Biology subjects

Kelly, J. T.

Publications and source records attributed to Kelly, J. T..

5 recordsLinked to original sources

bioRxiv2024

Induction of neutralising antibodies against conserved rhinovirus capsid protein VP4 depends on presenting VP4 in a virus-like conformation

Infection with rhinovirus (RV) is associated with significant morbidity and hospitalisation in people with chronic lung disease. At present there is no approved RV vaccine or antiviral. There are approximately 180 RV serotypes, classified into 3 species (RVA, RVB, RVC). There is no cross-protection between serotypes because of high diversity in immunodominant antigenic sites. This makes it impractical to create a broadly protective vaccine using traditional methods, involving whole capsids. A more feasible strategy is to direct the immune response towards conserved but less dominant epitopes. The capsid protein VP4 is highly conserved within each RV genotype and some antibodies that target VP4 are neutralising. This makes VP4 vulnerable to antibodies and a promising vaccine target. Here we investigate the ability of RV VP4 N-terminal peptides presented on different display systems to initiate a neutralising immune response in mice. We compared three different-sized VP4 peptides (spanning residues, 1-15, 1-30 and 1-45) displayed on two different display systems-SpyCatcher Virus-like particles (VLPs) or Keyhole Limpet Hemocyanin (KLH). Overlapping regions of VP4 were antigenically different when presented on different platforms and in peptides with different length. The conformation of the 1-15 region of VP4 was critical for inducing antibodies that were both neutralising and able to bind VP4 in the context of the virus particle. Therefore, correctly displayed VP4 peptides can recapitulate virus-like antigenicity. These findings improve our understanding of VP4 antigenicity and will inform the design of future RV vaccines. This work could also impact the design of other peptide vaccines, since a variable antigenic conformation is a common characteristic of pathogen-derived peptide targets. Impact statementRhinovirus (RV) is a highly prevalent respiratory virus that is a frequent cause of common cold symptoms. For people with chronic lung diseases such as asthma, infection can cause significant worsening of disease, leading to increased suffering and hospitalisation. There are currently no vaccines or anti-viral drugs that target RV infections. Development of a RV vaccine would be hugely beneficial to suffers of chronic lung diseases. Attempts to develop a broadly protective RV vaccine have been hindered by the presence of over 180 serotypes which have little or no natural cross-reactivity. Previous studies have identified the highly conserved VP4 epitope as a potential target for broadly protective vaccines. However, there has been little progress in evaluating its effectiveness as a vaccine candidate. In this study we assessed the ability of different RV VP4 immunogens to induce neutralising antibodies in mice. We demonstrated that antigenic conformation of VP4 varies greatly between immunogens and presentation of the first 15 N-terminal residues in a virus-like conformation is important for generating neutralising antibodies. This knowledge could help to maximise the production of neutralising VP4-specific antibodies in future studies which could ultimately lead to a universal RV vaccine.

microbiology↗

bioRxiv2023

Viral pIC-pocketing: RSV sequestration of eIF4F Initiation Complexes into bi-phasic biomolecular condensates

Orthopneumoviruses characteristically form membrane-less cytoplasmic inclusion bodies (IBs) wherein RNA replication and transcription occur. Herein, we report a strategy whereby the orthopneumoviruses sequester various components of the eiF4F Initiation Complex machinery into viral IBs to facilitate translation of their own mRNAs; pIC-pocketing. Mass spectrometry analysis of sub-cellular fractions from RSV-infected cells identified significant modification of the cellular translation machinery; however; interestingly, ribopuromycylation assays showed no changes to global levels of translation. Electron micrographs of RSV-infected cells revealed bi-phasic organisation of IBs; specifically, spherical "droplets" nested within the larger inclusion. Using correlative light and electron microscopy (CLEM), combined with fluorescence in situ hybridisation (FISH), we showed that the observed bi-phasic morphology represents functional compartmentalisation of the IB and that these domains are synonymous with the previously reported inclusion body associated granules (IBAGs). Detailed analysis demonstrated that IBAGs concentrate nascent viral mRNA, the viral M2-1 protein as well as many components of the eIF4F complex, involved in translation initiation. Interestingly, although ribopuromycylation-based imaging indicates the majority of viral mRNA translation likely occurs in the cytoplasm, there was some evidence for intra-IBAG translation, consistent with the likely presence of ribosomes in a subset of IBAGs imaged by electron microscopy. The mechanistic basis for this pathway was subsequently determined; the viral M2-1 protein interacting with eukaryotic translation initiation factor 4G (eIF4G) to facilitate its transport between the cytoplasm and the separate phases of the viral IB. In summary, our data shows that IBs function to spatially regulate early steps in viral translation within a highly selective biphasic liquid organelle.

