Development of advanced medical imaging technologies using synthetic biology tools

Regenerative medicine is at the forefront of medical research, providing patients with the ability of wound recovery, efficiently and effectively. This is due to the synthetic nature of the engineered treatment, which is created by studying cellular activity at the site of damage. Over

the past few decades, various such strategies have been developed, including engineering pluripotency with stem cells, mesenchymal stromal cell therapy, and immune cell therapy in many diseases including sickle cell aneamia, other medical applications such as skin rejuvenation, or tissue regeneration. These therapies revolve around understanding and controlling cell fate.

This can be done via the use of biomarkers in real time. Rather than fixing cells, which is invasive and static, live imaging using biomarkers allows for observing biological changes in a dynamic natural

environemnt of the cell - something I will explore during this project. The low concentrations of many of these biomarkers (which include, for example, DNA, RNA, proteins) demand an amplification system to augment their detection, via systems such as quantum dot labeling or in

situ molecular amplification. With the variety of biomarkers available today, including specific DNA and RNA biomarkers, advances in oncological diagnosis have been facilitated, for instance, via in vitro diagnostic tests, with the main advantages being the high-throughout, low cost and non-invasive aspects. As such, in this PhD, I would like to participate in synthetically enhancing such biomarkers.

These include possible CRISPR-Cas based biomarkers, such as those developed by Huyen et al, 2024, for meningitis detection. I am also eager to enhance mRNA biomarkers during this project, because although such markers are able to detect disease status, they are not always accurate, as found by Baghela et al., 2022, in relation to their mRNA biomarkers detecting specific cytokines, but not being able to predict the immune response involved in sepsis.

In addition, I am interested in developing new tools with which such activity can be studied. Traditional techniques including FISH, microarrays, ELISA, and flourescence microscopy, though essential biotechnological tools, have limitations to the study of live cellular activity deep within soft and hard tissue, such as in bone regeneration. These limitations include the hybridization step, signal overlapping and labour intensity. Newer tools must be less invasive, costly, and laborious for better and faster diagnosis.

Working within the group of Advanced Bioengineering (AB Group in the Division of Biomedical Engineering), we will apply synthetic biology tools to develop devices that can monitor and manipulate cell activity. I plan to implement my practical knowledge in molecular biology techniques, specifically in vitro work and high-throughput technology, while gaining new skills in engineering techniques.

The tools will enable us to use advanced imaging techniques which will generate high resolution images (sub-100nm) or explore dynamics (e.g. fluorescence lifetime imaging), for instance by creating specific biosensors and recognition elements to control cell activity, including using the CRISPR system. Depending on the progress, we may be able to engineer, through synthetic biology, different imaging modalities, including, photoacoustics in which synthetically created resolutions will be used to manipulate sound-active cells.

This will further allow for in-depth and noninvasive visualization of biological material, which enhances the opportunity for highly efficient, low-cost medical diagnostics.