Biology subjects

Wilson, T.

Publications and source records attributed to Wilson, T..

26 records · Page 2Linked to original sources

bioRxiv2023

A generalizable Cas9/sgRNA prediction model using machine transfer learning with small high-quality datasets

The CRISPR/Cas9 nuclease from Streptococcus pyogenes (SpCas9) can be used with single guide RNAs (sgRNAs) as a sequence-specific antimicrobial agent and as a genome-engineering tool. However, current bacterial sgRNA activity models poorly predict SpCas9/sgRNA activity and are not generalizable, possibly because the underlying datasets used to train the models do not accurately measure SpCas9/sgRNA cleavage activity and cannot distinguish cleavage activity from toxicity. We solved this problem by using a two-plasmid positive selection system to generate high-quality biologically-relevant data that more accurately reports on SpCas9/sgRNA cleavage activity and that separates activity from toxicity. We developed a new machine transfer learning architecture (crisprHAL) that can be trained on existing datasets and that shows marked improvements in sgRNA activity prediction accuracy when transfer learning is used with small amounts of high-quality data. The crisprHAL model recapitulates known SpCas9/sgRNA-target DNA interactions and provides a pathway to a generalizable sgRNA bacterial activity prediction tool.

bioinformatics↗

bioRxiv2022

Synchronisation of apical constriction and cell cycle progression is a conserved behaviour of pseudostratified neuroepithelia informed by their tissue geometry

Neuroepithelial cells balance tissue growth requirement with the morphogenetic imperative of closing the neural tube. They apically constrict to generate mechanical forces which elevate the neural folds, but are thought to apically dilate during mitosis. However, we previously reported that mitotic neuroepithelial cells in the mouse posterior neuropore have smaller apical surfaces than non-mitotic cells. Here, we document progressive apical enrichment of non-muscle myosin-II in mitotic, but not non-mitotic, neuroepithelial cells with smaller apical areas. Live-imaging of the chick posterior neuropore confirms apical constriction synchronised with mitosis, reaching maximal constriction by anaphase, before division and re-dilation. Mitotic apical constriction amplitude is significantly greater than interphase constrictions. To investigate conservation in humans, we characterised early stages of iPSC differentiation through dual SMAD-inhibition to robustly produce pseudostratified neuroepithelia with apically enriched actomyosin. These cultured neuroepithelial cells achieve an equivalent apical area to those in mouse embryos. iPSC-derived neuroepithelial cells have large apical areas in G2 which constrict in M phase and retain this constriction in G1/S. Given that this differentiation method produces anterior neural identities, we studied the anterior neuroepithelium of the elevating mouse mid-brain neural tube. Instead of constricting, mid-brain mitotic neuroepithelial cells have larger apical areas than interphase cells. Tissue geometry differs between the apically convex early midbrain and flat posterior neuropore. Culturing human neuroepithelia on equivalently convex surfaces prevents mitotic apical constriction. Thus, neuroepithelial cells undergo high-amplitude apical constriction synchronised with cell cycle progression but the timing of their constriction if influenced by tissue geometry.

cell biology↗

bioRxiv2022

Genetic exchange in Leishmania is facilitated by IgM natural antibodies

Host factors mediating Leishmania genetic exchange are not well defined. Here, we demonstrate that IgM antibodies, but not IgG or IgA, facilitate parasite genetic hybridization in vitro and in vivo. IgM induces the gradual and transient formation of a structured parasite clump in a process essential for L. major and L. tropica hybridization in vitro. Parasite hybrids and 3-nucleated parasites were observed inside this structure, named the Leishmania mating clump. IgM was also required for or significantly increased Leishmania hybrid formation in vivo. At minimum, we observed a 12-fold increase in the proportion of hybrids recovered from sand flies provided a second blood meal containing IgM compared to controls. Notably, genetic backcross events in sand flies were only observed in the presence of IgM, and were reproducibly recovered, reinforcing the relevance of IgM for Leishmania genetic exchange in vivo. The in vitro and in vivo Leishmania crosses from these studies resulted in full genome hybrids. Leishmania co-option of a host antibody to facilitate mating in the insect vector establishes a new paradigm of parasite-host-vector coevolution that promotes parasite diversity and fitness through genetic exchange.

microbiology↗

bioRxiv2021

Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales

Stable carbon ({delta}13C) and nitrogen ({delta}15N) isotope compositions of bone and dentine collagen extracted from museum specimens have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values need to be transformed into bone-collagen equivalent using a correction factor to allow comparisons between the two collagen sources. Here, we provide correction factors to transform dentine{delta} 13C and{delta} 15N values into bone-collagen equivalent for two toothed whales: narwhal and beluga. We sampled bone and tooth dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in beluga, dentine was sampled from tooth.{delta} 13C and{delta} 15N were measured and intraindividual bone and dentine isotopic compositions were used to calculate correction factors for each species. We detected differences in{delta} 13C and{delta} 15N. In narwhals, we found (i) lower average{delta} 13C and{delta} 15N in bone compared with dentine; (ii) no difference in dentine{delta} 13C between tusk and embedded tooth. For belugas, we also detected lower{delta} 13C and{delta} 15N in bone compared with tooth dentine. The correction factors provided by the study enable the combined analysis of stable isotope data from bone and dentine in these species.

