Biology subjects

Stevens, E.

Publications and source records attributed to Stevens, E..

8 recordsLinked to original sources

bioRxiv2025

A robust platform for recombinant production of animal venom toxin modulators of ion channels

Background and PurposePeptide toxins isolated from animal venom are potent and selective modulators of ion channels, and promising therapeutic leads. Due to intricate disulphide bridge patterns, they are often challenging to produce in standard laboratory settings, which limits engineering approaches to manipulate their structure-function properties. Given the low cost, wide accessibility, and versatility of recombinant expression systems for protein production, we set out to establish a straightforward high-yield strategy across a broad panel of peptide toxins from snakes, spiders and scorpions. Experimental Approach13 toxin DNA sequences were genetically fused to the C-terminus of either bivalent or monovalent human IgG1 antibody fragment crystallisable (Fc) domain sequences and expressed recombinantly from mammalian Expi293F cells. Affinity-purified proteins were evaluated by SDS-PAGE and size-exclusion chromatography (SEC). Function was assessed by Ca2+ flux assays on CN21 cells, or whole-cell electrophysiology on human embryonic kidney (HEK293T) cells, Chinese hamster ovary (CHO) cells, or dorsal root ganglion (DRG) neurons. Immunocytochemistry using HEK293T cells and mouse DRG neurons assessed Fc-toxin fusion binding. Key ResultsMonovalent Fc-toxin fusions consistently yielded 1-6 mg of pure, non-proteolytically cleaved protein from 20-70 ml cultures for several toxin types, including three-finger toxins from snakes, inhibitory cystine knot (ICK) toxins from spiders, and -toxins from scorpions, substantially surpassing the performance of unfused toxins or bivalent Fc-toxin fusions which gave low or no yield. Snake toxins targeting nicotinic acetylcholine receptors retained high single digit nanomolar inhibitory potency. Spider and scorpion toxins targeting the voltage-gated Na+ channel Nav1.7 retained pharmacological function and selectivity across a panel of five Nav subtypes, albeit with reduced potencies that did not exceed [~]70 nM. Conclusions and ImplicationsWe present a strategy for straightforward robust production of pure, monodisperse, and functional animal venom-derived toxins. This lowers the barrier to toxin production in a standard laboratory setting for follow-on engineering purposes.

pharmacology and toxicology↗

bioRxiv2025

Unveiling Interaction Signatures Across Viral Pathogens through VASCO: Viral Antigen-Antibody Structural COmplex dataset

Viral antigen-antibody (Ag-Ab) interactions shape immune responses, drive pathogen neutralization, and inform vaccine strategies. Understanding their structural basis is crucial for predicting immune recognition, optimizing immunogen design to induce broadly neutralizing antibodies (bnAbs), and developing antiviral therapeutics. However, curated structural benchmarks for viral Ag-Ab interactions remain scarce. To address this, we present VASCO (Viral Antibody-antigen Structural COmplex dataset), a high-resolution, non-redundant collection of [~]1225 viral Ag-Ab complexes sourced from the Protein Data Bank (PDB) and refined via energy minimization. Spanning Coronaviruses, Influenza, Ebola, HIV, and others, VASCO provides a comprehensive structural reference for viral immune recognition. By comparing VASCO against general protein-protein interactions (GPPI), we identify distinct sequence and structural features that define viral Ag-Ab binding. While conventional descriptors show broad similarities across datasets, deeper analyses reveal key sequence-space interactions, secondary structure preferences, and manifold-derived latent features that distinguish viral complexes. These insights highlight the limitations of GPPI-trained predictive models and the need for specialized computational frameworks. VASCO serves as a critical resource for advancing viral immunology, improving predictive modeling, and guiding immunogen design to elicit protective antibody responses. By bridging sequence and structural immunological datasets, VASCO should enable better docking, affinity prediction, and antiviral therapeutic development--key to pandemic preparedness and emerging pathogen response.

biophysics↗

bioRxiv2024

Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift

The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved epitopes capable of inducing protection. In this study, we explore the influence of glycan evolution on H3 hemagglutinin from 1968 to present day and its impacts on antigenicity and immunogenicity. We observe that the appearance of potential N-linked glycosylation sites in Sing/16 hemagglutinin head domain reduces the binding of broadly neutralizing antibodies and shifts the polyclonal immune response upon vaccination to target the stem. Furthermore, structural characterization of HK/68 and Sing/16 by cryo-electron microscopy shows that while HK/68 is resistant to enzymatic deglycosylation, removal of glycans destabilizes the hyperglycosylated head and membrane-proximal region in Sing/16. These insights expand our understanding of glycans beyond their role in protein folding and highlight the interplay among glycan integration and immune recognition to design a universal influenza vaccine.

immunology↗

bioRxiv2023

Changes in lipid metabolism track with the progression of neurofibrillary pathology in tauopathies.

