Biology subjects

McBride, M.

Publications and source records attributed to McBride, M..

5 recordsLinked to original sources

bioRxiv2023

Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing

BackgroundDominance and other non-additive genetic effects arise from the interaction between alleles, and historically these phenomena played a major role in quantitative genetics. However, today most genome-wide association studies (GWAS) assume alleles act additively. MethodsWe systematically investigated both dominance - here representing any non-additive effect - and additivity across 574 physiological and gene expression traits in three mammalian models: a Pig F2 Intercross, a Rat Heterogeneous Stock and a Mouse Heterogeneous Stock. ResultsIn all species, and across all physiological traits, dominance accounts for about one quarter of the heritable variance. Hematological and immunological traits exhibit the highest dominance variance, possibly reflecting balancing selection in response to pathogens. Although most quantitative trait loci (QTLs) are detectable assuming additivity, we identified 154, 64 and 62 novel dominance QTLs in pigs, rats and mice respectively, that were undetectable as additive QTLs. Similarly, even though most cis-acting eQTLs are additive, we observed a large fraction of dominance variance in gene expression, and trans-acting eQTLs are enriched for dominance. Genes causal for dominance physiological QTLs are less likely to be physically linked to their QTLs but instead act via trans-acting dominance eQTLs. In addition, in HS rat transcriptomes, thousands of eQTLs associate with alternate transcripts and exhibit complex additive and dominant architectures, suggesting a mechanism for dominance. ConclusionsAlthough heritability is predominantly additive, many mammalian genetic effects are dominant and likely arise through distinct mechanisms. It is therefore advantageous to consider both additive and dominance effects in GWAS to improve power and uncover causality.

genetics↗

bioRxiv2021

Dynamic proton-dependent motors power Type IX secretion and gliding adhesin movement in Flavobacterium

Motile bacteria usually rely on external apparatus like flagella for swimming or pili for twitching. By contrast, gliding bacteria do not rely on obvious surface appendages to move on solid surfaces. Flavobacterium johnsoniae and other bacteria in the Bacteroidetes phylum use adhesins whose movement on the cell surface supports motility. In F. johnsoniae, secretion and helicoidal motion of the main adhesin SprB are intimately linked and depend on the type IX secretion system (T9SS). Both processes necessitate the proton motive force (PMF), which is thought to fuel a molecular motor that comprises the GldL and GldM cytoplasmic membrane proteins. Here we show that F. johnsoniae gliding motility is powered by the pH gradient component of the PMF. We further delineate the interaction network between the GldLM transmembrane helices (TMH) and show that conserved glutamate residues in GldL TMH are essential for gliding motility, although having distinct roles in SprB secretion and motion. We then demonstrate that the PMF and GldL trigger conformational changes in the GldM periplasmic domain. We finally show that multiple GldLM complexes are distributed in the membrane suggesting that a network of motors may be present to move SprB along a helical path on the cell surface. Altogether, our results provide evidence that GldL and GldM assemble dynamic membrane channels that use the proton gradient to power both T9SS-dependent secretion of SprB and its motion at the cell surface.

microbiology↗

bioRxiv2019

Transforming growth factor-beta signaling via ALK1 and ALK5 regulates distinct functional pathways in vein graft intimal hyperplasia

RationaleTransforming growth factor-beta (TGF{beta}) is tightly regulated at multiple levels, with regulation at the receptor level now recognized as a key determinant of the cellular response to this pleiotropic cytokine. TGF{beta} promotes saphenous vein graft neointima formation after coronary artery bypass graft (CABG) surgery, inducing smooth muscle cell (SMC) hyperplasia and fibrosis by signaling via activin receptor-like kinase 5(ALK5). However, the role of the alternate TGF{beta} receptor ALK1 remains completely unknown. ObjectiveTo define the receptor pathways activated by TGF{beta} in SMCs and their mechanistic importance during CABG neointima formation. Methods and resultsRadioligand co-IP assays revealed direct interactions between TGF{beta}, ALK5 and ALK1 in primary saphenous vein graft SMC (HSVSMC) from patients undergoing CABG. Knockdown and pharmacological inhibition of ALK5 or ALK1 in HSVSMC significantly attenuated TGF{beta}-induced phosphorylation of receptor-regulated (R)-Smads 2/3 and 1/5, respectively. Microarray profiling followed by qRT-PCR validation showed that TGF{beta} induced distinct transcriptional networks downstream of ALK5 or ALK1, associated with HSVSMC contractility and migration, respectively and confirmed using migration assays as well as qRT-PCR and western blot assays of contractile SMC markers. scRNAseq analysis of TGF{beta}-treated HSVSMC identified distinct subgroups of cells showing ALK5 or ALK1 transcriptional responses, while RNA velocity analyses indicated divergence in differentiation towards ALK5 or ALK1-dominant lineages. ALK1, ALK5 and their downstream effectors pSmad1/5 and pSmad2/3 were localized to SMA+ neointimal SMCs in remodelled mouse vein grafts. Pharmacological inhibition or genetic ablation of Smad1/5 substantially reducing neointima formation following acute vascular injury. Notably, expression and activation of ALK1, ALK5 and their respective downstream R-Smads was already evident in hyperplastic saphenous veins prior to grafting. ConclusionsWhilst canonical TGF{beta} signaling via ALK5 promotes a contractile HSVSMC phenotype, transactivation of ALK1 by TGF{beta} induces neointima formation by driving cell migration. Restoring the balance between ALK1 and ALK5 in HSVSMC may represent a novel therapeutic strategy for vein graft failure.

