activated piezoelectric nanofiber substrate (PES) that converted audible sound into programmable electrical stimulation to enhance sEV biogenesis while tuning macrophage polarization. Adjusting acoustic parameters increased sEV yield, while musically inspired "assemblies" biased macrophage phenotypes: dissonant, low-frequency stimuli promoted M1-like inflammation, whereas consonant, higher-frequency stimuli favored M2-like, regenerative states. These shifts produced distinct sEV cargo and bioactivities. We rationally designed customized music stimulus that maximized both vesicle production and M2 bias, yielding sEVs exhibited regeneration potentials. This work establishes a programmable acoustic-piezoelectric strategy to scale macrophage sEV production while tailoring their therapeutic potency.

bioengineering↗

bioRxiv2025

Coordinated overexpression of miR398 and miR408 confers broad-spectrum abiotic stress tolerance in melon.

MicroRNAs (miRNAs) in general and miR398 and miR408 in particular, have emerged as key regulators of plant adaptation to individual stress, yet their roles regulating the crop response to diverse unfavorable environments remain poorly explored. Here, we present the first melon (Cucumis melo) plants overexpressing miR398 and miR408 precursors, two conserved miRNAs involved in the regulation of cooper (Cu) homeostasis and associated with stress-response. Engineered plants exhibited enhanced vegetative development, including stem elongation, internode formation, root architecture, and leaf production. The significant increased accumulation of well-processed miR398 and miR408, along with the downregulation of their respective targets (Copper/Zinc Superoxide Dismutase and Basic Blue Protein) demonstrating the functional activity of the transgenes. Sequencing analysis revealed positive correlation in accumulation of miR398 and miR408, suggesting a previously undescribed form of coordinated miRNA regulation, potentially independent of conventional transcription factor activity. Transgenic plants showed improved tolerance to drought, salinity, heat, and cold stress, validating the role of miR398 and miR408 as master regulators of abiotic stress resilience in melon. This work highlights the potential of biotechnological strategies based on engineering Cu-related miRNAs to enhance crop performance under different adverse environments, thereby contributing to agricultural sustainability in the face of climate change.

plant biology↗

bioRxiv2025

Chlorpyrifos and tamoxifen co-pretreatment promotes stem-like phenotype and upregulation of anti-estrogen therapy resistance markers in ERα breast cancer cells

Endocrine therapy (ET) is the standard first-line treatment for hormone receptor positive breast cancer but about 30% of patients develop resistance. Chlorpyrifos (CPF), is an endocrine disruptor pesticide that promotes a stemness phenotype and triggers molecular mechanisms involved in ET resistance. The goal of this study is to assess whether CPF induces tamoxifen (TAM) resistance by modulating estrogen receptor alpha (RE) expression through histone deacetylase 1 (HDAC1) regulation. We analyzed public databases of breast cancer patients and performed in vitro experiments using the MCF-7 cell line. We evaluated whether the co-pretreatment with CPF and TAM (CPF+TAM) modulates stemness and ET resistance markers. We found that CPF+TAM selects cells that exhibit increased clonogenicity, enhanced mammosphere-forming ability, and upregulates the stemness markers CD44, NANOG and POU5F1 while decreasing CD24. This selected cell subpopulation shows higher levels of mRNA and elevated protein expression of RE and HDAC1. Finally, we identified a resistance and stemness marker signature induced by CPF+TAM that closely resembles the profile observed in the dataset of patients who acquired tamoxifen resistance. Our findings show that CPF promotes an undifferentiated basal-like cell phenotype that contributes to TAM resistance, reinforcing the need for global restrictions to safeguard public health.

cancer biology↗

bioRxiv2025

Epigenetic Subtypes of High-Grade T1 Bladder Cancer Reveal Intra-Tumor Heterogeneity and Distinct Interactions with Tumor Microenvironment.

