Biology subjects

Williams, R. J.

Publications and source records attributed to Williams, R. J..

6 recordsLinked to original sources

bioRxiv2025

A Minimally Invasive, Scalable and Reproducible Neonatal Rat Model of Severe Focal Brain Injury

BackgroundNeonatal brain injuries such as stroke cause focal ischemic lesions that often result in lifelong neurological disabilities, as treatment options are limited. To speed up the discovery of potential therapies, early-phase screening with models that reliably reproduce brain injury, with scalable injury volume and minimal confounders, such as varying anaesthesia duration and painful procedures, is essential. MethodsPostnatal day 10 Sprague-Dawley rats of both sexes, with four litters per group and timepoint, were randomly allocated to delivery of intraperitoneal Rose Bengal (25, 40, or 60 mg/kg) and 10 minutes of light-emitting diode illumination through the intact scalp and skull. Infarct progression and reproducibility were assessed at 24 hours, 7 days, and 14 days post-injury. Outcomes included infarct volume and sensorimotor function, and cleaved caspase-3, glial fibrillary acidic protein (GFAP), and ionised calcium-binding adaptor molecule 1 (Iba1) immunoreactivity, with analysis of sex differences. Data were analysed using one-way or two-way ANOVA with Sidaks post-hoc tests. ResultsThere was no mortality due to the infarct, and procedure time was approximately 19 minutes across all groups; the lesion was consistent and supported scalability. The 25 mg/kg dose produced a reproducible cortical infarct (3.74 {+/-} 0.58 mm3; CV = 31%). Lesion size increased with dose and decreased over time (11.15 {+/-} 0.63 mm3 at 60 mg/kg versus 0.05 {+/-} 0.007 mm3 at 14 days; p < 0.0001). Cleaved caspase-3 and glial activation persisted for 14 days, indicating ongoing apoptosis and gliosis. No sex-dependent effects were observed in lesion volume, behaviour, or gliosis. ConclusionsThis refined neonatal photothrombotic ischaemia model is reproducible, scalable, and ethically improved, requiring no skin incision. Its minimal surgical burden, absence of mortality, consistent histopathology, and measurable functional outcomes make it an ideal platform for preclinical screening of neuroprotective and reparative interventions in the developing brain.

developmental biology↗

bioRxiv2023

Epigallocatechin Gallate Modulates Microglia Phenotype to Suppress Pro-Inflammatory Signalling Cues and Inhibit Phagocytosis

Microglia are crucial players in the pathogenesis of late onset Alzheimers Disease (AD), with evidence for both deleterious and beneficial effects. Identifying interventions to modulate microglial responsiveness, to promote Amyloid {beta} (A{beta}) clearance, disrupt plaque formation or to dampen excessive inflammation has therapeutic potential. Bioavailable flavonoids such as the flavan 3-ols are of interest due to their antioxidant, metal chelating, signalling and anti-inflammatory potential. Primary microglia were treated with a series of structurally related flavanol 3-ols to assess effects on phagocytosis, cytokine release and transcriptional responses by RNA sequencing. Data indicated that the extent of hydroxylation and the presence of the galloyl moiety were strong determinants of flavan 3-ol activity. Epigallocatechin gallate (EGCG) was the most effective flavan-3-ol tested and strongly inhibited phagocytosis of A{beta} independent of any metal chelating properties suggesting a more direct modulation of microglia responsiveness. EGCG was broadly anti-inflammatory, reducing cytokine release and downregulating transcription particularly of components of the microglia extracellular matrix such as MMP3 and SerpinB2. Collectively this brings new insight into the actions of flavonoids on microglial responsiveness with potential implications for the therapeutic use of EGCG and structurally related flavanol-3-ols in AD.

