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Third NATURE-ETN training Week in Munich, Germany

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From the 16th to the 20th of May 2022, our fifteen NATURE-ETN early-stage researchers (ESRs) were finally reunited in Munich, Germany, for the third training week. The event was held in the recently built Institute of Chemical Epigenetics Munich (ICEM), in the Ludwig-Maximilian University of Munich (LMU). The ICEM building is funded by the Federal Republic of Germany and the state of Bavaria and results from the initiative of Prof. Thomas Carell, Principal Investigator in NATURE-ETN. It hosts two of our ESRs from the Carell group who recently moved to this new building.

On the first day of the training week, the ESRs received a guided tour of ICEM and introductory sessions on mass-spectrometry-based proteomics by Dr. Pavel Kielkowski and sequencing technology by Dr. Markus Müller.

On the second day, the scientific training was pursued with morning sessions on epigenome sequencing by Dr. Müller and Dr. Pascal Giehr. In the afternoon, Dr. Müller provided a bioinformatics crash-course with RNAseq and Prof. Carell gave a lecture on the synthetic chemistry of nucleosides.

On the third day, the ESRs formed groups to discuss ways of enhancing science communication to different audiences.

The training programme also covered industry-relevant skills, with a stimulating session on Quality Management delivered by Alexander Schalk, Quality Manager at the company Baseclick GmbH, also a beneficiary in NATURE-ETN.

The ESRs had the afternoon free to visit Munich and better get to know each other, in the first in-person meeting since the start of the project.

On the fourth and fifth days, the ESRs, along with other researchers from the LMU Department of Chemistry, attended the Nature masterclass delivered by Dr. Véronique Gebala, Senior Editor at Nature, and Dr. Ilse A. Valtierra-Gutierrez, Associate Editor at Nature Communications.

The comprehensive training included sessions on the preparation and submission of high-quality papers, the editorial and peer-review processes, and best practices in scientific publishing. The trainers also take the time to review abstracts prepared in advance by the ESRs.

We thank the organisers at LMU and the trainers for this successful event and already look forward to the 4th training week, to be held this Autumn in Dublin, Ireland.

In the meantime, most ESRs will meet again on the 5th to 10th of June for the XVIIIth Symposium on Chemistry of Nucleic Acids, in Český Krumlov, Czechia, organised by the Hocek group.

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)

New publication on the cytotoxic activity of organometallic di-iron complexes in cancer cell lines

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Recent collaborative work from NATURE-ETN and the University of Pisa has been published in Organometallics by ESR Maria Dalla Pozza from the group of Gilles Gasser at Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences (France), in collaboration with the team of Prof. Fabio Marchetti at the University of Pisa (Italy). The scientists investigated the anticancer activity of some di-iron compounds functionalised with sugar moieties to increase their cellular uptake and possibly their selectivity for cancer cells. The compounds, synthesised by Marchetti’s group, were tested against a panel of cancerous cells by ESR Maria Dalla Pozza.

Among the different categories of metal drug candidates, iron complexes based on the ferrocene scaffold have aroused notable interest. The antiproliferative activity of these compounds is ascribable to the redox chemistry of the ferrocenyl iron(II) center, which undergoes oxidation to Fe(III) in the tumour cells. This enhances the formation of toxic metabolites that lead to cell death. Di-iron compounds have been less investigated, however recent studies have disclosed a promising anticancer potential. In this study, the sugar functionalisation was performed on di-iron complexes to optimise the cytotoxic properties by exploiting the Warburg effect. Specifically, the anticancer activity of the compounds was evaluated using the resazurin assay and the scratch assay. Overall, this study pointed out that the antiproliferative activities of the new complexes correlate with their lipophilicity, ranging from moderate cytotoxicity to inactivity, and showing an absence of appreciable selectivity with respect to a non-cancerous cell line. On the other hand, analogous diiron complexes without the sugar moiety functionalisation, analysed as references, performed better in the same conditions. This confirms the potential of the present category of organometallics in the medicinal field.

