Biology subjects

Graham, S.

Publications and source records attributed to Graham, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Dual ATPase-activated DNA hemimethylation and cleavage by the MANTIS defence system

Bacterial defence systems are diverse and form major barriers to horizontal gene transfer and bacteriophage (phage) infection. Though restriction-modification systems were the first such defences discovered and remain the most widespread, the basis of self/non-self discrimination in many newly identified methylation-based systems remains unclear. Here, we define the mechanism of a widely distributed BREX-related defence family, previously termed Gao_RL, which we rename MANTIS (Methyltransferase, ATPases and Nuclease Targeting Inverted-repeat Sequences). Using phage infection and plasmid transformation assays in Pseudomonas aeruginosa, biochemical reconstitution, and structural biology, we show that MANTIS establishes self-identity through adenine hemimethylation of short asymmetric DNA sequences. Unexpectedly, a AAA+ ATPase (MtsA) and a co-regulator (MtsB) are both required to recruit and activate the methyltransferase MtsC, revealing a previously unknown ATP-dependent mode of epigenetic modification. DNA recognition by the MtsABC complex then triggers restriction by a dimeric helicase-nuclease effector (MtsD), with activity dependent on target-site architecture: inverted pairs of unmodified sites support robust restriction, whereas direct repeats or single sites are restricted less efficiently. Consistent with this model, virulent phages show strand-biased depletion of MANTIS target sites, indicating evolutionary pressure to evade restriction. Together, these findings reveal how dual ATPases couple self-modification to non-self restriction and provide a framework for understanding the expanding landscape of methylation-based defence systems.

molecular biology↗

bioRxiv2026

Correlating Structure and Rheology in Ionically Crosslinked Alginate Biopolymer Hydrogels - A Case for Why "Less" can be "More"

We probe the structural and rheological properties of ionically crosslinked alginate, a model biopolymer hydrogel, using microscopy, rheology and viscosity dependent molecular probes. This combination of techniques enables the quantification and correlation of microstructure, microviscosity, bulk viscoelasticity and yielding dynamics. By adjusting the stoichiometric ratio, R, between the alginate biopolymer and its cation crosslinks, we observe a transition from a homogeneous network-like structure to a coarse bundle-like structure at high (R>0.67) stoichiometric ratio. Intriguingly, these bundle-like structures have distinct and counter-intuitive rheological properties. Using molecular probes, we observe a continuous decrease in microviscosity that is correlated with a decrease in bulk elastic modulus and an increase in energy dissipation. This is accompanied by a transition in the hydrogel yielding under strain from a sharp, well-defined yield point to a continuous ductile-like yielding. We ascribe these surprising transitions to the looser intermolecular interaction between alginate biopolymers in the bundle-like state, as previously predicted by x-ray scattering experiments. These findings reveal new and counter-intuitive structure-property relations that demonstrate high crosslink concentration does not necessarily translate to optimal mechanical performance. SignificanceAlginate is a polysaccharide biopolymer naturally found in brown seaweed cell walls. Extracted alginate forms ionically crosslinked hydrogels that are strong, flexible and increasingly valuable in the biomedical, packaging and food industries. A large part of the utility of these hydrogels stems from the ease with which their mechanics can be tuned through adjusting the stoichiometry between alginate and its ionic crosslinks. However, little is known about how the material properties of alginate hydrogels, in particular their rheology and dynamics, are affected by microscale structural transitions at high stoichiometric ratios. Here, we use a multi-modal approach to describe and correlate hydrogel material properties and to demonstrate that increased polymer crosslinking can, counterintuitively, sometimes weaken hydrogel performance.

