We have two main focus areas - related to basic and applied neuroscience. These divisions are not discrete, and some projects are on the interface of the two, with some aspects of both. Below is a generic description of the nature of projects. 
 

We are obsessed by the vexing problem of cytosolic slow axonal transport (nicely articulated here by Scott Brady). Specifically, while membranous proteins simply latch on to vesicles and are transported by motors in "fast" axonal transport , hundreds of soluble or cytosolic proteins are known to march along axons in a slow, concerted manner, with overall velocities that are several orders of magnitude slower (called "slow" axonal transport). As diffusion cannot supply molecules over these enormous distances (diffudion also exponentially decays over time); this slow movement must use some motor-driven mechanism. However, almost nothing is known about how cytosolic proteins move in slow axonal transport. In our lab, we have developed new model-systems that allow us to visualize this phenomena (see paper) and dissect the molecular mechanisms.

As many disease-associated cytosolic proteins also move in slow axonal transport (alpha-synuclein and tau for example), and their axonal transport has been implicated in disease (see reviews here and here), a related interest is to uncover the transport/trafficking of these cytosolic proteins under pathologic conditions.  

These experiments involve extensive live imaging using photoactivable vectors, image-analysis, immunofluorescence, biochemistry, proteomics/bioinformatics (in collaboration with John Yates, Scripps) and computational modeling, as/if needed. As almost nothing is known about cytosolic transport, chances of making a new discovery - on virtually every carefully-executed experiment - is rather high.

Alpha-synuclein is a tiny 14kDa protein involved in several neurodegenerative diseases including Parkinson's disease. While there is little agreement among researchers on the exact pathologic processes, it is clear that excessive amounts of wild-type alpha-synuclein can be pathologic. Gene multiplications leading to increased protein levels cause disease in some families, and increases in alpha-synuclein protein levels are also seen in affected brain regions from patients with the sporadic forms of disease. Thus increases in alpha-synuclein levels likely play an important role in the synaptic dysfunction (and eventual dementia) seen in these diseases.

We recently developed an experimentally tractable model-system to evaluate evolving alpha-synuclein-induced pathology in living neurons (see paper). In this system, a small (~ two fold) increase in human alpha-synuclein levels lead to synaptic deficits, including reduced neurotransmission, diminished recycling pools, and a curious decrease of presynaptic protein levels at the synapse. Projects in this domain are centered around unraveling the exact sequence of pathologic events that result from increased alpha-synuclein levels in neurons; culminating in decreased neurotransmitter release. A related area of interest is the normal role of alpha-synuclein at synapses.

We also find it interesting that though alpha-synuclein is a presynaptic protein under physiologic conditions, in diseased human brains, large amounts of the protein are found within the soma and proximal axons. This leads to the hypothesis that axonal transport of alpha-synuclein is altered in pathologic states ("the synuclein paradox", reviewed here). Using the slow axonal transport model-systems described here, we aim to directly test if pathologic forms of alpha-synuclein are aberrantly transported. Tools used are: live imaging of transgenic neurons/animals, image analysis, immunofluorescence, biochemistry and electrophysiology.

Picking up almost any review on the cell biology of Azheimer's disease (AD), one finds a detailed figure of the exact steps that are involved in the cleavage of the amyloid precursor protein (APP) into Amyloid-beta (Abeta) - a key step in the pathogenesis of AD, also called the "amyloidogenic pathway". All these processes occur within a neuron, yet surprisingly, virtually every detail regarding the cleavage and processing of APP is derived from studies in non-neuronal CHO cells.

A defining feature of neurons differentiating them from other cells is their polarized processes - the axons and the dendrites - and almost every known function of the neuron is critically related to this unique geometry (neurotransmission, for instance).  Though work in CHO cells have given us meaningful insights into APP processing with a generic cell, the fact remains that the trafficking of APP/BACE in axons and dendrites, their sites of association/cleavage within these domains, and even their normal neuronal localization - are all open questions.

We believe that as we move forward, these questions are critical not only from a scientific standpoint, but also in designing focused therapeutic targets for AD. Ongoing studies in the lab are addressing these questions by live imaging, image analysis, immunofluorescence and biochemistry. Other projects are examining effects of Abeta oligomers on axonal transport.      

If you are interested in a graduate student or post-doctoral position, please contact Dr. Roy at s1roy[at]ucsd[dot]edu