Biology subjects

Bailey, B.

Publications and source records attributed to Bailey, B..

10 recordsLinked to original sources

bioRxiv2026

Loss of Farnesoid X Receptor Signaling Promotes Choroidal Neovascularization in Mice

Choroidal neovascularization (CNV) is a defining feature of neovascular age-related macular degeneration (nAMD). Although anti-vascular endothelial growth factor (VEGF) therapies suppress neovascular activity, incomplete responses, recurrent leakage, and subretinal fibrosis remain important clinical challenges. The farnesoid X receptor (FXR) is a bile acid-activated nuclear receptor with anti-inflammatory, anti-fibrotic, and anti-angiogenic functions in other tissues, but its role in CNV is unknown. Analysis of publicly available human transcriptomic data (GSE135092) showed FXR expression in the retinal pigment epithelium (RPE)/choroid and significant downregulation in AMD-affected macular RPE/choroid. To define the role of FXR in CNV, laser photocoagulation was performed in wild-type (WT) and FXR-deficient (FXR-KO) mice, with disease progression assessed by in vivo imaging, histology, ex vivo choroidal sprouting, and endothelial cell assays. FXR expression in the RPE/choroid was reduced 14 days after laser injury. Compared with WT mice, FXR-KO mice developed larger CNV lesions, more extensive hyperfluorescence on fluorescein angiography, and increased lesion area during disease progression. FXR deficiency also impaired resolution of fibrotic remodeling. In WT mice, alpha-SMA peaked at day 14 and declined by day 21, whereas collagen I remained low throughout; in FXR-KO mice, both collagen I and alpha-SMA were significantly elevated relative to WT and remained significantly higher than WT at day 21. Consistent with these findings, FXR-deficient choroidal explants exhibited increased vascular sprouting, and FXR-KO endothelial cells formed more extensive capillary-like networks. Together, these findings identify FXR as an endogenous regulator of pathological angiogenesis, vascular leakage, mesenchymal activation, and fibrotic remodeling during CNV and provide a rationale for investigating FXR-directed strategies for nAMD.

biochemistry↗

bioRxiv2026

Vape Aerosol Exposure Decreases Voluntary Exercise in Mice

Electronic cigarette use (vaping) is generally accepted as a less harmful alternative to traditional cigarette smoking. However, so called "never smokers" including young adults and teenagers are often recruited through targeted advertising and appealing vape juice flavors. Any fitness cost of vaping matters for young people who exercise or play sports. We therefore tracked running distance in a mouse model of voluntary exercise to assess the effect of vaping. Specifically, we asked whether vaping decreases exercise performance, and whether there is progressive change over time. Experimental groups of mice subjected to whole-body inhalation exposure and corresponding non-exposed controls were housed in cages with running wheels. Daily wheel laps were recorded over the 8-week exposure period and analyzed using hierarchical generalized additive mixed models. Vape-exposed females ran 32% fewer laps than control females. Vape-exposed males showed a smaller reduction of 15% that did not reach statistical significance. The reduction was 10,025 laps per day larger in females than in males (p = 0.02). In females, the difference was present from the first weeks of exposure and was larger by the end of the study. The results demonstrate that vape exposure is associated with reduced voluntary aerobic activity. The analysis illustrates how nonlinear longitudinal modeling clarifies both the size and the temporal character of treatment effect in this experimental model. These findings reveal that nicotine-free components of vape aerosol reduce voluntary aerobic activity, highlighting an overlooked facet of vaping toxicity research which is particularly relevant for young and physically active users.

pharmacology and toxicology↗

bioRxiv2025

CYP46A1 Activation Improves Retinal Neovascularization in a Mouse Model of Retinopathy of Prematurity

Previous studies have shown the metabolic and regulatory significance of CYP46A1 in the adult retina; however, its role in the developing retina is unknown. Here, we evaluate CYP46A1 expression and the impact of its activation in the developing mouse retina under normal and pathological conditions. Seven-day-old (P7) C57BL/6J mice maintained in room air (controls) or subjected to oxygen-induced retinopathy (OIR) were treated with/without 20 mg/kg efavirenz (EFV), a CYP46A1 activator administered intraperitoneally from P7 to P17. Retinal cross sections and flat mounts were prepared to study retinal vasculature morphology, Muller and microglia activation, and ganglion cell viability. EFV treatment significantly reduced pathological neovascularization and the size of avascular and hypoxic areas in OIR mice retinas. EFV treatment additionally limited reactive gliosis and microglia activation and improved retinal ganglion cell survival in OIR mice. The current study demonstrates the developmental regulation of CYP46A1 and the dysregulated expression and levels of the downstream metabolite 24-Hydroxycholesterol (24HC) in OIR mice. The study further suggests that pharmacological CYP46A1 activation may improve key pathological features associated with pathological neovascularization in OIR mice.

