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The biocide triclosan induces (p)ppGpp dependent antibiotic tolerance and alters SarA dependent biofilm structures in Staphylococcus aureus (2023)
Working Paper
Walsh, D., Salzer, A., Wolz, C., Aylott, J., & Hardie, K. R. The biocide triclosan induces (p)ppGpp dependent antibiotic tolerance and alters SarA dependent biofilm structures in Staphylococcus aureus

The biocide triclosan is used extensively in both household and hospital settings. The chronic exposure to the biocide occurring in individuals that use triclosan-containing products results in low levels of triclosan present in the human body that h... Read More about The biocide triclosan induces (p)ppGpp dependent antibiotic tolerance and alters SarA dependent biofilm structures in Staphylococcus aureus.

Evaluating the potential of natural product combinations with sorbic acid for improving preservative action against food-spoilage yeasts (2023)
Journal Article
Harvey, H. J., Hendry, A. C., Archer, D. B., & Avery, S. V. (2023). Evaluating the potential of natural product combinations with sorbic acid for improving preservative action against food-spoilage yeasts. Fungal Biology, 127(7-8), 1218-1223. https://doi.org/10.1016/j.funbio.2023.01.004

Fungal control methods commonly involve the use of antifungals or preservatives, which can raise concerns about broader effects of these stressors on non-target organisms, spread of resistance and regulatory hurdles. Consequently, control methods ena... Read More about Evaluating the potential of natural product combinations with sorbic acid for improving preservative action against food-spoilage yeasts.

Interaction of human HelQ with DNA polymerase delta halts DNA synthesis and stimulates DNA single-strand annealing (2023)
Journal Article
He, L., Lever, R., Cubbon, A., Tehseen, M., Jenkins, T., Nottingham, A. O., …Bolt, E. L. (2023). Interaction of human HelQ with DNA polymerase delta halts DNA synthesis and stimulates DNA single-strand annealing. Nucleic Acids Research, 51(4), 1740-1749. https://doi.org/10.1093/nar/gkad032

DNA strand breaks are repaired by DNA synthesis from an exposed DNA end paired with a homologous DNA template. DNA polymerase delta (Pol δ) catalyses DNA synthesis in multiple eukaryotic DNA break repair pathways but triggers genome instability unles... Read More about Interaction of human HelQ with DNA polymerase delta halts DNA synthesis and stimulates DNA single-strand annealing.

Fourth Report on Chicken Genes and Chromosomes 2022 (2023)
Journal Article
Smith, J., Alfieri, J. M., Anthony, N., Arensburger, P., Athrey, G. N., Balacco, J., …Zhou, H. (2023). Fourth Report on Chicken Genes and Chromosomes 2022. Cytogenetic and Genome Research, 162(8-9), 405–528. https://doi.org/10.1159/000529376

The chicken continues to hold its position as a leading model organism within many areas of research, as well as being a major source of protein for human consumption. The First Report on Chicken Genes and Chromosomes [Schmid et al., 2000], which was... Read More about Fourth Report on Chicken Genes and Chromosomes 2022.

Delivery of biannual ultrasound surveillance for individuals with cirrhosis and cured hepatitis C in the UK (2023)
Journal Article
Hamill, V., Gelson, W., MacDonald, D., Richardson, P., Ryder, S. D., Aldersley, M., …Innes, H. (2023). Delivery of biannual ultrasound surveillance for individuals with cirrhosis and cured hepatitis C in the UK. Liver International, 43(4), 917-927. https://doi.org/10.1111/liv.15528

Background: Previous studies show the uptake of biannual ultrasound (US) surveillance in patients with cirrhosis is suboptimal. Here, our goal was to understand in broader terms how surveillance is being delivered to cirrhosis patients with cured hep... Read More about Delivery of biannual ultrasound surveillance for individuals with cirrhosis and cured hepatitis C in the UK.

A primer to directed evolution: current methodologies and future directions (2023)
Journal Article
Sellés Vidal, L., Isalan, M., Heap, J. T., & Ledesma-Amaro, R. (2023). A primer to directed evolution: current methodologies and future directions. RSC Chemical Biology, 2023(4), 271-291. https://doi.org/10.1039/d2cb00231k

Directed evolution is one of the most powerful tools for protein engineering and functions by harnessing natural evolution, but on a shorter timescale. It enables the rapid selection of variants of biomolecules with properties that make them more sui... Read More about A primer to directed evolution: current methodologies and future directions.

