New UK-wide nucleic acid network launches

This week a new national network led by the University of Portsmouth and including the University of Sheffield has launched to accelerate innovation across nucleic acids, bringing together researchers, industry partners and policymakers from across the UK.

Supported by over £900,000 in combined funding, including £650,000 from the Biotechnology and Biological Sciences Research Council (BBSRC) and £267,000 in partner contributions, the initiative will create a coordinated, cross-disciplinary community focused on advancing nucleic acid research and innovation.

Alice, who is leading the University of Sheffield input, said: “The creation of a nucleic acids network to promote innovation across sectors, from blue sky research to biotechnology, diagnostics, and manufacturing, is a huge opportunity to kickstart and promote growth in this area across the UK. This is reflected in the level of support from industry for this network, spanning leading global players through to innovative, growing startups. The network will be truly national, with a leadership team distributed across disciplines and across the UK, bringing different viewpoints and insights to support research across the nucleic acid space."

You can read more about this network here and here.

Join the conversation in our NEW LinkedIn Page here:

https://www.linkedin.com/company/iana-network

Join the network here: signing up page

New paper on mapping the conformational landscape of DNA minicircles

Our new paper titled “Mapping the conformational landscape of DNA minicircles through atomic force microscopy and shape space analysis” has been published in Small today! The work, lead by Dr. Laura Wiggins, gives us new insight into the dynamic conformations of DNA by developing an automated framework that quantifies shape from AFM images.

You can read the full paper here

New Nature Paper on CRISPR/Cas9!

We are thrilled to share our latest collaborative research with Imperial College London and the MRC Laboratory of Medical Sciences (LMS), recently published in Nature. The study reveals that DNA supercoiling of the molecule is a critical factor in the accuracy of CRISPR-Cas9 gene editing. By utilizing our lab’s high-resolution AFM to visualize DNA minicircles, we were able to demonstrate how the mechanical stress of "underwound" DNA can lead to off-target binding. The fantastic images were collected by Eddie Rollins and the analysis was performed by Sylvia Whittle. This complements the stunning cryoEM data obtained by Quentin Smith from David Rueda’s lab. These insights provide a new framework for improving the safety and precision of gene therapies.

You can read the full press release from Imperial College here and the full article here.

New paper investigating the role of DNA structure in cancer response

Our new research published today in Cell Reports gives new insights into how G-quadruplexes formed in the DNA of certain cancer cell lines can effect the way our immune system is able to respond to the disease. In collaboration with Shayla Mosley and Kristi Baker at the University of Alberta we discovered how the presence of G4s in the DNA which exists in the cytosol of cancer cells can stimulate the cGAS/STING pathway in our immune response, possibly leading to better outcomes. This work was supported by a University of Sheffield Global Partnership Development Fund Grant awarded to Thomas Catley.

Read more here

Paper Published on Self-Assembled G-quadruplexes

We have recently published an article in collaboration with researchers at the Globe Institute Copenhagen exploring the formation of G-quadruplex structures from single nucleotide monomers. Through repeated heating and cooling cycles we see extended filamentous G4 structures self-assemble, which could give hints as to the conditions that were required to form life in prebiotic environments.

Read more about this work here

Paper published in nature communications

Our latest research on the “Oligomerisation of Ku from Mycobacterium Tuberculosis promotes DNA synapsis” has recently been published in Nature Communications. In this work we explored the importance of the bacterial protein, Ku, on forming DNA-Protein oligomers. This DNA-protein oligomerisations points towards the mechanisms of the vital DNA repair mechanism in Mycobacterium Tuberculosis, which ultimately is responsible for the spread and rising cases of Tuberculosis. This research poses an exciting insight into the causes of rising issues with antimicrobial drug resistance and highlights a potential target for therapeutics. This work was done as part of a collaboration with Dr Amanda Chaplin and Dr Sayma Zahid from the University of Leicester.

The full paper can be found here.

SPM4.0 midterm meeting and first training workshop held in Berlin

The MSCA SPM4.0 consortium gathered in Berlin from 17–21 November for an intensive week that combined the project’s midterm meeting with its first training workshop. Hosted by Charité Berlin, the event offered a unique opportunity for the 15 doctoral candidates, including our student Attila, to meet in person for the first time and engage directly with the wider consortium.

As part of the training workshops, Tom delivered a session on “Introduction to SPM image processing” which included a hands-on demonstration of image processing in both Gwyddion and TopoStats.

