Biology subjects

Russell, D.

Publications and source records attributed to Russell, D..

13 recordsLinked to original sources

bioRxiv2026

Discovery of novel antimicrobial resistance genes in food and fertiliser using a high-throughput gene capture and functional screening platform

Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it diNicult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed an integron gene cassette capture system, a functional screening platform that captures environmental gene cassettes for direct phenotypic testing. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food items. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches. Environmental implicationAntimicrobial resistance (AMR) genes are hazardous biological contaminants, yet the vast majority of environmental integron gene cassettes remain functionally uncharacterised. This study addresses this sequence-to-function gap by deploying a novel functional capture platform directly on realistic environmental matrices, including agricultural fertilisers, coastal seawater, and commercial food products. By characterising these cassettes, we uncovered hidden reservoirs of both novel and clinically established AMR genes circulating in critical exposure pathways. This work reveals the true hazardous potential of the mobile environmental resistome, validating a proactive One Health surveillance tool for monitoring emerging biological threats.

microbiology↗

bioRxiv2025

Co-circulation of distinct high pathogenicity avian influenza virus (HPAIV) subtypes in a mass mortality event in wild seabirds and co-location with dead seals

H5Nx clade 2.3.4.4b high pathogenicity avian influenza viruses (HPAIV) have been detected repeatedly in Great Britain (GB) since autumn 2020, with H5N1 dominating detections but with low level detection of H5N5 during 2025. Globally, these viruses have caused mass mortalities in captive and wild avian and mammalian populations, including terrestrial and marine mammals. H5N1 has been the dominant subtype, and whilst incursions have overlapped temporally, occurrences have often been spatially distinct. Here, we report the detection of a mortality event in wild birds on the Norfolk coastline in the east of England, where H5N1 HPAIV was detected in five Great Black-backed Gulls (Larus marinus) and a Northern Fulmar (Fulmarus glacialis). Interestingly, at the same site, and as part of the same mortality event, a total of 17 Great Black-backed Gulls, one Herring Gull (Larus argentatus), one Atlantic Puffin (Fratercula arctica) and one Northern Fulmar tested positive for H5N5 HPAIV. Additionally, H5N5 was also detected in 17 co-located Grey Seal carcases (Halichoerus grypus). The H5N1 HPAIV from an infected bird belonged to genotype DI.2, closely related to contemporaneous detections in GB wild birds and poultry. In contrast, all H5N5 HPAIVs from birds and seals were genotype I with a 22-amino acid stalk deletion in NA and the 627K polymorphism in PB2. This represents the first recorded instance in GB of two subtypes being detected within the same avian population at the same location. It is also the first mass detection of HPAIV H5N5 in mammals within GB. Potential infection mechanisms are discussed.

genetics↗

bioRxiv2025

EcoFoldDB: Protein structure-guided functional profiling of ecologically relevant microbial traits at the metagenome scale

Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence, and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8,000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes, and accelerate discoveries in microbial ecology.

microbiology↗

bioRxiv2025

Molecular basis for the activation of Pseudomonas aeruginosa MsbA by Zn2+

Proteins involved in the biogenesis of lipopolysaccharide (LPS), a lipid exclusive to Gram-negative bacteria, are promising candidates for drug discovery. Specifically, the ABC transporter MsbA plays a crucial role in translocating an LPS precursor from the cytoplasmic to periplasmic facing leaflet of the inner membrane, and small molecules that inhibit its function exhibit bactericidal activity. Here, we use native mass spectrometry (MS) to determine lipid binding affinities of MsbA from P. aeruginosa (PaMsbA), a Gram-negative bacteria associated with hospital-acquired infections, in different conformations. We show the ATPase activity of the transporter is stimulated by Zn2+ and successfully trapping the protein with vanadate requires Zn2+ not Mg2+, which is necessary to trap MsbA from E. coli. We also present cryogenic-electron microscopy structures of PaMsbA in occluded and open outward-facing conformations determined to a resolution of 2.98 and 2.72 angstroms, respectively. The structures reveal a triad of histidine residues and mutation of these residues abolishes Zn2+ stimulation of PaMsbA activity. Together our studies provide detailed insight into PaMsbA structure, lipid binding preferences, and uncover a mechanism through which Zn2+ promotes the dimerization of the transporter, resulting in enhanced ATPase activity.

biochemistry↗

bioRxiv2024

Cortical synaptic vulnerabilities revealed in a α-synuclein aggregation model of Parkinson's disease

