Biology subjects

Flores, J. R.

Publications and source records attributed to Flores, J. R..

7 recordsLinked to original sources

bioRxiv2023

Preliminary cross-sectional investigations into the human glymphatic system using multiple novel non-contrast MRI methods.

We discuss two potential non-invasive MRI methods to cross-sectionally study two distinct facets of the glymphatic system and its association with sleep and aging. We apply diffusion-based intravoxel incoherent motion (IVIM) imaging to evaluate pseudodiffusion coefficient, D*, or cerebrospinal fluid (CSF) movement across large spaces like the subarachnoid space (SAS). We also performed perfusion-based multi-echo, Hadamard encoded multi-delay arterial spin labeling (ASL) to evaluate whole brain cortical cerebral blood flow (CBF) and transendothelial exchange (Tex) of water from the vasculature into the perivascular space and parenchyma. Both methods were used in young adults (N=9, 6F, 23{+/-}3 years old) in the setting of sleep and sleep deprivation. To study aging, 10 older adults, (6F, 67{+/-}3 years old) were imaged after a night of normal sleep only and compared with the young adults. D* in SAS was significantly (p<0.05) lesser after sleep deprivation (0.014{+/-}0.001 mm2/s) than after normal sleep (0.016{+/-}0.001 mm2/s), but was unchanged with aging. Cortical CBF and Tex on the other hand, were unchanged after sleep deprivation but were significantly lower in older adults (37{+/-}3 ml/100g/min, 476{+/-}66 ms) than young adults (42{+/-}2 ml/100g/min, 624{+/-}66 ms). IVIM was thus, sensitive to sleep physiology and multi-echo, multi-delay ASL was sensitive to aging.

neuroscience↗

bioRxiv2021

Intermediary role of lung alveolar type 1 cells in epithelial repair upon Sendai virus infection

The lung epithelium forms the first barrier against respiratory pathogens and noxious chemicals; however, little is known about how >90% of this barrier - made of alveolar type 1 (AT1) cells - responds to injury, in contrast to our accumulating knowledge of epithelial progenitor and stem cells whose importance lies in their ability to restore the barrier. Using Sendai virus to model natural infection in mice, we combine 3D imaging, lineage-tracing, and single-cell genomics to show that AT1 cells have an intermediary role by persisting in areas depleted of alveolar type 2 (AT2) cells, mounting an interferon response, and receding from invading airway cells. Sendai virus infection mobilizes airway cells to form alveolar SOX2+ clusters without differentiating into AT1 or AT2 cells, as shown in influenza models. Intriguingly, large AT2-cell-depleted areas remain covered by AT1 cells, which we name "AT2-less regions", and are replaced by SOX2+ clusters spreading both basally and luminally around AT1 cell extensions. AT2 cell proliferation and differentiation are largely confined to topologically distal regions - the end of airspace that could be in the periphery or middle of the lung - and form de novo alveolar surface, with limited contribution to in situ repair of AT2-less regions. Time course single-cell RNA-seq and AT1-cell interactome analyses suggest enhanced recognition of AT1 cells by immune cells and altered growth signals. Our comprehensive spatiotemporal and genome-wide study highlights the hitherto unappreciated role of AT1 cells during Sendai virus infection and possibly other injury-repair processes.

developmental biology↗

bioRxiv2021

Living apart if you can - how genetically and developmentally controlled sex has shaped the evolution of liverworts

Sexual differentiation in bryophytes occurs in the dominant gametophytic generation. Over half of bryophytes are dioicous, and this pattern in liverworts is even more profound as over 70% of species are dioicous. However, the evolutionary mechanisms leading to the prevalence of dioicy and the shifts of sexual systems between dioicy and monoicy have remained poorly known. These essential factors in reproductive biology are explored here in light of phylogenetics combined with evidence of genomic characterization of sex chromosomes and sex-determination, as well as cytology. Our analyses and discussions on liverworts are focused on: (1) ancestry and shifts in sexuality, (2) evolution of sex chromosomes and maintenance of haploid dioicy, and (3) environmental impact on the evolution of monoicism. We show that the dioicous condition is ancestral in liverworts, and the evolution of sexual systems is both conserved and stable with an ancient origin, but also highly dynamic in certain more recently diverged lineages. We assume that the haploid dioicy maintained in the course of evolution must be linked to the genetically controlled sex-determination, and transition from genetically to developmentally controlled sex determination, the evolution of monoicism, is driven by ephemeral and unstable environments. Monoicy is less stable in the long-term than dioicy, and thus, ultimately, dioicy is selected in liverworts. It is concluded that sexual dimorphism is maintained through a highly dynamic evolutionary process, sex chromosomes bearing distinct set of evolutionary forces that can have large impacts on genome evolution and may also promote speciation.

evolutionary biology↗

bioRxiv2020

Immune modulation to improve survival of respiratory virus infections in mice

Viral pneumonia remains a global health threat requiring novel treatment strategies, as strikingly exemplified in the SARS-CoV-2 pandemic of 2019-2020. We have reported that mice treated with a combination of inhaled Toll-like receptor (TLR) 2/6 and TLR 9 agonists (Pam2-ODN) to stimulate innate immunity are broadly protected against respiratory pathogens, but the mechanisms underlying this protection remain incompletely elucidated. Here, we show in a lethal paramyxovirus model that Pam2-ODN-enhanced survival is associated with robust virus inactivation by reactive oxygen species (ROS), which occurs prior to internalization by lung epithelial cells. However, we also found that mortality in sham-treated mice temporally corresponded with CD8+ T cell-enriched lung inflammation that peaks on days 11-12 after viral challenge, when the viral burden has waned to a scarcely detectable level. Pam2-ODN treatment blocked this injurious inflammation by reducing the viral burden, and alternatively, depleting CD8+ T cells 8 days after viral challenge also decreased mortality. These findings reveal opportunities for targeted immunomodulation to protect susceptible individuals against the morbidity and mortality of respiratory viral infections.

