Dudman Lab — Resources

Thalamoseq

Deep sequencing of the cellular transcriptome has provided unprecedented access to the molecular diversity of neurons. However, it remains a challenge to make sense of the observed molecular diversity — including relating it to projection patterns, dendritic morphology, and cellular biophysics.

A joint graduate student in our lab and the Hantman lab began a project to assess the molecular diversity of the mouse thalamus, seeking to understand the logic by which the ~30 thalamic nuclei are organized and to provide molecular entry points for precise manipulation of thalamic function.

The data is publicly available at thalamoseq.janelia.org and described in a paper in Nature Neuroscience. This work was led by Adam Hantman's lab in collaboration with Sacha Nelson's lab.

FLInChR

Optogenetics provides an exceptional and powerful toolkit for brain exploration by allowing precise manipulation of individual cell types and circuits. While remarkably efficient tools exist for stimulation, tools for inhibition are generally less robust for many neuroscience applications.

In collaboration with Alla Karpova's lab we sought to produce hybrid reagents through modular combination of existing reagents and targeting domains. We described FLInChR (Full Length Inversion of Channelrhodopsin) — a topological inversion of ChR that converts a neuronal activator into a potent neuronal silencer, as summarized in several places.

The plasmid is available at AddGene. Through ongoing efforts we continue to explore this method of diversification of our toolkit for systems neuroscience.

retro-AAV

Efficient retrograde access to projection neurons for delivering sensors and effectors constitutes an important avenue for circuit dissection. Viral vectors are powerful gene delivery vehicles for the nervous system, but all available viral tools suffer from inefficient retrograde transport.

Using directed molecular evolution together with our collaborators, we engineered potent retrograde functionality into the capsid of AAV. The newly evolved AAV2-retro variant permits robust retrograde access to projection neurons with efficiency comparable to classical synthetic retrograde labeling reagents, and supports high-level payload expression adequate for functional circuit interrogation.

The plasmid is available at AddGene. Tester preps are available from Janelia Virus Services.

Skilled Movements & Decisions

We have argued that measurement of kinematic parameters of goal-directed movements is important for understanding the function of basal ganglia circuits that control purposive behavior.

We developed a behavioral task in which mice displace a spring-loaded 2D joystick past a hidden threshold to receive reward. By using a continuous analog signal proportional to movement kinematics we can study how effort is traded off against reward, continuous neural representations of movement kinematics, and perform rapid (kHz) closed-loop feedback.

The system has 3 key parts: a hall-effect sensor based, spring loaded joystick; a mechanical system for stable head fixation using RIVETS; and an embedded controller with fast A/D conversion — the BCS.

Software & Hardware