High-Grade T1 (HGT1) Non-Muscle Invasive Bladder Cancer (NMIBC) is a clinically heterogeneous disease, characterized by unpredictable treatment responses and limited tools for recurrence prediction. Although molecular classification efforts have been made, patient stratification still primarily relies on clinicopathological features, which offer limited clinical precision. In this study, we integrated chromatin profiling in bulk with single-nuclei(sn) RNA-seq, immunohistochemistry and spatial transcriptomics to define epigenetic subtypes of HGT1, characterize their heterogeneity, and investigate tumor-microenvironment interactions. Our findings reveal distinct chromatin profiles differentiating urothelial (URO) and micropapillary (MP) histological variants of high-risk HGT1. We identified three epigenetic states: two within the URO group, luminal-like inflammatory (LLI) and basal-like (BL), and a separate signature unique to MP tumors. Single-cell and spatial resolution approaches validated intratumoral heterogeneity and provided insight into subtype-specific microenvironmental contexts. Notably, [~]40% of URO tumors exhibited spatially distinct coexisting LLI and BL components. BL regions showed enrichment for angiogenesis and hypoxia pathways and were preferentially located near vascular stroma, while LLI regions showed to be located at the core of the tumor. MP tumors featured a markedly different microenvironment, characterized by diverse populations of cancer-associated fibroblasts (CAFs) and M2-polarized macrophages intermingled with tumor cells, suggesting a more immunosuppressive niche which could account for their worse clinical outcome. URO tumors, by comparison, showed a more immune-excluded phenotype. These findings provide a detailed molecular and spatial map of bladder cancer heterogeneity, highlighting how distinct epigenetic subtypes and histological variants are associated with tumor architecture and microenvironmental interactions. Our data underscore the need for subtype-specific therapeutic strategies to more effectively address the complexity already existing at HGT1 bladder cancer.

cancer biology↗

bioRxiv2024

Hydrocarbon effects on cell survival and antioxidant system of breast tumorigenic and non-tumorigenic cells.

Over the last decades, environmental pollution with polycyclic aromatic hydrocarbons (PAH) has risen due to human development and industrial activities. The consequences of potential contamination with oil or any of its components must be evaluated. Here, we faced the effects on cell growth and detoxification that might arise from the exposure to hydrocarbons sourced from contaminated waters. MCF-7 and MDA-MB-231 human breast cancer cells and/or MCF-10A epithelial non-tumorigenic cells were exposed to water-accommodated oil fraction (WAF) or anthracene as a PAH currently found in the environment to evaluate clonogenicity, viability, GST and CAT activities. WAF decreased MDA-MB-231 cells clonogenicity and MDA-MB-231 and MCF-7 cells viability. Anthracene significantly reduced non-tumorigenic cells viability and clonogenicity, without affecting the survival of tumorigenic cells. Both tumorigenic cells responded mainly by activating the antioxidant system through the increment of CAT when exposed to low concentrations of WAF. In both cell lines, WAF also increased GST. Anthracene exposure significantly decreased CAT activity of the three cell lines evaluated. GST activity decreased 38% after 28 {micro}M anthracene exposure in MDA-MB-231 cells (p<0.05) and 15, 17 and 21% after 7 (p<0.05), 14 and 28 {micro}M (p<0.01) in MCF-10A cells, while in MCF-7 cells 28 {micro}M anthracene increased GST activity by 75% (p<0.001). We conclude that the sensitivity of cells to the different contaminants evaluated is affected by the degree of cellular tumorigenicity and exposure to WAF or anthracene may exacerbate malignant conditions. The integration of multiple parameters, analyzed through multivariate methods, offers a comprehensive evaluation of toxicant effects. HIGHLIGHTSO_LIWAF and anthracene affect tumorigenic mammary cells viability and clonogenicity C_LIO_LINon tumorigenic mammary cells show more sensitivity to anthracene exposure C_LIO_LIWAF activates antioxidant and detoxicant system in tumorigenic mammary cells C_LIO_LIAnthracene decreased CAT activity of tumorigenic and non-tumorigenic mammary cells C_LIO_LIAnthracene affected GST activity of tumorigenic and non-tumorigenic mammary cells C_LI

cell biology↗

bioRxiv2024

Chlorpyrifos induces lung metastases and modulation of cancer stem cell markers in triple negative breast cancer model

