Biology subjects

Fraser, J.

Publications and source records attributed to Fraser, J..

11 recordsLinked to original sources

bioRxiv2025

Integrating Behavioural Science and Epidemiology to Improve Early Detection of Zoonotic Swine Influenza in the Netherlands

Background and ObjectivesThe Netherlands faces zoonotic disease risks due to its dense human and livestock populations. The 2009 H1N1 outbreak highlighted the pandemic potential of influenza virus reassortment. Effective preparedness requires integrating behavioural and epidemiological models. Human behaviour, shaped by personal, social, and institutional factors, is critical in detecting, intervening, and treating diseases. Using the Theory of Planned Behaviour (TPB), a framework was developed integrating knowledge from the TPB to improve early detection and response, using (zoonotic) swine influenza as a case study. Material and MethodsWithin the framework we defined the desired outcome: timely detection and notification of symptomatic (and hypothetical zoonotic) swine influenza to prevent its spread. Actions, such as symptom recognition and disease reporting, were linked to key drivers extracted from the TPB and disease transmission modelling. Expert elicitation estimated the likelihood of action for different farmer profiles, while disease transmission modelling assessed farm-to-farm spread probabilities. Simulations integrated these probabilities to evaluate intervention effectiveness across different scenarios. ResultsThe framework successfully combined behavioural science and epidemiology, offering nuanced estimates of intervention effectiveness. For early detection, 95% of farmers were estimated to notify their veterinarian within 13 days post-infection. Key factors influencing action included symptom recognition and disease spread extent. The farmer profiles influenced response likelihood, while human infections linked to outbreaks had minimal impact. Farm density and assumptions about transmission probabilities significantly affected the likelihood of spread before notification. Discussion and ConclusionThe framework provides a systematic approach for integrating social and epidemiological insights to support evidence-based policies. The work can be further enhanced by complementing expert judgement with more extensive stakeholder surveys, randomized scenario presentations, and immersive methods. This pragmatic tool aids policymakers in designing targeted interventions for zoonotic disease preparedness.

systems biology↗

bioRxiv2025

Rosace-AA: Enhancing Interpretation of Deep Mutational Scanning Data with Amino Acid Substitution and Position-Specific Insights

Proteins are dynamic systems whose function and behavior are sensitive to environmental conditions and often involve multiple cellular roles. Deep mutational scanning (DMS) experiments generate extensive datasets to capture the functional consequences of mutations. However, the sheer volume of data presents challenges in visualization and interpretation. Current approaches often rely on heatmaps, but these methods fail to capture the nuanced effects of amino acid (AA) substitutions, which are essential for understanding mutational impact. To address this, we extend the Rosace framework with Rosace-AA, a model that incorporates both position-specific information and AA substitution trends. Using substitution matrices like BLOSUM90, Rosace-AA offers a flexible and interpretable approach to summarize DMS data oil both protein-level and position-level. We demonstrate its utility across datasets, including OCTI and MET kinase, showing that Rosace-AA highlights key positions where mutations deviate from expected substitution patterns and captures functionally relevant variation in protein behavior across multiple DMS screens. These results suggest that Rosace-AA enables more robust and interpretable analysis of complex DMS datasets.

bioinformatics↗

bioRxiv2024

PRISM: A Python Package for Interactive and Integrated Analysis of Multiplexed Tissue Microarrays

Tissue microarrays (TMAs) enable researchers to analyse hundreds of tissue samples simultaneously by embedding multiple samples into single arrays, enabling conservation of valuable tissue samples and experimental reagents. Moreover, profiling TMAs allows efficient screening of tissue samples for translational and clinical applications. Multiplexed imaging technologies allow for spatial profiling of proteins at single cell resolution, providing insights into tumour microenvironments (TMEs) and disease mechanisms. High-plex spatial single cell protein profiling is a powerful tool for biomarker discovery and translational cancer research, however, there remain limited options for end-to-end computational analysis of this type of data. Here, we introduce PRISM, a Python package for interactive, end-to-end analyses of TMAs with a focus on translational and clinical research using multiplexed proteomic data from the CODEX, Phenocycler Fusion (Akoya Biosciences), Comet (Lunaphore), MACSima (Miltenyi Biotec), CosMx and Cellscape (Bruker Spatial Biology) platforms. PRISM leverages the SpatialData framework to standardise data storage and ensure interoperability with single cell and spatial analysis tools. It consists of two main components: TMA Image Analysis for marker-based tissue masking, TMA dearraying, cell segmentation, and single cell feature extraction; and AnnData Analysis for quality control, clustering, iterative cell-type annotation, and spatial analysis. Integrated as a plugin within napari, PRISM provides an intuitive and purely interactive graphical interface for real-time and human-in-the-loop analyses. PRISM supports efficient multi-resolution image processing and accelerates bioinformatics workflows using efficient scalable data structures, parallelisation and GPU acceleration. By combining modular flexibility, computational efficiency, and a completely interactive interface, PRISM simplifies the translation of raw multiplexed images to actionable clinical insights, empowering researchers to explore and interact effectively with spatial omics data.

