1. Research Background

Organisms, cells, and molecules are continuously subjected to damage from external and internal sources. Although organisms employ sophisticated mechanisms to monitor and repair many forms of damage, their performance is imperfect, and the resulting accumulation of damage likely underlies the aging process. Historically, this imperfect repair has been viewed as an evolutionary trade-off between the energetic cost of maintenance against rapid growth. However, it is only recently that high-resolution methods have been developed to dynamically quantify this energy flux and allocation.

2. Research questions addressed by the group:

Our group develops novel methods to quantify energy expenditure and allocation, investigating how these drive the aging process. By combining approaches from molecular biology, biochemistry, and biophysics, we aim to understand mechanistic connections between energy constraints, dormancy, and longevity.

3. Possible project(s):

1. Worm Dormancy and Energy Dynamics
   In response to starvation at different developmental stages, C. elegans can transition into dormancy (dauer, L1 arrest, late larval arrest, adult reproductive diapause). These states are associated with extensions of longevity and stress resistance, requiring significant metabolic reprogramming. However, the real-time dynamics of energy metabolism throughout these stages are not known. Our lab has developed microfluidic devices that trap single worms for their full lifespans, allowing high-resolution fluorescence microscopy. We have used this setup to quantify the dynamics of glycolytic flux in individual worms with a recently developed fluorescence sensor. Building on these results, we aim to continuously quantify energy metabolism in worms as they enter, maintain and exit these long-lived, dormant states.

2. Ribosome Activity Sensors
   Translation and ribogenesis demand a significant fraction of the total energy budget in growing cells. When energy becomes scarce, some existing proteins and ribosomes are scavenged, while others must be preserved in a protected state. This decision is especially crucial in transitions to dormancy such as sporulation, diapause, and quiescence. Using structural information, our lab has designed sensors for ribosome abundance based on Förster resonance energy transfer (FRET). Building on this work, we will develop new sensors for ribosome activity and ribosomal dormancy, and use them to study the dynamics of energy allocation to translation during variations in energy availability.

3. Flux-sensing Metabolites
   Until recently, it has been difficult to measure metabolic fluxes at the scale of single cells. Two advances have made such measurements possible: the discovery that the concentrations of certain metabolites correlate with particular metabolic fluxes, and the development of fluorescent sensors for these metabolites - in this case, HYLIGHT as a sensor for fructose 1,6-bisphosphate and glycolytic flux. Do flux-sensing metabolites exist for other metabolic pathways? We aim to answer this question using systematic metabolic perturbations, stable isotope metabolomics, and fluorescent biosensors.

4. Applied Methods and model organisms:

We work with simple model systems, including budding yeast, C. elegans, and cultured cells. The methods we commonly use are quantitative fluorescence microscopy (including FLIM, FRET, and super-resolution), time-lapse microscopy and microfluidics, image analysis, metabolomics, and protein sensor design.

5. Desirable skills and qualifications:

We are looking for motivated and curious students with strong backgrounds in biology.

6. References and key publications:

Kirkwood, T. B. (1987). Immortality of the germ-line versus disposability of the soma. In Evolution of longevity in animals: a comparative approach (pp. 209-218). Boston, MA: Springer US.

Baugh, L. R., Hu, P. J. (2020). Starvation responses throughout the Caenorhabditis elegans life cycle. Genetics, 216(4), 837-878.

Frentz, Z., & Dworkin, J. (2020). Bioluminescence dynamics in single germinating bacterial spores reveal metabolic heterogeneity. Journal of the Royal Society Interface, 17(170), 20200350.

Kochanowski, K., Volkmer, B., Gerosa, L., Haverkorn van Rijsewijk, B. R., Schmidt, A., Heinemann, M. (2013). Functioning of a metabolic flux sensor in Escherichia coli. Proceedings of the National Academy of Sciences, 110(3), 1130-1135.

Koberstein, J. N., Stewart, M. L., Smith, C. B., Tarasov, A. I., Ashcroft, F. M., Stork, P. J., Goodman, R. H. (2022). Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1, 6-bisphosphate. Proceedings of the National Academy of Sciences, 119(31), e2204407119.