Breast cancer is a major public health problem, and distant metastases are the main cause of morbidity and mortality. Chlorpyrifos is an organophosphate that promotes Epithelial-Mesenchymal Transition-like phenotype in breast cancer cell lines and modulates the Breast Cancer Stem Cells activating two key processes related to the metastatic cascade. Here, we investigated whether Chlorpyrifos may induce distant metastases in an in vivo triple negative tumor model. Also, we studied the expression of Breast Cancer Stem Cell and Epithelial-Mesenchymal Transition activation-markers in Triple Negative Breast Cancer mice tumors and human cells. We demonstrate that Chlorpyrifos modulates stem cell plasticity as a function of growth conditions in monolayer or three-dimensional culture. Furthermore, Chlorpyrifos decreased the doubling period, increased tumor volume, stimulated the infiltration of adjacent muscle fibers and induced lung metastases in mice. Finally, Chlorpyrifos modulated the expression of Epithelial-Mesenchymal Transition and BCSC markers in mice exposed to the pesticide. All our findings confirm that Chlorpyrifos promotes breast cancer progression, enhances stemness and Epithelial-Mesenchymal Transition marker expression and generates lung metastases in an in vivo model induced in mice.

cancer biology↗

bioRxiv2024

The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicenter prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n=24), moderate (n=51), and severe/critical (n=31). Faecal and nasopharyngeal samples were taken, and the microbiota was analyzed. Linear discriminant analysis identified M. salivarium, P. dentalis, and H. parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while P. bivia and P. timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.

microbiology↗

bioRxiv2023

Probabilistic Coverage of the Frontal Aslant Tract in Young Adults: Insights into Individual Variability, Lateralization, and Language Functions

The frontal aslant tract (FAT) is a crucial neural pathway of language and speech, but little is known about its connectivity and segmentation differences across populations. In this study, we utilized diffusion MRI automatic tractography to investigate the probabilistic coverage of the FAT in a large sample of 1065 young adults. Our primary goal was to reveal individual variability and lateralization of FAT and its structure-function correlations in language processing. Our results showed that the left anterior FAT exhibited the most substantial individual differences, particularly in the superior and middle frontal gyrus, with greater variability in the superior than the inferior region. Furthermore, we found significant left lateralization in FAT, with a greater difference in innervation coverage in the inferior and posterior portions. Additionally, our analysis revealed a significant correlation between the size of left FAT inferior innervation areas and Picture Vocabulary function, highlighting the structural and functional importance of the left FAT in language processing. In comparison, the anisotropy of FAT did not show significant correlation. Overall, our study provides valuable insights into individual and population differences in FAT connectivity and segmentation and sheds light on its critical role in language functions.

neuroscience↗

bioRxiv2023

Repeated Plasmodium vivax blood stage infection provides sterile protection against homologous challenge in non-human primates

The malaria parasite Plasmodium vivax remains a major global public health challenge, causing major morbidity across tropical and subtropical regions. Several candidate vaccines are in preclinical and clinical trials, however no vaccine against P. vivax malaria is approved for use in humans. Here we assessed whether P. vivax strain-transcendent immunity can be achieved by repeated infection in Aotus monkeys. For this purpose, we repeatedly infected six animals with blood stages of the P. vivax Salvador 1 (SAL-1) strain until sterile immune, and then challenged with the AMRU-1 strain. Sterile immunity was achieved in 4/4 Aotus monkeys after two homologous infections with the SAL-1 strain, while partial protection against a heterologous AMRU-1 challenge (i.e., delay to infection and reduction in peak parasitemia compared to control) was achieved in 3/3 monkeys. IgG levels based on P. vivax lysate ELISA and protein microarray increased with repeated infections and correlated with the level of homologous protection. Analysis of parasite transcriptional profiles across inoculation levels provided no evidence of major antigenic switching upon homologous or heterologous challenge. In contrast, we observed significant transcriptional differences in the P. vivax core gene repertoire between SAL-1 and AMRU-1. Together with the strain-specific genetic diversity between SAL-1 and AMRU-1 these data suggest that the partial protection upon heterologous challenge is due to molecular differences between strains (at genome and transcriptome level) rather than immune evasion by antigenic switching. Our study demonstrates that sterile immunity against P. vivax can be achieved by repeated homologous blood stage infection in Aotus monkeys, thus providing a benchmark to test the efficacy of candidate blood stage P. vivax malaria vaccines. Author summaryPlasmodium vivax is the most widespread human malaria parasite. Elimination efforts are complicated due to the peculiar biology of P. vivax including dormant liver forms, cryptic reservoirs in bone marrow and spleen and a large asymptomatic infectious reservoir in affected populations. Currently there is no vaccine against malaria caused by P. vivax. Here we induce sterile immunity by repeated P. vivax infection with the SAL-1 strain in non-human primates. In contrast, heterologous challenge with the AMRU-1 strain only provided partial protection. Antibody levels against a crude antigen and a protein microarray correlated with the level of homologous protection. Parasite transcriptional profiles across inoculation levels failed to show major antigenic switching across SAL-1 infections or upon heterologous challenge, instead suggesting other mechanisms of immune evasion. Our study demonstrates that sterile immunity against P. vivax can be achieved by repeated blood stage infection in Aotus monkeys, thus providing a benchmark to test the efficacy of candidate blood stage P. vivax malaria vaccines.

