Biology subjects

Ortiz, L.

Publications and source records attributed to Ortiz, L..

9 recordsLinked to original sources

bioRxiv2026

Viral dispersal drives changes in population composition

In an acute viral infection, a small seeding population expands rapidly over several orders of magnitude, then declines. This vast population growth is accompanied by spatial expansion as infection spreads to new anatomical sites within the host. Evolutionary theory predicts that spatially expanding populations experience more extreme stochastic losses of genetic diversity than spatially unstructured populations. To test this prediction in the context of viral dynamics, we evaluated the impact of spatial expansion on viral population genetic structure and assessed how modulators of viral dispersal affected this structure. To this end, we developed a means of implementing the spatial expansion of influenza A virus in cell culture and applied it to a viral population carrying a diverse genetic barcode. Across this simplified cellular landscape, we found that spatial expansion produces a patchwork of distinct viral subpopulations. We then evaluated the consequences for population structure of two modulators of viral dispersal: extracellular viscosity and a common polymorphism in the viral attachment protein. Both physical constraint and viral phenotype altered the extent of genetic bottlenecking and spatial heterogeneity that developed during expansion, indicating that environmental features and viral traits that modulate dispersal also modulate viral population composition, diversity and evolution.

microbiology↗

bioRxiv2026

Within-host antigenic selection of influenza A virus dominates over stochasticity but is limited by fitness tradeoffs and timing of the immune response

Despite antigenic evolution at the global scale, positive selection of influenza virus antigenic variants is not readily observed within hosts. Here, we tested the extent to which fitness tradeoffs, the timing of immune pressure, and stochastic effects impede antigenic selection within pre-immune hosts. We used genetically barcoded influenza A/Texas/50/2012 (H3N2) viruses (Tx/12) in a guinea pig model to probe these dynamics. Positive selection of an antigenic variant was reliant on a high strength of immune pressure acting early in infection. However, when fitness tradeoffs of the antigenic change were lessened, a lower strength and later introduction of immune pressure favored the antigenic variant. In all conditions, barcode dynamics revealed moderate stochastic effects. Our results suggest that stochastic evolution does not impede selection during acute influenza virus infection. The rarity of antigenic escape may instead stem from low mutational supply, fitness tradeoffs, and the intrinsic delay between infection and antibody recall.

microbiology↗

bioRxiv2026

Aging reveals domain-specific vulnerability to the chronic behavioral consequences of repetitive mild traumatic brain injury

Older adults are among the fastest growing groups of traumatic brain injury (TBI) patients and sustain disproportionately poor chronic outcomes. Despite this, the preclinical aging-TBI literature is limited. Beyond the limited presence of aging TBI studies, most studies published in this domain use moderate-to-severe, open head models of TBI, rather than closed head models of mild TBI (mTBI) and repetitive mTBI (rmTBI), the most clinically prevalent presentation. Whether age modulates the chronic behavioral consequences of rmTBI is unknown. In the current study, young (3-4 months) and aged (18-19 months) male C57BL/6 mice received either five mTBIs on alternating days to model rmTBI or sham procedures and underwent behavioral testing in the chronic phase for spatial memory and anxiety-related behavior. Because cross-age behavioral comparisons are confounded by age-related declines in activity and by large sample sizes necessary to detection interaction effects, we applied a three-tier analytical framework combining within-age comparisons, sham-normalized inter-age comparisons, and factorial two-way ANOVA. Contrary to our hypothesis that aging would worsen rmTBI behavioral deficits, age produced domain-divergent effects. Spatial memory deficits were directionally consistent in both young and aged mice but was attenuated in the aged group. Conversely, anxiety-related behavior emerged selectively in the aged mice showing increased thigmotaxis. Locomotion was driven by age alone, with no injury effect, confirming that the aged anxiety signal was not a locomotor artifact. A post-hoc sensitivity analysis indicated that resolving the Age x Injury interaction effect would require at least 44 animals per group. These findings show that age shapes the affective, but not the cognitive, consequences of chronic rmTBI, and underscoring that statistical strategy is inseparable from design in factorial injury studies.

neuroscience↗

bioRxiv2025

A genetic platform for a biocementation bacterium

Sporosarcina pasteurii is the most widely studied bacterium for microbially-induced calcium carbonate precipitation (MICP), a process of intense interest for materials and construction applications. Despite two decades of investigation, S. pasteurii has remained genetically intractable, limiting our mechanistic understanding of biomineralization pathways and constraining efforts to engineer scalable solutions. Here, we present the first genetic toolkit for S. pasteurii, including a stable replicating plasmid, a conjugation-based DNA delivery protocol, engineered inducible promoters, and methods for genome modification. Using homologous recombination, we precisely deleted 5.7 kb of the genome spanning two operons encoding urease activity and demonstrated complete loss of biocementation. We also screened a library of engineered transposon constructs for activity in S. pasteurii and generated a genome-wide mutant library with >15,000 unique insertion sites. Using this library, we identified putative genes affecting ureolytic growth, revealing previously inaccessible aspects of S. pasteurii genetics. This work establishes S. pasteurii as a genetically tractable platform for rational engineering of MICP and constitutes the first genetic modification capability within the Sporosarcina genus.

