Biology subjects

Humphries, J.

Publications and source records attributed to Humphries, J..

5 recordsLinked to original sources

bioRxiv2026

Poor foam stability in gluten-free beers is associated with distinct protein composition compared with barley-malt beers

Why was the work done?: Gluten-free (GF) beers typically exhibit poorer foam stability than conventional barley malt-based beers, yet the molecular basis underlying this difference remains poorly understood. This study aimed to investigate protein-level factors associated with foam stability in GF and barley beers. How was the work done?: Three commercially produced GF beers, comprising two lagers brewed from rice or sorghum, and one pale ale brewed from a millet-buckwheat-rice blend, were compared with two commercially produced barley-malt beers, comprising a lager and a pale ale. Soluble protein was isolated from freeze-dried beer powder using TCA-acetone. Protein profiles were examined using SDS-PAGE, and proteomes were characterised and compared using label-free quantitative LC-MS/MS. What are the main findings?: GF beers showed lower soluble protein concentrations and significantly lower foam stability than the barley beers. SDS-PAGE revealed fewer and weaker protein bands in GF beers compared with barley beers. Proteomic analysis showed that barley beers were enriched in known foam-active proteins, particularly lipid transfer protein 1 (LTP1) and Protein Z (serpin family members), whereas these proteins were not detected or were detected only at very low levels in GF beers.

biochemistry↗

bioRxiv2026

Developmental and regulatory logic of cannabis glandular trichomes resolved by single cell multiomics

Glandular trichomes of Cannabis sativa produce specialised metabolites including cannabinoids and terpenes, yet the cellular basis of trichome development and metabolic specialisation remains unresolved. Here we reconstruct the glandular trichome lineage within the C. sativa inflorescence using single-cell transcriptomics and chromatin accessibility profiling. We identify a continuous developmental trajectory from the protoderm, linking bulbous, sessile, and capitate-stalked trichomes, indicating that these morphologies represent sequential stages rather than distinct trichome types. We further identify a previously undescribed neck cell that shares a developmental origin with secretory disc cells before lineage bifurcation. Integration of chromatin accessibility with transcription factor (TF) binding reveals cell state specific regulatory programs coordinating neck cell development and specialised metabolism, redox homeostasis, and secretion in mature secretory disc cells. Methyl jasmonate elicitation induces extensive transcriptional and chromatin landscape reprogramming in mature secretory disc cells and transient repression of specialised metabolic pathways. Together, these findings provide a cell-resolved regulatory framework for glandular trichome development and function, revising prevailing models of trichome identity, maturation and defence associated metabolic regulation.

plant biology↗

bioRxiv2025

Oscillatory and elevated flow distinctly regulate gene expression in human coronary artery endothelial cells

BackgroundAtherosclerosis develops at arterial sites exposed to disturbed flow, while plaque rupture and plaque erosion predominantly occur in regions subjected to elevated flow. The impact of elevated flow on regulation of endothelial gene expression is less well studied; therefore, we undertook a comprehensive analysis of primary human coronary artery endothelial cell (HCAEC) gene expression under elevated flow, comparing it to gene expression induced by normal physiological and oscillatory flow. MethodsAnalysis of HCAEC mRNA, microRNA and protein expression cultured under oscillatory shear stress (OSS), physiological laminar shear stress (LSS), and elevated shear stress (ESS) for 72 hours. Identification of changes in RNA isoform expression and proximity of flow-responsive genes to established coronary artery disease (CAD) risk loci were also performed. Results2,175 shear-regulated genes were identified, with 665 uniquely responsive to ESS. Both ESS and OSS induced significant changes in RNA isoform selection, predicted to affect 848 and 580 genes respectively. Signalling pathways regulating CAD pathogenesis including HIPPO, TGF{beta}/BMP, and IRF, showed altered RNA isoform selection which may influence plaque development and plaque erosion. 65% of linkage disequilibrium (LD)-filtered CAD-associated genetic variants contained at least one OSS or ESS-regulated gene within 250Kb. Proteomic analysis identified 289 proteins differentially expressed under OSS and 171 under ESS, with notable discordance between mRNA and protein changes observed in 28.7% (OSS vs LSS) and 16.6% (ESS vs LSS) genes. Additionally, 40 shear-responsive microRNAs were identified. ConclusionElevated flow elicits a distinct gene expression programme in HCAECs, modulating pathways central to CAD pathogenesis. Research PerspectiveWhat New Question Does This Study Raise? O_LIPlaque erosion predominantly occurs on the upstream surface of the plaque, where the endothelium is exposed to elevated flow, which we show within this study to evoke a significant and largely unique regulation of the transcriptome, miRome and proteome within primary human coronary artery endothelial cells. C_LIO_LIIdentify shear stress as a significant regulator of alternative splicing, with elevated flow causing the greatest shift in alternative transcript selection. C_LIO_LIIdentify 135 oscillatory, and 101 elevated differentially expressed genes in proximity to CAD risk loci. C_LI What Question Should be Addressed Next? O_LIStudy of the response of the coronary endothelium directly in patients to understand how the risk factors involved in plaque erosion change endothelial function. C_LIO_LICreation of physiological 3D arterial models replicating in vivo observations to study the precipitating factors involved in plaque erosion. C_LI

