Periodic Reporting for period 1 - UPFs_NMD (Up-frameshift protein interactions in translation termination and nonsense-mediated mRNA decay)
Okres sprawozdawczy: 2022-03-01 do 2024-02-29
The genetic code is often compared to a "blueprint" because it holds the essential instructions for a cell's survival. Think of DNA like a book - but how does the cell actually "read" it? The instructions stored within DNA are "read" in two steps: transcription and translation. Transcription is the first step in gene expression, Transcription is like making a copy of a specific page in the book. This copy, called messenger RNA (mRNA) is needed to make a protein. This translation happens with the help of machines called ribosomes. Nonsense-mediated mRNA decay (NMD) is a quality control system found in all eukaryotic cells. Its job is to spot specific errors namely translation stop signals in the mRNA - like typos in a text - and get rid of the mRNA. This prevents the cell from making incomplete or harmful proteins. NMD proteins get activated when the ribosome encounters a stop sign at an inappropriate position in the mRNA.
This area of research is highly important for both medicine and society because NMD plays a key role in numerous human genetic diseases like β-thalassemia, cystic fibrosis, Becker muscular dystrophy, and Duchenne muscular dystrophy. Furthermore, disruption of NMD can lead to neurodevelopmental disorders, immune diseases, and cancer. Understanding how NMD works is crucial for developing new treatment strategies. To that end, there are still big questions to answer, including how NMD proteins recognize substrates and become activated.
This project had several primary goals. I studied the interactions among NMD proteins to better understand their molecular function. Secondly, I carried out structural investigations to visualize these interactions of NMD components. The MSCA Individual Fellowship had the parallel aims of advancing my personal and professional development and undertaking outreach initiatives such as public engagement and dissemination of findings – this project was ideally suited for me to learn new practical skills, gain leadership experience, and engage in outreach activities.
This area of research is highly important for both medicine and society because NMD plays a key role in numerous human genetic diseases like β-thalassemia, cystic fibrosis, Becker muscular dystrophy, and Duchenne muscular dystrophy. Furthermore, disruption of NMD can lead to neurodevelopmental disorders, immune diseases, and cancer. Understanding how NMD works is crucial for developing new treatment strategies. To that end, there are still big questions to answer, including how NMD proteins recognize substrates and become activated.
This project had several primary goals. I studied the interactions among NMD proteins to better understand their molecular function. Secondly, I carried out structural investigations to visualize these interactions of NMD components. The MSCA Individual Fellowship had the parallel aims of advancing my personal and professional development and undertaking outreach initiatives such as public engagement and dissemination of findings – this project was ideally suited for me to learn new practical skills, gain leadership experience, and engage in outreach activities.
Work was conducted via 3 work packages (WPs).
The goal of Work Package 1 (WP1) was to improve my expertise in new methodologies, in particular baculovirus insect cell expression and electron microscopy (EM). I became proficient in both techniques. I applied my new skills to produce NMD proteins, reconstitute NMD complexes and analyse their structure by single-particle EM. This resulted in one publication and 2 manuscripts underway.
WP2 was focussed on my research skills and helping me to teach and share with others what I've learned. I attended several workshops to learn electron microscopy technique and others to further develop soft skills. Additionally, I have attended a one-year course in Leadership (Female leadership initiative, FLi, 2023) organized by University of Bristol, which gave me the opportunity to participate, learn and apply the new skills. I was also asked to share my experience at the introduction session of the subsequent, FLi 2024, course and to become an Action Learning facilitator for the FLi course 2024. I further attended the training sessions organized by the CREATE (Cultivating Research-rich Education and Teaching Excellence) HEA Fellowship scheme at the University of Bristol. I recently completed the submission of my portfolio for consideration as an HEA Associate Fellow (AFHEA) and expect to receive the outcome in mid-May 2024. I further developed skills in management, governance, communication, networking and funding seeking. In these two years I have actively participated in co-organising the Southwest Structural Biology conference 2022, organising seminars for the cryo-EM community in the southwest of UK, and I am a Biochemical Society Ambassador at the School of Biochemistry in Bristol. Ambassadors support the transfer of ideas between local molecular biologists and the Society, and also help to organise local events such as student receptions and sponsored seminars.
WP3 comprised the transfer of knowledge. I supervised and mentored for undergraduate Biochemistry students and PhD students, and new researchers in the team. I conducted workshops covering research techniques tailored for both Early-Stage Researchers and experienced researchers. I regularly presented my research progress at informal group meetings in the lab to discuss the advancement, experiments and technical problems encountered with other colleagues, at the electron microscopy user’s meetings, and at the whole-department seminars. I gave a seminar on research processes and research culture to Year 3 Students in Biochemistry.
I gave two lectures for the Biochemical methodologies course (Master’s level in Biochemistry) in April 2023 at University of Rome, Italy as invited lecturer.