synthetic biology↗

bioRxiv2024

Anaerobiosis modulates the performance of antimicrobial resistance genes in Enterobacteriaceae

Bacteria must face and adapt to a variety of physicochemical conditions in the environment and during infection. A key condition is the concentration of dissolved oxygen, proportional to the partial pressure of oxygen (PO2), which is extremely variable among environmental biogeographical areas and also compartments of the human and animal body. Here, we sought to understand if the phenotype of resistance determinants commonly found in Enterobacterales can be influenced by oxygen pressure. To do so, we have compared the MIC in aerobic and anaerobic conditions of isogenic Escherichia coli strains containing 136 different resistance genes against 9 antibiotic families. Our results show a complex landscape of changes in the performance of resistance genes in anaerobiosis. Certain changes are especially relevant for their intensity and the importance of the antibiotic family, like the large decreases in resistance observed against ertapenem and fosfomycin among blaVIM {beta}-lactamases and certain fos genes, respectively; however, the blaOXA-48 {beta}-lactamase from the clinically relevant pOXA-48 plasmid conferred 4-fold higher ertapenem resistance in anaerobiosis. Strong changes in resistance patterns in anaerobiosis were also conserved in Klebsiella pneumoniae. Our results suggest that anaerobiosis is a relevant aspect that can affect the action and selective power of antibiotics for specific AMRs in different environments.

microbiology↗

bioRxiv2022

Independent evolution of influenza A virus H1N1 in pigs in Guatemala

Commercial swine farms provide unique systems for interspecies transmission of influenza A viruses (FLUAVs) at the animal-human interface. Bidirectional transmission of FLUAVs between pigs and humans plays a significant role in the generation of novel strains that become established in the new host population. Active FLUAV surveillance was conducted for two years on a commercial pig farm in Southern Guatemala with no history of FLUAV vaccination. Nasal swabs (n=2,094) from fattening pigs (6 to 24 weeks old) with respiratory signs were collected from May 2016 to February 2018. Swabs were screened for FLUAV by RRT-PCR and full virus genomes of FLUAV-positive swabs were sequenced by next-generation sequencing (NGS). FLUAV prevalence was 12.0% (95% CI: 10.6% - 13.4%) with two distinct periods of high infection. All samples were identified as FLUAVs of the H1N1 subtype within the H1 swine clade 1A.3.3.2 and whose ancestors are the human origin 2009 H1N1 influenza pandemic virus (H1N1 pdm09). Compared to the prototypic reference segment sequence, 10 amino acid signatures were observed on relevant antigenic sites on the hemagglutinin. We also found that Guatemalan swine-origin FLUAVs show independent evolution from other H1N1 pdm09 FLUAVs circulating in Central America. The zoonotic risk of these viruses remains unknown, but strongly calls for continued FLUAV surveillance in pigs in Guatemala. ImportanceDespite increased surveillance efforts, the epidemiology of FLUAVs circulating in swine in Latin America remains understudied. For instance, the 2009 H1N1 influenza pandemic strain (H1N1 pdm09) emerged in Mexico, but its circulation remained undetected in pigs. In Central America, Guatemala is the country with the largest swine industry. We found a unique group of H1N1 pdm09 sequences that suggests independent evolution from similar viruses circulating in Central America. These viruses may represent the establishment of a novel genetic lineage with the potential to reassort with other co-circulating viruses, and whose zoonotic risk remains to be determined.

