The Coupling of Alternative Splicing and Nonsense-Mediated mRNA Decay

Most human genes exhibit alternative splicing, but not all alternatively spliced transcripts produce functional proteins. Computational and experimental results indicate that a substantial fraction of alternative splicing events in humans result in mRNA isoforms that harbor a premature termination codon (PTC). These transcripts are predicted to be degraded by the nonsense-mediated mRNA decay (NMD) pathway. One explanation for the abundance of PTC-containing isoforms is that they represent splicing errors that are identified and degraded by the NMD pathway. Another potential explanation for this startling observation is that cells may link alternative splicing and NMD to regulate the abundance of mRNA transcripts. This mechanism, which we call "Regulated Unproductive Splicing and Translation" (RUST), has been experimentally shown to regulate expression of a wide variety of genes in many organisms from yeast to human. It is frequently employed for autoregulation of proteins that affect the splicing process itself. Thus, alternative splicing and NMD act together to play an important role in regulating gene expression

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript

Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease

One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain–gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials

The effect of water dispersion and absorption on axial resolution in ultrahigh-resolution optical coherence tomography

We examine the effects of dispersion and absorption in ultrahigh-resolution optical coherence tomography (OCT), particularly the necessity to compensate for high dispersion orders in order to narrow the axial point-spread function envelope. We present a numerical expansion in which the impact of the various dispersion orders is quantified; absorption effects are evaluated numerically. Assuming a Gaussian source spectrum (in the optical frequency domain), we focus on imaging through water as a first approximation to biological materials. Both dispersion and absorption are found to be most significant for wavelengths above ~1µm, so that optimizing the system effective resolution (ER) requires choosing an operating wavelength below this limit. As an example, for 1-µm source resolution (FWHM), and propagation through a 1-mm water cell, if up to third-order dispersion compensation is applied, then the optimal center wavelength is 0.8µm, which generates an ER of 1.5µm (in air). The incorporation of additional bandwidth yields no ER improvement, due to uncompensated high-order dispersion and long-wavelength absorption

The effect of water dispersion and absorption on axial resolution in ultrahigh-resolution optical coherence tomography

We examine the effects of dispersion and absorption in ultrahigh-resolution optical coherence tomography (OCT), particularly the necessity to compensate for high dispersion orders in order to narrow the axial point-spread function envelope. We present a numerical expansion in which the impact of the various dispersion orders is quantified; absorption effects are evaluated numerically. Assuming a Gaussian source spectrum (in the optical frequency domain), we focus on imaging through water as a first approximation to biological materials. Both dispersion and absorption are found to be most significant for wavelengths above ~1µm, so that optimizing the system effective resolution (ER) requires choosing an operating wavelength below this limit. As an example, for 1-µm source resolution (FWHM), and propagation through a 1-mm water cell, if up to third-order dispersion compensation is applied, then the optimal center wavelength is 0.8µm, which generates an ER of 1.5µm (in air). The incorporation of additional bandwidth yields no ER improvement, due to uncompensated high-order dispersion and long-wavelength absorption

Spatially resolved Fourier holographic light scattering angular spectroscopy

We show for what is the first time to our knowledge that digital Fourier holography can be used to record spatially resolved angular light scattering spectra from microscopically structured samples. This is achieved in one or a few digital image captures over large millimeter-scale fields of view. Such spectra are a sensitive measure of microscopic morphology, with wide applications in biological and medical imaging. We demonstrate good agreement between results of experiment and Mie theory for the angular scattering spectra of microspheres in water extracted from local regions within reconstructed 2 x 1 millimeter image sets

Modified discrete particle model of optical scattering in skin tissue accounting for multiparticle scattering

We rigorously account for the effects of multiparticle light scattering from a fractal sphere aggregate in order to simulate the optical properties of a soft biological tissue, human skin. Using a computational method that extends Mie theory to the multisphere case, we show that multiparticle scattering significantly affects the computed optical properties, resulting in a reduction in both scattering coefficient and anisotropy for the wavelengths simulated, as well as a significantly enhanced forward peak in the simulated phase function. The model is extended to incorporate the contribution of Rayleigh scatterers, which we show is required to obtain reasonable agreement with experimentally measured optical properties of skin tissue

Modified discrete particle model of optical scattering in skin tissue accounting for multiparticle scattering

We rigorously account for the effects of multiparticle light scattering from a fractal sphere aggregate in order to simulate the optical properties of a soft biological tissue, human skin. Using a computational method that extends Mie theory to the multisphere case, we show that multiparticle scattering significantly affects the computed optical properties, resulting in a reduction in both scattering coefficient and anisotropy for the wavelengths simulated, as well as a significantly enhanced forward peak in the simulated phase function. The model is extended to incorporate the contribution of Rayleigh scatterers, which we show is required to obtain reasonable agreement with experimentally measured optical properties of skin tissue

Detection of multiple scattering in optical coherence tomography using the spatial distribution of Stokes vectors

Multiple scattering is one of the main degrading influences in optical coherence tomography, but to date its presence in an image can only be indirectly inferred. We present a polarization-sensitive method that shows the potential to detect it more directly, based on the degree to which the detected polarization state at any given image point is correlated with the mean state over the surrounding region. We report the validation of the method in microsphere suspensions, showing a strong dependence of the degree of correlation upon the extent to which multiply scattered light is coherently detected. We demonstrate the method's utility in various tissues, including chicken breast ex vivo and human skin and nailfold in vivo

Investigation of speckle contrast ratio in optical coherence tomography

The speckle contrast ratio in optical coherence tomography images has been shown to depend on scatterer density when the detected signal is dominated by single backscattering. Here we investigate the influence of multiple scattering on the speckle contrast ratio, and also on the parallel and perpendicular polarization channels in polarization-sensitive optical coherence tomography images, including the correlation between them. Conditions under which the contrast ratio and polarization sensitive detection can be used to discriminate regions of OCT images affected by multiple scattering are discussed. The contrast ratio and the correlation between polarization channels were both found to markedly decrease as the ratio of multiple to single scattering increased. A high correlation between polarization channels, indicating that imaging is being performed in the single-scattering regime, provides greater confidence in interpreting the value of scatterer density obtained from the contrast ratio