-Synuclein aggregates characterize -synucleinopathies, including Parkinsons disease and Dementia with Lewy bodies. A majority of people with these disorders experience cognitive decline, and its extent correlates with cortical -synuclein pathology. Mechanisms by which pathology targets cortical circuits remain to be understood so that the debilitating non-motor impairments can be addressed. Overt neuronal loss is not a major feature of cortical pathology, but a reduction of presynaptic sites has been reported at late stages of PD. We here define excitatory synapses as neuronal loci affected by -synuclein aggregation, showing that they are progressively lost, and identify temporal and spatial patterns of synaptic vulnerability. Results were obtained in a mouse model using intrastriatal injection of pre-formed -synuclein fibrils to template the aggregation of endogenous -synuclein in cortical neurons. Lewy neurite-like aggregates were predominantly observed in axons. Super-resolved imaging showed -synuclein aggregation within cortical synapses and revealed that synaptic aggregation is most severe proximal to Lewy neurite-like structures and linked to the earliest detectable loss of excitatory synapses. Excitatory synapses also exhibited ultrastructural aberrations, including a redistribution of pre- and post-synaptic protein clusters away from contact sites and reduced synaptic vesicle size. As pathology advanced, VGLUT1-positive intracortical synapses, enriched in -synuclein, were progressively vulnerable in this striatal seeding model, while VGLUT2-positive long-range synapses with minimal -synuclein were spared. Inhibitory synapses were not affected. In agreement with a disruptive role of synaptic -synuclein aggregation, super-resolved mesoscale imaging determined that synaptic but not non-synaptic -synuclein pathology is correlated with excitatory synapse loss. Physiological recordings confirmed impaired excitatory neurotransmission. Pathology propagation tracked cortical connectivity, with intra-column synapse loss correlated between interconnected layers V and II/III. Contralateral areas receiving projections from pathologic layer V also exhibited synapse loss. These findings reveal synapses as principal cellular loci of -synuclein pathology and define how molecular and circuit-based mechanisms underlie the cortical progression of synaptic pathology in -synucleinopathies.

neuroscience↗

bioRxiv2024

Designing Bt constructs for Brassicas, with minimal IP issues: A case study

As part of a publicly funded initiative to develop genetically engineered Brassicas (cabbage, cauliflower, and canola) expressing Bacillus thuringiensis Cry-encoded insecticidal (Bt) toxin for Indian and Australian farmers, we designed several constructs that drive high-level expression of modified Cry1B and Cry1C genes (referred to as Cry1BM and Cry1CM). The two main motivations for modifying the DNA sequences of these genes were to minimise any licencing cost associated with the commercial cultivation of transgenic crop plants expressing CryM genes, and to remove or alter sequences that might affect gene activity in plants. To assess the insecticidal efficacy of the Cry1BM/Cry1CM genes, constructs were introduced into the model Brassica Arabidopsis thaliana in which Cry1BM/Cry1CM expression was directed from either single (S4/S7) or double (S4S4/S7S7) Subterranean Clover Stunt Virus promoters. The resulting transgenic plants displayed a high-level of Cry1BM/Cry1CM expression. Protein accumulation for Cry1CM ranged from 0.81 to 17.69 g Cry1CM/g fresh weight of leaves. Contrary to previous work on stunt promoters, we found no correlation between the use of either single or double stunt promoters and the expression levels of Cry1BM/Cry1CM genes, with a similar range of Cry1CM transcript abundance and protein content observed from both constructs. First instar Diamondback moth (Plutella xylostella) larvae fed on transgenic Arabidopsis leaves expressing the Cry1BM/Cry1CM genes showed 100% mortality, with a mean leaf damage score on a scale of zero to five of 0.125 for transgenic leaves and 4.2 for wild-type leaves. Under laboratory conditions, even low-level expression of Cry1BM and Cry1CM was sufficient to cause insect mortality, suggesting that these modified CryM genes are suitable for the development of insect resistant GM crops. Except for the Cry1B/Cry1C genes themselves, which remain under patent until 2027 and the PAT gene in the USA, our assessment of the intellectual property landscape of the constructs described here suggest that they can be used without the need for further licencing. This has the capacity to significantly reduce the cost of developing and using these Cry1M genes in GM crop plants in the future.

plant biology↗

bioRxiv2023

The Soil Food Web Ontology: aligning trophic groups, processes, and resources to harmonise and automatise soil food web reconstructions

