The paper uses time-resolved infrared spectroscopy to study electron density flow in coenzyme B12 of CarH, showing how the protein avoids radical photoproducts during its photoresponse.

bioRxiv · Aug 11, 2023 · PreprintBiophysics

A bespoke analytical workflow for the confident identification of sulfopeptides and their discrimination from phosphopeptides

L. A. Daly, D. P. Byrne, S. Perkins, P. J. Brownridge, E. McDonnell, A. R. Jones, P. A. Eyers, C. E. Eyers

This study develops a mass spectrometry workflow to identify sulfotyrosine peptides and distinguish them from phosphotyrosine peptides, identifying 21 new sulfotyrosine-containing proteins.

bioRxiv · Jul 15, 2023 · PreprintBiochemistry

A Panel of Diverse Klebsiella pneumoniae Clinical Isolates for Research and Development

M. J. Martin, W. C. Stribling, A. C. Ong, R. A. Maybank, Y. I. Kwak, J. A. Rosado-Mendez, L. Preston, K. F. Lane, M. Julius, A. R. Jones, M. K. Hinkle, P. E. Waterman, E. Lesho, F. Lebreton, J. W. Bennett, P. McGann

The paper describes a panel of 100 diverse Klebsiella pneumoniae isolates selected from 3,878 clinical isolates to support research on antimicrobial resistance and pathogenesis.

bioRxiv · Aug 17, 2022Microbiology

A systems approach reveals species differences in hepatic stress response capacity

G. Russomanno, R. Sison-Young, L. A. Livoti, H. Coghlan, R. E. Jenkins, S. J. Kunnen, C. P. Fisher, D. Reddyhoff, I. Gardner, A. H. Rehman, S. W. Fenwick, A. R. Jones, G. Vermeil De Conchard, G. Simonin, H. Bertheux, , I. M. Copple

The paper compares hepatic stress responses in mice and rats using pharmacokinetic modeling and omics data, finding greater liver injury in mice despite similar toxicant exposure.

bioRxiv · Apr 13, 2022Pharmacology & Toxicology

Essential elements of radical pair magnetosensitivity in Drosophila

A. Bradlaugh, G. Fedele, A. Munro, C. Hansen, S. Patel, C. Kyriacou, A. R. Jones, E. Rosato, R. Baines

This study identifies the essential components of a magnetoreceptor in Drosophila, showing that the C-terminal domain of CRY and intracellular FAD are sufficient for magnetoreception and MF response potentiation.

bioRxiv · Oct 29, 2021 · PreprintPhysiology

A thermodynamic model for interpreting tryptophan excitation-energy-dependent fluorescence spectra provides insight into protein conformational sampling and stability

A. Kwok, I. Camacho, S. Winter, M. Knight, R. Meade, M. van der Kamp, A. Turner, J. O'Hara, J. Mason, A. R. Jones, V. Arcus, C. R. Pudney

The paper develops a thermodynamic model to quantify the relationship between the tryptophan red edge excitation shift effect and protein flexibility, using examples across multiple scales and protein types.

bioRxiv · Sep 9, 2021Biophysics

A Panel of Diverse Pseudomonas aeruginosa Clinical Isolates for Research and Development

F. Lebreton, E. Snesrud, L. Hall, E. G. Mills, M. R. Galac, J. Stam, A. C. Ong, R. A. Maybank, Y. I. Kwak, S. Johnson, M. Julius, B. E. Swierczewski, P. E. Waterman, M. K. Hinkle, A. R. Jones, , P. McGann

The paper describes a panel of 100 diverse Pseudomonas aeruginosa clinical isolates selected to represent genetic and antibiotic susceptibility diversity for research and development.

bioRxiv · Apr 23, 2021Microbiology

Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets with therapeutic potential

B. Meyer, J. Chiaravalli, S. Gellenoncourt, P. Brownridge, D. P. Bryne, L. A. Daly, A. Grauslys, M. Walter, F. Agou, L. A. Chakrabarti, C. S. Craik, C. E. Eyers, P. A. Eyers, Y. Gambin, A. R. Jones, , E. Emmott

This study identifies novel SARS-CoV-2 protease cleavage sites and cellular targets using mass spectrometry, showing that targeting these proteins can inhibit viral replication.

bioRxiv · Sep 16, 2020Microbiology

Temporal modulation of the NF-κB RelA network in response to different types of DNA damage

A. Campbell, C. Ferraz Franco, L.-I. Su, S. Perkins, A. R. Jones, P. J. Brownridge, N. D. Perkins, C. E. Eyers

This study examines how different DNA damage agents modulate the phosphorylation of RelA and its interactome over time, revealing distinct signaling pathways and cellular outcomes.

bioRxiv · Aug 11, 2020Biochemistry

SDC3 acts as a timekeeper of myogenic differentiation by regulating the insulin/AKT/mTOR axis in muscle stem cell progeny

F. K. Jones, A. Phillips, A. R. Jones, A. Pisconti

This study identifies SDC3 as a regulator of myogenic differentiation by modulating the insulin/AKT/mTOR pathway in muscle stem cells.

bioRxiv · Aug 10, 2020 · PreprintCell Biology

Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signaling networks using SILAC-based phosphoproteomics

D. P. Byrne, C. J. Clarke, P. Brownridge, A. Kalyuzhnyy, S. Perkins, A. Campbell, D. Mason, A. R. Jones, P. A. Eyers, C. E. Eyers

This study uses centrinone and SILAC-based phosphoproteomics to identify PLK4 substrates and reveal a network of PLK4-regulated phosphorylation motifs in human cells.

bioRxiv · May 22, 2020Biochemistry

Native Mass Spectrometry Reveals the Conformational Diversity of the UVR8 Photoreceptor

I. S. Camacho, A. Theisen, L. O. Johannissen, L. A. Diaz-Ramos, J. M. Christie, G. I. Jenkins, B. Bellina, P. Barran, A. R. Jones

This study uses native mass spectrometry to show that full-length UVR8 exists in multiple conformational states, unlike truncated versions, and identifies active conformations that bind COP1.

bioRxiv · Jul 18, 2018Biochemistry

Improvements to the rice genome annotation through large-scale analysis of RNA-Seq and proteomics datasets

Z. Ren, D. Qi, N. Pugh, K. Li, B. Wen, R. Zhou, S. Xu, S. Liu, A. R. Jones

The paper improves rice genome annotation by analyzing RNA-Seq and proteomics data, identifying 692 genomic loci with potential annotation updates.

bioRxiv · Apr 12, 2018Plant Biology

Chromosomally Encoded mcr-5 in Colistin Non-susceptible Pseudomonas aeruginosa

E. Snesrud, R. A. Maybank, Y. I. Kwak, A. R. Jones, M. K. Hinkle, P. McGann

The paper identifies a chromosomal mcr-5 gene in a colistin-resistant Pseudomonas aeruginosa isolate using whole genome sequencing.

bioRxiv · Apr 9, 2018Microbiology