Biology subjects

Bird, S.

Publications and source records attributed to Bird, S..

6 recordsLinked to original sources

bioRxiv2026

Complementary Single-Cell Microflow HILIC and Ion Pair LC-MS Reveal Bystander Metabolic Effects in a Macrophage Model of Tuberculosis

Single-cell metabolomics remains analytically challenging due to the low abundance and chemical diversity of metabolites in individual cells. We have developed complementary microflow HILIC and ion pair LC-MS methods to expand metabolite coverage in single macrophages. Ion pair LC-MS was applied to single cells for the first time, enabling retention of highly polar and ionic metabolites that elute early under conventional reversed-phase conditions. Across Mycobacterium bovis BCG infected, uninfected bystander, and control unexposed THP-1 macrophages, both microflow methods detected significantly more features than a previously reported analytical-flow HILIC method. The two microflow methods provided complementary chemical space, together yielding 633 unique named metabolites with MS2 spectra. This depth enabled pathway-level interpretation at single-cell resolution, revealing infection-associated changes in purine-, arginine-, glutathione-, and one-carbon folate-associated metabolism. Metabolite-level interrogation indicated shared purine and amino acid changes in both infected and neighbouring macrophages, while revealing a distinct bystander phenotype characterised by elevated glycine and heterogeneous ATP levels. Finally, we demonstrate sequential IP and HILIC analysis of the same single cell, establishing a route toward maximal coverage from individual cells. These results position microflow HILIC and IP LC-MS as powerful, orthogonal strategies for advancing single-cell metabolomics and unveiling heterogeneity within complex biological microenvironments. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/733771v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@103ecfforg.highwire.dtl.DTLVardef@bc6734org.highwire.dtl.DTLVardef@11b96aforg.highwire.dtl.DTLVardef@41edfe_HPS_FORMAT_FIGEXP M_FIG Figure made in BioRender. C_FIG

microbiology↗

bioRxiv2025

A cationic liposome-formulated Toll Like Receptor (TLR)7/8 agonist enhances the efficacy of a vaccine against fentanyl toxicity

The U.S. opioid epidemic is an extraordinary public health crisis that started in 1990 and significantly accelerated in the last decade. Since 2020, over 100,000 fatal drug overdoses have been reported annually, and 75% of those involved fentanyl and its analogs (F/FA). Accelerating the translation of innovative, effective, and safe treatments is needed to augment existing measures to counteract such a crisis. Active immunization against F/FA and other opioids represents a promising therapeutic and prophylactic strategy for opioid use disorder (OUD) and opioid-induced overdose toxicity. Previously we demonstrated that the anti-fentanyl vaccine comprising a fentanyl-based hapten (F) conjugated to the diphtheria cross-reactive material (CRM), admixed with the novel lipidated toll-like receptor 7/8 (TLR7/8) agonist INI-4001 adsorbed on Alhydrogel(R) (alum) induced high-affinity fentanyl-specific polyclonal antibodies that protected against fentanyl-induced pharmacological effects in mice, rats, and mini-pigs. Here, INI-4001 was formulated into liposomes with different surface charges, and their impact on F-CRM adsorption, INI-4001 adjuvanticity, and vaccine efficacy were explored. Additionally, as the role of innate immunity in mediating the efficacy of addiction vaccines is largely unknown, we tested these formulations on the activation of innate immunity in vitro. Cationic INI-4001 liposomes surpassed other liposomal and aluminum-based formulations of INI-4001 by enhancing the efficacy of fentanyl vaccines and protecting rats against bradycardia and respiratory depression by blocking the distribution of fentanyl to the brain. Fentanyl vaccines adjuvanted with either cationic INI-4001 liposomes or the aqueous INI-4001 adsorbed to alum induced significant surface expression of co-stimulatory molecules and maturation markers in a murine dendritic cell line (JAWS II), while the former was superior in enhancing the macrophages surface expression of CD40, CD86 and inducible nitric oxide synthase (iNOS), indicative of maturation and activation. These results warrant further investigation of liposome-based formulations of TLR7/8 agonists for improving the efficacy of vaccines targeting F/FA and other opioids of public health interest. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/631964v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@178c8fdorg.highwire.dtl.DTLVardef@d38c09org.highwire.dtl.DTLVardef@8ec41forg.highwire.dtl.DTLVardef@edcf82_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Whole genome structural predictions reveal hidden diversity in putative oxidative enzymes of the lignocellulose degrading ascomycete Parascedosporium putredinis NO1

