Dr Alice Pyne
MSci, MRes, EngD
Department of Materials Science and Engineering
Senior Lecturer in Soft Matter & Polymers
a.l.pyne@sheffield.ac.uk
+44 114 222 5969
+44 114 222 5969
Sir Robert Hadfield Building
Full contact details
Dr Alice Pyne
Department of Materials Science and Engineering
Sir Robert Hadfield Building
Mappin Street
Sheffield
S1 3JD
Department of Materials Science and Engineering
Sir Robert Hadfield Building
Mappin Street
Sheffield
S1 3JD
- Profile
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Alice is a Senior Lecturer in Polymers & Soft Matter and head of the Henry Royce Nanocharacterisation laboratory. Her research focusses on developing high-resolution Atomic Force Microscopy (AFM) imaging methods for structural characterisation of biomolecules in solution. She has pioneered single-molecule imaging studies of the DNA double helix, including unique time-resolved imaging at the atomic scale, showing DNA molecules twisting and “dancing” in ways that had not previously been imaged. Alice has a keen interest in bioimage analysis, and has developed an automated image analysis pipeline, TopoStats, that combines AFM image correction, molecule identification, and tracing into a single tool.
Prior to moving to Sheffield, Alice completed an EngD in Biophysics at the London Centre for Nanotechnology, UCL and was awarded two postdoctoral fellowships during which she established a track record in high resolution biomolecular AFM.
- Qualifications
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- EngD Biophysics, University College London & the National Physical Laboratory, High Resolution Atomic Force Microscopy of Functional Biological Molecules (2015)
- MRes (Hons) Distinction, UCL, Molecular Modelling and Materials Science (2011)
- MSci (Hons) Physics, University of Bristol (2009)
- Research interests
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Alice’s current projects combine high-resolution AFM and cutting-edge bioimage analysis to determine how structural and conformational heterogeneity in individual DNA molecules affects fundamental biological processes.
- Publications
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Journal articles
- Atomic force microscopy—A tool for structural and translational DNA research. APL Bioengineering, 5(3), 031504-031504.
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nature Communications, 12. View this article in WRRO
- TopoStats – A program for automated tracing of biomolecules from AFM images. Methods. View this article in WRRO
- Imaging the Effects of Peptide Materials on Phospholipid Membranes by Atomic Force Microscopy, 225-235.
- Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing. ACS Sensors, 5(10), 3133-3139. View this article in WRRO
- Imaging live bacteria at the nanoscale: comparison of immobilisation strategies. The Analyst, 144(23), 6944-6952. View this article in WRRO
- Single-molecule kinetics of pore assembly by the membrane attack complex. Nature Communications, 10(1), ---. View this article in WRRO
- PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy. Nanoscale, 11(42), 20072-20080. View this article in WRRO
- Bacterial killing by complement requires membrane attack complex formation via surface‐bound C5 convertases. The EMBO Journal, 38(4).
- Author Correction: Tuneable poration: host defense peptides as sequence probes for antimicrobial mechanisms. Scientific Reports, 8(1).
- Tuneable poration : host defense peptides as sequence probes for antimicrobial mechanisms. Scientific Reports, 8(1). View this article in WRRO
- DNA Origami Inside-Out Viruses. ACS Synthetic Biology, 7(3), 767-773.
- The role of C5 convertases in membrane attack complex dependent killing of Gram-negative bacteria. Molecular Immunology, 89, 154-154.
- Engineering monolayer poration for rapid exfoliation of microbial membranes. Chemical Science, 8(2), 1105-1115.
- Biomimetic Hybrid Nanocontainers with Selective Permeability. Angewandte Chemie, 128(37), 11272-11275.
- Biomimetic Hybrid Nanocontainers with Selective Permeability. Angewandte Chemie International Edition, 55(37), 11106-11109.
- Single-Molecule Reconstruction of Oligonucleotide Secondary Structure by Atomic Force Microscopy. Small, 10(16), 3257-3261. View this article in WRRO
- Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers. Proceedings of the National Academy of Sciences, 110(22), 8918-8923.
- Atomic Force Microscopy with Nanoscale Cantilevers Resolves Different Structural Conformations of the DNA Double Helix. Nano Letters, 12(7), 3846-3850.
- High-speed atomic force microscopy of dental enamel dissolution in citric acid. Archives of Histology and Cytology, 72(4/5), 209-215.
- Cantilever Sensors for Rapid Optical Antimicrobial Sensitivity Testing.
- Studies of G-quadruplexes formed within self-assembled DNA mini-circles. Chemical Communications, 52(84), 12454-12457.
- TopoStats - an automated tracing program for AFM images.
Chapters
- Imaging DNA Structure by Atomic Force Microscopy, Methods in Molecular Biology (pp. 47-60). Springer New York
Conference proceedings papers
- Probing antimicrobial mechanisms for effective strategies to overcome resistance. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 48 (pp S223-S223)
- Visualisation of DNA conformational changes in situ at nanometre resolution. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S369-S369)
- A combinatorial single-molecule study of ligand-gated ion channels and monoclonal antibodies. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S371-S371)
- Investigating the mechanism of action of a novel antimicrobial peptide on live E. coli cells. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, Vol. 46 (pp S389-S389)
Software / Code
Datasets
- 2 Methods for DNA Adsorption on a Mica Substrate for AFM Imaging in Fluid v1 (protocols.io.bncjmaun).
- Atomic Force Microscopy of DNA and DNA-Protein Interactions v1 (protocols.io.bncemate).
- 3 Pre-imaging Setup for High Resolution AFM in Fluid v1 (protocols.io.bncnmave).
- 5 Methods for DNA-protein imaging by AFM in fluid v1 (protocols.io.bncqmavw).
- 1 Preparation of Mica Substrate v1 (protocols.io.bnb2maqe).
- 4 Optimizing AFM Imaging in PFT for High Resolution AFM Imaging on DNA v1 (protocols.io.bncpmavn).
Other
- Atomic force microscopy—A tool for structural and translational DNA research. APL Bioengineering, 5(3), 031504-031504.
- Research group
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PhD Students:
- Daniel Rollins (AFM analysis of supercoiled DNA interactions)
- Mingxue Du (TopoStats: Automating AFM analysis of DNA & protein interactions)
- Libby Holmes (Complex DNA structures in cancer)
- Max Gamil (Deep probabilistic models for analysing complex DNA structures)
PhD Students (UCL):
Kavit Main (Single molecule insights into DNA-Topoiomerase interactions)
- Teaching activities
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- BIE103 (Introduction to Bioengineering)
- MAT360 (Research skills)
- MAT408 (Bioimaging)
- MEC438 (Preparation for Practice)
- Professional activities
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Professional Activities:
- British Biophysical Society committee member
- Royal Microscopical Society Data Analysis in Imaging committee member
- Wiley Biopolymers editorial board member
- Co-director of the INSIGNEO biomedical imaging pillar
- Head of the Henry Royce Nanocharacterisation Laboratory
- Co-organiser of the international Royal Microscopical Society ‘SPM and AFM’ conference series
- Co-organiser of the first international Royal Microscopical Society ‘AFM data analysis’ conference
Awards:
- Young Investigator Award - DNA, UK Nucleic Acids Forum 2019
- Journal of Molecular Recognition Award 2014
- National Physical Laboratory’s Raleigh Prize 2013