biochemistry↗

bioRxiv2024

Chromatin architecture mapping by multiplex proximity tagging

Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method - Proximity Copy Paste (PCP) - we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. By analyzing nucleosome positions and spacing on single molecule fibers, we show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. Basic features of nucleosome arrays are generally explained by gene size and transcription. PCP can also map long-range, multi-way interactions and we provide the first direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that non-canonical nucleosomes, notably Overlapping-Di-Nucleosomes (OLDN) are a stable feature of chromatin. PCP is a versatile method allowing the detection of the connectivity of individual molecules locally and over large distance to be mapped at high-resolution in a single experiment.

molecular biology↗

bioRxiv2024

Cardiac p16 Expression Following Vape Exposure with Nicotine Shows Sex-Specific Induction in Males but not Females

Vaping is marketed as a safe alternative to traditional cigarette smoking, but multiple studies demonstrate deleterious cardiopulmonary effects including cardiac function decline and fibrotic remodeling with alveolar size enlargement. Nicotine, a common constituent of vaping aerosol, stimulates p16 expression in pulmonary tissue but the impact on cardiac tissue remains unclear. In this study, mice were exposed to e-cigarette vape aerosol either containing nicotine (Vape Nicotine; VN) or without nicotine (Vape 0; V0). Non-exposed (No Vape; NoV) mice were used as controls. Cardiac effects were assessed by echocardiography, histology, and immunofluorescence to determine changes in function, morphology, p16, and Discoidin Domain Receptor 2 (DDR2). VN depressed cardiac function and increased collagen deposition relative to V0 and NoV. Interestingly, p16 expression was increased in cardiomyocytes and interstitial cells of male mice while remaining unchanged in females. In contrast to VN, V0 had no significant impact on cardiac function or p16 expression in males. Furthermore, collagen deposition in the V0 group was significantly lower than the VN group. Subsequent cardiac fibroblast analysis using DDR2 revealed increased expression within the V0 group relative to VN and NoV. Collectively, these findings show collagen accumulation as well as p16 expression prompted by vaping is mediated by nicotine as a constituent of vape juice. In contrast, vape aerosol alone promotes accrual of cardiac fibroblasts without concomitant changes in collagen accumulation or p16 expression. These results are the first to identify p16 induction with pathologic collagen deposition by exposure to vape aerosol containing nicotine in male cardiac tissue. The underlying basis for sex-specific differences in cardiac responses to vape aerosol exposure warrant further investigation, particularly those involving cellular and molecular changes that may lead to pathologic changes later in life.

molecular biology↗

bioRxiv2024

Myocardial infarction injury is exacerbated by nicotine in vape aerosol exposure

RationaleVaping is touted as a safer alternative to traditional cigarette smoking but the full spectrum of harm reduction versus comparable risk remains unresolved. Elevated bioavailability of nicotine in vape aerosol together with known risks of nicotine exposure may result in previously uncharacterized cardiovascular consequences of vaping. ObjectiveAssess the impact of nicotine exposure via vape aerosol inhalation upon myocardial response to infarction injury. Methods and ResultsFlavored vape juice containing nicotine (5 mg / ml) or vehicle alone (0 mg) was delivered using identical 4-week treatment protocols. Mice were subjected to acute myocardial infarction injury and evaluated for outcomes of cardiac structure and function. Findings reveal that nicotine exposure leads to worse outcomes with respect to contractile performance regardless of sex. Non-myocyte interstitial cell accumulation following infarction significantly increased with exposure to vape aerosol alone, but a comparable increase was not present when nicotine was included. ConclusionsMyocardial function after infarction is significantly decreased after exposure to nicotine vape aerosol irrespective of sex. Comparable loss of contractile function was not observed in mice exposed to vape aerosol alone, highlighting the essential role of nicotine in loss of contractile function. Increased vimentin immunoreactivity was observed in the vape alone group compared to control and vape nicotine. The correlation between vaping, interstitial cell responses, and cardiac remodeling leading to impaired contractility warrants further investigation. Public health experts seeking to reduce vaping-related health risks should consider messaging that highlights the increased cardiovascular risk especially with nicotine-containing aerosols.