BackgroundAbnormal aggregation of tau protein that leads to brain inclusions is a common feature of neurodegenerative disorders called tauopathies. Recent evidence suggests the involvement of lipid metabolic deregulations in the pathogenesis of tauopathies. However, the role of tau protein in the regulation of lipid metabolism is much less characterized and not well understood. MethodsWe used a transgenic rat model for tauopathy to reveal metabolic alterations induced by neurofibrillary pathology. Transgenic rats express a tau fragment truncated at the N-and C-terminals. For phenotypic profiling, we performed targeted metabolomic and lipidomic analysis of brain tissue, CSF, and plasma, based on the LC-MS platform. To monitor disease progression, we employed samples from transgenic and control rats aged 4, 6, 8, 10, 12, and 14 months. To study neuron-glia interplay in lipidome changes induced by pathological tau we used well well-established multicomponent cell model system. Univariate and multivariate statistical approaches were used for data evaluation. ResultsWe showed that tau has an important role in the deregulation of lipid metabolism. In the lipidomic study, pathological tau was associated with higher production of lipids participating in protein fibrillization, membrane reorganization, and inflammation. Interestingly, significant changes have been found in the early stages of tauopathy before the formation of high-molecular-weight tau aggregates and neurofibrillary pathology. Increased secretion of pathological tau protein in vivo and in vitro induced upregulated production of phospholipids and sphingolipids and accumulation of lipid droplets in microglia. During the later stages of tauopathy, we found a connection between the transition of tau into an insoluble fraction and changes in brain metabolism. The results showed that dysregulation of lipid composition by pathological tau leads to disruption of the microenvironment and further propagation of pathology. ConclusionOur results revealed that lipid metabolism is significantly affected during different stages of tau pathology and provide new evidence that supports the contribution of pathological tau proteins in individual lipid pathways. Our data suggests that biologically active membrane lipids such as phospholipids and sphingolipids could represent new potential next-generation therapeutic targets in tauopathies.

neuroscience↗

bioRxiv2021

Longitudinal immune cell profiling in early systemic lupus erythematosus

ObjectiveTo investigate the immune cell profiling and their longitudinal changes in systemic lupus erythematosus (SLE). MethodsWe employed mass cytometry with three different 38-39 marker panels (Immunophenotyping, T cell/monocyte, and B cell) in cryopreserved peripheral blood mononuclear cells (PBMCs) from nine patients with early SLE, 15 patients with established SLE, and 14 non-inflammatory controls. We used machine learning-driven clustering, FlowSOM (Flow Self-Organizing Maps) and dimensional reduction with tSNE (t-distributed Stochastic Neighbor Embedding) to identify unique cell populations in early and established SLE. For the nine early SLE patients, longitudinal mass cytometry analysis was applied to PBMCs at three time points (at enrollment, six months post-enrollment, and one year post-enrollment). Serum samples were also assayed for 65 cytokines by Luminex multiplex assay, and associations between cell types and cytokines/chemokines assessed. ResultsT peripheral helper cells (Tph cells), T follicular helper cells (Tfh cells) and several Ki67+ proliferating subsets (ICOS+ Ki67+ CD8 T cells, Ki67+ regulatory T cells, CD19int Ki67hi plasmablasts, and Ki67hi PU.1hi monocytes) were increased in early SLE. Longitudinal mass cytometry and multiplex serum cytokine assays of samples from early SLE patients revealed that Tfh cells and CXCL10 decreased at one year post-enrollment. CXCL13 correlated positively with several of the expanded cell populations in early SLE. ConclusionsTwo major helper T cell subsets and unique Ki67+ proliferating immune cell subsets were expanded in the early phase of SLE, and the immunologic features characteristic of early SLE evolved over time.

immunology↗

bioRxiv2021

A chemically-defined growth medium to support Lactobacillus-Acetobacter community analysis