Discovery of a polymer resistant to bacterial biofilm, swarming, and encrustation (2023)
Journal Article
Dubern, J. F., Hook, A. L., Carabelli, A. M., Chang, C. Y., Lewis-Lloyd, C. A., Luckett, J. C., …Williams, P. (2023). Discovery of a polymer resistant to bacterial biofilm, swarming, and encrustation. Science Advances, 9(4), Article eadd7474. https://doi.org/10.1126/sciadv.add7474

Innovative approaches to prevent catheter-associated urinary tract infections (CAUTIs) are urgently required. Here, we describe the discovery of an acrylate copolymer capable of resisting single- and multispecies bacterial biofilm formation, swarming... Read More about Discovery of a polymer resistant to bacterial biofilm, swarming, and encrustation.

Innate immune cell instruction using micron-scale 3D objects of varied architecture and polymer chemistry: The ChemoArchiChip (2023)
Journal Article
Vassey, M., Ma, L., Kämmerling, L., Mbadugha, C., Trindade, G. F., Figueredo, G. P., …Alexander, M. R. (2023). Innate immune cell instruction using micron-scale 3D objects of varied architecture and polymer chemistry: The ChemoArchiChip. Matter, 6(3), 887-906. https://doi.org/10.1016/j.matt.2023.01.002

To design effective immunomodulatory implants, innate immune cell interactions at the surface of biomaterials need to be controlled and understood. The architectural design freedom of two-photon polymerization is used to produce arrays of surface-mou... Read More about Innate immune cell instruction using micron-scale 3D objects of varied architecture and polymer chemistry: The ChemoArchiChip.

Cocoa Flavanol Supplementation and the Effect on Insulin Resistance in Females Who Are Overweight or Obese: A Randomized, Placebo-Controlled Trial (2023)
Journal Article
Simpson, E. J., Mendis, B., Dunlop, M., Schroeter, H., Kwik-Uribe, C., & Macdonald, I. A. (2023). Cocoa Flavanol Supplementation and the Effect on Insulin Resistance in Females Who Are Overweight or Obese: A Randomized, Placebo-Controlled Trial. Nutrients, 15(3), Article 565. https://doi.org/10.3390/nu15030565

There is interest in the impact that dietary interventions can have on preventing the transition from insulin resistance to type 2 diabetes, including a suggestion that the bioactive components of cocoa may enhance fasting insulin sensitivity. Howeve... Read More about Cocoa Flavanol Supplementation and the Effect on Insulin Resistance in Females Who Are Overweight or Obese: A Randomized, Placebo-Controlled Trial.

Liver glycogen stores via 13C magnetic resonance spectroscopy in healthy children: randomized, controlled study (2023)
Journal Article
Horstman, A. M., Bawden, S. J., Spicer, A., Darwish, N., Goyer, A., Egli, L., …Simpson, E. J. (2023). Liver glycogen stores via 13C magnetic resonance spectroscopy in healthy children: randomized, controlled study. American Journal of Clinical Nutrition, 117(4), 709-716. https://doi.org/10.1016/j.ajcnut.2023.01.014

Background: Owing to its role in glucose homeostasis, liver glycogen concentration ([LGly]) can be a marker of altered metabolism seen in disorders that impact the health of children. However, there is a paucity of normative data for this measure in... Read More about Liver glycogen stores via 13C magnetic resonance spectroscopy in healthy children: randomized, controlled study.

The Isoleucine at Position 118 in Transmembrane 2 Is Responsible for the Selectivity of Xamoterol, Nebivolol, and ICI89406 for the Human β1-Adrenoceptor (2023)
Journal Article
Lim, V. J. Y., Proudman, R. G. W., Monteleone, S., Kolb, P., & Baker, J. G. (2023). The Isoleucine at Position 118 in Transmembrane 2 Is Responsible for the Selectivity of Xamoterol, Nebivolol, and ICI89406 for the Human β1-Adrenoceptor. Molecular Pharmacology, 103(2), 89-99. https://doi.org/10.1124/molpharm.122.000583

Known off-target interactions frequently cause predictable drug side-effects (e.g., β1-antagonists used for heart disease, risk β2-mediated bronchospasm). Computer-aided drug design would improve if the structural basis of existing drug selectivity w... Read More about The Isoleucine at Position 118 in Transmembrane 2 Is Responsible for the Selectivity of Xamoterol, Nebivolol, and ICI89406 for the Human β1-Adrenoceptor.

