Biology subjects

Blake, R.

Publications and source records attributed to Blake, R..

9 recordsLinked to original sources

bioRxiv2026

A genome-wide CRISPR knockout screen identifies host dependency factors and potential viral-induced cell death regulators for porcine deltacoronavirus infection

Porcine deltacoronavirus (PDCoV) is a globally circulating coronavirus of swine that causes severe enteric disease and mortality in neonatal piglets. Its broad host range and zoonotic potential raises concerns about continued spillover into human populations. However, the host factors that govern PDCoV infection remain largely unexplored. Identifying host factors involved in virus infection may uncover novel therapeutic targets for antiviral drug development or targets for gene editing to create resistant pigs. Here, we conducted a genome-wide CRISPR knockout (GeCKO) screen to identify host factors contributing to PDCoV infection in swine testicular (ST) cells. Small guide RNAs (sgRNAs) targeting the ANPEP gene, expressing the main receptor porcine aminopeptidase N for PDCoV, were enriched in PDCoV-resistant cells, demonstrating the validity of the screen. Moreover, we identified transmembrane protein 30A (TMEM30A), an accessory {beta}-subunit of the P4-ATPase flippase complex, as a host dependency factor for PDCoV infection along with several potential PDCoV-induced cell death regulators, including DET1, IFNAR1, RFWD2, STAT1 and TP53. We further demonstrated that PDCoV attachment and internalization into cells were significantly impaired in TMEM30A knockout ST cells, suggesting that TMEM30A is important in the early stages of the PDCoV life cycle. Because TMEM30A also contributes to SARS-CoV-2 replication, future studies are warranted to investigate its mechanistic role in the context of coronavirus infection.

molecular biology↗

bioRxiv2023

Investigating the role of Mce proteins in Mycobacterium avium paratuberculosis infection

Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johnes Disease, a chronic granulomatous enteritis of ruminants. MAP establishes an infection in the host via the small intestine. This requires the bacteria to adhere to and be internalised by cells of the intestinal tract. The effector molecules expressed by MAP for this remain to be fully identified and understood. The mammalian cell entry (Mce) proteins play an essential role for other Mycobacterial species to facilitate the attachment and invasion of host epithelial cells. Here, we have expressed Mce1A, Mce1D, Mce3C and Mce4A proteins derived from MAP on the surface of a non-invasive E. coli host to characterise their role in the initial interaction between MAP and the host. To this end, mce1A was found to significantly increase the ability of the E. coli to attach and survive intracellularly in THP-1 cells, and mce1D was found to significantly increase attachment and invasion of MDBK cells. Both genes were implicated in the increased ability of E. coli to infect 3D bovine basal-out enteroids. Together, these results have identified two effector molecules used by MAP with a degree of cell-type specificity.

microbiology↗

bioRxiv2023

tCFS: A new 'CFS tracking' paradigm reveals uniform suppression depth regardless of target complexity or salience

When the eyes view separate and incompatible images, the brain suppresses one image and promotes the other into visual awareness. Periods of interocular suppression can be prolonged during continuous flash suppression (CFS) - when one eye views a static target while the other views a complex dynamic stimulus. Measuring the time needed for a suppressed image to break CFS (bCFS) has been widely used to investigate unconscious processing, and the results have generated controversy regarding the scope of visual processing without awareness. Here, we address this controversy with a new CFS tracking paradigm (tCFS) in which the suppressed monocular target steadily increases in contrast until breaking into awareness (as in bCFS) after which it decreases until it again disappears (reCFS), with this cycle continuing for many reversals. Unlike bCFS, tCFS provides a measure of suppression depth by quantifying the difference between breakthrough and suppression thresholds. tCFS confirms that: (i) breakthrough thresholds indeed differ across target types (e.g., faces vs gratings, as bCFS has shown) - but (ii) suppression depth does not vary across target types. Once the breakthrough contrast is reached for a given stimulus, all stimuli require a strikingly uniform reduction in contrast to reach the corresponding suppression threshold. This uniform suppression depth points to a single mechanism of CFS suppression, one that likely occurs early in visual processing because suppression depth was not modulated by target salience or complexity. More fundamentally, it shows that variations in bCFS thresholds alone are insufficient for inferring whether the barrier to achieving awareness exerted by interocular suppression is weaker for some categories of visual stimuli compared to others. Significance statementResearch on unconscious vision has proliferated recently, often employing the continuous flash suppression (CFS) method in which rapidly changing shapes viewed by one eye suppress the other eyes image from awareness. If that suppressed image is progressively strengthened in contrast it will eventually break suppression and emerge into visible awareness. Low breakthrough thresholds are claimed to indicate unconscious processing during suppression. We introduce a method that quantifies breakthrough thresholds and suppression thresholds, thus providing a lower bound missing from previous CFS research. Comparing various image types, including those claimed to undergo unconscious processing, all images show equal suppression when both thresholds are measured. We thus find no evidence of differential unconscious processing and conclude reliance on breakthrough thresholds is misleading without considering suppression thresholds and leads to spurious claims about unconscious processing.

