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Training

Exchanges with ClickGene Alumni for the final event

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On September 25, the NATURE-ETN ESRs got together for the final project event.

During this online session, the NATURE-ETN ESRs had the chance to hear from alumni of the ClickGene project, a European Training Network in click chemistry and gene therapy, coordinated by Prof. Kellett (DCU) in collaboration with other NATURE-ETN PIs, including Prof. Brown (UOXF), Prof. Carell (LMU), Prof. Hocek (IOCB), and the companies baseclick and ATDBio.

The four ClickGene alumni shared diverse career paths spanning academia, start-ups, and major pharmaceutical companies. Dr. Bastien Viverge (Senior Manager, Regulatory CMC – Clinical Lead, Biogen, CH), Dr. Sarah Walsh (Applied Platform Workflows Manager, Oxford Nanopore Technologies, UK), Dr. Nicolò Zuin Fantoni (Senior Scientist – Oligonucleotides, Roche, CH), and Dr. Georgia Menounou (Postdoctoral Researcher, DCU, IE) each discussed their post-PhD journeys.

We thank the ClickGene alumni for their time and valuable advice to our ESRs.

Dr. Marco Cavallaro (accelCH) also introduced the ESRs to EU funding opportunities for postdocs, industry-academia collaborations, and start-ups/SMEs, highlighting resources that could be useful after obtaining their PhD, whether they pursue careers in academia or industry.

NATURE-ETN counts two new Doctors

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We are delighted to announce that our ESRs Eva Sophie Schönegger (baseclick/LMU) and Ahmad Abdullrahman (University of Reading) recently passed their viva. Eva spent her NATURE-ETN journey at the company baseclick and the Carell group at LMU Munich, while Ahmad completed his PhD at the University of Reading under the co-supervision of Dr. James Hall and Prof. Christine Cardin.

We congratulate Dr. Schönegger and Dr. Abdullrahman on this key milestone in their career!

Maria’s secondment experience in Oxford, UK

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After the great experience I had during my first secondment at the University of Reading, I had the chance to spend one month at the University of Oxford, in the UK, supervised by Prof. Tom Brown and Prof. Afaf El-Sagheer.

This time I was not alone, but Tania (ESR9) and Malou (ESR5) came for their secondment in the same period. The first day I went to the lab I was very excited about the new experience in such an important group and university. The group gave me a warm welcome when I arrived, and I felt happy and thrilled to be there.

During this secondment, I learnt many new techniques and developed new skills, supervised by very professional and passionate scientists, always keen to teach me.

During my stay, I used click chemistry reactions to link the Ruthenium compounds I synthesised at Chimie ParisTech – PSL to some triplex-forming oligonucleotides. I learnt how the oligonucleotides are synthesised, thanks to Prof. Afaf El-Sagheer who was always keen to teach me, and I performed the reactions helped by Diallo (ESR 6), who kindly and patiently taught and illustrated the techniques.

During this experience, I had the opportunity to learn, develop my scientific skills, and know a different scientific environment.

But it was not just science! I had great experiences like visiting the beautiful Oxford, and getting into some of the Colleges – thanks to the “local”, Sebastian (ESR1). The cherry on top was the fairy tale experience of having a formal dinner in a College!

Overall, this experience was magic! From the scientific and personal point of view. I am very happy and grateful I had the chance to live all these great adventures thanks to the NATURE-ETN project!

By Maria Dalla Pozza (ESR3)

Tania’s secondments from Warsaw to Oxford

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Our ESR Tania Sánchez Quirante from the Hocek group at the Institute of Organic Chemistry and Biochemistry in Czechia recently did two secondments at the Universities of Warsaw (Poland) and Oxford (UK).

From January to February 2023, Tania did her first secondment at the Laboratory of Chemical Biology and Biophysical Chemistry at the University of Warsaw, where she synthesized and purified modified cap RNA 70nt long and modified mRNA by in-vitro transcription. She also learned how to do in-vitro translation using the rabbit reticulocyte system.