microbiology↗

bioRxiv2022

Habitat use differences mediate anthropogenic threat exposure in white sturgeon

Understanding intraspecific variation in habitat use, particularly of long-lived fishes across multiple life history stages, is core to improved conservation management. Here, we present results from a synthesis of acoustic telemetry data for large juvenile and adult white sturgeon (Acipenser transmontanus) from 2010 to 2017 in the San Francisco Estuary and Sacramento River ecosystems. We focused primarily on uncovering spatial patterns of inferred habitat occupancy across life stages, and on linking habitat use to population threats. We found substantial differences in habitat use across individuals and over time that was related to fish age class. However, differences in habitat use were not explained by fish sex or water year flow conditions. We estimated an index of angling exposure, which showed that fish entering reproductive maturity, which historically were of harvestable size, were detected less often than other sizes in areas with high angler pressure, suggesting possible behavioral avoidance of areas of high angler pressure. Additionally, we used historical data to evaluate potential exposure of white sturgeon to a severe red tide event in late summer 2022. We found that >50% of reproductive-age fish may have been residing in areas affected by the red tide. Future monitoring and management of white sturgeon might benefit from examining multiple phases of white sturgeon life history. For example, additional tracking studies could improve understanding of juvenile habitat use, adult survival rates, patterns of anadromy, and cross-basin habitat utilization.

ecology↗

bioRxiv2021

Intraspecific variation in migration timing of green sturgeon in the Sacramento River system

BackgroundUnderstanding movement patterns of anadromous fishes is critical to conservation management of declining wild populations and preservation of habitats. Yet, infrequent observations of individual animals fundamentally constrain accurate descriptions of movement dynamics. MethodsIn this study, we synthesized over a decade (2006-2018) of acoustic telemetry tracking observations of green sturgeon (Acipenser medirostris) in the Sacramento River system to describe major anadromous movement patterns. ResultsWe observed that green sturgeon exhibited a unimodal in-migration during the spring months but had a bimodal distribution of out-migration timing, split between an early out-migration (32%) group during May - June, or alternatively, holding in the river until a late out-migration (68%), November - January. Focusing on these out-migration groups, we found that river discharge, but not water temperature, may cue the timing of migration, and that fish showed a tendency to maintain out-migration timing between subsequent spawning migration events. ConclusionsWe recommend that life history descriptions of green sturgeon in this region reflect the distinct out-migration periods described here. Furthermore, we encourage the continued use of biotelemetry to describe migration timing and life history variation, not only this population but other green sturgeon populations and other species.

ecology↗

bioRxiv2020

The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins

SARS-CoV-2 emerged in late 2019, leading to the COVID-19 pandemic that continues to cause significant global mortality in human populations. Given its sequence similarity to SARS-CoV, as well as related coronaviruses circulating in bats, SARS-CoV-2 is thought to have originated in Chiroptera species in China. However, whether the virus spread directly to humans or through an intermediate host is currently unclear, as is the potential for this virus to infect companion animals, livestock and wildlife that could act as viral reservoirs. Using a combination of surrogate entry assays and live virus we demonstrate that, in addition to human ACE2, the Spike glycoprotein of SARS-CoV-2 has a broad host tropism for mammalian ACE2 receptors, despite divergence in the amino acids at the Spike receptor binding site on these proteins. Of the twenty-two different hosts we investigated, ACE2 proteins from dog, cat and rabbit were the most permissive to SARS-CoV-2, while bat and bird ACE2 proteins were the least efficiently used receptors. The absence of a significant tropism for any of the three genetically distinct bat ACE2 proteins we examined indicates that SARS-CoV-2 receptor usage likely shifted during zoonotic transmission from bats into people, possibly in an intermediate reservoir. Interestingly, while SARS-CoV-2 pseudoparticle entry was inefficient in cells bearing the ACE2 receptor from bats or birds the live virus was still able to enter these cells, albeit with markedly lower efficiency. The apparently broad tropism of SARS-CoV-2 at the point of viral entry confirms the potential risk of infection to a wide range of companion animals, livestock and wildlife.

microbiology↗