bioinformatics↗

bioRxiv2023

Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from FDG yield potent sensors of living bacteria in vivo

Chemoenzymatic techniques have been applied extensively to pharmaceutical development, most effectively when routine synthetic methods fail. The regioselective and stereoselective construction of structurally complex glycans is an elegant application of this approach, that is seldom applied to positron emission tomography (PET) tracers. We sought a method to dimerize 2-deoxy-[18F]-fluoro-D-glucose ([18F]FDG), the most common tracer used in clinical imaging, to form [18F]-labeled disaccharides for detecting microorganisms in vivo based on their bacteria-specific glycan incorporation. When [18F]FDG was reacted with {beta}-D-glucose-1-phosphate in the presence of maltose phosphorylase, both the -1,4 and -1,3-linked products 2-deoxy-[18F]-fluoro-maltose ([18F]FDM) and 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK) were obtained. This method was further extended with the use of trehalose (,-1,1), laminaribiose ({beta}-1,3), and cellobiose ({beta}-1,4) phosphorylases to synthesize 2-deoxy-2-[18F]fluoro-trehalose ([18F]FDT), 2-deoxy-2-[18F]fluoro-laminaribiose ([18F]FDL), and 2-deoxy-2-[18F]fluoro-cellobiose ([18F]FDC). We subsequently tested [18F]FDM and [18F]FSK in vitro, showing accumulation by several clinically relevant pathogens including Staphylococcus aureus and Acinetobacter baumannii, and demonstrated their specific uptake in vivo. The lead sakebiose-derived tracer [18F]FSK was stable in human serum and showed high uptake in preclinical models of myositis and vertebral discitis-osteomyelitis. Both the synthetic ease, and high sensitivity of [18F]FSK to S. aureus including methicillin-resistant (MRSA) strains strongly justify clinical translation of this tracer to infected patients. Furthermore, this work suggests that chemoenzymatic radiosyntheses of complex [18F]FDG-derived oligomers will afford a wide array of PET radiotracers for infectious and oncologic applications.

microbiology↗

bioRxiv2022

Design, development, and preliminary assessment of a novel peripheral intravenous catheter aimed at reducing early failure rates

BackgroundPeripheral intravenous catheters (PIVCs) are the most commonly used invasive medical device, yet despite best efforts by end-users, PIVCs experience unacceptably high early failure rates. We aimed to design a new PIVC that reduces the early failure rate of in-dwelling PIVCs and we conducted preliminary tests to assess its efficacy and safety in a large animal model of intravenous access. MethodsWe used computer-aided design and simulation to create a PIVC with a ramped tip geometry, which directs the infused fluid away from the vein wall; we called the design the FloRamp. We created FloRamp prototypes (test device) and tested them against a market-leading device (BD Insyte; control device) in a highly-controlled setting with five insertion sites per device in four pigs. We measured resistance to infusion and visual infusion phlebitis (VIP) every six hours and terminated the experiment at 48 hours. Veins were harvested for histology and seven pathological markers were assessed. ResultsComputer simulations showed that the optimum FloRamp tip reduced maximum endothelial shear stress by 60%, from 12.7Pa to 5.1Pa, compared to a typical PIVC tip, and improved the infusion dynamics of saline in the blood stream. In the animal study, we found that 2/5 of the control devices were occluded after 24 hours, whereas all test devices remained patent and functional. The FloRamp created less resistance to infusion (0.73{+/-}0.81 vs 0.47{+/-}0.50, p=0.06) and lower VIP scores (0.60{+/-}0.93 vs 0.31{+/-}0.70, p=0.09) that the control device, although neither findings were significantly different. Histopathology revealed that 5/7 of the assessed markers were lower in veins with the FloRamp. ConclusionsAs PIVCs are used in almost every hospitalized patient, there is an urgent need to reduce failure rates. Herein we report preliminary assessment of a novel PIVC design, which could be advantageous in clinical settings through decreased device occlusion.

bioengineering↗

bioRxiv2021

Ensemble-function relationships to evaluate catalysis in the ketosteroid isomerase oxyanion hole