biophysics↗

bioRxiv2026

Cortical Excitation-Inhibition Balance in Autism Varies by Brain Region and Age

Autism spectrum disorder (ASD) is characterized by differences in social communication, interaction, and restricted and repetitive behaviors. The hypothesis that ASD involves altered cortical excitation-inhibition (EI) balance has been extensively investigated, yet evidence remains mixed, partly because EI balance changes substantially during typical maturation. We used resting-state magnetoencephalography (MEG) to examine developmental trajectories of cortical EI alterations with regional specificity in a large cross-sectional cohort (N = 172; 92 typically developing, 80 ASD; ages 6-32). Functional EI (fEI), derived from critical brain dynamics, was estimated across 500 cortical parcellations. Group-averaged fEI maps revealed broadly similar large-scale topographic patterns across groups. Age-stratified analyses revealed increased global fEI in childhood and decreased fEI in adolescence in ASD, with no evidence of a group difference in adulthood. Parcel-wise regressions identified a significant main effect of diagnosis in right dorsolateral prefrontal cortex, where typically developing individuals showed higher fEI across all ages. A significant group-by-age interaction in left inferior parietal cortex indicated diverging developmental trajectories. Finally, fEI in paracentral and precuneus regions was associated with the magnitude of ASD symptoms. These findings indicate that EI imbalance in ASD is neither globally distributed nor static, but expressed through regionally and developmentally specific differences, with relevance for ASD heterogeneity.

neuroscience↗

bioRxiv2026

Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector

Cyclic nucleotide second messengers are used in all domains of life to amplify viral infection signals and activate cellular defences. In prokaryotes, CBASS (cyclic nucleotide based antiphage signalling system) and type III CRISPR-Cas systems generate a range of cyclic nucleotides which bind and allosterically activate effector proteins to mount an anti-viral response. Viruses have evolved counter-measures to antagonise these signalling pathways in the form of cyclic nucleotide sponges and phosphodiesterases that sequester or degrade these molecules to subvert immunity. Recently, the Panoptes system was shown to function as a guard against these viral tactics. The type I Panoptes polymerase, mCpol, generates cyclic dinucleotides as decoy molecules that, when sequestered by phage proteins, results in the activation of the membrane-permeabilising effector 2TM{beta} to halt the phage infection cycle. Here, we investigate the type II Panoptes system, demonstrating that it generates cyclic tri-adenylate (cA3) to maintain a CRISPR-associated Rossmann fold-transmembrane (CARF-TM) effector in an inactive, dimeric state. When cA3 is sequestered or degraded, the CARF-TM protein oligomerises, resulting in increased outer membrane permeability and growth arrest. These findings expand our understanding of the guard systems that constitute a fascinating component of the bacterial immune system.

biochemistry↗

bioRxiv2026

The CRISPR ring nuclease Csx15 oligomerises on cyclic nucleotide binding to regulate antiviral defence

Prokaryotic type III CRISPR systems signal infection by generating cyclic oligoadenylate (cOA) second messengers, which activate defence proteins allosterically, providing immunity. cOA molecules are typically degraded by extrinsic, stand-alone ring nuclease (RN) enzymes with phosphodiesterase activity, or by the intrinsic RN activity of the effectors themselves. Viruses and plasmids also encode RNs, which can function as anti-CRISPRs (Acr). Eight different families of extrinsic RNs are currently known. Here, we report the structural and biochemical analysis of one of these families: Csx15. We show that Csx15 is a dimeric protein with the ability to bind cyclic tetra-adenylate (cA4) molecules in a shared binding site formed by the head-to-tail stacking of dimers in a filament conformation. Some family members are non-enzymatic, relying on the sequestration (sponging) of cA4 to regulate the host immune response, while others act as canonical RNs, slowly degrading cA4.

biochemistry↗

bioRxiv2025

Global phylogeography of Amrasca biguttula (Hemiptera: Cicadellidae) across eight countries reveals a single-haplotype incursion into the United States beyond its putative native range