ecology↗

bioRxiv2021

The type and source of reactive oxygen species influences the outcome of oxidative stress in cultured cells

Oxidative stress can be modeled using various different experimental approaches, such as exposing the cells or organisms to oxidative chemicals. However, the actual effects of these chemicals, outside of the immediate measured effect, have attracted relatively little attention. We show here that three commonly used oxidants, menadione, potassium bromate and hydrogen peroxide, while known to function differently, also elicit different types of responses in cultured cells. While cells response to menadione and bromate exposure mainly by an integrated stress response, hydrogen peroxide has more indirect effects. Primary oxidative stress does not induce DNA repair or antioxidant defense mechanisms. However, cells with previous experience of oxidative stress show adaptive changes when the stress is renewed. Our results urge caution when comparing studies using different sources of oxidative stress or generalizing the findings of these studies to different tissue or oxidant types.

cell biology↗

bioRxiv2020

Heme dependent transcriptional regulation of the Pseudomonas aeruginosa tandem sRNA prrF1,F2 locus by the cytoplasmic heme binding protein PhuS

Pseudomonas aeruginosa is an opportunistic pathogen requiring iron for its survival and virulence. P. aeruginosa can acquire iron from heme via the heme assimilation system (Has) and Pseudomonas heme uptake (Phu) systems. The Has and Phu systems have non-redundant roles in heme sensing and transport, respectively. However, despite their respective roles heme taken up by either the Has or Phu system is regulated at the metabolic level by the cytoplasmic heme binding protein PhuS, which controls heme flux through the iron-regulated heme oxygenase HemO. Herein, through a combination of CHIP-PCR, EMSA and fluorescence anisotropy we show PhuS binds upstream of the tandem iron-responsive sRNAs prrF1,F2. Furthermore, qPCR analysis of the PAO1 WT and {Delta}phuS allelic strain shows loss of PhuS abrogates the heme dependent regulation of PrrH. Taken together our data shows PhuS, in addition to its role in regulating extracellular heme metabolism also functions as a transcriptional regulator of the heme-dependent sRNA, PrrH. This dual function of PhuS is central to integrating extracellular heme utilization into the PrrF/PrrH sRNA regulatory network critical for P. aeruginosa adaptation and virulence within the host.

microbiology↗

bioRxiv2019

Mouse and human microglial phenotypes in Alzheimer’s disease are controlled by amyloid plaque phagocytosis through Hif1α

The important role of microglia, the brains resident immune cells, in Alzheimers disease (AD) is now well recognized, however their molecular and functional diversity and underlying mechanisms still remain controversial. To transcriptionally and functionally characterize the diversity of microglia in AD and aging, we isolated the amyloid plaque-containing (XO4+) and non-containing (XO4-) microglia from an AD mouse model. Transcriptomics analysis unveiled independent transcriptional trajectories in ageing and AD. XO4+ microglial transcriptomes linked plaque phagocytosis to altered [Formula] expression of bona fide late onset AD genetic risk factors. We further revealed that the XO4+ transcriptional program is present in a subset of human microglia from AD patients and is a direct and reversible consequence of A{beta} plaque phagocytosis. Conversely, XO4- microglia in AD displayed an accelerated ageing signature and contained more intracellular post synaptic material than plaque-containing microglia, despite reduced active synaptosome phagocytosis. Mechanistically, we predicted HIF1 as a core regulator of the XO4-/XO4+ axis, and further validated the mechanism in vitro using human stem cell-derived microglia like cells and primary human microglia. Together these findings unveiled the molecular mechanism underpinning the functional diversity of microglia in AD, providing opportunities to develop treatments targeted at subset specific manipulation of the microglial niche.

neuroscience↗

bioRxiv2019

Missense mutations in the MLKL brace region lead to lethal neonatal inflammation in mice and are present in high frequency in humans.

We have isolated a mouse strain with a single missense mutation in the gene encoding MLKL, the essential effector of necroptotic cell death. The resulting substitution lies within the two-helix brace and confers constitutive, RIPK3 independent, killing activity to MLKL. Mice homozygous for MlklD139V develop lethal inflammation within days of birth, implicating the salivary glands and pericardium as hotspots for necroptosis and inflammatory infiltration. The normal development of MlklD139V homozygotes until birth, and the absence of any overt phenotype in heterozygotes provides important in vivo precedent for the capacity of cells to clear activated MLKL. These observations offer an important insight into the potential disease-modulating roles of three common human MLKL polymorphisms that encode amino acid substitutions within or adjacent to the brace region. Compound heterozygosity of these variants is found at up to 12-fold the expected frequency in patients that suffer from a pediatric autoinflammatory disease, CRMO.

cell biology↗