John J Tomes

Dr. John J Tomes

orcid

Research Focus & Metrics

Academic Career Length

11Years (2016-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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30 April 2020 in Journal of Extracellular Vesicles
Verified
Journal Article
Open access
MKMarije E. Kuipers
Marije E. Kuipers
EHEsther N.M. Nolte‐‘t Hoen
Esther N.M. Nolte‐‘t Hoen
AHAlwin J. van der Ham
Alwin J. van der Ham
AOArifa Ozir‐Fazalalikhan
Arifa Ozir‐Fazalalikhan
DND. Linh Nguyen
D. Linh Nguyen
CHCornelis H. Hokke
Cornelis H. Hokke
Helminths like Schistosoma mansoni release excretory/secretory (E/S) products that modulate host immunity to enable infection. Extracellular vesicles (EVs) are among these E/S products, yet molecular mechanisms and functionality of S. mansoni EV interaction with host immune cells is unknown. Here we demonstrate that EVs released by S. mansoni schistosomula are internalised by human monocyte‐derived dendritic cells (moDCs). Importantly, we show that this uptake was mainly mediated via DC‐SIGN (CD209). Blocking DC‐SIGN almost completely abrogated EV uptake, while blocking mannose receptor (MR, CD206) or dendritic cell immunoreceptor (DCIR, CLEC4A) had no effect on EV uptake. Mass spectrometric analysis of EV glycans revealed the presence of surface N‐glycans with terminal Galβ1‐4(Fucα1‐3)GlcNAc (LewisX) motifs, and a wide array of fucosylated lipid‐linked glycans, including LewisX, a known ligand for DC‐SIGN. Stimulation of moDCs with schistosomula EVs led to increased expression of costimulatory molecules CD86 and CD80 and regulatory surface marker PD‐L1. Furthermore, schistosomula EVs increased expression of IL‐12 and IL‐10 by moDCs, which was partly dependent on the interaction with DC‐SIGN. These results provide the first evidence that glycosylation of S. mansoni EVs facilitates the interaction with host immune cells and reveals a role for DC‐SIGN and EV‐associated glycoconjugates in parasite‐induced immune modulation.

27 February 2019 in PLOS Neglected Tropical Diseases
Verified
Journal Article
Open access
PDF file
CDchelsea davis
chelsea davis
HPHelen Phillips
Helen Phillips
JTJohn J Tomes
John J Tomes
MSMartin T. Swain
Martin T. Swain
TWToby J. Wilkinson
Toby J. Wilkinson
Russell M MorphewRussell M Morphew
Russell M Morphew
Robust protocols for the isolation of extracellular vesicles (EVs) from the rest of their excretory-secretory products are necessary for downstream studies and application development. The most widely used purification method of EVs for helminth pathogens is currently differential centrifugation (DC). In contrast, size exclusion chromatography (SEC) has been included in the purification pipeline for EVs from other pathogens, highlighting there is not an agreed research community ‘gold standard’ for EV isolation. In this case study, Fasciola hepatica from natural populations were cultured in order to collect EVs from culture media and evaluate a SEC or DC approach to pathogen helminth EV purification. Transmission electron and atomic force microscopy demonstrated that EVs prepared by SEC were both smaller in size and less diverse than EV resolved by DC. Protein quantification and Western blotting further demonstrated that SEC purification realised a higher EV purity to free excretory-secretory protein (ESP) yield ratio compared to DC approaches as evident by the reduction of soluble free cathepsin L proteases in SEC EV preparations. Proteomic analysis further highlighted DC contamination from ESP as shown by an increased diversity of protein identifications and unique peptide hits in DC EVs as compared to SEC EVs. In addition, SEC purified EVs contained less tegumental based proteins than DC purified EVs. The data suggests that DC and SEC purification methods do not isolate equivalent EV population profiles and caution should be taken in the choice of EV purification utilised, with certain protocols for DC preparations including more free ES proteins and tegumental artefacts. We propose that SEC methods should be used for EV purification prior to downstream studies. Recent pathogen research has identified extracellular vesicle (EV) release from many organisms. EVs are small membrane bound organelles, which have different origins, sizes and composition. It is important that the optimal EV purification method is realised in order to obtain high quality EVs to have confidence in understanding EV biology and function. In this study, the zoonotic parasite, Fasciola hepatica, was cultured as a case study to investigate the importance of EV purification from helminth culture media. Investigating two purification methods, it was found that size exclusion chromatography EV isolation led to a reduction of contaminating excretory-secretory and tegumental proteins. This research highlighted that purification methods do not isolate equivalent EV population profiles with similar EV purities and that size exclusion chromatography methods are likely better suited for downstream helminth EV studies and application development, compared to a differential centrifugation method.