neuroscience↗

bioRxiv2022

Epigenetic cell memory: The gene's inner chromatin modification circuit

Epigenetic cell memory allows distinct gene expression patterns to persist in different cell types despite a common genotype. Although different patterns can be maintained by the concerted action of transcription factors (TFs), it was proposed that long-term persistence hinges on chromatin state. Here, we study how the dynamics of chromatin state affect memory, and focus on a biologically motivated circuit motif, among histones and DNA modifications, that mediates the action of TFs on gene expression. Memory arises from time-scale separation among three circuits constituent processes: basal erasure, auto and cross-catalysis, and recruited erasure of modifications. When the two latter processes are sufficiently faster than the former, the circuit exhibits bistability and hysteresis, allowing active and repressed gene states to coexist and persist after TF stimulus removal. The duration of memory is stochastic with a mean value that increases as time-scale separation increases, but more so for the repressed state. This asymmetry stems from the cross-catalysis between repressive histone modifications and DNA methylation and is enhanced by the relatively slower decay rate of the latter. Nevertheless, TF-mediated positive autoregulation can rebalance this asymmetry and even confers robustness of active states to repressive stimuli. More generally, by wiring positively autoregulated chromatin modification circuits under time scale separation, long-term distinct gene expression patterns arise, which are also robust to failure in the regulatory links.

synthetic biology↗

bioRxiv2021

Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells

Central nervous system-expressed long non-coding RNAs (lncRNAs) are often located in the genome close to protein coding genes involved in transcriptional control. Such lncRNA-protein coding gene pairs are frequently temporally and spatially co-expressed in the nervous system and are predicted to act together to regulate neuronal development and function. Although some of these lncRNAs also bind and modulate the activity of the encoded transcription factors, the regulatory mechanisms controlling co-expression of neighbouring lncRNA-protein coding genes remain unclear. Here, we used high resolution NG Capture-C to map the cis-regulatory interaction landscape of the key neuro-developmental Paupar-Pax6 lncRNA-mRNA locus. The results defined chromatin architecture changes associated with high Paupar-Pax6 expression in neurons and identified both promoter selective as well as shared cis-regulatory interactions with the Paupar and Pax6 promoters involved in regulating Paupar-Pax6 co-expression in neuronal cells. The TCF7L2 transcription factor, a major regulator of chromatin architecture and effector of the Wnt signalling pathway, binds to a subset of these candidate cis-regulatory elements to coordinate Paupar and Pax6 co-expression. We identify a functional TCF7L2 bound cis-regulatory element within the Paupar gene, suggesting that the Paupar DNA locus itself regulates Pax6 expression in addition to its previously described transcriptdependent modes of action. Our work provides important insights into the chromatin interactions, signalling pathways and transcription factors controlling co-expression of adjacent lncRNAs and protein coding genes in the brain.

genomics↗

bioRxiv2020

PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation

Pel is an N-acetylgalactosamine rich polysaccharide that contributes to the structure and function of Pseudomonas aeruginosa biofilms. The pelABCDEFG operon is highly conserved among diverse bacterial species, and thus Pel may be a widespread biofilm determinant. Previous annotation of pel gene clusters led us to identify an additional gene, pelX, that is found adjacent to pelABCDEFG in over 100 different bacterial species. The pelX gene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily of enzymes, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have used Pseudomonas protegens Pf-5 as a model to understand PelX function as P. aeruginosa lacks a pelX homologue in its pel gene cluster. We find that P. protegens forms Pel-dependent biofilms, however, despite expression of pelX under these conditions, biofilm formation was unaffected in a {Delta}pelX strain. This observation led to our identification of the pelX paralogue, PFL_5533, which we designate pgnE, that appears to be functionally redundant to pelX. In line with this, a {Delta}pelX {Delta}pgnE double mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1[A] resolution. The structure revealed that PelX resembles UDP-N-acetylglucosamine (UDP-GlcNAc) C4-epimerases and, using 1H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Taken together, our results demonstrate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.

microbiology↗

bioRxiv2019

Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses.

Herpes Simplex Virus type 1 (HSV-1) chronically infects over 70% of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. By contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.

evolutionary biology↗