molecular biology↗

bioRxiv2020

Phage and bacteria diversification through a prophage acquisition ratchet

Lysogeny is prevalent in the microbial-dense mammalian gut. This contrasts the classical view of lysogeny as a refuge used by phages under poor host growth conditions. Here we hypothesize that as carrying capacity increases, lysogens escape phage top-down control through superinfection exclusion, overcoming the canonical trade-off between competition and resistance. This hypothesis was tested by developing an ecological model that combined lytic and lysogenic communities and a diversification model that estimated the accumulation of prophages in bacterial genomes. The ecological model sampled phage-bacteria traits stochastically for communities ranging from 1 to 1000 phage-bacteria pairs, and it included a fraction of escaping lysogens proportional to the increase in carrying capacity. The diversification model introduced new prophages at each diversification step and estimated the distribution of prophages per bacteria using combinatorics. The ecological model recovered the range of abundances and sublinear relationship between phage and bacteria observed across eleven ecosystems. The diversification model predicted an increase in the number of prophages per genome as bacterial abundances increased, in agreement with the distribution of prophages on 833 genomes from marine and human-associated bacteria. The study of lysogeny presented here offers a framework to interpret viral and microbial abundances and reconciles the Kill-the-Winner and Piggyback-the-Winner paradigms in viral ecology.

ecology↗

bioRxiv2018

Biophysical and physiological causes of coral reef microbialization

Coral reefs are declining globally as their primary producer communities shift from stony coral to fleshy macroalgae dominance. Previously, we have shown that the rise of fleshy macroalgae produces dissolved organic carbon (DOC) that lead to microbialization and coral death. Here we test the hypothesis that the biophysical cause of bacterial biomass accumulation is a relative decrease in electron acceptors relative to electron donors due to O2 loss from macroalgae. We show that 37 % of photosynthetic O2 produced by reef fleshy macroalgae is lost in the form of gas through ebullition from algae surfaces. O2 loss increases DOC:O2 ratios, decoupling the photosynthetically fixed carbon from oxidative potential for respiration. This biogeochemical environment drives heterotrophic microbes to increase cell-specific DOC consumption and cell sizes, accumulating biomass. In contrast, corals do not lose oxygen and support the growth of smaller and fewer bacteria. In situ biomass and metagenomic analyses of 87 reefs across the Pacific and Caribbean show that on algae-dominated reefs bacteria accumulate organic carbon through a Warburg-like increase in aerobic glycolytic metabolism. Because of its biophysical basis, microbialization is predicted to occur in other marine ecosystems shifting primary producer assemblages, such as planktonic communities in warming and acidifying conditions.

ecology↗

bioRxiv2018

Relevance of coral geometry in the outcomes of the coral-algal benthic war

Corals have built reefs on the benthos for millennia, becoming an essential element in marine ecosystems. Climate change and human impact, however, are favoring the invasion of non-calcifying benthic algae and reducing coral coverage. Corals rely on energy derived from photosynthesis and heterotrophic feeding, which depends on their surface area, to defend their outer perimeter. But the relation between geometric properties of corals and the outcome of competitive coral-algal interactions is not well known. To address this, 50 coral colonies interacting with algae were sampled in the Caribbean island of Curacao. 3D and 2D digital models of corals were reconstructed to measure their surface area, perimeter, and polyp sizes. A box counting algorithm was applied to calculate their fractal dimension. The perimeter and surface dimensions were statistically non-fractal, but differences in the mean surface fractal dimension captured relevant features in the structure of corals. The mean fractal dimension and surface area were negatively correlated with the percentage of losing perimeter and positively correlated with the percentage of winning perimeter. The combination of coral perimeter, mean surface fractal dimension, and coral species explained 19% of the variability of losing regions, while the surface area, perimeter, and perimeter-to-surface area ratio explained 27% of the variability of winning regions. Corals with surface fractal dimensions smaller than two and small perimeters displayed the highest percentage of losing perimeter, while corals with large surface areas and low perimeter-to-surface ratios displayed the largest percentage of winning perimeter. This study confirms the importance of fractal surface dimension, surface area, and perimeter of corals in coral-algal interactions. In combination with non-geometrical measurements such as microbial composition, this approach could facilitate environmental conservation and restoration efforts on coral reefs.

ecology↗

bioRxiv2017

Prophage genomics reveals patterns in phage genome organization and replication

Temperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the hosts genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution.

biochemistry↗