Following the training sessions, the midterm project meeting (M12) took place on 21 November, bringing together doctoral candidates, principal investigators, supervisors, the project manager and the communication officer to review the progress evolution of the project. As part of this Attila presented an introduction to himself and his research project to the consortium.

This was a fantastic week - it was great to see so much engagement from everyone and was a brilliant start to this training programme!

Sheffield hosts AFMBioMed Summer School

In September the University of Sheffield and the Pyne Lab hosted the 2025 AFMBioMed summer school. This brought participants from across the globe together with experts from the AFM community for a week of seminars and practical activities. We enjoyed an excellent range of talks including stand-outs by Ionna Mela and Georgina Benn. Laura, Sylvia and Tom all delivered a series of workshops on TopoStats and imaging DNA with AFM. The event was a tremendous success all around!

You can find out more about the next AFMBioMed conference and workshops here.

Paper on R-Loop formation and structure published in PNAS

Our latest research on “Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro” has been published in the prestigious journal PNAS, with colleagues from the University of California, Davis; Ethan Holleman, Tadas Sereiva, Stella Hartono and Frederic Chedin. This work demonstrates how nicking the non-template strand before transcription can significantly increase the formation of three-strand nucleic acid structures known as R-Loops. Our high-resolution Atomic Force Microscopy revealed that nicks change the morphology of the R-Loop, allowing the formation of previously unreported forked structures.

You can read the press release from the Royce team here: Royce Linkedin Post

and you can read the full paper here: https://doi.org/10.1073/pnas.2509309122

Press release for our work on tracing complex DNA topologies!

A press release reporting on our recently published work on automated tracing of complex DNA topologies is now available here. We’re delighted to see this work gaining recognition from the wider community!

Within the press release, Alice states “This is the first time we have been able to determine the structure of individual complex DNA structures found in cells with nanometre precision. We have done that by developing advanced new image analysis tools that can do in a matter of seconds that before may have taken hours.”

Paper on automated tracing of complex DNA topologies published in Nature Communications

Our group’s latest research on “Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy“ has been published in Nature Communications. In this work, we present a novel approach for automated tracing of complex DNA molecules from AFM images, showcasing how this enables detailed quantification of individual DNA conformations and accurate classification of their topological states. The paper was an exciting collaboration between experimental and computational members of the Pyne lab, as well as Dr. James Provan and Prof. Sean Colloms (University of Glasgow), Dr. Renáta Rusková and Dr. Dušan Račko (Polymer Institute of the Slovak Academy of Sciences), and Dr. Neville S. Gilhooly and Prof. Agnieszka Gambus (University of Birmingham). You can read the full paper here!

The timing of the paper’s acceptance was especially meaningful, coinciding with first authors Dr. Elizabeth Holmes and Dr. Max Gamill’s PhD vivas… a well-earned highlight they were proud to share with their examiners!

Physics of Life 2025

This week Tom, Tobi, Sylvia, Eva, Kinga and Alice attended the Physics of Life conference at Harrogate Convention Centre. This was the second edition of this biennial event, representing science at the interface between biology and physics. Tobi has provided his perspective on the conference -

“It was an absolute joy to attend POL 2025 in Harrogate this week. This conference brings together biophysicists from around the world for four days of fascinating talks, discussions, and discoveries. From single-molecule techniques to organism development, from computational simulations to cutting-edge microscopy, the breadth of topics covered was truly inspiring.

One of the most exciting aspects of POL is how it showcases the diversity and dynamism of biophysics. The field is constantly evolving, integrating new technologies and ideas to uncover the fundamental principles of life. Each talk and conversation reinforced just how interconnected different disciplines are—whether it’s physics, biology, chemistry, or data science, biophysics sits at the heart of them all.
Beyond the science, what made this conference truly special was the people. Engaging with researchers from all over the world, hearing about their work, and sharing ideas was a fantastic experience. The passion and enthusiasm in every discussion reminded me why I love being part of this community.

As I leave POL 2025, I feel energised, inspired, and more excited than ever about the future of biophysics.”

The group took advantage of the gorgeous Yorkshire weather and visited the Harrogate Gardens

There were many excellent talks on offer, but the standouts included Lorna Dougan’s fantastic talk on studies of protein networks, Erin Cutts discussing her brilliant work on Top2a using optical tweezers, and Aakash Basu explaining the use of his Loop-seq technique to study DNA flexibility.