In April 2023, she stayed at the Tom Brown group at the University of Oxford. She synthesized modified single-guide RNA 99nt long by in-vitro transcription reaction and used this sgRNA to perform CRISPR-Cas experiments. In addition, she did stability experiments of the modified sgRNA in Human serum.

Crystal clear insight: ESRs explore the world of crystallography and structural biology

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The Early-Stage Researchers (ESRs) were thrilled to participate in the 5th training week about nucleic acids and crystallography. The first two days were spent attending the Oligo 2023 conference in Oxford. They listened to experts talk about nucleic acid, base modification, aptamers, and more. They were fascinated by the new developments and ideas in this field.

After the conference, the ESRs visited the Oxford Nanopore Technologies research facilities. They gained a deep understanding of how the research industry works and how scientists turn their ideas into reality. The ESRs were impressed by the state-of-the-art facilities and the advanced equipment used for research.

The next two days were spent at the University of Reading, where the ESRs attended engaging talks about crystallography and data processing. They had the opportunity to participate in hands-on activities such as crystallisation, plate preparation, high throughput robot, and learning to recognise and collect good crystals. Finally, they collected data from the X-ray, which was an exciting experience for them.

After a free afternoon spent in London, the ESRs were welcomed at Diamond Light Source. They were given an intense tour of the different facilities and beam lines available at the synchrotron. They gained an understanding of the Cryo-EM and laser technology used in the field of structural biology for protein and nucleic acids. It was an eye-opening experience for them, and they had a lot of fun learning about this exciting field. Overall, the ESRs found the 5th training week about nucleic acids and crystallography to be an enlightening experience. They were exposed to the latest developments in the field, and the hands-on experience provided them with a deeper understanding of the processes involved. They were inspired to continue their research with renewed enthusiasm and curiosity.

By Ahmad Abdullrahman (ESR4)

Eva’s secondment at the Kellett Group in DCU

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baseclick GmbH and the Kellett group at DCU have an ongoing research collaboration upon a potential oligonucleotide-based SARS-CoV2 drug, whereas our baseclick ESR Eva Sophie Schönegger, one PostDoc (Dr. Brionna McGroman) and one PhD Student from the Kellett group are working together.

During the secondment in October 2022, Eva learned new techniques and developed new skills. At DCU, Eva was analyzing binding affinities of ligand-clicked oligonucleotides, which she had previously prepared in Munich. Therefore, different approaches were investigated, based on thermal melting, microscale thermophoresis and gel electrophoresis. Moreover, she performed first cleavage assays with the best-performing oligonucleotides

The 4th training week – In the core of NATURE-ETN

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Early-stage researchers (ESRs) and principal investigators have been invited to attend the 4th training week at Dublin City University where this EU-funded research consortium was born.

Prof. Andrew Kellett first gave an update on the project before introducing Prof. Nicholas Farrell from Virginia Commonwealth University (US), who is one of the scientific advisors of NATURE-ETN and is interested in Glycosaminoglycans as signalling molecules. He talked about his latest results and joked about how retiring is difficult when you can’t stop looking for more results.

Each ESR presented their results obtained so far followed by questions, comments, and discussions for future ideas. On Thursday, a team from the German biophysical instrument manufacturer NanoTemper delivered training on the Monolith technologies in Andrew Kellett’s lab to ESRs who had the opportunity to prepare the samples, learn how to read the results, and think about how this technology can be applied to their projects.

Finally, on the last day of the training week, ESRs were hosted by Prof. Niall Barron at the National Institute for Bioprocessing Research and Training (NIBRT). Prof. Barron explained the advanced therapy medicinal products, emphasizing the need to keep in mind the patient delivery process while obtaining basic research results. ESRs conducted a complete tour guided by Dr Adam Pritchard who showed and explained the technologies behind the bioproduction of recombinant proteins, vaccines, and cell and gene therapies.