cell biology↗

bioRxiv2025

A Standardized Protocol to Investigate Trans-Endothelial Trafficking in Zebrafish: Nano-bio Interactions of PEG-based Nanoparticles in Live Vasculature

Trans-endothelial transport of nanoparticles remains poorly characterized in live organisms. The zebrafish is a well-established model for direct in vivo imaging; however, standardized controls are not consistently applied across studies. Here, we developed a standardized protocol to assess nanoparticle trans-endothelial trafficking in live zebrafish. We tested a range of tracers and identified 2000 kDa dextran as an optimal control for standardizing microinjections and quantifying nanoparticle transport in a systematic unbiased manner. As validation, we identified the early physiological trans-endothelial transport pathways in zebrafish embryos using 40 kDa dextran as a nanoparticle surrogate. Using our workflow, we assessed the extravasation of 3, 7, 32 and 47 nm polyethylene glycol (PEG)-based nanoparticles. Using cAMP stimulation to restrict paracellular routes, and inhibitors to impede dynamin-dependent endocytosis, we demonstrated that PEG-based hyperbranched polymer (HBP) nanoparticles of 3 to 7 nm traverse the endothelial barrier via paracellular routes and 32 and 47 nm PEG micelles adopt dynamin- dependent endocytic trafficking over paracellular transport. We characterized the emergence of caveolae in the vasculature up to 17 days post-fertilization (dpf) using a cavin1b knock-in zebrafish line. Using cavin1a/cavin1b double knockout (DKO) zebrafish, and tumor-bearing Cavin-1 null mice, we showed that caveolae do not contribute to the transvascular transport of these PEG-based nanoparticles. This work highlights the rigour of the standardized protocol for assessing nanoparticle trans-endothelial transport in the live zebrafish, providing a systematic approach for quantification using a standardized control.

cell biology↗

bioRxiv2024

Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell-surface markers

Efficient delivery of mRNA-LNPs to specific cell-types remains a major challenge in the widespread application of mRNA therapeutics. Conventional targeting approaches involve modifying the lipid composition or functionalising the surface of lipid nanoparticles (LNPs), which complicates manufacturing, alters nanoparticle size, charge and stealth, impacting their delivery and immunogenicity. Here we present a generalisable method for targeted mRNA-LNP delivery that uses bispecific antibodies (BsAbs) to form a bridge between LNPs and cell-surface markers. Instead of attaching the targeting agent to the nanocarrier, BsAbs are administered first, bind to surface proteins on target cells, and later retain unmodified LNPs in affected tissues. We demonstrate efficient and cell-type-specific delivery of mRNA-LNPs to epidermal growth factor receptor (EGFR), and folate hydrolase 1 (PSMA) positive cells in vitro and in vivo. The flexibility of this technology, achieved by substitution of the cell-targeting region of the BsAbs, enables rapid development of next-generation targeted mRNA drugs.

molecular biology↗