During the conference, Tom, Tobi, Sylvia and our visiting PhD student Eva presented posters on their current work in the lab. These sparked lots of interesting discussion and questions!

Tobi and Eva presenting their posters

Alice also chaired an interesting discussion with Raveen Tank on the future and direction of the Physics of Life community. Lots of interesting and important points were discussed including how to support researchers within the community (especially ECRs) and how important it is to remain strong in the goal of improving inclusivity and diversity within research.

Alice and Raveen chairing the culture and environment roadmap session

Tom attends AFM Outreach workshop in Manchester

Earlier this month Tom attended the '“Knowledge of the Nanoscale: Developing AFM Activities for Outreach” workshop hosted by the Royce Institute in Manchester. It was a fantastic two days of talks, break-out sessions and discussion about everything outreach! Talks included a fantastic one by Edwin Hwu who described how to ‘hack’ an AFM with everyday consumer electrical including a Nintendo Wii! There was also sessions dedicated to assembling a home-made AFM from scratch (which you can see in the picture below) and then designing outreach activities which could be used in schools to inspired the next generation of AFMers!

Paper on copper metallodrugs published in Nucleic Acids Research

Tom and Alice have published a paper with collaborators from Dublin City University on the “Design and in vitro anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease”. The work was an exciting collaboration with Andrew Kellett and his lab, in which we visualised the DNA-condensing effects of their novel anti-cancer metallodrug compounds. If you would like to now more you can access the paper here.

Alice hosts the Insigneo Institute "Imaging Life" workshop

We kicked off the festive season this year with the Insigneo Institute’s first workshop on “Imaging Life”, co-organised by Alice and Jamie Hobbs. It was a real pleasure to host our external speakers Gail McConnell from the University of Strathclyde and Dr. Raveen K.G. Tank from The University of Manchester for our Insigneo Imaging workshop. Thanks to them both for coming and for giving such engaging and inspiring talks 🔬

The day was a real success, with excellent talks from Ankita Ray, Ruby Peters, Andy Swift, our close collaborator and friend Matt Newton and Laura! We had a very engaging flash talk session sponsored by Exciting Instruments featuring Libby and Tom!

The day included a discussion session where we talked about what’s next for “Imaging Life” at Sheffield and what we can do to best support our members, as a result, we’re already planning our next event, which will focus on Data Analysis in early 2025.

Alice attends EU Project SPM4.0 kick-off meeting - PhD position opening soon

In November, Alice travelled to Barcelona for the kick-off meeting of the SPM4.0 project, an innovative Marie Curie Skłodowska Doctoral Network (MSCA-DN) designed to advance the capabilities of Scanning Probe Microscopy (SPM) and revolutionise its application in Life Sciences and Medicine.

SPM4.0 researchers meet for the first time at IBEC, Catalunya

As part of the Marie Skłodowska-Curie Actions Doctoral Networks (MSCA-DN) programme, the SPM4.0 project will be funded for 4 years with around 4 million euros. During this period, 16 young researchers will be trained in the science and technology of autonomous Scanning Probe Microscopes powered by Artificial Intelligence.

One of these positions will be based in our group at the University of Sheffield and will be advertised shortly. The recruited researcher will receive state-of-the-art multidisciplinary scientific training in advanced scanning probe microscopy and machine learning, and its application in biological and medical contexts, focussing on the recognition of essential DNA-protein interactions. They will have the opportunity to undertake secondments at Sorbonne University, IBEC and Bruker Nano in Berlin, supported by a generous training budget. If you’re interested in this project, please get in touch with Alice.

In addition to their scientific education, this new generation of researchers will receive training in complementary skills to prepare them for the research job market. They will participate in training sessions on data management, open science, scientific communication, intellectual property rights and entrepreneurship.

For more information, please check out the press release from IBEC here.

Genomics to Whole Cell Conference Hosted in Sheffield

Marina attended the Genomics to Whole Cell workshop in Sheffield, a three-day event that brought together leading experts from the genomics, whole-cell, and modelling communities. As a first-year PhD student, Marina found the workshop to be a unique opportunity to observe how researchers from diverse fields collaborate to tackle complex scientific questions. It was inspiring and enlightening for her to see how ideas from different fields work together to solve shared challenges.