Amrasca biguttula is a pest of cotton, ornamentals, and vegetables, and is invading the southeastern United States. We addressed five questions: (1) Are US populations genetically identical to those in the putative native range? (2) Does the southeastern US outbreak extend the recent Puerto Rico and Florida invasion or represent separate introductions? (3) Does the lineage infesting ornamentals match that on other crops? (4) What is the mitochondrial cytochrome oxidase subunit 1 (mtCOI) diversity of A. biguttula? (5) Which regions constitute its native versus invaded range? Adults were collected from Florida, Georgia, South Carolina, Texas, and Puerto Rico. Species identity was confirmed morphologically and by sequencing mtCOI, where possible, from five individuals per site, yielding consensus haplotypes. We analyzed 11 US, 20 Puerto Rican, and 342 sequences originating from publicly available databases (n = 373). Phylogenetic analysis confirmed monophyly of this species. A haplotype network recovered 70 unique haplotypes, including a star-like core of 68 radiating from Hap01 and two divergent singletons. The mainland US and Chinese populations were fixed for Hap01, indicating recent introductions. Puerto Rico exhibited Hap01, Hap52, and Hap70, reflecting multiple introductions, but could also result from haplotype diversity carried within a single introduction involving many individuals. Furthermore, southeastern US sites were fixed for Hap01, indicating extension from Puerto Rico and Florida. No haplotype was host-specific, confirming a lineage across crops. Diversity metrics indicate recent expansion in Iraq, Hong Kong, and Puerto Rico. South Asia, particularly Bangladesh, India, and Pakistan, showed the highest haplotype diversity, supporting its role as the putative native range. In contrast, low diversity in China and the US is consistent with recent invasion. Curation yielded 373 high-quality sequences, providing a unified database to support quarantine and management strategies.

genetics↗

bioRxiv2025

Structure and mechanism of the broad spectrum CRISPR-associated ring nuclease Crn4

Type III CRISPR systems detect the presence of RNA from mobile genetic elements (MGE) in prokaryotes, providing antiviral immunity. On activation, the catalytic Cas10 subunit conjugates ATP to form cyclic oligoadenylate (cOA) signalling molecules that activate ancillary e\ectors, providing an immune response. Cellular ring nucleases degrade cOA to reset the system. Here, we describe the structure and mechanism of a new family of ring nucleases, Crn4, associated with type III-D CRISPR systems. The crystal structure of Crn4 reveals a small homodimeric protein with a fold unrelated to any known ring nuclease or, indeed, any known protein structure. Crn4 degrades a range of cOA species to linear oligoadenylates in vitro and ameliorates type III CRISPR immunity in vivo. Phage and plasmids also encode Crn4 orthologues that may function as anti-CRISPRs. These observations expand our understanding of ring nucleases and reveal a new protein fold for cyclic nucleotide recognition.

biochemistry↗

bioRxiv2025

SAM-AMP lyases in CRISPR defence and anti-defence

Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation of ancillary effectors. Although most signal via cyclic oligoadenylate (cOA), an alternative class of signalling molecule SAM-AMP, formed by conjugating ATP and S-adenosyl methionine, was described recently. SAM-AMP activates a trans-membrane effector of the CorA magnesium transporter family to provide anti-phage defence. Intriguingly, immunity also requires SAM-AMP degradation by means of a specialised CRISPR-encoded NrN family phosphodiesterase in Bacteroides fragilis. In Clostridium botulinum, the nrn gene is replaced by a gene encoding a SAM-AMP lyase. Here, we investigate the structure and activity of C. botulinum SAM-AMP lyase, which can substitute for the nrn gene to provide CorA-mediated immunity in Escherichia coli. The structure of SAM-AMP lyase bound to its reaction product methylthioadenosine-AMP (MTA-AMP) reveals key details of substrate binding and turnover by this PII superfamily protein. Bioinformatic analyses reveal candidate phage-encoded SAM-AMP lyases and we demonstrate that one, hereafter named AcrIIIB4, degrades SAM-AMP efficiently in vitro.

biochemistry↗

bioRxiv2025

A Multi-Organ Murine Metabolomics Atlas Reveals Molecular Dysregulations in Alzheimer's Disease

The etiology of Alzheimers Disease (AD) remains largely unclear but is likely driven by gene-environment interactions. Here, we present a multi-organ untargeted metabolomics dataset (2,271 samples) generated from five tissue types in two genetic AD mouse models under colonized or germ-free conditions, complemented by shotgun metagenomics sequencing data (666 samples). Systems-level analyses of 3xTg and 5xFAD mice reveal clusters of dysregulated molecular classes across tissues including carnitines, bile acids, B vitamins, and neurotransmitters. This signature, coupled with microbiome profiles, suggests increased oxidative stress via mitochondrial dysfunction. Molecular feature tracking via tissueMASST, a mass spectrometry search tool we developed to bridge animal model findings with human data, identifies microbially-modulated phenylacetyl-carnitine as positively associated with aging and cognitive impairment across human AD studies. With hundreds of yet-to-be-characterized metabolites, this public resource and its associated tools will aid future research in the pathophysiology of AD.