Lactobacilli and acetobacters are commercially important bacteria that often form communities in natural fermentations, including food preparations, spoilage, and in the digestive tract of Drosophila melanogaster fruit flies. Communities of these bacteria are widespread and prolific, despite numerous strain-specific auxotrophies, suggesting they have evolved nutrient interdependencies that regulate their growths. The use of a chemically-defined medium (CDM) supporting the growth of both groups of bacteria would greatly facilitate identification of the precise metabolic interactions between these two groups of bacteria. While numerous such media have been developed that support specific strains of lactobacilli and acetobacters, there has not been a medium formulated to support both genera. We developed such a medium, based on a previous Lactobacillus CDM, by modifying the nutrient abundances to improve growth of both groups of bacteria. We further simplified the medium by substituting casamino acids for individual amino acids and the standard Wolfes vitamins and mineral stocks for individual vitamins and minerals, resulting in a reduction from 40 to 8 stock solutions. The new CDM and variations of it support robust growth of lactobacilli and acetobacters. We provide the composition and an example of its use to measure nutritional interactions.

microbiology↗

bioRxiv2020

Online milk composition analysis with an on-farm near-infrared sensor

On-farm monitoring of milk composition can support close control of the udder and metabolic health of individual dairy cows. In previous studies, near-infrared (NIR) spectroscopy applied to milk analysis has proven useful for predicting the main components of raw milk (fat, protein, and lactose). In this contribution, we present and evaluate a precise tool for online milk composition analysis on the farm. For each milking, the online analyzer automatically collects and analyses a representative milk sample. The system acquires the NIR transmission spectra of the milk samples in the wavelength range from 960 to 1690 nm and performs a milk composition prediction afterward. Over a testing period of 8 weeks, the sensor collected 1165 NIR transmittance spectra of raw milk samples originating from 36 cows for which reference chemical analyses were performed for fat, protein, and lactose. For the same online sensor system, two calibration scenarios were evaluated: training post-hoc prediction models based on a representative set of calibration samples (n = 319) acquired over the entire testing period, and training real-time prediction models exclusively on the samples acquired in the first week of the testing period (n = 308). The obtained prediction models were thoroughly tested on all the remaining samples not included in the calibration sets (n respectively 846 and 857). For the post-hoc prediction models, this resulted in an overall prediction error (root-mean-squared error of prediction, RMSEP) smaller than 0.08% (all % are in w/w) for milk fat (range 1.5-6.3%), protein (2.6-4.3%) and lactose (4-5.1%), while for the real-time prediction models the RMSEP was smaller than 0.09% for milk fat and lactose, and smaller than 0.11% for protein. The milk lactose predictions could be further improved by taking into account a cow-specific bias. The presented online sensor system using the real-time prediction approach can thus be used for detailed and autonomous on-farm monitoring of milk composition after each individual milking, as its accuracy is well within the ICAR requirements for on-farm milk analyzers and even meet the ICAR standards for laboratory analysis systems for fat and lactose. For this real-time prediction approach, a drift was observed in the predictions, especially for protein. Therefore, further research on the development of online calibration maintenance techniques is required to correct for this model drift and further improve the performance of this sensor system.

bioengineering↗

bioRxiv2017

Epistasis mediated alleviation of the cost of antibiotic resistance for MRSA

Understanding how multi-drug resistant pathogens evolve is key to identifying means of curtailing their further emergence and dissemination. Fitness costs imposed on bacteria by resistance mechanisms are believed to hamper their dissemination in an antibiotic free environment, however, some have been reported to have little or no cost, which suggests there are few barriers preventing their global spread. One such apparently cost-free resistance mechanism acquired by the major human pathogen Staphylococcus aureus is to the clinically important antibiotic mupirocin, which is mediated by mutation of the highly-conserved and essential isoleucyl-tRNA synthethase (ileS) gene. In Genome Wide Association Studies (GWAS) on two genetically and geographically distinct MRSA lineages we have found this mutation to be associated with changes in bacterial virulence, driven through epistatic interactions with other loci. Given the potential dual effect of this mutation on both antibiotic resistance and virulence we adopted a proteomic approach and observed pleiotropic effects. This analysis revealed that the activity of the secretory apparatus of the PSM family of cytolytic toxins, the Pmt system, is affected in the mupirocin resistant mutant, which explains why it is less toxic. As an energetically costly activity, this reduction in toxicity masks the fitness costs associated with this resistance mutation, a cost that becomes apparent when toxin production is required. Given the widespread use of this antibiotic, and that this resistance often results from a single nucleotide substitution in the ileS gene, these hidden fitness costs provide an explanation for why this resistance mechanism is not more prevalent. This work also demonstrates how population-based genomic analysis of virulence and antibiotic resistance can contribute to uncovering hidden features of the biology of microbial pathogens.

microbiology↗