Economic valorisation of lignocellulose is paramount to realising a true circular bioeconomy; however, this requires the development of systems and processes to expand the repertoire of bioproducts beyond current renewable fuels, chemicals, and sustainable materials. Parascedosporium putredinis NO1 is an ascomycete that thrived at the later stages of a wheat- straw composting community culture, indicating a propensity to degrade recalcitrant lignin- enriched biomass, but exists within an underrepresented and underexplored fungal lineage. This strain has proven an exciting candidate for the identification of new enzymes targeting recalcitrant components of lignocellulose following the recent discovery of a new lignin {beta}-ether linkage cleaving enzyme. The first genome for the genus Parascedosporium for P. putredinis NO1 genome was sequenced, assembled, and annotated. The genome is 39 Mb in size, consisting of 21 contigs annotated to contain 9.998 protein-coding sequences. The carbohydrate-active enzyme (CAZyme) repertoire was compared to 2570 ascomycete genomes and in detail with Trichoderma reesei, Fusarium oxysporum, and sister taxa Scedosporium boydii. Significant expansion in the oxidative auxiliary activity class of CAZymes was observed in the P. putredinis NO1 genome resulting from increased sequences encoding putative lytic polysaccharide monooxygenases (LPMOs), oxidative enzymes acting within LPMO redox systems, and lignin-degrading laccases. P. putredinis NO1 scored above the 95th percentile for AA gene density across the ascomycete phylum, suggesting a primarily oxidative strategy for lignocellulose breakdown. Novel structure-based searching approaches were employed, revealing 17 new sequences with structural similarity to LPMO, laccase, and peroxidase sequences and which are potentially new lignocellulose-degrading enzymes. ImportanceAn annotated reference genome has revealed P. putredinis NO1 as a useful resource for the identification of new lignocellulose degrading enzymes for biorefining of woody plant biomass. Utilising a structure-omics based searching strategy, new potentially lignocellulose-active sequences were identified that would have been missed by traditional sequence searching methods. These new identifications, alongside the discovery of novel enzymatic functions from this underexplored lineage with the recent discovery of a new phenol oxidase that cleaves the main structural {beta}-O-4 linkage in lignin from P. putredinis NO1 highlights the underexplored and poorly represented family Microascaceae as particularly interesting candidates worthy of further exploration toward the valorisation of high value biorenewable products.

genomics↗

bioRxiv2022

Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities

Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their natural environmental niche.

microbiology↗

bioRxiv2022

Plasmid manipulation of bacterial behaviour through translational regulatory crosstalk

Beyond their role in horizontal gene transfer, conjugative plasmids commonly encode homologues of bacterial regulators. Known plasmid regulator homologues have highly targeted effects upon the transcription of specific bacterial traits. Here, we characterise a plasmid translational regulator, RsmQ, capable of taking global regulatory control in Pseudomonas fluorescens and causing a behavioural switch from motile to sessile lifestyle. RsmQ acts as a global regulator controlling the host proteome through direct interaction with host mRNAs and interference with the hosts translational regulatory network. This mRNA interference leads to largescale proteomic changes in metabolic genes, key regulators and genes involved in chemotaxis, thus controlling bacterial metabolism and motility. Moreover, comparative analyses found RsmQ on a large number of divergent plasmids isolated from multiple bacterial host taxa, suggesting the widespread importance of RsmQ for manipulating bacterial behaviour across clinical, environmental, and agricultural niches. RsmQ is a widespread plasmid global translational regulator primarily evolved for host chromosomal control to manipulate bacterial behaviour and lifestyle. Significance StatementPlasmids are recognised for their important role in bacterial evolution as drivers of horizontal gene transfer. Less well understood are the effects of plasmids upon bacterial behaviours by manipulating the expression of key bacterial phenotypes. Until now, examples of plasmid manipulation of their bacterial hosts were limited to highly targeted transcriptional control of a few related traits. In contrast, here we describe the first plasmid global translational regulator evolved to control the bacterial behavioural switch from a motile to a sessile lifestyle and bacterial metabolism, mediated through manipulation of the bacterial proteome. Moreover, this global translational regulator is common across divergent plasmids in a wide range of bacterial host taxa, suggesting that plasmids may commonly control bacterial lifestyle in the clinic, agricultural fields, and beyond.

microbiology↗

bioRxiv2021

Predation risk differentially affects aphid morphotypes: impacts on prey behavior, fecundity and transgenerational dispersal morphology

To avoid predation, prey initiate anti-predator defenses such as altered behavior, physiology and/or morphology. Prey trait changes in response to perceived predation risk can influence several aspects of prey biology that collectively contribute to individual success and thus population growth. However, studies often focus on single trait changes in a discrete life stage or morphotype. We assessed how predation risk by Harmonia axyridis affects several important traits in the aphid, Myzus persicae: host plant preference, fecundity and investment in dispersal. Importantly, we examined whether these traits changed in a similar way between winged (alate) and wingless (apterous) adult aphid morphotypes, which differ in morphology, but also in life-history characteristics important for reproduction and dispersal. Host plant preference was influenced by the presence of H.axyridis odors in choice tests; wingless aphids were deterred by the odor of plants with H.axyridis whereas winged aphids preferred plants with H.axyridis present. Wingless aphids reared in the presence of ladybeetle cues produced fewer offspring in the short-term, but significantly more when reared with exposure to predator cues for multiple generations. However, winged aphid fecundity was unaffected by H.axyridis cues. Lastly, transgenerational plasticity was demonstrated in response to predation risk via increased formation of winged aphid morphotypes in the offspring of predator cue-exposed wingless mothers. Importantly, we found that responses to risk differ across aphid polyphenism and that plasticity in aphid morphology occurs in response to predation risk. Together our results highlight the importance of considering how predation risk affects multiple life stages and morphotypes.

ecology↗