Hunt, D. | Search bioRxiv

bioRxiv2018

Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device

Coral reefs, and their associated diverse ecosystems, are of enormous ecological importance. In recent years, coral health has been severely impacted by environmental stressors brought on by human activity and climate change, threatening the extinction of several major reef ecosystems. Reef damage is mediated by a process called coral bleaching where corals, sea anemones, and other cnidarians lose their photosynthetic algal symbionts (genus Symbiodinium) upon stress induction, resulting in drastically decreased host energy harvest and, ultimately, coral death. The mechanism by which this critical cnidarian-algal symbiosis is lost remains poorly understood. Here, we report Traptasia, a simple microfluidic device with multiple traps designed to isolate and image individual live larvae of Aiptasia, a sea anemone model organism, and their algal symbionts over extended time courses. Aiptasia larvae are ~100 m in length, deformable, and highly motile, posing particular challenges for long-term imaging. Using a trap design optimized via fluid flow simulations and polymer bead loading tests, we trapped Aiptasia larvae containing algal symbionts and demonstrated stable imaging for >10 hours. We visualized algal migration within Aiptasia larvae and observed algal expulsion under an environmental stressor. To our knowledge, this device is the first to enable live imaging of cnidarian larvae and their algal symbionts and, in further implementation, could provide important insights into the cellular mechanisms of coral bleaching under different environmental stressors. The device is simple to use, requires minimal external equipment and no specialized training to operate, and can easily be adapted to study a variety of large, motile organisms.

ecology↗

bioRxiv2017

ShuTu: Open-Source Software for Efficient and Accurate Reconstruction of Dendritic Morphology

Neurons perform computations by integrating inputs from thousands of synapses - mostly in the dendritic tree - to drive action potential firing in the axon. One fruitful approach to understanding this process is to record from neurons using patch-clamp electrodes, fill the recorded neuron with a substance that allows subsequent staining, reconstruct the three-dimensional architecture of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic process, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.\n\nSignificance StatementWe developed a software package - ShuTu - that integrates automated reconstruction of stained neurons with manual error correction. This package facilitates rapid reconstruction of the three-dimensional geometry of neuronal dendritic trees, often needed for computational simulations of the functional properties of these structures.

neuroscience↗