microbiology↗

bioRxiv2025

Decreased auditory cortical activations and altered long-range alpha-band connectivity characterize passive auditory spatial attention in ASD

Autism Spectrum Disorder (ASD) is a developmental condition characterized by difficulties in social interaction, communication and sensory processing. The ability to orient towards sounds is a key component of social interactions, yet auditory spatial attention remains relatively understudied in ASD, despite prior research indicating differences in this domain. Here, we investigate the neural signatures associated with passive auditory spatial attention in children with ASD (n = 21, ages 6-17) relative to age- and IQ-matched typically developing (TD) children (n = 31), using source-localized magnetoencephalography (MEG). Participants listened passively, while watching a silenced movie, to non-social auditory stimuli designed to either remain lateralized to one hemifield (stay trials), or to change in location from one side to the contralateral hemifield (jump trials). Linear mixed effects modeling showed lower cortical activation in the auditory cortex in the ASD group in response to jump trials, relative to the TD group. Additionally, functional connectivity analyses showed higher alpha-band functional connectivity in the ASD group between left auditory cortex seeds and right prefrontal and left parietal regions known to be recruited during auditory spatial attention. Right prefrontal alpha-band connectivity estimates were associated with behaviorally assessed auditory processing scores, whereas left parietal connectivity estimates were associated with ASD symptomatology. Our results align with the hypothesis that auditory spatial attention generally, and specifically orientation to sounds even when experienced passively, differs in ASD individuals.

neuroscience↗

bioRxiv2024

Characterising alphacoronavirus phenotypic traits through diversity-driven selection of spike

The capacity for viruses to spillover from one host to another is dependent on their ability to bind to and enter cells from a new host. Using a computational approach that maximises phylogenetic diversity, we selected an optimal subset of 40 alphacoronavirus spike proteins, including the two human viruses NL63 and 229E, and characterised their host-range using broad mammalian APN and ACE2 receptor libraries. Based on this data, we were able to determine molecular genotypes that contribute to receptor tropism and identify alphacoronaviruses with broad (generalist) or restricted (specialist) receptor usage. Strikingly, we observed that generalism and specialism can vary significantly between closely related viruses. Using structural information, we identified key residues that determine the bat tropism of 229E-like viruses, as well as residues in the ACE2 receptor that likely restrict NL63 infection of certain mammals. Furthermore, we observed that the host range of certain bat alphacoronaviruses is expanded by TMPRSS2 priming of spike. All APN- and ACE2-using alphaCoVs in our study interacted with the receptor of at least one animal species within ecological proximity to humans, suggesting new routes for spillover. However, most bat alphacoronaviruses did not use any of receptors in our screen, refining our understanding of coronavirus entry. We propose a new approach to investigating receptor usage for viral orders/families/genera, which is not constrained by focused analysis of a limited number of sequences from human-tropic viruses. Understanding phenotypic traits, such as entry, at this genus-wide level can revolutionise our ability to predict zoonotic potential.

microbiology↗

bioRxiv2024

The splicing factor kinase, SR protein kinase 1 (SRPK1) is essential for late events in the human papillomavirus life cycle.