Before saying goodbye, the ESRs decided to go for a walk together. This time down to the lighthouse at Dún Laoghaire, a small town outside the busy Dublin. Prof. Barron mentioned Emerson who said, “Science does not know its debt to imagination”, and isn’t the sea the best place to clear the mind and fire the imagination?

In this training week, new collaborations were created between ESRs, wrapping up before departing to their different locations in Europe, where they will bring home new ideas to apply in their labs and Irish souvenirs!

By Ahmad Abdullrahman (ESR4)

Jamie’s secondment at the MRC Laboratory of Molecular Biology completed

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Our ESR Chun Yin (Jamie) Chan from the Carell group at LMU had the opportunity to go on secondment at the MRC Laboratory of Molecular Biology (LMB) in Cambridge, UK, from July to October 2022.

The MRC LMB is one of the world’s leading research institutes in molecular biology. Jamie joined the group led by Dr. Philipp Holliger, which focuses on chemical biology, synthetic biology and in vitro evolution. The Holliger lab investigates fundamental questions of the chemical logic and constraints of molecular information encoding and the encoded synthesis; replication and evolution of novel sequence-defined biopolymers for applications in biotechnology and medicine; and the emergence of genetic function in chemical systems.

During his stay, Jamie explored the capacity of a recently discovered RNA polymerase ribozyme utilising trinucleotide triphosphates (triplets) as substrates to incorporate chemically modified triplets, for example, for the template-directed and sequence-specific positioning of chemical groups in nucleic acid polymers, and investigated how could these modifications possibly impact the ribozyme’s polymerisation in terms of fidelity, activity and chemical space for evolution in a prebiotic scenario.

From Paris to Reading – Maria’s secondment in the UK

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During my NATURE-ETN PhD program, I had the chance to spend two months at the University of Reading, in the UK, supervised by Prof. Christine Cardin and Dr. James Hall.

Even if changing country and environment are always challenging, I realised how a great experience I had the chance to come across from the first moment I arrived in the UK. The first day I went to the lab, the group gave me a very warm welcome, and I felt at home from the beginning.

During this secondment, I learnt many new techniques and developed new skills, supervised by very professional and passionate scientists, always keen to teach me.

During these two months, I evaluated the interaction between the compounds I synthesised at Chimie ParisTech and the DNA, through thermal stability studies. Also, I learned how to use a chiral HPLC and crystallise the compounds and the DNA. These topics and techniques are really fascinating to me, and this experience helped me to better understand my project and its very important aim. Overall, during my secondment, I had the opportunity to learn, develop my scientific skills, and know a different scientific environment.

To be fair, that was not only work… I fell in love with the UK! During the weekend I visited many different places like London, Oxford, and the beautiful British countryside. I spent some evenings in the pubs drinking beers with my new friends and having tea with the delicious scones with clotted cream and jam (the “cream tea”) in the afternoon.

Also, we went out with the group for a beer a few times, as you can see in the picture.

This was a very great experience from both a professional and personal point of view, and I am grateful to be part of this fantastic ETN project.

By Maria Dalla Pozza (PSL)

Second training week – Entrepreneurship, IP and ESR updates

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From the 13th to the 15th of September 2021, the ESRs took part in the second online NATURE-ETN training week.

In the first two days, the ESRs updated each other on their progress and receive valuable feedback from their peers and PIs. Potential opportunities for collaboration and secondments were also explored.

On the third day, Dr. Thomas Frischmuth, CEO of baseclick GmbH, provided two training sessions on entrepreneurship and Intellectual Property (IP). Using the leading biotechnological company and NATURE-ETN beneficiary baseclick as a basis, Dr. Frischmuth shared his experience and perspectives in terms of business models and company growth. During the IP session, the ESRs were introduced to internal vs. external IP, patent filing strategies, and examples of European and national patenting processes.