evolutionary biology↗

bioRxiv2022

Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS2) affected the geriatric population. Among research models, Golden Syrian hamsters (GSH) are one of the most representative to study SARS2 pathogenesis and host responses. However, animal studies that recapitulate the effects of SARS2 in the human geriatric population are lacking. To address this gap, we inoculated 14 months old GSH (resembling people over 60 years old) with a prototypic ancestral strain of SARS2 and studied the effects on virus pathogenesis, virus shedding, and respiratory and gastrointestinal microbiome changes. SARS2 infection led to high vRNA loads in the nasal turbinates (NT), lungs, and trachea as well as higher pulmonary lesions scores later in infection. Dysbiosis throughout SARS2 disease progression was observed in the pulmonary microbial dynamics with the enrichment of opportunistic pathogens (Haemophilus, Fusobacterium, Streptococcus, Campylobacter, and Johnsonella) and microbes associated with inflammation (Prevotella). Changes in the gut microbial community also reflected an increase in multiple genera previously associated with intestinal inflammation and disease (Helicobacter, Mucispirillum, Streptococcus, unclassified Erysipelotrichaceae, and Spirochaetaceae). Influenza A virus (FLUAV) pre-exposure resulted in slightly more pronounced pathology in the NT and lungs early on (3 dpc), and more notable changes in lungs compared to the gut microbiome dynamics. Similarities among aged GSH and the microbiome in critically ill COVID-19 patients, particularly in the lower respiratory tract, suggest that GSHs are a representative model to investigate microbial changes during SARS2 infection. The relationship between the residential microbiome and other confounding factors, such as SARS2 infection, in a widely used animal model, contributes to a better understanding of the complexities associated with the host responses during viral infections. Author SummaryThe SARS-CoV-2 pandemic led to millions of human losses, notably affecting the geriatric population, who are at greater risk of developing acute respiratory distress infection leading to prolonged hospitalization and death. However, the mechanism of age-related pathogenicity is not fully understood. Here, we utilized an aged Syrian hamster model resembling ~60-year-old humans to analyze the pathobiology, host response, and effects of SARS2 on the respiratory and intestinal microbiome. We identified specific microbial markers observed in severe COVID-19 patients within the lungs of aged hamsters infected with SARS-CoV-2. Prior influenza A virus (H1N1) exposure amplified these changes. Similarities among aged GSH and critically ill COVID-19 patients suggest that GSHs are a valuable model for investigating microbial changes during SARS2 infection. The relationship between the age, residential microbiome and viral pathogens contributes to a better understanding of the complexities associated with the host responses during viral infection while limiting potential environmental factors that may contribute to inter-individual variation.

microbiology↗

bioRxiv2020

Editing of the TRIM5 gene decreases the permissiveness of human T lymphocytic cells to HIV-1

TRIM5 is a cytoplasmic antiretroviral effector upregulated by type I interferons (IFN-I). We previously showed that two points mutations, R332G/R335G, in the retroviral capsid-binding region confer human TRIM5 the capacity to target and strongly restrict HIV-1 upon over-expression of the mutated protein. Here, we used CRISPR-Cas9-mediated homology-directed repair (HDR) to introduce these two mutations in the endogenous human TRIM5 gene. We found 6 out of 47 isolated cell clones containing at least one HDR-edited allele. One clone (Clone 6) had both alleles containing R332G but only one of the two alleles containing R335G. Upon challenge with an HIV-1 vector, clone 6 was significantly less permissive compared to unmodified cells, whereas the cell clones with monoallelic modifications were only slightly less permissive. Following IFN-{beta} treatment, inhibition of HIV-1 infection in clone 6 was significantly enhanced (~40-fold inhibition). TRIM5 knockdown confirmed that HIV-1 was inhibited by the edited TRIM5 gene products. Quantification of HIV-1 reverse transcription products showed that inhibition occurred through the expected mechanism. In conclusion, we demonstrate the feasibility of potently inhibiting a viral infection through editing of innate effector genes. Our results also emphasize the importance of biallelic modification in order to reach significant levels of inhibition by TRIM5.

microbiology↗

bioRxiv2018

Real Time PCR for the Evaluation of Treatment Response in Clinical Trials of Adult Chronic Chagas Disease: Usefulness of Serial Blood Sampling and qPCR Replicates.

This work evaluated a serial blood sampling procedure to enhance the sensitivity of duplex real time PCR (qPCR) for baseline detection and quantification of parasitic loads and post-treatment identification of failure in the context of clinical trials for treatment of chronic Chagas disease, namely DNDi-CH-E1224-001 (NCT01489228) and MSF-DNDi PCR sampling optimization study (NCT01678599). Patients from Cochabamba (N= 294), Tarija (N = 257), and Aiquile (N= 220) were enrolled. Three serial blood samples were collected at each time-point, and qPCR triplicates were tested per sample. The first two samples were collected during the same day and the third one seven days later.\n\nA patient was considered PCR positive if at least one qPCR replicate was detectable. Cumulative results of multiple samples and qPCR replicates enhanced the proportion of pre-treatment sample positivity from 54.8 to 76.2%, 59.5 to 77.8%, and 73.5 to 90.2% in Cochabamba, Tarija, and Aiquile cohorts, respectively and increased cumulative detection of treatment failure from 72.9 to 91.7%, 77.8 to 88.9%, and 42.9 to 69.1% for E1224 low, short, and high dosage regimes, respectively; and from 4.6 to 15.9% and 9.5 to 32.1% for the benznidazole (BZN) arm in the DNDi-CH-E1224-001 and MSF-DNDi studies, respectively. The monitoring of patients treated with placebo in the DNDi-CH-E1224-001 trial revealed fluctuations in parasitic loads and occasional non-detectable results. This serial sampling strategy enhanced PCR sensitivity to detecting treatment failure during follow-up and has the potential for improving recruitment capacity in Chagas disease trials which require an initial positive qPCR result for patient admission.

microbiology↗