Reference:
Schoch, S., Iacopini, D., Dalla Pozza, M., Di Pietro, S., Degano, I., Gasser, G., Di Bussolo, V., and Marchetti, F. Tethering Carbohydrates to the Vinyliminium Ligand of Antiproliferative Organometallic Diiron Complexes. 
Organometallics (2022). https://doi.org/10.1021/acs.organomet.1c00519

New publication examines the multi-modal activity of copper(II) and silver (I)-phendione complexes on DNA scission within P. aeruginosa

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Recent collaborative work from NATURE-ETN has been published in the Journal of Biological Inorganic Chemistry by researchers in the Kellett lab at DCU. Co-authors include NATURE-ETN coordinator Dr. Andrew Kellett, co-supervisor Dr. Georgia Menounou, and ESR Conor Bain. The paper investigated the multi-modal activity of copper(II) and silver(I) complexes with the N,N-coordinating ligand, 1,10-phenanthroline-5,6-dione, with particular focus on DNA damage within Pseudomonas aeruginosa.

The emergence of microbial drug-resistance in recent decades has given rise to the need for novel antimicrobial therapeutics. The metal-based complexes [Ag(1,10-phenanthroline-5,6- dione)2]ClO4 (Ag-phendione) and [Cu(1,10-phenanthroline-5,6-dione)3](ClO4)2.4H2O (Cu-phendione) have previously demonstrated efficient antimicrobial action against multidrug-resistant species. The focus of the study was to understand the binding potential of these complexes with double-stranded DNA using a combination of in silico and in vitro approaches. Promising results arising from this work revealed a potentially new class of antimicrobial drug candidate with a distinct therapeutic mechanism against the multidrug-resistant pathogen P. aeruginosa.

Molecular docking studies showed both complexes elicit a multi-mechanistic approach to DNA-binding via hydrogen bonding, hydrophobic and electrostatic interactions, with both complexes favouring minor groove binding. Of the two complexes, Cu-phendione achieved the highest binding affinity for both major and minor grooves with nearly 10x greater affinity to DNA than Ag-phendione and nearly 20x greater affinity than the phendione ligand alone. Cu-phendione achieved DNA scission through free radical oxidative damage, as well as DNA-nicking and relaxation of supercoiled plasmid DNA. It was concluded that both complexes elicit a dose-dependent effect, with successful DNA fragmentation within multi-drug resistant pathogen P. aeruginosa when treated with a single dose of Cu-phendione. This work proposes a novel dose-regulated class of metal-based antimicrobial therapeutics.

Reference:

Galdino, A.C.M., Viganor, L., Pereira, M.M., Devereux, M., McCann, M., Branquinha, M.H., Molphy, Z., O’Carroll, S., Bain, C., Menounou, G., Kellett, A., Dos Santos, A.L.S. Copper(II) and silver(I)-1,10-phenanthroline-5,6-dione complexes interact with double-stranded DNA: further evidence of their apparent multi-modal activity towards Pseudomonas aeruginosa. J Biol Inorg Chem (2022). https://doi.org/10.1007/s00775-021-01922-3

Global Tech Company Biotage acquires ATDBio

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On 20 October 2021, one of NATURE-ETN’s partners, ATDBio has announced that it has been acquired by Swedish multinational life sciences company Biotage for approximately £ 45 million. The acquisition will bring many years of experience and expertise in highly complex DNA and RNA production to Biotage. As a new part of the Biotage Group, the ATDBio founders will continue to work on these technologies with existing and new customers. While ATDBio is undergoing major changes, R&D projects such as the ones that are ongoing as part of NATURE-ETN – with early-stage researcher Diallo Traore on CRISPR-Cas 9 in live-cell imaging – will continue as planned.

“ATDBio is very proud to become part of the Biotage family, which shares our passion for innovation, customer focus and sustainability. With our deep understanding of nucleic acid chemistry, we can ensure superior quality oligonucleotide synthesis, and supply highly pure products. We make oligonucleotides for a broad range of academic and commercial customers, including some of the most significant biotech and pharma companies globally. We will now be able to scale up even further thanks to the global presence and world-leading separation science expertise of Biotage.  We will continue to innovate, helping our customers to bring the next generation of nucleic acid molecular diagnostics, vaccines and therapeutics to the market”, said Dr Tom Brown Jr, Director of ATDBio.

ATDBio was founded in 2004 by Professor Tom Brown (Snr), one of the world’s leading nucleic acids chemists, Dr Dorcas Brown, an expert in oligonucleotide synthesis, Dr Tom Brown (Jnr) and Dr Asha Brown. It has laboratories in Oxford and Southampton, UK. As a leader in complex oligonucleotide synthesis, ATDBio has been working on molecular diagnostics, nucleic acid-based therapeutics and vaccines in addition to a new generation of DNA and RNA sequencing technologies.

Press release (Biotage)

Press release (ATDBio)

Successful NATURE-ETN check meeting

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The NATURE-ETN check meeting with our European Commission Research Executive Agency (REA) Project Officer took place online on the 5th of October 2021. Our Coordinator reported on the progress of the project and the COVID-19- and Brexit-induced challenges encountered and successfully solved through effective mitigation measures and collaboration. On their side, our 15 ESRs introduced themselves, their project objectives and training ambitions. The discussions on the next steps and upcoming milestones with the REA Project Officer were both fruitful and informative.

This meeting was the occasion to highlight our appreciation for the REA’s flexibility and support in these uncertain times and our gratitude for being part of the Marie-Skłodowska-Curie Actions community. A community that now counts two Nobel Prize winners in Chemistry for the second year in a row.

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.

First training week – combining soft and technical skills

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From the 18th to the 22nd of June 2021, the ESRs took part in the first NATURE-ETN training week, which covered a mix between soft and technical skills. The training was held virtually due to the COVID-19 pandemic and subsequent travel limitations.

During the first day, the ESRs were introduced to Hugh Kearns’ (ThinkWell) Seven Secrets of Highly Successful Research Students.

In this workshop, Kearns described key habits that help PhD students complete their research project efficiently, ensuring appropriate work-life balance and overcoming issues such as writer’s block and imposter syndrome.  
 
The second day started with a training session on Research Project Management from the partner organisation accelopment Switzerland Ltd.
 
The training covered aspects such as project planning, project monitoring, reporting, risk management, and project communication.

The scientific training consisted of both live and pre-recorded (asynchronous) lectures and the materials will remain available to the ESRs for future references.

Prof Tom Brown from the University of Oxford gave introductory and advanced lectures on the Synthesis of Biomolecules. This training notably covered nucleic acid structures, as well as oligonucleotide synthesis and their use as drugs in genetic and forensic analyses.
 
Dr Tom Brown Jnr from the oligonucleotide synthesis company ATDBio provided additional insights from more applied and commercial perspectives, and an introduction to ATDBio’s activities.
 
On the third and last day, Prof Andrew Kellett, Coordinator of NATURE-ETN, and his team at the Dublin City University (DCU) introduced the ESRs to artificial gene editing systems and molecular methods.

Prof Andrew Kellett discussed in detail metallodrug-DNA interactions, chemical nucleases, and advanced hybrid biomaterials for gene editing using click chemistry. Pre-recorded lectures with the principles of novel methodologies, techniques, and biophysical assays developed within the Kellett group were followed by high-quality virtual laboratory sessions recorded at the exceptionally well-equipped facilities at DCU.

This was the first of a series of training events that will be held both online and in-person throughout the project duration.

1st Project meeting with the newly recruited ESRs

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On 16 December 2020, the NATURE-ETN team had a first network meeting with the 12 recruited ESRs.

This was the occasion for the consortium to virtually meet each other before the Holiday season and for the ESRs to introduce themselves and their research projects. After this round of introductions, the PIs and ESRs were divided into separate rooms to discuss next year’s activities for the former and simply to get to know each other for the latter.

To stay updated on the latest news from NATURE-ETN and ESRs’ research updates, you can now follow the project’s Twitter account @ETN_NATURE.