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University of Exeter

12 ARTICLES PUBLISHED IN JoVE

Immunology and Infection

Detection of Invasive Pulmonary Aspergillosis in Haematological Malignancy Patients by using Lateral-flow Technology

Christopher Thornton¹, Gemma Johnson², Samir Agrawal³

¹Biosciences, University of Exeter, ²BICMS, Queen Mary University of London, ³St. Bartholomew's Hospital and The London NHS Trust

A rapid and accurate point-of-care test for invasive pulmonary aspergillosis is presented. It takes advantage of lateral-flow technology using a specific monoclonal antibody that binds to an Aspergillus antigen secreted during pulmonary infections. The assay is compatible with serum and brochoalveolar lavage and represents a novel adjunct test for disease diagnosis.

Biology

Determination of Protein-ligand Interactions Using Differential Scanning Fluorimetry

Mirella Vivoli¹, Halina R. Novak¹, Jennifer A. Littlechild¹, Nicholas J. Harmer¹

¹Department of Biosciences, University of Exeter

Differential scanning fluorimetry is a widely used method for screening libraries of small molecules for interactions with proteins. Here, we present a straightforward method to extend these analyses to provide an estimate of the dissociation constant between a small molecule and its protein partner.

Biology

The Infiltration-centrifugation Technique for Extraction of Apoplastic Fluid from Plant Leaves Using Phaseolus vulgaris as an Example

Brendan M. O'Leary¹, Arantza Rico², Sarah McCraw¹, Helen N. Fones³, Gail M. Preston¹

¹Department of Plant Sciences, University of Oxford, ²School of Education of Vitoria-Gasteiz, University of the Basque Country (UPV/EHU), ³Biosciences, University of Exeter

This protocol details the optimized extraction of apoplast washing fluid from plant leaves, using French bean plants (Phaseolus vulgaris) as a model example.

Bioengineering

Preparation of Extracellular Matrix Protein Fibers for Brillouin Spectroscopy

Ryan S. Edginton¹, Sara Mattana², Silvia Caponi^2,3, Daniele Fioretto², Ellen Green¹, C. Peter Winlove¹, Francesca Palombo¹

¹School of Physics and Astronomy, University of Exeter, ²Department of Physics and Geology, University of Perugia, ³Istituto Officina dei Materiali del CNR, Unità di Perugia

We present a protocol for the application of Brillouin light scattering spectroscopy to elastin and trypsin-purified type I collagen fibers of the extracellular matrix to extract their full elastic properties.

Genetics

Metagenomic Analysis of Silage

Richard K. Tennant¹, Christine M. Sambles¹, Georgina E. Diffey¹, Karen A. Moore¹, John Love¹

¹Biosciences, University of Exeter

Metagenomics was used to investigate the microbiome of silage cattle feed. Analysis was performed by shotgun sequencing. This approach was used to characterize the composition of the microbial community within the cattle feed.

Bioengineering

Creating a Structurally Realistic Finite Element Geometric Model of a Cardiomyocyte to Study the Role of Cellular Architecture in Cardiomyocyte Systems Biology

Vijay Rajagopal^1,2,3, Gregory Bass^2,3, Shouryadipta Ghosh^1,2,3, Hilary Hunt^2,4, Cameron Walker⁵, Eric Hanssen⁶, Edmund Crampin^2,3,4,7,8, Christian Soeller⁹

¹Cell Structure and Mechanobiology Group, University of Melbourne, ²Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, ³Department of Biomedical Engineering, University of Melbourne, ⁴School of Mathematics and Statistics, Faculty of Science, University of Melbourne, ⁵Department of Engineering Science, University of Auckland, ⁶Advanced Microscopy Facility, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, ⁷ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, ⁸School of Medicine, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, ⁹Living Systems Institute, University of Exeter

This protocol outlines a novel method to create a spatially detailed finite element model of the intracellular architecture of cardiomyocytes from electron microscopy and confocal microscopy images. The power of this spatially detailed model is demonstrated using case studies in calcium signaling and bioenergetics.

