All Outputs (2179)

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?.

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.

A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus) (2023)
Journal Article
Barnes, M., Ebanks, B., MacColl, A., & Chakrabarti, L. (2023). A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus). Fishes, 8(1), Article 42. https://doi.org/10.3390/fishes8010042

Submersion in the anaesthetic MS-222 is a well-established and effective method used during the euthanasia of fish, but the consequences of treatment with this anaesthetic for mitochondrial respiration are yet to be established. This is important to... Read More about A Common Anaesthetic, MS-222, Alters Measurements Made Using High-Resolution Respirometry in the Three-Spined Stickleback (Gasterosteus aculeatus).

Analysis of tail morphology and osteology in Ethiopian indigenous sheep (2023)
Journal Article
Amane, A., Belay, G., Kebede, A., Dessie, T., Worku, S., Hanotte, O., & Vila, E. (2023). Analysis of tail morphology and osteology in Ethiopian indigenous sheep. Journal of Archaeological Science: Reports, 47, Article 103776. https://doi.org/10.1016/j.jasrep.2022.103776

Sheep adaptive diversity, including tail morphology, has been shaped by various factors, including natural and/or artificial selection for different traits. The Horn of Africa has historically been a major livestock entry point on the African contine... Read More about Analysis of tail morphology and osteology in Ethiopian indigenous sheep.

Predictive Molecular Design and Structure–Property Validation of Novel Terpene-Based, Sustainably Sourced Bacterial Biofilm-Resistant Materials (2023)
Journal Article
Cuzzucoli Crucitti, V., Ilchev, A., Moore, J. C., Fowler, H. R., Dubern, J., Sanni, O., …Irvine, D. J. (2023). Predictive Molecular Design and Structure–Property Validation of Novel Terpene-Based, Sustainably Sourced Bacterial Biofilm-Resistant Materials. Biomacromolecules, https://doi.org/10.1021/acs.biomac.2c00721

Presented in this work is the use of a molecular descriptor, termed the α parameter, to aid in the design of a series of novel, terpene-based, and sustainable polymers that were resistant to biofilm formation by the model bacterial pathogen Pseudomon... Read More about Predictive Molecular Design and Structure–Property Validation of Novel Terpene-Based, Sustainably Sourced Bacterial Biofilm-Resistant Materials.

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design (2023)
Journal Article
Weilguny, L., De Maio, N., Munro, R., Manser, C., Birney, E., Loose, M., & Goldman, N. (2023). Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design. Nature Biotechnology, 41, 1018–1025. https://doi.org/10.1038/s41587-022-01580-z

Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing... Read More about Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design.

Pharmacological and Physicochemical Properties Optimization for Dual-Target Dopamine D3 (D3R) and μ-Opioid (MOR) Receptor Ligands as Potentially Safer Analgesics (2023)
Journal Article
Bonifazi, A., Saab, E., Sanchez, J., Nazarova, A. L., Zaidi, S. A., Jahan, K., …Newman, A. H. (2023). Pharmacological and Physicochemical Properties Optimization for Dual-Target Dopamine D3 (D3R) and μ-Opioid (MOR) Receptor Ligands as Potentially Safer Analgesics. Journal of Medicinal Chemistry, 66(15), 10304–10341. https://doi.org/10.1021/acs.jmedchem.3c00417

A new generation of dual-target μ opioid receptor (MOR) agonist/dopamine D3 receptor (D3R) antagonist/partial agonists with optimized physicochemical properties was designed and synthesized. Combining in vitro cell-based on-target/off-target affinity... Read More about Pharmacological and Physicochemical Properties Optimization for Dual-Target Dopamine D3 (D3R) and μ-Opioid (MOR) Receptor Ligands as Potentially Safer Analgesics.

Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules (2023)
Journal Article
Gebru, G., Belay, G., Dessie, T., Zenebe Kelkay, M., Birhanie Dagnhegn, M., & Hanotte, O. (2023). Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules. Frontiers in Ecology and Evolution, 11, Article 1032082. https://doi.org/10.3389/fevo.2023.1032082

Ecogeographical habitat heterogeneity in wild endotherm species results in morphological variability associated with physiological mechanisms for maintaining their body temperature at a thermoneutral state in different environments. This habitat-indu... Read More about Morphological and osteological characterization of indigenous domestic chickens (Gallus gallus domesticus): validation of Rensch’s, Bergmann’s and Allen’s rules.

Base editing enables duplex point mutagenesis in Clostridium autoethanogenum at the price of numerous off-target mutations (2023)
Journal Article
Seys, F. M., Humphreys, C. M., Tomi-Andrino, C., Li, Q., Millat, T., Yang, S., & Minton, N. P. (2023). Base editing enables duplex point mutagenesis in Clostridium autoethanogenum at the price of numerous off-target mutations. Frontiers in Bioengineering and Biotechnology, 11, Article 1211197. https://doi.org/10.3389/fbioe.2023.1211197

Base editors are recent multiplex gene editing tools derived from the Cas9 nuclease of Streptomyces pyogenes. They can target and modify a single nucleotide in the genome without inducing double-strand breaks (DSB) of the DNA helix. As such, they hol... Read More about Base editing enables duplex point mutagenesis in Clostridium autoethanogenum at the price of numerous off-target mutations.