The workshop focused on current challenges and emerging opportunities in biological research, with a particular emphasis on advancements in AI. What stood out to Marina was the distinctive structure of the event. Unlike traditional conferences, the workshop focused on group discussions instead of lectures and presentations. Participants were divided into small groups and given specific questions to explore, covering topics such as automation, AI, data standards, and multi-model simulations for whole-cell modelling. This interactive format fostered deeper conversations and encouraged collaborative problem-solving.

For Marina, the highlight of the workshop was the strong collaboration across disciplines and the diversity of expertise among attendees. As someone at the beginning of her research journey, she found it incredibly motivating to witness the power of collective problem-solving and open dialogue.

Marina reflected on the workshop, saying, “Overall, the workshop left me feeling energised and inspired. The cross-disciplinary collaboration was a reminder of the importance of working together across fields to tackle the most challenging questions in science. This experience has given me valuable insights and a greater appreciation for the collaborative nature of research, which I look forward to applying in my PhD work.”

A Look Back at Our Trip to the I2K Conference in Milan!

We’re thrilled to share some highlights from our recent trip to a misty Milan for the Images 2 Knowledge conference! The conference was a fantastic opportunity to connect with passionate minds across the microscopy and data science communities and to see first-hand how work in image analysis is creating real interest and impact in the biological community.

Laura, Tom, Harriet and Max kicked off the event with excitement, especially knowing we had a workshop and live demo on deck! With some last-minute pull requests to tidy our outputs, we were prepared, if a bit nervous, to dive right into the capabilities of TopoStats. The workshop went off without a hitch and it was interesting to see the priorities of the wider image analysis community on using such a tool. There was particularly lively discussion about the participants loves, improvements, and future directions after seeing and using the tool for themselves, and how they would use the tool for their upcoming AFM data.

One of the most exciting moments was showcasing our AFMReader library (https://github.com/AFM-SPM/AFMReader/) in our workshop. We designed this to open-up the atomic force microscopy (AFM) community to use the tools developed by the wider microscopy image analysis world through Python. AFMReader provides essential tools for handling and analysing data specifically from AFM images, and it’s all built to be fully open and FAIR: Findable, Accessible, Interoperable, and Reusable. We were blown away by the response! The attendees were excited about how AFMReader could help them build their own pipelines and open their data up to the wealth of image analysis tools already being used by other microscopies.

In addition to our workshop, Laura present a fantastic flash talk highlight all of the amazing work our team does using TopoStats, and Max presented a beautiful poster showcasing his work developing deep learning methods for TopoStats!

Paper on kinetoplast DNA published in PCCP

Our former master’s student Bradley has published a paper from the work he carried out in our lab. “Multiscale topological analysis of kinetoplast DNA via high-resolution AFM” combined high-resolution AFM with a custom image analysis pipeline built in TopoStats to understand more about the topology of these unusual DNA structures. The work was carried out in collaboration with Patrick Doyle and Indresh Yadav from MIT, and was included as part of the PCCP Emerging Investigators collection, which highlights the excellent research done by Alice and the lab. 

Read more about the work here

UK & Ireland Single-Molecule Biology Meeting in London

On May 14-15, Alice, Libby and Slyvia travelled down to the MRC Laboratory of Medical Sciences at Imperial College London to attend the LUMICKS single-molecule research symposium. The two days consisted of a variety of wonderful talks, highlighting the importance of single-molecule techniques in biophysical research.

During the symposium, Alice gave an exciting talk entitled “Single molecule insights into how DNA supercoiling affects its interactions”, which was incredibly well received. In addition, Libby and Sylvia both gave flash talks and poster presentations talking about their current research during their PhD’s.

Alice giving her talk during the second day of the symposium.

The keynote speakers, Nynke Dekker and Simon Boulton both gave exceptionally stimulating talks on their research careers. As a PhD student, it was incredibly inspiring and motivating to watch. Two talk highlights were Lori Passmore who gave a talk on “insights into how the FANCD2-FANCI DNA repair clamp interacts with DNA” and Graeme King for “Probing the structure and interactions of negatively supercoiled DNA using optical tweezers and fluorescence imaging”. As a lab who’s main focus is singe-molecule imaging of DNA-protein interactions in solution, and the automation of analysis of these complexes, both these talks were very insightful into this field.

Thank you to David Rueda and Mina Brett-Pitt for organising this wonderful event!