Techniques to Assess Kidney Function in Mouse Models of Glomerular Disease

Megan Stevens^1,2,3, Sebastian Oltean^1,2,3

¹School of Physiology, Pharmacology and Neurosciences, University of Bristol, ²Bristol Renal, School of Clinical sciences, University of Bristol, ³Institute of Biomedical and Clinical Sciences, Medical School, University of Exeter

This protocol describes a full kidney work-up that should be carried out in mouse models of glomerular disease. The methods allow for detailed functional, structural, and mechanistic analysis of glomerular function, which can be applied to all mouse models of glomerular disease.

Medicine

Assessment of Kidney Function in Mouse Models of Glomerular Disease

Megan Stevens^1,2,3, Sebastian Oltean^1,2,3

¹Institute of Biomedical and Clinical Sciences, Medical School, University of Exeter, ²School of Physiology, Pharmacology and Neurosciences, University of Bristol, ³Bristol Renal, School of Clinical Sciences, University of Bristol

Biology

Preparation of Rat Skeletal Muscle Homogenates for Nitrate and Nitrite Measurements

Ji Won Park^*1, Samantha M. Thomas^*1, Lee J. Wylie², Andrew M. Jones², Anni Vanhatalo², Alan N. Schechter¹, Barbora Piknova¹

¹Molecular Medicine Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, ²Sport and Health Sciences, College of Life and Environmental Sciences, St Luke’s Campus, University of Exeter

We present protocols for three different methods for the homogenization of four different muscle groups of rat skeletal muscle tissue to measure and compare the levels of nitrate and nitrite. Furthermore, we compare different sample weights to investigate whether tissue sample size affects the results of homogenization.

Bioengineering

Biomolecular Imaging of Cellular Uptake of Nanoparticles using Multimodal Nonlinear Optical Microscopy

Chun-Chin Wang^*1, Jessica C. Mansfield^*1, Nicholas Stone¹, Julian Moger¹

¹Biomedical Physics, School of Physics and Astronomy, University of Exeter

This article presents the integration of a spectral-focusing module and a dual-output pulse laser, enabling rapid hyperspectral imaging of gold nanoparticles and cancer cells. This work aims to demonstrate the details of multimodal nonlinear optical techniques on a standard laser scanning microscope.

Chemistry

Uncovering Hidden Dynamics of Natural Photonic Structures Using Holographic Imaging

Marina Simovic-Pavlovic^1,2, Maja C. Pagnacco³, Dusan Grujic¹, Bojana Bokic¹, Darko Vasiljevic¹, Sébastien Mouchet^4,5, Thierry Verbiest⁶, Branko Kolaric^1,7

¹Institute of Physics, Photonics Center, University of Belgrade, ²Faculty of Mechanical Engineering, University of Belgrade, ³Institute of Chemistry, Technology and Metallurgy, University of Belgrade, ⁴School of Physics, University of Exeter, ⁵Department of Physics & Namur Institute of Structured Matter (NISM), University of Namur, ⁶Chemistry Department, Laboratory of Molecular Imaging and Photonics, KULeuven, ⁷Université de Mons

The paper is primarily focused on the combined power of optical (linear and nonlinear) and holographic methods used to reveal phenomena at the nanoscale. The results obtained from the biophotonic and oscillatory chemical reactions' studies are given as representative examples, highlighting holography's ability to reveal dynamics at a nanoscale.

Neuroscience

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions

Neeleema Seetaloo¹, Jonathan J. Phillips¹

¹Living Systems Institute, Department of Biosciences, University of Exeter

The structural ensemble of monomeric alpha-synuclein affects its physiological function and physicochemical properties. The present protocol describes how to perform millisecond hydrogen/deuterium-exchange mass spectrometry and subsequent data analyses to determine conformational information on the monomer of this intrinsically disordered protein under physiological conditions.