Biology subjects

Grant, O.

Publications and source records attributed to Grant, O..

5 recordsLinked to original sources

bioRxiv2026

Loss of hemagglutination ability by H3N2 influenza A virus, subclade K.

Seasonal human H3N2 influenza viruses, subclade K (J.2.4.1), have been the predominant influenza A viruses in the Northern hemisphere influenza season of 2025/2026. Since 2024, the vaccine virus A/Darwin/6/21 has emerged in different antigenic variants. Antigenic changes are frequently caused by amino acid substitutions near the hemagglutinin (HA) receptor-binding pocket, which can also affect receptor binding properties, such as hemagglutination. Hemagglutination is crucial for assessing antigenicity using the hemagglutination inhibition (HAI) assay, and a loss of binding to turkey erythrocytes could significantly hamper this process. In this study, we explored how substitutions in or around the HA receptor-binding site affect binding to glycans at the molecular level. We employed ELISA, glycan array, flow cytometry, hemagglutination assays, and tissue staining. Substitutions at positions 140, 192, and 223 establish clade J viruses that emerged in 2024. Computational analysis of HA in complex with an elongated glycan reveals that mutation F192 forms a CH-Pi interaction to stabilize the binding. Based on this background, substitutions in antigenic sites A and B within subclade K viruses exhibit a binding preference for elongated glycans, which are not displayed on turkey erythrocytes. Conversely, our previously established glyco-remodeled erythrocytes are efficiently bound by these subclade K H3N2 viruses and could support influenza surveillance and vaccine development.

microbiology↗

bioRxiv2025

Donor-derived airway ALI model for high-throughput screening of antiviral combinations with concurrent analysis of antiviral efficacy and epithelial toxicity using ciliR

Respiratory RNA viral infections significantly impact quality of life and productivity, both in terms of pandemics (e.g., SARS-CoV-2, influenza A viruses) and seasonal infections such as respiratory syncytial virus (RSV). Globally, RSV causes an estimated 33.8 million cases annually in children under five, leading to 2.8-4.3 million hospital admissions and up to 199,000 deaths. Human-relevant drug screening models are key to addressing the urgent need for effective antiviral treatments for RSV, particularly in vulnerable patient groups. Here, we present a donor-derived differentiated primary human nasal epithelial cell, 96-HTS Transwell air-liquid interface (ALI) model designed to investigate the effects of combination antiviral therapies on RSV infection in primary human ciliated airway epithelium. Additionally, we describe novel analytical tools using R (ciliR) to screen drug combinations by concurrently measuring efficacy and ciliary beat frequency as a sensitive marker of cell toxicity. Our results demonstrate that the smaller 96-HTS ALI cultures retain comparable epithelial composition and ciliary function to conventional ALI culture formats. These cultures are permissible to infection with an RSV-GFP reporter virus, enabling quantitative comparison and combination treatment across multiple epithelial cultures from the same donor. We anticipate that our disease-relevant system will serve as a foundation for larger-scale experiments aimed at optimizing combination therapy for RSV and other respiratory viruses.

microbiology↗

bioRxiv2024

Sex-specific DNA methylation differences in Amyotrophic lateral sclerosis

Sex is an important covariate in all genetic and epigenetic research due to its role in the incidence, progression and outcome of many phenotypic characteristics and human diseases. Amyotrophic lateral sclerosis (ALS) is a motor neuron disease with a sex bias towards higher incidence in males. Here, we report for the first time a blood-based epigenome-wide association study meta-analysis in 9274 individuals after stringent quality control (5529 males and 3975 females). We identified a total of 226 ALS saDMPs (sex-associated DMPs) annotated to a total of 159 unique genes. These ALS saDMPs were depleted at transposable elements yet significantly enriched at enhancers and slightly enriched at 3UTRs. These ALS saDMPs were enriched for transcription factor motifs such as ESR1 and REST. Moreover, we identified an additional 10 genes associated with ALS saDMPs through chromatin loop interactions, suggesting a potential regulatory role for these saDMPs on distant genes. Furthermore, we investigated the relationship between DNA methylation at specific CpG sites and overall survival in ALS using Cox proportional hazards models. We identified two ALS saDMPs, cg14380013 and cg06729676, that showed significant associations with survival. Overall, our study reports a reliable catalogue of sex-associated ALS saDMPs in ALS and elucidates several characteristics of these sites using a large-scale dataset. This resource will benefit future studies aiming to investigate the role of sex in the incidence, progression and risk for ALS.

genomics↗

bioRxiv2023

ciliR: a new R package for determining ciliary beat frequency using fast-Fourier transformation.

Cilia are motile hair-like structures that play a vital role in our body. Accurate assessment of ciliary beat frequency is pivotal for investigating ciliary dynamics and diagnosing ciliopathies. This study aims to develop software for accurately measuring the beat frequency of cilia captured using high-speed video microscopy. To achieve this, we developed the ciliR package in R, which was validated against manual counting and three other automated methods of counting cilia beat frequency. The results showed that ciliR produced results that were comparable to manual counting. The accuracy of ciliR was defined by its ability to reduce noise, including only counting data in a biologically significant range (0-60 Hz). Our software is a valuable tool for researchers in the field of ciliobiology as it offers a reliable method for detailed ciliary function analysis, thereby contributing to the broader understanding of mechanisms underlying ciliary-related disease. We encourage researchers to try this package and feed-back their findings to the authors. Instructions for use and processes for providing feedback are provided in supplementary material. SummaryciliR is a novel R package designed for analysing ciliary beat frequency (CBF) via ImageJ and RStudio. The advantage of the ciliR system, lies in its integration with the R environment, increasing processing speed and access to data visualization tools and analysis pipelines available in other R packages. The open-source platform invites community feedback to refine functionality, aiming to advance ciliopathy research with an accessible, comprehensive toolkit.

cell biology↗

bioRxiv2020

Allosteric regulation of lysosomal enzyme recognition by the cation-independent mannose 6-phosphate receptor

The cation-independent mannose 6-phosphate receptor (CI-MPR), also known as the IGF2 receptor or CD222, is a multifunctional type I transmembrane glycoprotein ubiquitously expressed in most eukaryotic cell types. Through the receptors ability to bind a variety of unrelated extracellular and intracellular ligands, it is involved in a wide array of functions including protein trafficking, lysosomal biogenesis, internalization, regulation of cell growth, cell migration and apoptosis. CI-MPR has a large extracellular region comprised of 15 contiguous domains, four of which interact with phosphorylated glycans on lysosomal enzymes. Here we present a series of biophysical studies, along with crystal structures, providing information on how the N-terminal 5 domains of this receptor work in concert to bind and release carbohydrates. High-resolution electron microscopy as well as hydroxyl radical protein footprinting (HRPF) of this multifunctional multidomain construct demonstrates dynamic conformational changes occur as a consequence of ligand binding and different pH conditions, These data, coupled with surface plasmon resonance studies and molecular modeling, allow us to propose a bi-dentate oligosaccharide binding model, which could explain how high affinity carbohydrate binding is achieved through allosteric domain cooperativity.

biochemistry↗