Human papillomaviruses (HPV) infect epithelial causing benign lesions. However, the so-called "high risk" HPVs that infect the anogenital regions and the oropharynx can cause precancerous lesions that can progress to malignant tumours. Understanding the HPV life cycle is important to the discovery of novel antiviral therapies. HPV uses cellular splicing for the production of the full suite of viral mRNAs. Members of the serine/arginine rich (SR) protein family can positively regulate splicing. SR protein activity and cellular location is regulated by kinases through phosphorylation of their serine-arginine domains. SR protein kinase 1 (SRPK1) phosphorylates SR proteins to licence their nuclear entry and can promote nuclear splicing in conjunction with another SR protein kinase, Clk1. SRPIN340 is a specific SRPK1 inhibitor that has been reported to inhibit replication of HCV, Sindbis virus and HIV. Using organotypic raft cultures supporting the HPV16 life cycle, we show that SRPIN340 inhibits the expression of the viral replication and transcription factor, E2. Drug-mediated loss of E2 is specifically associated with inhibition of late gene expression since early gene expression is unaffected. RNA sequencing revealed that SRPIN340 treatment resulted in many gene expression changes opposite to those induced by HPV16 infection. In particular, the loss of epithelial barrier structure and immune function was restored. SRPIN340 treatment resulted in changes in alternative splicing of 935 RNAs and pathway analysis showed a predominance of changes to RNAs encoding proteins involved in chromatin conformation, DNA repair and RNA processing. SRPIN340 treatment was not associated with changes in proliferation or differentiation of keratinocytes. Collectively, these results provide evidence that SRPK1 is a host factor that is essential for HPV16 replication and therefore, targeting this factor, or the phosphorylation events it mediates, could be considered as a therapeutic strategy for HPV16 infection. AUTHOR SUMMARYHuman papillomavirus (HPV) can cause precancerous and cancerous tumours of the anogenital region, for example, the cervix. HPV infects epithelial cells and utilizes the host cell gene expression machinery to produce its own proteins. Splicing is a key mechanism used by HPV to synthesise messenger RNAs that encode the viral proteins. Splicing is positively controlled by SR proteins which require to be phosphorylated by SR protein kinase (SRPK) to enter the nucleus and regulate splicing. SRPIN340 is a specific inhibitor of SRPK. SRPIN340 treatment of HPV16-infected epithelial cells resulted in loss of expression of the viral replication and transcription factor, E2 and abrogation of late events in the viral life cycle. SRPIN340 treatment counteracted some gene expression changes to the epithelium known to be cause by HPV infection. These data suggest that SRPK1 is essential for the HPV life cycle and that it could be a potential anti-viral target.

microbiology↗

bioRxiv2024

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) elicited dose-dependent shifts in the murine urinary metabolome associated with hepatic AHR-mediated differential gene expression

Epidemiological evidence suggests an association between dioxin and dioxin-like compound (DLC) exposure and human liver disease. The prototypical DLC, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), has been shown to induce the progression of reversible hepatic steatosis to steatohepatitis with periportal fibrosis and biliary hyperplasia in mice. Although the effects of TCDD toxicity are mediated by aryl hydrocarbon receptor (AHR) activation, the underlying mechanisms of TCDD-induced hepatotoxicity are unresolved. In the present study, male C57BL/6NCrl mice were gavaged every 4 days for 28 days with 0.03 - 30 g/kg TCDD and evaluated for liver histopathology and gene expression as well as complementary 1-dimensional proton magnetic resonance (1D-1H NMR) urinary metabolic profiling. Urinary trimethylamine (TMA), trimethylamine N-oxide (TMAO), and 1-methylnicotinamide (1MN) levels were altered by TCDD at doses [≤] 3 g/kg; other urinary metabolites, like glycolate, urocanate, and 3-hydroxyisovalerate, were only altered at doses that induced moderate to severe steatohepatitis. Bulk liver RNA-seq data suggested altered urinary metabolites correlated with hepatic differential gene expression corresponding to specific metabolic pathways. In addition to evaluating whether altered urinary metabolites were liver-dependent, published single-nuclear RNA-seq (snRNA-seq), AHR ChIP-seq, and AHR knockout gene expression datasets provide further support for hepatic cell-type and AHR-regulated dependency, respectively. Overall, TCDD-induced liver effects were preceded by and occurred with changes in urinary metabolite levels due to AHR-mediated changes in hepatic gene expression.