microbiology↗

bioRxiv2021

Anti-Bat Ultrasound Production in Moths is Globally and Phylogenetically Widespread

Warning signals are well known in the visual system, but rare in other modalities. Some moths produce ultrasonic sounds to warn bats of noxious taste or to mimic unpalatable models. Here we report results from a long-term study across the globe, assaying moth response to playback of bat echolocation. We tested 252 genera, spanning most families of large-bodied moths, and outline anti-bat ultrasound production in 52 genera, with eight new subfamily origins described. Based on acoustic analysis of ultrasonic emissions and palatability experiments with bats, it seems that acoustic warning and mimicry are the raison detre for sound production in most moths. However, some moths use high-density ultrasound capable of jamming bat sonar. In fact, we find preliminary evidence of independent origins of sonar jamming in at least six subfamilies. Palatability data indicates that jamming and warning are not mutually exclusive strategies. To explore the possible organization of anti-bat warning sounds into acoustic mimicry rings, we intensively studied a community of moths in Ecuador and found five distinct acoustic clusters using machine learning algorithms. While these data represent an early understanding of acoustic aposematism and mimicry across this megadiverse insect order, it is likely that ultrasonically-signaling moths comprise one of the largest mimicry complexes on earth.

evolutionary biology↗

bioRxiv2021

Recombinant NAGLU-IGF2 prevents physical and neurological disease and improves survival in Sanfilippo B syndrome

Recombinant human alpha-N-acetylglucosaminidase-insulin-like growth factor-2 (rhNAGLU-IGF2) is an investigational enzyme replacement therapy for Sanfilippo B, a lysosomal storage disease. Because recombinant human NAGLU (rhNAGLU) is poorly mannose 6-phosphorylated, we generated a fusion protein of NAGLU with IGF2 to permit its binding to the cation-independent mannose 6-phosphate receptor. We previously administered rhNAGLU-IGF2 intracerebroventricularly to Sanfilippo B mice, and demonstrated therapeutic restoration of NAGLU, normalization of lysosomal storage, and improvement in markers of neurodegeneration and inflammation. Here, we studied repeated intracerebroventricular rhNAGLU-IGF2 delivery in both murine and canine Sanfilippo B to determine potential effects on their behavioral phenotypes and survival. Treated mice showed improvement in disease markers such as heparan sulfate glycosaminoglycans, beta-hexosaminidase, microglial activation, and lysosomal-associated membrane protein-1. Sanfilippo B mice treated with rhNAGLU-IGF2 displayed partial normalization of their stretch attend postures, a defined fear pose in mice (p<0.001). We found an improved rotarod performance in Sanfilippo B mice treated with rhNAGLU-IGF2 compared to vehicle-treated Sanfilippo B mice (p=0.002). We also found a 61% increase in survival in Sanfilippo B mice treated with rhNAGLU-IGF2 (mean 53w, median 48w) compared to vehicle-treated Sanfilippo B mice (mean 33w, median 37w; p<0.001). In canine Sanfilippo B, we found that rhNAGLU-IGF2 administered into cerebrospinal fluid normalized HS and beta-hexosaminidase activity in gray and white matter brain regions. Proteomic analysis of cerebral cortex showed restoration of protein expression levels in pathways relevant to cognitive, synaptic, and lysosomal functions. These data suggest that treatment with rhNAGLU-IGF2 may improve the phenotype of Sanfilippo B disease.

neuroscience↗