neuroscience↗

bioRxiv2023

Drivers of asymmetrical insect invasions between three world regions

The geographical exchange of non-native insects can be highly asymmetrical, with some world regions exporting or importing more species than others. Several hypotheses have been proposed to explain such asymmetries, including differences in propagule pressure, environmental features in recipient regions, or biological traits of invaders. We tested aspects of these hypotheses in the context of the exchange of non-native insects between North America, Europe, and Australasia. Europe was the dominant exporter of non-native insect species between the three regions, with most of this asymmetry arising prior to 1950. The European dominance could not be explained by differences in import value, source species pool sizes, or native plant richness in the recipient regions. We identified that the introduction of non-native plants, driven in part by European colonization, best explains the asymmetrical exchange of non-native insects between our focal regions.

ecology↗

bioRxiv2022

Development of 3D bovine intestinal organoid derived models to investigate Mycobacterium avium ssp paratuberculosis pathogenesis

Mycobacterium avium subspecies paratuberculosis (MAP) is the etiologic agent of Johnes Disease, a chronic enteritis of ruminants prevalent across the world. It is estimated that approximately 50% of UK dairy herds are infected with MAP, but this is likely an underestimate of the true prevalence. Infection can result in reduced milk yield, infertility and premature culling of the animal, leading to significant losses to the farming economy and negatively affecting animal welfare. Understanding the initial interaction between MAP and the host is critical to develop improved diagnostic tools and novel vaccines. Here we describe the characterisation of three different multicellular in vitro models derived from bovine intestinal tissue, and their use for the study of cellular interactions with MAP. In addition to the previously described basal-out 3D bovine enteroids, we have established viable 2D monolayers and 3D apical-out organoids. The apical-out enteroids differ from previously described bovine enteroids as the apical surface is exposed on the exterior surface of the 3D structure, enabling study of host-pathogen interactions at the epithelial surface without the need for microinjection. We have characterised the cell types present in each model system using RT-qPCR to detect predicted cell type-specific gene expression and confocal microscopy for cell type-specific protein expression. Each model contained the cells present in the bovine ileum and were therefore representative of the bovine gut. Exposure of the three model systems to the reference strain MAP K10, and a recent Scottish isolate referred to as C49, led to the observation of intracellular bacteria by confocal microscopy. Enumeration of the bacteria by genome copy number quantification, indicated that K10 was less invasive than C49 at early time points in infection in all model systems. This study shows that bovine enteroid-based models are permissive to infection with MAP and that these models may be useful in investigating early stages of MAP pathogenesis in a physiologically relevant in vitro system, whilst reducing the use of animals in scientific research.

microbiology↗

bioRxiv2021

Getting the gist faster: Blurry images enhance the early temporal similarity between neural signals and convolutional neural networks