Although soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, data reuse for large-scale soil food-web reconstructions still faces challenges. These obstacles include: (1) most data on the trophic interactions and feeding behaviour of soil organisms being scattered across disparate repositories, without well-established standard for describing and structuring trophic datasets; (2) the existence of various competing terms, rather than consensus, to delineate feeding-related concepts such as diets, trophic groups, feeding processes, resource types, leading to ambiguities that hinder meaningful data integration from different studies; (3) considerable divergence in the trophic classification of numerous soil organisms, or even the lack of such classifications, leading to discrepancies in the resolution of reconstructed food webs and complicating the reuse and comparison of food-web models within synthetic studies. To address these issues, we introduce the Soil Food Web Ontology, a novel formal conceptual framework designed to foster agreement on the trophic ecology of soil organisms. This ontology represents a collaborative and ongoing endeavour aimed at establishing consensus and formal definitions for the array of concepts relevant to soil trophic ecology. Its primary objective is to enhance the accessibility, interpretation, combination, reuse, and automated processing of trophic data. By harmonising the terminology and fundamental principles of soil trophic ecology, we anticipate that the Soil Food Web Ontology will improve knowledge management within the field. It will help soil ecologists to better harness existing information regarding the feeding behaviours of soil organisms, facilitate more robust trophic classifications, streamline the reconstruction of soil food webs, and ultimately render food-web research more inclusive, reusable and reproducible.

ecology↗

bioRxiv2022

An Alzheimer's disease patient-derived olfactory cell model identifies gene expression changes associated with cognition

An early symptom of Alzheimers disease (AD) is an impaired sense of smell, for which the molecular basis remains elusive. Here, we generated human olfactory neurosphere-derived (ONS) cells from people with AD and mild cognitive impairment (MCI), and performed global RNA sequencing to determine gene expression changes. ONS cells expressed markers of neuroglial differentiation, providing a unique cellular model to explore early AD-associated disease pathways. Our transcriptomics data from ONS cells revealed differentially expressed genes (DEGs) associated with cognitive processes in AD cells compared to MCI, or matched healthy controls (HC). A-Kinase Anchoring Protein 6 (AKAP6) was the most significantly altered gene in AD compared to both MCI and HC, and has been linked to cognitive function. The greatest change in gene expression of all DEGs occurred between AD and MCI. Gene pathway analysis revealed defects in multiple cellular processes with aging, intellectual deficiency and alternative splicing being the most significantly dysregulated in AD ONS cells. Our results demonstrate that ONS cells can provide a cellular model for AD that recapitulates disease-associated differences. We have revealed potential novel genes, including AKAP6 that may have a role in AD, particularly MCI to AD transition, and should be further examined.

neuroscience↗

bioRxiv2022

Structural basis for lipid and copper regulation of the ABC transporter MsbA

A critical step in Lipopolysaccharide (LPS) biogenesis involves flipping lipooligosaccharide, an LPS precursor, from the cytoplasmic to the periplasmic leaflet of the inner membrane, an operation carried out by the ATP-binding cassette transporter MsbA. Although MsbA has been extensively studied, the selectivity of MsbA-lipid interactions remains poorly understood. Here we use native mass spectrometry (MS) to characterize MsbA-lipid interactions and guide structural studies. We show the transporter co-purifies with copper(II) and metal binding modulates protein-lipid interactions. A 2.15 [A] resolution structure of an N-terminal region of MsbA in complex with copper(II) is presented, revealing a structure reminiscent of the GHK peptide, a high-affinity copper(II) chelator. Our results demonstrate conformation-dependent lipid binding affinities, particularly for the LPS-precursor, 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KLA). We report a 3.6 [A]-resolution structure of MsbA trapped in an open, outward-facing conformation with adenosine 5-diphosphate and vanadate, revealing an unprecedented KLA binding site, wherein the lipid forms extensive interactions with the transporter. Additional studies provide evidence that the exterior KLA binding site is conserved and a positive allosteric modulator of ATPase activity, serving as a feedforward activation mechanism to couple transporter activity with LPS biosynthesis.

biochemistry↗

bioRxiv2022

Neuronopathic GBA1 L444P mutation accelerates glucosylsphingosine levels and formation of hippocampal alpha-synuclein inclusions