immunology↗

bioRxiv2020

Rooting morphologically divergent taxa - slow-evolving sequence data might help

When fossils are sparse and the lineages studied are very divergent morphologically, analyses based exclusively on morphology may lead to conflicting and unexpected hypotheses. Through integration of data from conservative genes/gene regions the terminals including these data can anchor or constrain the search, thereby practically circumscribing the search space of the combined analyses. In this study, we revisit the phylogeny of a highly divergent group of mosses, class Polytrichopsida. We supplemented the morphological matrix by adding sequence data of the nuclear gene 18S, chloroplast genes rbcL and rps4, plus the mitochondrial gene nad5. For the phylogenetic analyses we used parsimony as the optimality criterion. Analyses that included all the terminals resulted in one most parsimonious tree with a clade comprised of Alophosia azorica and the fossil Meantoinea alophosioides representing the basal-most lineage. Analyses with different outgroup sampling produced the same topology for most ingroup relationships. An analysis excluding morphological characters and the four terminals for which only morphological characters were scored (the two fossil and two extant terminals) resulted in one optimal tree with identical topology to the one obtained when including all terminals. These results are largely congruent with those obtained in the recent analyses based exclusively on sequence level data of a larger number of terminals. Our results indicate that large size and complexity of the gametophyte have evolved independently in several lineages. Notably, the nodes of the backbone of the most parsimonious tree have very low support values, thus these inferred relationships could change if new additional information conflicts with the current data. Future studies should be aimed at incorporating all terminals into phylogenetic analyses, which is not an unrealistic goal for a group with less than 200 species. Also, additional fossils, some of which await detailed examination and description, need to be included. Whether these will affect the overall pattern of phylogeny presented here remains to be seen. In a group that is obviously very ancient, we cannot assume, a priori, that currently known fossil taxa, which go back in time less than 140 Ma, represent the oldest lineages of the group.

evolutionary biology↗

bioRxiv2020

Inducible epithelial resistance improves survival of Sendai virus pneumonia in mice by both inactivating virus and preventing CD8+ T cell-mediated immunopathology

Viral pneumonias remain a global health threat necessitating novel strategies to prevent and treat these lower respiratory tract infections. We have reported that mice treated with a combination of inhaled Toll-like receptor (TLR) 2/6 and TLR 9 agonists (Pam2-ODN) are broadly protected against respiratory pathogens. Although a single inhalation of Pam-ODN prevents acute morbidity and chronic complications associated with viral pneumonias, the mechanisms underlying this protection remain incompletely elucidated. Here, we show in a lethal paramyxovirus model that Pam2-ODN-enhanced survival is associated with robust virus inactivation that occurs prior to internalization by lung epithelial cells. However, it was also noted that viral mortality in sham-treated mice temporally corresponded with CD8+ T cell-enriched lung inflammation that peaks after the viral burden wanes. Pam2-ODN treatment also blocked this injurious inflammation, but the attenuation of lymphocytic inflammation and the reduction in virus burden were both lost when inducible reactive oxygen species generation was inhibited. Depleting CD8+ T cells before or after viral challenge underscored the balanced roles of CD8+ T cells in antiviral immunity and fatal immunopathology, but did not obviate the Pam2-ODN antiviral protection. These findings identify multifunctional inducible antiviral mechanisms and may reveal means to protect susceptible individuals against respiratory infections.

immunology↗

bioRxiv2019

Aerosolized TLR Agonists Suppress Acute Sendai Virus Lung Infection and Chronic Airway Disease in Mice

Respiratory viral infections play central roles in the initiation, exacerbation and progression of asthma in humans. An acute paramyxoviral infection in mice can cause a chronic lung disease that resembles human asthma. We sought to determine whether reduction of Sendai virus lung burden in mice by stimulating innate immunity with aerosolized Toll-like receptor (TLR) agonists could attenuate the severity of chronic asthma-like lung disease. Treatment with 1 {micro}M oligodeoxynucleotide (ODN) M362, an agonist of the TLR9 homodimer, and 4 {micro}M Pam2CSK4 (Pam2), an agonist of the TLR2/6 heterodimer, within a few days before or after Sendai virus challenge, resulted in a [~]75% reduction in lung Sendai virus burden five days after challenge. The reduction in acute lung virus burden was associated with marked reductions 49 days after viral challenge in eosinophilic and lymphocytic lung inflammation, airway mucous metaplasia, lumenal mucus occlusion, and hyperresponsiveness to methacholine. Mechanistically, ODN/Pam2 treatment attenuated the chronic asthma phenotype by suppressing IL-33 production by type 2 pneumocytes, both by reducing the severity of acute infection and by downregulating Type 2 (allergic) inflammation. These data suggest that treatment of susceptible human hosts with aerosolized ODN and Pam2 at the time of a respiratory viral infection might attenuate the severity of the acute infection and reduce progression of asthma.\n\nOne Sentence SummaryRespiratory viral infections can induce chronic airway disease, and we find that stimulating innate immunity within the lungs of mice reduces the severity of acute infection and development of a chronic asthma phenotype.

immunology↗