20 July 2021 in Pathogens
Verified
Journal Article
Open access
PDF file
BWBoontarikaan Wititkornkul
Boontarikaan Wititkornkul
BHBenjamin J. Hulme
Benjamin J. Hulme
JTJohn J Tomes
John J Tomes
NANathan R. Allen
Nathan R. Allen
CDchelsea davis
chelsea davis
Russell M MorphewRussell M Morphew
Russell M Morphew
Anoplocephala perfoliata is a neglected gastro-intestinal tapeworm, commonly infecting horses worldwide. Molecular investigation of A. perfoliata is hampered by a lack of tools to better understand the host–parasite interface. This interface is likely influenced by parasite derived immune modulators released in the secretome as free proteins or components of extracellular vesicles (EVs). Therefore, adult RNA was sequenced and de novo assembled to generate the first A. perfoliata transcriptome. In addition, excretory secretory products (ESP) from adult A. perfoliata were collected and EVs isolated using size exclusion chromatography, prior to proteomic analysis of the EVs, the EV surface and EV depleted ESP. Transcriptome analysis revealed 454 sequences homologous to known helminth immune modulators including two novel Sigma class GSTs, five α-HSP90s, and three α-enolases with isoforms of all three observed within the proteomic analysis of the secretome. Furthermore, secretome proteomics identified common helminth proteins across each sample with known EV markers, such as annexins and tetraspanins, observed in EV fractions. Importantly, 49 of the 454 putative immune modulators were identified across the secretome proteomics contained within and on the surface of EVs in addition to those identified in free ESP. This work provides the molecular tools for A. perfoliata to reveal key players in the host–parasite interaction within the horse host.

13 July 2016 in European Journal of Physics
Verified
Journal Article
Closed access
PDF file
JTJohn J Tomes
John J Tomes
Chris FinlaysonChris Finlayson
Chris Finlayson
We report upon the exploitation of the latest 3D printing technologies to provide low-cost instrumentation solutions, for use in an undergraduate level final-year project. The project addresses prescient research issues in optoelectronics, which would otherwise be inaccessible to such undergraduate student projects. The experimental use of an integrating sphere in conjunction with a desktop spectrometer presents opportunities to use easily handled, low cost materials as a means to illustrate many areas of physics such as spectroscopy, lasers, optics, simple circuits, black body radiation and data gathering. Presented here is a 3rd year undergraduate physics project which developed a low cost (£25) method to manufacture an experimentally accurate integrating sphere by 3D printing. Details are given of both a homemade internal reflectance coating formulated from readily available materials, and a robust instrument calibration method using a tungsten bulb. The instrument is demonstrated to give accurate and reproducible experimental measurements of luminescence quantum yield of various semiconducting fluorophores, in excellent agreement with literature values.

12 May 2022 in Applied Sciences
Verified
Journal Article
Open access
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Chris FinlaysonChris Finlayson
Chris Finlayson
GRGiselle Rosetta
Giselle Rosetta
JTJohn J Tomes
John J Tomes
The method of spectroscopic ellipsometry is applied to complex periodic nanomaterials, consisting of shear-ordered polymeric nanosphere composites, with intense resonant structural color. A corresponding multilayer optical quasi-model of the system, parametrizing the inherent degree of sample disorder and encompassing key properties of effective refractive-index and index-contrast, is developed to elucidate the correlation between the ∆ and Ψ ellipsometric parameters and the shear-induced opaline crystallinity. These approaches offer reliable means of in-line tracking of the sample quality of such “polymer opals” in large scale processing and applications.

11 June 2022 in Molecules
Verified
Journal Article
Open access
PDF file
GRGiselle Rosetta
Giselle Rosetta
MGMatthew Gunn
Matthew Gunn
JTJohn J Tomes
John J Tomes
MBMichael Butters
Michael Butters
JPJens Pieschel
Jens Pieschel
Chris FinlaysonChris Finlayson
Chris Finlayson
We report on shear-ordered polymer photonic crystals demonstrating intense structural color with a photonic bandgap at 270 nm. Our work examines this UV structural color, originating from a low refractive index contrast polymer composite system as a function of the viewing angle. We report extensive characterization of the angle-dependent nature of this color in the form of ‘scattering cones’, which showed strong reflectivity in the 275–315 nm range. The viewing range of the scattering was fully quantified for a number of planes and angles, and we additionally discuss the unique spectral anisotropy observed in these structures. Such films could serve as low-cost UV reflection coatings with applications in photovoltaics due to the fact of their non-photobleaching and robust mechanical behavior in addition to their favorable optical properties.