molecular biology↗

bioRxiv2024

Diversity and abundance of ring nucleases in type III CRISPR-Cas loci

Most type III CRISPR-Cas systems facilitate immune responses against invading mobile genetic elements such as phages by generating cyclic oligoadenylates (cOAs). Downstream effectors activated by cOAs are typically non-specific proteins that induce damage to essential cellular components, thereby preventing phage epidemics. Due to these toxic effects, it is crucial that the production and concentration of cOAs remain under tight regulatory control during infection-free periods or when deactivating the immune response after clearing an infection. Type III CRISPR loci often encode enzymes known as ring nucleases (RNs) that bind and degrade specific cOAs, while some effectors are auto-deactivating. Despite the discovery of several classes of RNs, a comprehensive bioinformatic analysis of type III CRISPR-Cas loci in this context is lacking. Here, we examined 38,742 prokaryotic genomes to provide a global overview of type III CRISPR loci, focussing on the known and predicted RNs. The candidate RNs Csx16 and Csx20 are confirmed as active enzymes, joining Crn1-3. Distributions and patterns of co-occurrence of RNs and associated effectors are explored, allowing the conclusion that a sizeable majority of type III CRISPR systems regulate cOA levels by degrading the signalling molecules, which has implications for cell fate following viral infection.

bioinformatics↗

bioRxiv2024

Human iPSC-derived brain pericytes exhibit differences in inflammatory activation compared to primary human brain pericytes

BackgroundiPSC-derived cells are increasingly used to model complex diseases in vitro because they can be patient derived and can differentiate into any cell in the adult human body. Recent studies have demonstrated the generation of brain pericytes using a neural crest-based differentiation protocol. However, the inflammatory response of these iPSC-derived brain pericytes has not been investigated. We aimed to investigate the response of iPSC-derived brain pericytes to common inflammatory stimuli, thereby assessing the suitability of these cells to study inflammatory disease. MethodsBrain pericytes were differentiated from iPSCs for 42 days. The expression of brain pericyte markers was assessed by RT-qPCR and immunofluorescent staining at days 0, 15, 21, and 42 of differentiation to validate the brain pericyte-like phenotype. Nuclear localisation of NF{kappa}B and STAT1 was assessed by immunofluorescence following IL-1{beta}- and TNF-treatment in day 21 and day 42 iPSC-derived pericytes, and primary human pericytes. Cytometric bead array assessed the concentration of secreted inflammatory factors in the cell medium and phagocytosis was investigated using fluorescent carboxylated beads and flow cytometry. ResultsAt day 42 of differentiation, but not at day 21, cells expressed brain pericyte markers. Generally, iPSC-derived pericytes lacked consistent responses to inflammatory treatment compared to primary human pericytes. Day 21 and 42 iPSC-derived pericytes exhibited a NF{kappa}B response to IL-1{beta} treatment comparable to primary human pericytes. Day 21 iPSC-derived pericytes exhibited a STAT1 response with IL-1{beta} treatment which was absent in day 42 cells, but present in a subset of primary human pericytes. TNF treatment presented similar NF{kappa}B responses between day 21 and 42 iPSC-derived and primary human pericytes, but a STAT1 response was again present in a subset of primary human pericytes which was absent in both day 21 and day 42 iPSC-derived pericytes. Numerous differences were observed in the secretion of cytokines and chemokines following treatment of iPSC-derived and primary human pericytes with IL-1{beta} and TNF. iPSC-derived pericytes exhibited greater rates of phagocytosis than primary human pericytes. ConclusionsWith the increase in iPSC-derived cells in research, labs should undertake validation of lineage specificity when adapting an iPSC-derived differentiation protocol. In our hands, the inflammatory response of iPSC-derived pericytes was different to that of primary human pericytes, raising concern regarding the use of iPSC-derived pericytes to study neuroinflammatory disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/613375v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1e3612eorg.highwire.dtl.DTLVardef@1014537org.highwire.dtl.DTLVardef@6729adorg.highwire.dtl.DTLVardef@e14825_HPS_FORMAT_FIGEXP M_FIG C_FIG Brain pericytes can be generated from iPSCs. The work presented here shows the generation of phenotypically distinct pericytes from the original protocol, demonstrating the significant variability present within some iPSC differentiation protocols. Furthermore, functional differences are demonstrated between iPSC-derived brain pericytes and primary brain pericytes, revealing limitations in the use of iPSC-derived brain pericytes to model brain pericyte biology. Key PointsO_ST_ABSWhat is already known about this topic?C_ST_ABSBrain pericyte-like cells can be generated from induced pluripotent stem cells, however their responses to inflammatory stimuli has not been assessed. What does this study add?iPSC-derived brain pericytes exhibit different inflammatory responses compared to primary brain pericytes, showing that some iPSC-derived cell models are not appropriate for modelling all aspects of a cells biology. Furthermore, the iPSC-derived pericytes generated here were markedly different to those generated from the original article. It is therefore important for each lab to optimise the generation of iPSC-derived cell in their own hands to account for potential inter-lab variability.

