Biology subjects

Phillips, J. A.

Publications and source records attributed to Phillips, J. A..

7 recordsLinked to original sources

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

Intestinal Tissue Mechanics Regulate Angiogenesis and Stem Cell Proliferation via Vascular Piezo

The vasculature is a prominent component of developmental and adult tissue microenvironments. How tissue specific characteristics and environmental states influence vascular biology and function, remains largely understudied. Using the fruit fly Drosophila melanogaster midgut and its associated vascular-like tracheal system, we discover reciprocal, mechanochemical interorgan communication between the adult intestine and its vascular microenvironment, which influences vascular and stem cell adaptations during intestinal regeneration. Mechanistically, apoptotic epithelial cells contribute to biomechanical remodelling of the regenerating midgut, which is associated with activation of Piezo in a subset of gut tracheal cells. Piezo drives activation of the mechanosensitive transcription factor Yorkie/YAP, leading to tracheal remodelling and intestinal stem cell proliferation. Furthermore, we identify a conserved role of mammalian vascular Piezo1 influencing remodelling of the intestinal crypt vasculature, and intestinal regeneration upon DNA damage and inflammation in mice. Our cross-species in vivo study reveals the presence of biomechanically distinct compartments in the regenerative intestine and identifies mechanosensory interorgan signalling, which contributes to intestinal regeneration through the vascular-stem cell niche. Furthermore, our work highlights the importance of studying tissue- and context-specific vascular biology to better understand intestinal compartmentalization, plasticity, and the complexity of tissue/vasculature interactions within a living organ.

developmental 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↗

bioRxiv2020

Title: Acetylcholine regulates pulmonary inflammation and facilitates the transition from active immunity to tissue repair during respiratory viral infection

ABSTRACTInflammatory control is critical to recovery from respiratory viral infection. Acetylcholine (ACh) secreted from non-neuronal sources, including lymphocytes, plays an important, albeit underappreciated, role in regulating immune-mediated inflammation. This study was designed to explore the role of ACh in acute viral infection and recovery. Using the murine model of influenza A, cholinergic status in the lungs and airway was examined over the course of infection and recovery. The results showed that airway ACh remained constant through the early stage of infection and increased during the peak of the acquired immune response. As the concentration of ACh increased, cholinergic lymphocytes appeared in the airway and lungs. Cholinergic capacity was found primarily in CD4 T cells, but also in B cells and CD8 T cells. The cholinergic CD4+ T cells bound to influenza-specific tetramers at the same frequency as their conventional (i.e., non-cholinergic) counterparts. In addition, they were retained in the lungs throughout the recovery phase and could still be detected in the resident memory regions of the lung up to two months after infection. Histologically, cholinergic lymphocytes were found in direct physical contact with activated macrophages throughout the lung. When ACh production was inhibited, mice exhibited increased tissue inflammation, altered lung architecture, and delayed recovery. Together, these findings point to a previously unrecognized role for ACh in the transition from active immunity to recovery and pulmonary repair following respiratory viral infection.View Full Text

immunology↗

bioRxiv2020

Identifying digenic disease genes using machine learning in the undiagnosed diseases network

Rare diseases affect hundreds of millions of people worldwide, and diagnosing their genetic causes is challenging. The Undiagnosed Diseases Network (UDN) was formed in 2014 to identify and treat novel rare genetic diseases, and despite many successes, more than half of UDN patients remain undiagnosed. The central hypothesis of this work is that many unsolved rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating even just pairs of variants for potential to cause disease is currently infeasible. To address this challenge, we developed DiGePred, a random forest classifier for identifying candidate digenic disease gene pairs using features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier using DIDA, the largest available database of known digenic disease causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN patients. DiGePred achieved high precision and recall in cross-validation and on a held out test set (PR area under the curve >77%), and we further demonstrate its utility using novel digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings like the UDN. Finally, to facilitate the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work facilitates the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.

bioinformatics↗

bioRxiv2019

Flexible routing of motor control signals through neocortical projection neuron classes

The interaction of descending neocortical outputs and subcortical premotor circuits is critical for shaping the skilled movements. Two broad classes of motor cortical output projection neurons provide input to many subcortical motor areas: pyramidal tract neurons (PT), which project throughout the neuraxis; and intratelencephalic neurons (IT), which project within cortex and subcortical striatum. It is unclear whether these classes are functionally in series or whether separable components of descending motor control signals are distributed across these distinct classes of projection neurons. Here we combine large-scale neural recordings across all layers of motor cortex with cell-type specific perturbations to study cortically-dependent mouse motor behaviors: kinematically-variable manipulation of a joystick and a kinematically-precise reach-to-grasp. We find that striatum-projecting IT neuron activity preferentially represents amplitude whereas pons-projecting PT neurons preferentially represent the variable direction of forelimb movements. Thus, separable components of descending motor cortical commands are distributed across motor cortical projection cell classes. One-sentence summarySeparable components of cortical motor commands are distributed across distinct glutamatergic projection neuron cell-types.

neuroscience↗

bioRxiv2017

Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures

The spatial distribution of genetic variation within proteins is shaped by evolutionary constraint and thus can provide insights into the functional importance of protein regions and the potential pathogenicity of protein alterations. Here, we comprehensively evaluate the 3D spatial patterns of constraint on human germline and somatic variation in 4,568 solved protein structures. Different classes of coding variants have significantly different spatial distributions. Neutral missense variants exhibit a range of 3D constraint patterns, with a general trend of spatial dispersion driven by constraint on core residues. In contrast, germline and somatic disease-causing variants are significantly more likely to be clustered in protein structure space. We demonstrate that this difference in the spatial distributions of disease-associated and benign germline variants provides a signature for accurately classifying variants of unknown significance (VUS) that is complementary to current approaches for VUS classification. We further illustrate the clinical utility of our approach by classifying new mutations identified from patients with familial idiopathic pneumonia (FIP) that segregate with disease.

genetics↗