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny (2023)
Journal Article
McCarthy, C. G., Mulhair, P. O., Siu-Ting, K., Creevey, C. J., & O’Connell, M. J. (2023). Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny. Molecular Biology and Evolution, 40(1), Article msac276. https://doi.org/10.1093/molbev/msac276

There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of mode... Read More about Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny.

On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next? (2023)
Journal Article
Rauch, C., Wattis, J., & Bray, S. (2023). On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next?. Organisms, 6(1), 7-22. https://doi.org/10.13133/2532-5876/17811

Identifying the association between phenotypes and genotypes is the fundamental basis of genetic analyses. Although genomic technologies used to generate data have rapidly advanced within the last 20 years, the statistical models used in genome-wide... Read More about On the Meaning of Averages in Genome-wide Association Studies: What Should Come Next?.

Patient and Public Involvement and Engagement for PhD Students (2023)
Working Paper
Gladman, J. R. F., Stocks, J., Phillips, B., Horobin, A., Wragg, A., Mundey, M., …Humes, D. (2022). Patient and Public Involvement and Engagement for PhD Students

This paper aims to provide useful advice regarding the development of skills for patient and public involvement and engagement (PPIE) in research. The authors of this paper comprise experienced PhD supervisors and trainers, researchers leading PPIE a... Read More about Patient and Public Involvement and Engagement for PhD Students.

Differential expression of m5C RNA methyltransferase genes NSUN6 and NSUN7 in Alzheimer’s disease and traumatic brain injury (2023)
Journal Article
Perez Grovas-Saltijeral, A., Rajkumar, A. P., & Knight, H. M. (2023). Differential expression of m5C RNA methyltransferase genes NSUN6 and NSUN7 in Alzheimer’s disease and traumatic brain injury. Molecular Neurobiology, https://doi.org/10.1007/s12035-022-03195-6

Epigenetic processes have become increasingly relevant in understanding disease-modifying mechanisms. 5-Methylcytosine methylations of DNA (5mC) and RNA (m5C) have functional transcriptional and RNA translational consequences and are tightly regulate... Read More about Differential expression of m5C RNA methyltransferase genes NSUN6 and NSUN7 in Alzheimer’s disease and traumatic brain injury.

Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent (2023)
Journal Article
Wanelik, K. M., Begon, M., Bradley, J. E., Friberg, I. M., Jackson, J. A., Taylor, C. H., & Paterson, S. (2023). Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent. eLife, 12, Article e77666. https://doi.org/10.7554/eLife.77666

The genotype of an individual is an important predictor of their immune function, and subsequently, their ability to control or avoid infection and ultimately contribute offspring to the next generation. However, the same genotype, subjected to diffe... Read More about Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent.

A combinatorial DNA assembly approach to biosynthesis of N-linked glycans in E. coli (2023)
Journal Article
Passmore, I. J., Faulds-Pain, A., Abouelhadid, S., Harrison, M. A., Hall, C. L., Hitchen, P., …Wren, B. W. (2023). A combinatorial DNA assembly approach to biosynthesis of N-linked glycans in E. coli. Glycobiology, 33(2), 138-149. https://doi.org/10.1093/glycob/cwac082

Glycoengineering of recombinant glycans and glycoconjugates is a rapidly evolving field. However, the production and exploitation of glycans has lagged behind that of proteins and nucleic acids. Biosynthetic glycoconjugate production requires the coo... Read More about A combinatorial DNA assembly approach to biosynthesis of N-linked glycans in E. coli.

Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging (2023)
Journal Article
Linke, F., Johnson, J. E. C., Kern, S., Bennett, C. D., Lourdusamy, A., Lea, D., …Coyle, B. (2023). Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging. Acta Neuropathologica Communications, 11(1), Article 6. https://doi.org/10.1186/s40478-022-01496-4

The most common malignant brain tumour in children, medulloblastoma (MB), is subdivided into four clinically relevant molecular subgroups, although targeted therapy options informed by understanding of different cellular features are lacking. Here, b... Read More about Identifying new biomarkers of aggressive Group 3 and SHH medulloblastoma using 3D hydrogel models, single cell RNA sequencing and 3D OrbiSIMS imaging.

Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity (2023)
Journal Article
Humphreys, J. R., Debebe, B. J., Diggle, S. P., & Winzer, K. (2023). Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity. Frontiers in Microbiology, 13, Article 1075609. https://doi.org/10.3389/fmicb.2022.1075609

Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to... Read More about Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity.