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As the winter aura is still present in Gdańsk, we use to think back to our sunny stay at one of our SEA-EU Alliance partners,  University of Split, Croatia, in June 2022. The ICCVS Research Support Team consisting at that time of Wioleta Domańska-Babul, Małgorzata Bastian, Magdalena Dziki,  Anna Krajewska, Joanna Świerk, accompanied by a project manager colleague Marta Dziedzic from the Intercollegiate Faculty of Biotechnology had a very fruitful ERASMUS+ training & exchange stay at the University of Split.

The amazing views at literally every step one takes in Split on the beach and in the old town, although really hard to resist,  have not prevented us from  enjoying a day with Alexandra Banić from the Faculty of Maritime Studies, especially the exciting presentations during the Multiplier event of the MareMathics project. And hear, hear… two of us stood even on the podium as winners after a Kahoot competition.

At the School of Medicine we discussed with the Research Office various aspects of organization of research support in a biomed research environment as well as opportunities for collaboration in EU Horizon projects aiming at doctoral education. It was a pleasure to find out how much we have in common, talk about different ways of solving similar challenges in everyday work. We also presented opportunities for research funding for Croatian scientists who would like to do research in Poland, such as for example the Polonez funding from the National Science Centre, MSCA Fellowships, or NAWA Chair.

We met colleagues from the Project Implementation Support, Unit for Project Development, and Technology Transfer Office. We discussed the research support officers’ role in developing international networks and about the profession of  RMAs (research managers and administrators) in both countries. It was also fun to meet in person friends from the EU project ReSEArch EU with whom we until then had collaborated mainly in the online mode.

Last but not least, we also found time to visit the Diocletian Palace, climb the Marjan hill, and enter the Cathedral of Saint Domnius which is one with its seat in the oldest building among European cathedrals.

Looking back we can already reveal that our links do grow stronger and stronger in the following months – we have submitted an exciting joint Horizon Europe project proposal together with our Croatian friends who did an absolutely remarkable job as the proposal Coordinator’s team (huge thanks Bruna Pausic, Ivana Vuka & Tonka Petričević !). Do keep fingers crossed for a success, by the way.  We are working on the next project proposal which is due in a few months  –  this time in cooperation with the School of Medicine and other partners, mainly from the SEA-EU Alliance.

Izabela Raszczyk

From 19th till 22nd of October 2022, we – Malgorzta Kurkowiak and Aleksandra Domin, the current ICCVS editRNA project team – visited the Central European Institute of Technology (CEITEC, Brno, Czech Republic). CEITEC is an impressive scientific centre in the fields of life sciences, advanced materials and technologies. The stay was organized as a part of international cooperation activities in the bilateral research project from the  Weave-UNISONO funding programme. We had the opportunity to share aims of the forthcoming projects and discuss details of further collaboration with members of the RNA and Immunity group, led by prof. Mary O’Connell.

Moreover, we met prof. Matthias Hentze, who is the Director of the European Molecular Biology Laboratory and attended his lecture titled “Exploring the Underground of the RBP World: Riboregulation”. The speech was given as a part of the prestigious Mendel Lectures that host eminent guests from the field of medicine and natural sciences. Mendel Lectures have been organized for almost 20 years, hosted over 200 foreign scientists, including 15 Nobel prize laureates.

Continuing the ICCVS-CEITEC cooperation, Aleksandra will be joining Mary O’Connell’s team for a  6-months internship very soon, so stay tuned for future news from us.

Małgorzata Kurkowiak and Aleksandra Domin

from left: dr Małgorzata Kurkowiak and prof. Mary O’Connell

It was a windy eve of Halloween 2022, when two PhD candidates of our centre, myself – Mikołaj Kocikowski – and Katarzyna Dziubek – attended the prestigious “Science – Polish Perspectives” (SPP) conference at the University of Oxford. While truffle-parmegiano chips were one of the highlights of this adventure, it wasn’t the love of British cuisine that brought us back to the land of Earl Grey and double taps.

I had been invited to give a well-received talk entitled “Of Dogs and Men. How canines can help cure human cancers” while Kasia presented a poster – “Do we really know how cancer immunotherapy works? Shedding new light on the FDA-approved therapies and their safety”. Presenting our research to the top-tier researchers from a variety of backgrounds was a challenging, but ultimately successful, exercise in science communication.

Aside from a fantastic, inter-disciplinary menu of presentations and posters, ranging from the fates of Polish emigrants’ children, to quantum physics and beyond, other attractions were lurking at this gathering. Networking was supported by a workshop delivered by Olle Bergman, a Swedish communications consultant. A lot of inspiration and insight came from a talk by Joanna Bagniewska, a notable Polish science communicator and zoologist, who described the meanders of her own career, highlighted the importance of believing in ones own ideas and advised the audience on cooperating with scientific journalists.

The event provided numerous opportunities to talk and collaborate with colleagues from institutions such as EMBL, and to network with representatives of the key players of the Polish scientific landscape, such as the Foundation for Polish Science, Polpharma, or Łukasiewicz Network. It was very positive to observe the big institutions starting to compete for the best talent, aiming to man new Poland-based positions.

The annual SPP conference is run by Polonium Foundation, with the goal of bringing together the Polish scientific diaspora, according to their motto – “turning Polish brain drain into brain circulation”. Polonium acknowledges the reality of Polish scientists often choosing the most fertile ground for their research abroad and focuses on the potential of nation’s representatives working in the best scientific institutions of the world. The conference itself, like the foundation, is run purely through the unpaid effort of volunteers, their shared values and passion for this extraordinary event. That provides an authentic spirit and example to anyone who attends.

The conference left us with good memories. I only wish I could have spent more time following the footsteps of J.R.R. Tolkien through the stunning parks of Oxford. To quote one of the works by the father of British fantasy and remarkable researcher of myths and languages, whose ancestors lived in Gdansk, “It’s a dangerous business, Frodo, going out your door. You step onto the road, and if you don’t keep your feet, there’s no knowing where you might be swept off to.” I’m sure though my feet will deliver me again to Oxford and SPP.

Mikołaj Kocikowski

At the beginning of October 2022 two ICCVS scientists, Zuzanna Trybała and Łukasz Arcimowicz spent two weeks with the team of professor Bořivoj Vojtěšek at the Regional Centre for Applied Molecular Oncology (RECAMO) at Masaryk Memorial Cancer Institute in Brno. They had a unique opportunity to learn the process of protein production in the mammalian expression system utilizing the ExpiCHO system. The antibodies obtained at RECAMO will be useful in future projects led by Dr Małgorzata Lisowska at ICCVS in the field of antibody design. Our scientists found the method very practical and are excited about implementing it at our Centre.

ICCVS employees were impressed by RECAMO with modern laboratories, high-end equipment and world-leading research. They received a warm welcome and guidance from RECAMO researchers: dr Martin Krkoška, dr Zuzka Tylichová, dr Pavlina Zatloukalová, dr Radovan Krejčíř, Soňa Babčanová and others. Our scientists had many inspiring discussions and conversations about differences and similarities between our countries, science, and future possibilites that led to valuable friendships.

During their stay, our scientists visited also another research centre based in Brno that collaborates with the ICCVS – CEITEC and professor Mary O’Connell’s group where they had the pleasure join dr Pavla Musilová and dr Janka Melicherová in their daily experiments. It was a valuable experience seeing state-of-the-art laboratories and visiting the Masaryk University campus.

The city of Brno surprised our researchers and turned out to be a vivid city, full of breathtaking landmarks and tourist attractions, not to mention the delicious smažený sýr! It is a beautiful city that in many ways may be even considered better then Prague! The trip was made possible thanks to NAWA Prom and ERASMUS+ programmes.

From the left: Zuzanna Trybała, Martin Krkoska, Łukasz Arcimowicz and Zuzka Tylichova at RECAMO	Martin and Vaclav in their office
Janka, Pavla, Zuzanna and Łukasz at CEITEC	Zuzanna and Łukasz during their daily work at RECAMO
Zuzanna during her daily work at RECAMO	Łukasz and Zuzanna sightseeing Brno

Georges Bedran performed a 5-month internship at the University of Michigan in prof. Alexey Nesvizhskii’s lab. Using the state-of-the-art tools developed by the Nesvizhskii lab and the computational knowledge in immuno-oncology at ICCVS, Georges explored novel sources of tumour specific antigens (TSAs). This work will fill a specific gap in the literature and provide a well trusted resource for future studies aiming to understand immune-evasion or develop a new category of antigens.

Georges Bedran

The workshop was conducted at the University of Split, Croatia, between 4-6 July. We were two – dr Sachin Kote and prof. Adam Jagiełło-Rusiłowski – representatives from the University of Gdansk (UG). The workshop was led by a renowned, experienced international expert from the University of Edinburgh (UoE) in speculative and creative design, applied in the research context. The workshop was coordinated and facilitated by assistant professor Ivica Mitrovic, Art Academy, and Nikola Balic, Head of Science and Innovation, University of Split (US).

Dr Sachin Kote from the ICCVS (UG) has given valuable insight as a wet laboratory scientist who provided the vision to develop an “artifact” whose form and function of a possible future research lab in 2040. With other group members, dr Kote presented a vision of a speculative research future. The vision called HEER (Her Eternal Ephemeral Resources) imagined the life of a scientist in 2040 as a love story between Artificial Intelligence (AI) and a scientist. Conversational problem solving enabled by data hoarding and secondary research opportunities could be one of the plausible futures.

Besides the workshop, dr Kote visited prof. Janos Terzic from the School of Medicine (US), for the scientific collaboration between Poland and Croatia.

Application of Ashwin Kallor a PhD student form computational biology group at ICCVS was selected in a competitive recruitment process to participate in the International High Performance Computing Summer School 2022. Below Ashwin’s reminiscences about the event.

The International High Performance Computing Summer School (IHPCSS) was held this year at Athens, Greece between 20 and 26 June. This is an annual event which is hosted jointly by the Partnership for Advanced Computing in Europe (PRACE), XSEDE (USA), SciNet (Canada) and RIKEN Center for Advanced Computing (Japan) where participating students are provided training on various topics related to high performance computing, ranging from parallelization to big data techniques. Hands-on classroom lectures are supplemented with learning materials and take-home exercises to impart a holistic and rigorous grounding in the underlying concepts of HPC while exposing the students to real-world applications through examples derived from engineering, astrophysics and the biomedical sciences. The participants are also given an opportunity to present their doctoral/post-doctoral research during a two day electronic poster session and connect with academicians/industry professionals during a career fair held during the latter half of the program. Beyond didactics, each student is assigned a specific mentor, who is expected to provide the student with professional, academic and even personal guidance on various issues faced by them.

The summer school was an enriching experience. Through the classroom sessions, I was able to learn new techniques in parallelization and big data processing such as OpenMP and PySpark, both of which are expected to be implemented in my computational workflows in due course. Outside the classroom, I was able to present the work conducted by the computational biology group at ICCVS during the e-poster session with a poster titled “Utilizing high performance computing for cancer vaccine discovery”. Meeting students, academicians and industry professionals from around the world was eye-opening since we were able to exchange ideas around HPC-related techniques and discuss our work. The networking sessions were further enhanced through the career and resume/interview sessions, where industry professionals and academicians provided advice on how to approach job interviews, how to frame and develop resumes and also the skill-sets required for each industry. In this regard, it is fitting to acknowledge the contribution of my mentor, Dr Pawel Janowski, who, through his constant support and encouragement, ensured that my time at the summer school was stimulating, both at the intellectual and personal level. Of course, the summer school was not entirely work and career-oriented as trips to a musical performance at the ancient Odeon theatre, the Athenian Acropolis and the Lycabettus Hill provided much-needed recreation during a week of intensive learning.

I take this opportunity to acknowledge Dr Natalia Marek-Trzonkowska and Dr Javier Alfaro, without whose assistance and encouragement this trip would not have been possible.

Ashwin Kallor

During 28 June – 4 July I spent the training days at the University of Pisa.

I visited the laboratory of Prof. Chiara Gabelli and Prof. Vittoria Raffa where I learnt how to perform a gene editing protocol based on CRISPR-Cas9 technique, applied to human cancer cells as well as to the teleost zebrafish.

I prepared ribonucleoprotein complexes (RNP). I performed transfection of RNP and after I analyzed cell internalization of RNP using immunofluorescence. I learnt basic technique employing zebrafish including adults fish crossing, embryo collection, microinjection of RNP in embryos in 1-cell stage. In addition, I performed genomic DNA extraction from embryo and I gained basic knowledge in data analysis of High Resolution Melting technique. I received a valuable training on the new and very potent techniques.

Visiting the University of Pisa and being welcomed by the very hospitable people working there was a wonderful experience for me. In the broader perspective, the mobility can initiate the establishment of the research collaboration and staff exchange between University of Gdańsk and University of Pisa.

Alicja Dziadosz

Our employee, M.Sc. Eng. Balbina Surma, participated in the 23^rd STP VALENCIA: LANGUAGES & IT TRAINING FOR UNIVERSITY STAFF. The event took place at the beginning of June 2022 at the Universitat Polite.

Over 120 participants from different parts of the world and various fields of science attended this event. It was a great opportunity to exchange experiences and interdisciplinary approaches for further development.

The supervisor of IT group, Eduardo Blasco Talavan, shared his knowledge on the use of database management system tools such as MS Access.

During the training importance of  cybersecurity was highlighted. The  participants also learned the secrets of the art of presentation with Prezi software, which enables multi-level content visualization.

During the intensive course, participants also had the opportunity to become acquainted with the art, culture and traditions of Valencia.

Balbina Surma

The 1st Progress and Assembly meeting of KATY (Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity) was held on 24th/25th May, 2022 in Rome.

The KATY project is about developing an AI enabled prognostic platform in cancer focused on Renal Cancer as an application.

Work Package “Large Scale Pilot and Validation” of the project is led by dr Javier Alfaro, a PI of Computational Science Group at the ICCVS and co-led by dr Emilia Daghir-Wojtkowiak.  Working on a proof-of-concept application of the KATY platform on a renal cancer dataset, they coordinate scientific activity of people of different backgrounds and professions to make a patient-centric interface available through the KATY platform.

The 1st Progress and Assembly Meeting provided an opportunity to report scientific highlights (20 partners out of 11 countries gathering people of different background), focused on:

1) Clinical Scenarios and Pilots (clinicians, biologists, bioinformaticians)

2) Data engineering through the development of a DataLake and Distributed Knowledge Graph (data scientists, mathematicians, biologists),

3) Predictive modelling using Artificial Intelligence (data scientists, mathematicians, informaticians, computer infrastructure experts),

4) Making models accessible through the KATY platform (front-end and back-end developers, bioinformaticians).

During the Meeting, Javier Alfaro, Emilia Daghir-Wojtkowiak and Ashwin Kallor were reporting the on-going work focused on various aspects of clinical scenarios, proteomics and immunopeptidomics.

It is worth adding that the KATY consortium is a very interactive environment and during the Meeting, many questions, untouched issues/problems have been addressed and solved by mutual discussion. All participants finally had the opportunity to meet not only on-line but face-to-face in the heart of Rome and each person had a chance to eat his self-made pizza!

Emilia Daghir-Wojtkowiak