I have enthusiastically contributed to outreach events. I participated in the Researcher’s night (Sep 2021 and 2022) and talked about my work to 11-years old pupils. As ongoing activity, I am currently exchanging mails with students at a secondary school in Italy, to talk about my role as a biochemist, how research is conducted and what the implications and applications of my research projects are.
My results will be reported in forthcoming papers providing structural and functional insights into NMD protein complexes which further our understanding of mRNA quality control mechanism. The new skills I gained during the grant helped me build a research network, lead a project, and provide the basis for my career as independent scientist.
The goal of Work Package 1 (WP1) was to improve my expertise in new methodologies, in particular baculovirus insect cell expression and electron microscopy (EM). I became proficient in both techniques. I applied my new skills to produce NMD proteins, reconstitute NMD complexes and analyse their structure by single-particle EM. This resulted in one publication and 2 manuscripts underway.
WP2 was focussed on my research skills and helping me to teach and share with others what I've learned. I attended several workshops to learn electron microscopy technique and others to further develop soft skills. Additionally, I have attended a one-year course in Leadership (Female leadership initiative, FLi, 2023) organized by University of Bristol, which gave me the opportunity to participate, learn and apply the new skills. I was also asked to share my experience at the introduction session of the subsequent, FLi 2024, course and to become an Action Learning facilitator for the FLi course 2024. I further attended the training sessions organized by the CREATE (Cultivating Research-rich Education and Teaching Excellence) HEA Fellowship scheme at the University of Bristol. I recently completed the submission of my portfolio for consideration as an HEA Associate Fellow (AFHEA) and expect to receive the outcome in mid-May 2024. I further developed skills in management, governance, communication, networking and funding seeking. In these two years I have actively participated in co-organising the Southwest Structural Biology conference 2022, organising seminars for the cryo-EM community in the southwest of UK, and I am a Biochemical Society Ambassador at the School of Biochemistry in Bristol. Ambassadors support the transfer of ideas between local molecular biologists and the Society, and also help to organise local events such as student receptions and sponsored seminars.
WP3 comprised the transfer of knowledge. I supervised and mentored for undergraduate Biochemistry students and PhD students, and new researchers in the team. I conducted workshops covering research techniques tailored for both Early-Stage Researchers and experienced researchers. I regularly presented my research progress at informal group meetings in the lab to discuss the advancement, experiments and technical problems encountered with other colleagues, at the electron microscopy user’s meetings, and at the whole-department seminars. I gave a seminar on research processes and research culture to Year 3 Students in Biochemistry.
I gave two lectures for the Biochemical methodologies course (Master’s level in Biochemistry) in April 2023 at University of Rome, Italy as invited lecturer.
I have enthusiastically contributed to outreach events. I participated in the Researcher’s night (Sep 2021 and 2022) and talked about my work to 11-years old pupils. As ongoing activity, I am currently exchanging mails with students at a secondary school in Italy, to talk about my role as a biochemist, how research is conducted and what the implications and applications of my research projects are.
My results will be reported in forthcoming papers providing structural and functional insights into NMD protein complexes which further our understanding of mRNA quality control mechanism. The new skills I gained during the grant helped me build a research network, lead a project, and provide the basis for my career as independent scientist.
For one, scientists who study how cells control the quality of mRNA will directly profit from the new structures and protocols. Also, structural biologists studying protein complexes and protein-nucleic acid complexes will benefit from the new protocols. Finally, our structures provide important insights into the molecular interaction of NMD proteins and how disease-causing mutations interfere with complex formation, which is of interest to medical doctors, affected patients, the general public and pharmaceutical companies looking for new treatment strategies.
Working with collaborators, team members, and students has helped me develop the skills needed to lead a team. I was able to improve my communication of scientific ideas, mentoring others, and planning research projects. This fellowship has been crucial for me in shaping a research program and giving me a platform to start my career as an independent researcher. Through this project, I obtained the opportunity to explore new ideas, new technology and tackle important research questions. In particular, learning advanced technologies like electron microscopy and image processing. These new skills have really shaped my professional profile and given me a strong foundation to take on new research projects as a leader. Teaching and leadership courses helped me improve how I communicate and gave me the tools to lead and inspire my colleagues. By engaging in outreach activities, I've been able to talk to the public about my project as well as biochemistry and structural biology in general, highlighting the importance and fascination of basic research.
Working with collaborators, team members, and students has helped me develop the skills needed to lead a team. I was able to improve my communication of scientific ideas, mentoring others, and planning research projects. This fellowship has been crucial for me in shaping a research program and giving me a platform to start my career as an independent researcher. Through this project, I obtained the opportunity to explore new ideas, new technology and tackle important research questions. In particular, learning advanced technologies like electron microscopy and image processing. These new skills have really shaped my professional profile and given me a strong foundation to take on new research projects as a leader. Teaching and leadership courses helped me improve how I communicate and gave me the tools to lead and inspire my colleagues. By engaging in outreach activities, I've been able to talk to the public about my project as well as biochemistry and structural biology in general, highlighting the importance and fascination of basic research.