The most common genetic risk factor for Parkinsons disease (PD) is heterozygous mutations in the GBA1 gene which encodes for the lysosomal enzyme, glucocerebrosidase (GCase). GCase impairments are associated with an accumulation of abnormal -synuclein (-syn) called Lewy pathology, which characterizes PD. PD patients heterozygous for the GBA1 L444P mutation (GBA1+/L444P) have a 5.6-fold increased risk of cognitive impairments. In this study, we used GBA1+/L444P mice to determine the effects of this severe GBA1 mutation on lipid metabolism, expression of synaptic proteins, behavior, and -syn inclusion formation. GBA1+/L444P mice showed reduced GCase activity in limbic brain regions and expressed lower levels of hippocampal vGLUT1 compared to wildtype (GBA1+/+) mice. GBA+/L444P mice also demonstrated impaired fear conditioning, but no motor deficits. We show, using mass spectrometry, that mutant GCase and age increased levels of glucosylsphingosine (GlcSph), but not glucosylceramide (GlcCer), in the brains and serum of GBA1+/L444P mice. Aged GBA1+/+ mice also showed increased levels of GlcSph, and decreased GlcCer. To model disease pathology, templated -syn pathology was used. -Syn inclusions were increased in the hippocampus of GBA1+/L444P mice compared to GBA1+/+ mice, but not in the cortex, or substantia nigra pars compacta (SNc). Pathologic -syn did not cause a loss of dopamine neurons in the SNc. Treatment with a GlcCer synthase inhibitor prevented loss of cortical -syn inclusions, but not loss of dopamine neurons. Overall, these data suggest the critical importance to evaluate the contribution of hippocampal pathologic -syn and brain and serum glucosylsphingosine in synucleinopathies. SIGNIFICANCE STATEMENTSynucleinopathies, such as Parkinsons disease (PD) and Dementia with Lewy bodies (DLB), are both pathologically characterized by abnormal -synuclein (-syn). Mutant GBA1 is a risk factor for both PD and DLB where a reduction of glucocerebrosidase (GCase) activity is seen. Collectively, this indicates the significance of evaluating mutant GCase in synucleinopathies. Our data suggest the critical importance to evaluate the contribution of hippocampal pathologic -syn and brain and serum glucosylsphingosine (GlcSph) accumulation in synucleinopathies. Moreover, these pathologic outcomes may contribute to the nonmotor symptoms clinically observed in PD and DLB. Our findings highlight the importance of GlcSph as a relevant biomarker for future therapeutics.

neuroscience↗

bioRxiv2021

Triazolopyrimidines target aerobic respiration in Mycobacterium tuberculosis

We previously identified a series of triazolopyrimidines with anti-tubercular activity. We determined that Mycobacterium tuberculosis strains with mutations in a component of the cytochrome bc1 system (QcrB) were resistant to the series. A cytochrome bd oxidase deletion strain was also more sensitive to this series. We isolated resistant mutants, all of which had mutations in Rv1339. Compounds were active against intracellular bacteria but did not inhibit mitochondrial respiration in human HepG2 cells. These data are consistent with triazolopyrimidines acting via inhibition of M. tuberculosis QcrB.

microbiology↗

bioRxiv2019

Inter-reader agreement of 18F-FDG PET/CT for the quantification of carotid artery plaque inflammation

BackgroundA significant proportion of ischemic strokes are caused by emboli from unstable atherosclerotic carotid artery plaques with inflammation being a key feature of plaque instability and stroke risk. Positron emission tomography (PET) depicting the uptake of 2-deoxy-2-(18F)-fluoro-D-glucose (18F-FDG) in carotid artery plaques is a promising technique to quantify plaque inflammation. A consensus on the methodology for plaque localization and quantification of inflammation by 18F-FDG PET/computed tomography (CT) in atherosclerosis has not been established. High inter-reader agreement is essential if 18F-FDG PET/CT is to be used as a clinical tool for the assessment of unstable plaques and stroke risk. The aim of our study was to assess the inter-reader variability of different methods for quantification of 18F-FDG uptake in carotid atherosclerotic plaques with a separate CT angiography (CTA) providing anatomical guidance. Methods and resultsForty-three patients with carotid artery stenosis [≥]70% underwent 18F-FDG PET/CT. Two independent readers separately delineated the plaque in all axial PET slices containing the atherosclerotic plaque and the maximum standardized uptake value (SUVmax) from each slice was measured. Uptake values with and without background correction were calculated. Intraclass correlation coefficients were highest for uncorrected uptake values (0.97-0.98) followed by those background corrected by subtraction (0.89-0.94) and lowest for those background corrected by division (0.74-0.79). There was a significant difference between the two readers definition of plaque extension, but this did not affect the inter-reader agreement of the uptake parameters. ConclusionsQuantification methods without background correction have the highest inter-reader agreement for 18F-FDG PET of carotid artery plaque inflammation. The use of the single highest uptake value (max SUVmax) from the plaque will facilitate the methods clinical utility in stroke prevention.

pathology↗

bioRxiv2019

Global distribution of earthworm diversity

Soil organisms provide crucial ecosystem services that support human life. However, little is known about their diversity, distribution, and the threats affecting them. Here, we compiled a global dataset of sampled earthworm communities from over 7000 sites in 56 countries to predict patterns in earthworm diversity, abundance, and biomass. We identify the environmental drivers shaping these patterns. Local species richness and abundance typically peaked at higher latitudes, while biomass peaked in the tropics, patterns opposite to those observed in aboveground organisms. Similar to many aboveground taxa, climate variables were more important in shaping earthworm communities than soil properties or habitat cover. These findings highlight that, while the environmental drivers are similar, conservation strategies to conserve aboveground biodiversity might not be appropriate for earthworm diversity, especially in a changing climate.\n\nOne sentence summaryGlobal patterns of earthworm diversity, abundance and biomass are driven by climate but patterns differ from many aboveground taxa.

ecology↗