cell biology↗

bioRxiv2024

Screening activity of brain cancer-derived factors on primary human brain pericytes

Brain cancers offer poor prognoses to patients accompanied by symptoms that drastically impact the patient and their family. Brain tumours recruit local non-transformed cells to provide trophic support and immunosuppression within the tumour microenvironment, supporting tumour progression. Given the localization and supportive role of pericytes at the brain vasculature, we explored the potential for brain pericytes to contribute to the brain cancer microenvironment. To investigate this, primary brain pericytes were treated with factors commonly upregulated in brain cancers. Changes to brain pericyte cell signalling, inflammatory secretion, and phagocytosis were investigated. The TGF{beta} superfamily cytokines TGF{beta} and GDF-15 activated SMAD2/3 and inhibited C/EBP-{delta}, revealing a potential mechanism behind the pleiotropic action of TGF{beta} on brain pericytes. IL-17 induced secretion of IL-6 without activating NF{kappa}B, STAT1, SMAD2/3, or C/EBP-{delta} signalling pathways. IL-27 and IFN{gamma} induced STAT1 signalling and significantly reduced pericyte phagocytosis. The remaining brain cancer-derived factors did not induce a measured response, indicating that these factors may act on other cell types or require co-stimulation with other factors to produce significant effects. Together, these findings show potential mechanisms by which brain pericytes contribute to aspects of inflammation and starts to uncover the supportive role brain pericytes may play in brain cancers.

cancer biology↗

bioRxiv2023

Reversible conjugation of a CBASS nucleotide cyclase regulates immune response to phage infection

Antiviral defence systems build the prokaryotic immune system and their proper regulation is vital for survival and fitness. While it is important that they are readily available in case of infection, they need to be tightly controlled to prevent activation of an unnecessary cellular response. Here we describe how the bacterial cyclic oligonucleotide-based antiphage signalling system (CBASS) uses its intrinsic protein modification system to regulate the nucleotide cyclase. By integrating a Type II CBASS system from Bacillus cereus into the cognate host Bacillus subtilis, we show that the Cap2 protein conjugates the cyclase exclusively to the conserved phage shock protein A (PspA) in the absence of phage. This cyclase-PspA conjugation is reversed after infection by the isopeptidase Cap3. Finally, we propose a model in which the cyclase is held in an inactive state by conjugation to PspA in the absence of phage and that this conjugation is released upon infection, priming the cyclase for activation.

microbiology↗

bioRxiv2023

High standing diversity masks extreme genetic erosion in a declining snake.

Average heterozygosity is frequently used as a proxy for genetic health, and to compare genetic diversity between species and populations. However, this measurement could be misleading if the distribution of heterozygosity across the genome is highly skewed. We investigated this pitfall in methodology using whole-genome sequencing of the adder (Vipera berus), a species experiencing dramatic declines in the UK. We find that mean heterozygosity in adders is notably high, exceeding that of other vertebrates typically regarded as genetically diverse. Their genome-wide distribution of heterozygosity, however, approximates a negative exponential distribution, with most genome regions showing extremely low heterozygosity. Modelling approaches show that this pattern is likely to have resulted from a recent, severe bottleneck and fragmentation most likely caused by anthropogenic activity in a previously large, interconnected adder population. Our results highlight that high standing diversity may mask severe genetic erosion when declines are recent and rapid. In such situations, whole-genome sequencing may provide the best option for genetic risk assessment and targeted conservation actions.

genomics↗