Using novel fluorescence lifetime imaging methods to study molecular dynamics and their influence on circuits and homeostasis in vivo

  • English language proficiency required
  • Boston
  • This position has been filled

Website Harvard Medical school

Supervisor: Bart Lodder, MSc (former Dutch master student) at Sabatini lab at Harvard medical school

Project description:

In recent years, through optical methods such as optogenetics and calcium/voltage imaging, there has been an explosion in the possibilities to study the brain on a circuit and cellular level. These methods allow for precise control and measurement of neuronal firing, allowing us to derive behavioral/cellular functionality of molecularly and spatially defined neuronal populations. However, there is a key point of information missing that is both relevant on a fundamental and clinical level: How are the signals of neuronal populations integrated in an intact neuronal environment (i.e. in vivo)? Neurotransmitters activate a plethora of receptors and each have subtle and distinct effects on the molecular architecture of the cell. My PhD is focused on developing new optical methods, creating new molecular sensors and use these tools to understand how downstream molecular mechanisms react to behavioral states, neurotransmitter release and medication. Subsequently, I investigate the effect of these changes on behavior, neuronal state and disease progression. Specifically, I am currently pursuing the following projects:

1) PKA activity in microglia during inflammation (e.g. during stroke) and homeostasis (e.g. Alzheimer disease): PKA activity is an important driver for microglia function. For example, when microglia transition from a homeostatic state into an inflammatory state there is a large shift in PKA pathway associated gene expression, which tailor the microglia for their specific function. We make use of fluorescent lifetime photometry and microscopy to try to understand the effect of peripheral pain, sleep, injury, Alzheimer’s disease and several widely used and available drugs on PKA activity, to gain a deeper understanding how microglia are regulated. This project contains: In vivo mouse behavior, pharmacological administration, fluorescence lifetime photometry and microscopy, histology and fluorescent microscopy and potentially optical window in vivo fluorescence lifetime microscopy and using an Alzheimer’s mouse model.

2) Creating a GSK3B sensor to understand molecular mechanisms underlying the treatment of bipolar disorder in vitro: GSK3B is a central effector protein that relays signals from multiple signaling pathways and causes wide transcriptional changes. Interestingly, GSK3B is thought to be the main target of lithium when treating bipolar disorder. Over the last few months we have designed and cloned multiple potential GSK3B sensors. We are currently validating our sensors using in vivo methods. In future steps we will use these sensors to test the effect of multiple GSK3B targeting drugs in vitro and in vivo. This project contains: fluorescence lifetime microscopy, cell culturing, transfection and fluorescence microscopy.

3) Development of a tapered fluorescence lifetime photometry device to look at the heterogeneity of dopamine dependent PKA activity in the striatum: The tapered fluorescent lifetime photometry system is able to measure lifetime sensors across a dorsal ventral axis in the mouse brain. This device is currently in development and needs to be calibrated and validated, before we can use it for biological discovery. This project entails testing new software, performing calibrations and measuring dopamine dependent PKA signaling across the striatum, an important region for learning, choice and reward. This project contains: creative troubleshooting, modifying/building optical devices, mouse behavior, tapered photometry and fluorescence lifetime photometry.

4) (Collaboration with the Ed Boyden lab at MIT) to create a new way to identify and multiplex sensors (SIRIs), allowing for the simultaneous measurement of many molecular processes in the same cell (in vitro and in vivo): We are using fluorescent lifetime microscopy to identify the fluorescent lifetime of clustered sensors, allowing for their identification in vivo. This project contains: fluorescence lifetime microscopy in cells, slice and possibly in vivo, cell culturing, transfection and viral injection.

If you have any questions and/or if you are interested in one or more of these projects, please send me an email at For applications, please include in your email a few sentences about your motivation/interests/experience accompanied by a CV.


Bart Lodder