Expanding Horizons Through Research Mobility
Secondments
Our doctoral researchers gain a unique opportunity to work across institutions and sectors through secondments. These placements enhance their training, foster collaboration, and strengthen the impact of their research.
Secondments are a vital component of the RepState MSC Doctoral Network, offering our doctoral candidates the opportunity to engage in collaborative research, gain valuable skills, and build professional networks across academic and non-academic sectors. These short-term placements play a key role in strengthening the interdisciplinary and intersectoral dimensions of the project, while deepening the scientific impact of each researcher’s work.
We have already organized a number of successful secondments across our partner institutions and industry collaborators, and several are currently ongoing. Each secondment is carefully tailored to support the individual research goals of the doctoral candidates while contributing to the broader objectives of the RepState network.
Short reports and insights from completed and ongoing secondments can be found below, providing a glimpse into the diverse experiences and outcomes emerging from these exchanges.
Shiksha Saraogi (JLU) about her secondment at Erasmus MC, Rotterdam, NL, August– October 2024
Investigating UvrD Helicase
Research Focus
The secondment at EMC centered on two major objectives:
- Optimizing Mass Spectrometry (MS) Buffer Conditions – Ensuring protein integrity for structural and functional MS studies of protein-protein and protein-DNA interactions.
- Studying the Tudor Domain of UvrD in DNA Unwinding – Assessing its role in helicase activity using gel-based unwinding assays.
Key Findings & Outcomes
Mass Spectrometry Buffer Optimization
- Identified 250mM ammonium acetate as the optimal buffer for maintaining UvrD stability and functionality in MS.
- This buffer is now being used for continued MS-based structural studies.
Role of Tudor Domain in DNA Unwinding
- UvrD ΔTudor could not unwind GT-mismatched and gapped DNA, highlighting its essential role in processing specific DNA structures.
- Despite this, MutL still stimulated UvrD ΔTudor in unwinding smaller DNA substrates, suggesting alternative interaction interfaces facilitate helicase activity.
Kinetic & Functional Studies:
- Use stopped-flow fluorescence assays to measure unwinding rates.
- Perform ATP hydrolysis assays to determine the Tudor domain’s effect on helicase energy consumption.
Structural Investigations:
- Apply native MS and cross-linking MS to characterize MutL-UvrD interactions.
- Collaborate on single-molecule imaging to track UvrD’s real-time unwinding dynamics.
Emma Arean-Ulloa (LUMC) about her secondment at Erasmus MC, Rotterdam, NL, October-November 2024
As part of my PhD programme, I spent a month in Joyce Lebbink’s laboratory in Rotterdam, where I focused on assessing the activity of purified proteins. The methods I learnt provided valuable insights for my research. I carried out biochemical assays, including the use of circular DNA substrates to study replication in vitro and refined protocols for testing UvrD helicase activity.
The opportunity to collaborate with my peers enriched the experience, providing both professional development and networking opportunities.
Dennis Winter (CUT) about his secondment at Erasmus MC, Rotterdam, NL, November-December 2024
I did my first research secondment of the doctoral network RepState at the Erasmus University Rotterdam from 08.11. to 20.12.2024.
As part of the research secondment, I learnt how to make the necessary constructs and perform the in-bulk assays for the proteins involved in E. coli DNA mismatch repair (MMR). This involved making a phagemid construct containing a G/T mismatch and a hemimethylated GATC site, and performing several DNA repair assays to assess successful recognition and subsequent repair by the primary repair proteins involved, MutS, MutL and MutH.
By using a fluorescently labelled Cas9, successful MMR can be detected using a fluorescence microscope.
The resulting constructs are returned to Chalmers University for single-molecule analysis using chemically prepared glass slides and nanofluidic devices.
Khalid Rasheed (JLU) about his secondment at Erasmus MC, Rotterdam, NL, August-October 2024
I have completed a two-month secondment at Erasmus MC Rotterdam, focusing on two key research objectives:
- To check the activity of my labeled and unlabelled proteins in the Nicking assay.
- Optimization of Native Mass spec. Buffer by using different techniques with my colleagues.
Techniques learned: Nicking assay, Size Exclusion Chromatography (SEC), Thermal melt assay, and Unwinding assay.
During my stay, I had the opportunity to:
- Engage with the international community of scientists/researchers.
- Explore ongoing research at Erasmus MC.
- Exchange ideas with fellow researchers.
I contributed to the academic environment by:
- Participating in research seminars.
- Conducting a short research project related to my deliverables and milestones.
- Writing a report on my experiences and research findings.
The visit allowed me to enhance my skills and knowledge:
- I followed a lecture and practical course programme on Alpha fold prediction and PyMol.
- I engaged in lifelong learning skills for my personal and professional development.
This research visit at Erasmus MC has been an enriching experience. It has contributed to my academic growth and facilitated potential future collaborations.
Hien Le (UEF) about her secondment at Erasmus MC, Rotterdam, NL, August-September 2024
As a part of the RepState project, I had my first secondment at the research group of Assoc. Prof. Joyce Lebbink at Erasmus MC (Rotterdam, Netherlands), focusing on studying the DNA mismatch repair mechanism.
During the secondment, I worked closely with colleagues and peers within the RepState project. This collaboration extended my knowledge and equipped new techniques for my upcoming research. Additionally, the secondment allows me to build a strong connection with peers who share a passion for research on DNA mismatch repair. I highly appreciate my mentors and peers’ unwavering support and guidance throughout my secondment.
Beyond the academics, the secondment also gave me a great personal experience. Approaching the new culture and exploring new places after work made my time in the Netherlands fulfilling.