Humans are able to recognize objects under a variety of noisy conditions, so models of the human visual system must account for how this feat is accomplished. In this study, we investigated how image perturbations, specifically reducing images to their low spatial frequency (LSF) components, affected correspondence between convolutional neural networks (CNNs) and brain signals recorded using magnetoencephalography (MEG). Using the high temporal resolution of MEG, we found that CNN-Brain correspondence for deeper and more complex layers across CNN architectures emerged earlier for LSF images than for their unfiltered broadband counterparts. The early emergence of LSF components is consistent with the coarse-to-fine theoretical framework for visual image processing, but surprisingly shows that LSF signals from images are more prominent when high spatial frequencies are removed. In addition, we decomposed MEG signals into oscillatory components and found correspondence varied based on frequency bands, painting a full picture of how CNN-Brain correspondence varies with time, frequency, and MEG sensor locations. Finally, we varied image properties of CNN training sets, and found marked changes in CNN processing dynamics and correspondence to brain activity. In sum, we show that image perturbations affect CNN-Brain correspondence in unexpected ways, as well as provide a rich methodological framework for assessing CNN-Brain correspondence across space, time, and frequency.

neuroscience↗

bioRxiv2021

Seeing the World Like Never Before: Human stereovision through perfect optics

Stereovision is the ability to perceive fine depth variations from small differences in the two eyes images. Using adaptive optics, we show that even minute optical aberrations that are not clinically correctable, and go unnoticed in everyday vision, can affect stereo acuity. Hence, the human binocular system is capable of using unnaturally fine details that are not encountered in everyday vision. More importantly, stereoacuity was still considerably variable even with perfect optics. This variability can be attributed to neural adaptation. Our visual system tries to compensate for these aberrations through neural adaptation that optimizes stereovision when viewing stimuli through ones habitual optics. However, the same adaptation becomes ineffective when the optics are changed, even if improved. Beyond optical imperfections, we show that stereovision is limited by neural adaptation to ones own optics. Significance statementHumans, and animals with front-facing eyes, view the world from slightly different vantage points. This creates small differences in the left and right images that can be utilized for fine depth perception (stereovision). Retinal images are also subject to imperfections that are often different in the optics of the two eyes. Using advanced optical correction techniques, we show that even the smallest imperfections that escape clinical detection affect stereovision. We also find that neural processes become adapted to a persons own optics. Hence, stereovision is directly impacted by the optics of the eyes, and indirectly via neural adaptation. Since the optics change over the lifespan, our results imply that the adult binocular system is adaptable with possibilities for binocular rehabilitation.

neuroscience↗

bioRxiv2019

ZMIZ1 - A novel Estrogen Receptor co-activator that enhances the growth of ER+ breast cancer

The Estrogen Receptor (ER) drives 75% of breast cancers. On activation, the ER recruits co-factors to form a transcriptionally active complex. These co-factors can modulate tumour growth, and understanding their roles can help to identify new therapeutic targets. Here, we present the discovery of an ER-ZMIZ1 interaction by quantitative proteomics, and validated by proximity ligation assay. We characterise ZMIZ1 function by demonstrating that targeting ZMIZ1 results in the reduction of ER transcriptional activity at estrogen response elements and a significant decrease in the proliferation of ER-positive cancer cell lines. To establish a role for the ER-ZMIZ1 interaction, we measured the transcriptional changes in the estrogen response post-ZMIZ1 knockdown using an RNA-seq time-course over 24 hours. GSEA analysis of the ZMIZ1-knockdown data identified a specific delay in the response of estradiol-induced cell-cycle genes. Integration of ENCODE data with our RNA-seq results identified ER and ZMIZ1 binding at the promoter of E2F2. We therefore propose that ER and ZMIZ1 co-regulate an important subset of cell cycle genes via a novel ER-ZMIZ1-E2F2 signalling axis. Finally, we show that high ZMIZ1 expression is predictive of worse patient outcome, ER and ZMIZ1 are co-expressed in breast cancer patients in TCGA, METABRIC, and the proteins are co-localised within the nuclei of tumours cell in patient biopsies. In conclusion, we establish that ZMIZ1 is a regulator of the estrogenic cell cycle response and provide evidence of the biological importance of the ER-ZMIZ1 interaction ER+ patient tumours, supporting potential clinical relevance.

cancer biology↗

bioRxiv2019

Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain

Neuronal cell types are the nodes of neural circuits that determine the flow of information within the brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of cell type and reveals how individual neurons route their output across the brain. Despite the importance of morphology, few projection neurons in the mouse brain have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the brain. We used this platform to reconstruct more than 1,000 projection neurons in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed neurons comprise more than 75 meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of projection neurons and suggest organizational principles of long-range connectivity.

neuroscience↗