Following decades of insights from structure-function studies, there is now a need to progress from a static to dynamic view of enzymes. Comparison of prior cryo X-ray structures suggested that deleterious effects from ketosteroid isomerase (KSI) mutants arise from misalignment of the oxyanion hole catalytic residue, Y16. However, multi-conformer models from room temperature X-ray diffraction revealed an ensemble of Y16 conformers indistinguishable from WT for Y32F/Y57F KSI and a distinct, non-native ensemble for Y16 in Y57F KSI. Functional analyses suggested rate effects arise from weakened hydrogen bonding, due to disruption of the Y16/Y57/Y32 hydrogen bond network, and repositioning of the general base. In general, catalytic changes can be deconvoluted into effects on the probability of occupying a state (P-effects) and the reactivity of each state (k-effects). Our results underscore the need for ensemble-function analysis to decipher enzyme function and ultimately manipulate their extraordinary capabilities.

biochemistry↗

bioRxiv2019

Pharmacological inhibition of acid sensing ion channel 1a protects the heart from ischemia-reperfusion injury

The proton-gated acid-sensing ion channel 1a (ASIC1a) is implicated in the injury response to cerebral ischemia but little is known about its role in cardiac ischemia. We provide genetic evidence that ASIC1a is involved in myocardial ischemia-reperfusion injury (IRI) and show that pharmacological inhibition of ASIC1a yields robust cardioprotection in rodent and human models of cardiac ischemia, resulting in improved post-IRI cardiac viability and function. Consistent with a key role for ASIC1a in cardiac ischemia, we show that polymorphisms in the ASIC1 genetic locus are strongly associated with myocardial infarction. Collectively, our data provide compelling evidence that ASIC1a is a key target for cardioprotective drugs to reduce the burden of disease associated with myocardial ischemia.

physiology↗

bioRxiv2019

High-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit and validation of nucleotide modifications

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides positions, a task that has previously been accomplished by X-ray crystallography. Here we present a cryo-electron microscopy (cryo-EM) structure of Escherichia coli (E. coli) 50S subunit at an average resolution of 2.2[A] as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for identification of post-transcriptional rRNA modifications using a cryo-EM map. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.

biochemistry↗

bioRxiv2019

Effects of α-tubulin acetylation on microtubule structure and stability

Acetylation of K40 in -tubulin is the sole post-translational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy reconstructions of pure samples of TAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as the structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains K40. Modification of K40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.

biophysics↗

bioRxiv2018

Synthetic essentiality of metabolic regulator PDHK1 in PTEN-deficient cells and cancers

PTEN is a tumor suppressor that is often inactivated in cancer and possesses both lipid and protein phosphatase activities. We report the metabolic regulator PDHK1 (pyruvate dehydrogenase kinase1) is a synthetic-essential gene in PTEN-deficient cancer and normal cells. The predominant mechanism of PDHK1 regulation and dependency is the PTEN protein phosphatase dephosphorylates NF{kappa};B activating protein (NKAP) and limits NF{kappa}B activation to suppress expression of PDHK1, a NF{kappa}B target gene. Loss of the PTEN protein phosphatase upregulates PDHK1 to drive aerobic glycolysis and induce PDHK1 cellular dependence. PTEN-deficient human tumors harbor increased PDHK1, which is a biomarker of decreased patient survival, establishing clinical relevance. This study uncovers a PTEN-regulated signaling pathway and reveals PDHK1 as a potential target in PTEN-deficient cancers.\n\nSIGNIFICANCEThe tumor suppressor PTEN is widely inactivated in cancers and tumor syndromes. PTEN antagonizes PI3K/AKT signaling via its lipid phosphatase activity. The modest success of PI3K/AKT inhibition in PTEN-deficient cancer patients provides rationale for identifying other vulnerabilities in PTEN-deficient cancers to improve clinical outcomes. We show that PTEN-deficient cells are uniquely sensitive to PDHK1 inhibition. PTEN and PDHK1 co-suppression reduced colony formation and induced cell death in vitro and tumor regression in vivo. PDHK1 levels were high in PTEN-deficient patient tumors and associated with inferior patient survival, establishing clinical relevance. Our study identifies a PTEN-regulated signaling pathway linking the PTEN protein phosphatase to the metabolic regulator PDHK1 and provides a mechanistic basis for PDHK1 targeting in PTEN-deficient cancers.

cancer biology↗

bioRxiv2017

A multi-model approach to assessing local and global cryo-EM map quality

There does not currently exist a standardized indicator of how well a cryo-EM-derived model represents the density from which it was generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected model-model agreement criterion for EM maps reported to be at 5 [A] resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.

biophysics↗