Biology subjects

Robinson, J. T.

Publications and source records attributed to Robinson, J. T..

3 recordsLinked to original sources

bioRxiv2017

cytoNet: Network Analysis of Cell Communities

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNets capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin 4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains. Availability and ImplementationQutubLab.org/how | cytoNet contact: cytoNetProject@gmail.com Brain Initiative Alliance Toolmaker cytoNet site: https://www.braininitiative.org/toolmakers/resources/cytonet/ Author / Lay SummarycytoNet provides an online tool to rapidly characterize relationships between objects within images and video frames. To study complex tissue, cell and subcellular topologies, cytoNet integrates vision science with the mathematical technique of graph theory. This allows the method to simultaneously identify environmental effects on single cells and on network topology. cytoNet has versatile use across neuroscience, stem cell biology and regenerative medicine. cytoNet applications described in this study include: (1) characterizing how sensing pain alters neural circuit activity, (2) quantifying how vascular cells respond to neurotrophic stimuli overexpressed in the brain after injury or exercise, (3) delineating features of fat tissue that may confer resistance to obesity and (4) uncovering structure-function relationships of human stem cells as they transform into neurons.

bioengineering↗

bioRxiv2017

Fluidic Microactuation of Flexible Electrodes for Neural Recording

Ultra-flexible microelectrodes that can bend and flex with the natural movement of the brain reduce the inflammatory response and improve the stability of long-term neural recordings.1-5 However, current methods to implant these highly flexible electrodes rely on temporary stiffening agents that increase the electrode size6-10 thus aggravating neural damage during implantation, which leads to cell loss and glial activation that persists even after the stiffening agents are removed or dissolve.11-13 A method to deliver thin, ultra-flexible electrodes deep into neural tissue without increasing the stiffness or size of the electrodes will enable minimally invasive electrical recordings from within the brain. Here we show that specially designed microfluidic devices can apply a tension force to ultra-flexible electrodes that prevents buckling without increasing the thickness or stiffness of the electrode during implantation. Additionally, these \"fluidic microdrives\" allow us to precisely actuate the electrode position with micron-scale accuracy. To demonstrate the efficacy of our fluidic microdrives, we used them to actuate highly flexible carbon nanotube fiber (CNTf) microelectrodes11,14 for electrophysiology. We used this approach in three proof-of-concept experiments. First, we recorded compound action potentials in a soft model organism, the small cnidarian Hydra. Second, we targeted electrodes precisely to the thalamic reticular nucleus in brain slices and recorded spontaneous and optogenetically-evoked extracellular action potentials. Finally, we inserted electrodes more than 4 mm deep into the brain of rats and detected spontaneous individual unit activity in both cortical and subcortical regions. Compared to syringe injection, fluidic microdrives do not penetrate the brain and prevent changes in intracranial pressure by diverting fluid away from the injection site during insertion and actuation. Overall, the fluidic microdrive technology provides a robust new method to implant and actuate ultra-flexible neural electrodes.

neuroscience↗

bioRxiv2017

Magnetic Entropy as a Gating Mechanism for Magnetogenetic Ion Channels

Magnetically sensitive ion channels would allow researchers to better study how specific brain cells affect behavior in freely moving animals; however, recent reports of \"magnetogenetic\" ion channels have been questioned because known biophysical mechanisms cannot explain experimental observations. Here we show that magnetic fields can produce a change in the magnetic entropy of biogenic nanoparticles, which in turn may generate sufficient heat to gate temperature-sensitive ion channels. This magnetocaloric effect provides a rational approach for developing future magnetogenetic channels.

neuroscience↗