cell biology↗

bioRxiv2019

Endothelial pannexin 1 channels control inflammation by regulating intracellular calcium

In BriefInterleukine-1 beta (IL-1{beta}) has been identified as a critical factor that contributes to the inflammatory response in cardiovascular disease (e.g., atherosclerosis). Pannexin 1 (Panx1) channel activity in endothelial cells regulates localized inflammatory cell recruitment. In response to prolonged tumor necrosis factor alpha (TNF) treatment, Yang et al. found that the Panx1 channel is targeted to the plasma membrane, where it facilitates an increase in intracellular calcium to control the production and release of cytokines including IL-1{beta}.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC=\"FIGDIR/small/750323v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@59e72borg.highwire.dtl.DTLVardef@57bd5corg.highwire.dtl.DTLVardef@50ed73org.highwire.dtl.DTLVardef@1151f56_HPS_FORMAT_FIGEXP M_FIG C_FIG AbstractThe proinflammatory cytokine IL-1{beta} is a significant risk factor in cardiovascular disease that can be targeted to reduce major cardiovascular events. IL-1{beta} expression and release are tightly controlled by changes in intracellular Ca2+. In addition, purinergic signaling through ATP release has also been reported to promote IL-1{beta} production. Despite this, the mechanisms that control IL-1{beta} synthesis and expression have not been identified. The pannexin 1 (Panx1) channel has canonically been implicated in ATP release, especially during inflammation. However, resolution of purinergic signaling occurs quickly due to blood flow and the presence of ectonucleotidases. We examined Panx1 in human endothelial cells following treatment with the pro-inflammatory cytokine tumor necrosis alpha (TNF). In response to long-term TNF treatment, we identified a dramatic increase in Panx1 protein expression at the plasma membrane. Analysis by whole transcriptome sequencing (RNA-seq), qPCR, and treatment with specific kinase inhibitors, revealed that TNF signaling induced NF{kappa}{beta}-associated Panx1 transcription. Genetic inhibition of Panx1 reduced the expression and secretion of IL-1{beta}. We initially hypothesized that increased Panx1-mediated ATP release acted in a paracrine fashion to control cytokine expression. However, our data demonstrate that IL1-{beta} expression was not altered after direct ATP stimulation, following degradation of ATP by apyrase, or after pharmacological blockade of P2 receptors. These data suggest that non-purinergic pathways, involving Panx1, control IL-1{beta} production. Because Panx1 forms a large pore channel, we hypothesized it may act to passively diffuse Ca2+ into the cell upon opening to regulate IL-1{beta}. High-throughput flow cytometric analysis demonstrated that TNF treatments lead to elevated intracellular Ca2+. Genetic or pharmacological inhibition of Panx1 reduced TNF-associated increases in intracellular Ca2+, and IL-1{beta} transcription. Furthermore, we found that the Ca2+-sensitive NF{kappa}{beta}-p65 protein failed to localize to the nucleus after genetic or pharmacological block of Panx1. Taken together, our study provides the first evidence that intracellular Ca2+ regulation via the Panx1 channel induces a feed-forward effect on NF{kappa}{beta} to regulate IL-1{beta} synthesis and release in endothelium during inflammation.

cell biology↗

bioRxiv2019

Spatial simulation of co-designed land-cover change scenarios in New England: Alternative futures and their consequences for conservation priorities

To help prepare for an uncertain future, planners and scientists often engage with stakeholders to co-design alternative scenarios of land-use change. Methods to translate the resulting qualitative scenarios into quantitative simulations that characterize the future landscape condition are needed to understand consequences of the scenarios while maintaining the legitimacy of the process. We use the New England Landscape Futures (NELF) project as a case study to demonstrate a transparent method for translating participatory scenarios to simulations of Land-Use and Land-Cover (LULC) change and for understanding the major drivers of land-use change and diversity of plausible scenarios and the consequences of alternative land-use pathways for conservation priorities. The NELF project co-designed four narrative scenarios that contrast with a Recent Trends scenario that projects a continuation of observed changes across the 18-million-hectare region during the past 20 years. Here, we (1) describe the process and utility of translating qualitative scenarios into spatial simulations using a dynamic cellular land change model; (2) evaluate the outcomes of the scenarios in terms of the differences in the LULC configuration relative to the Recent Trends scenario and to each other; (3) compare the fate of forests within key areas of concern to the stakeholders; and (4) describe how a user-inspired outreach tool was developed to make the simulations and analyses accessible to diverse users. The four alternative scenarios populate a quadrant of future conditions that crosses high to low natural resource planning and innovation with local to global socio-economic connectedness. The associated simulations are strongly divergent in terms of the amount of LULC change and the spatial pattern of change. Features of the simulations can be linked back to the original storylines. Among the scenarios there is a fivefold difference in the amount of high-density development, and a twofold difference in the amount of protected land. Overall, the rate of LULC change has a greater influence on forestlands of concern to the stakeholders than does the spatial configuration. The simulated scenarios have been integrated into an online mapping tool that was designed via a user-engagement process to meet the needs of diverse stakeholders who are interested the future of the land and in using future scenarios to guide land use planning and conservation priorities.

ecology↗