A microfluidic device and computational platform for high-throughput live imaging of gene expression

Abstract

To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics device, the RootArray, in which 64 Arabidopsis thaliana seedlings can be grown and their roots imaged by confocal microscopy over several days without manual intervention. To achieve high throughput, we decoupled acquisition from analysis. In the acquisition phase, we obtain images at low magnification and segment to identify regions of interest. Coordinates are communicated to the microscope to record the regions of interest at high magnification. In the analysis phase, we reconstruct 3D objects from stitched high magnification images, and extract quantitative measurements from a virtual medial section of the root. We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions.

Time-resolved NMR metabolomics of plant cells based on a microfluidic chip

“…Although microfluidic devices have been used to study different aspects of plant cell biology such as gene expression (Busch et al, 2012), cell biomechanics (Sanati Nezhad et al, 2013a, b), cellular mechanism of growth (Agudelo et al, 2013;Grossmann et al, 2011;Sanati Nezhad et al, 2014), phenotyping of plant organs (Jiang et al, 2014), and chemical stimulation of plant cells (Sanati Nezhad et al, 2013c), they had not been performed adequately enough with walled plant cells, so far. The reason is that these cells are not attached to a surface as mammalian cells, but have to be cultivated in suspension.…”

Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering

“…It is shown that the methods implementing continuous cell tracking have a promising potential to overcome the complexity of investigation of tissue growth and hemostasis at the cellular level [222]. Analysis of cell tracking within microfluidic devices which provide a real time monitoring of biological samples in a controllable condition is a desirable achievement that can reveal the extensive unknown factors in tissue development studies [223,224]. However, these techniques are not applicable without implementing computational and statistical analyses to process large data obtained from monitoring the samples [225].…”

Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel

“…Physiological growing conditions in the microscope specimen chamber are crucial for long-term experiments. There are a number of protocols available that describe imaging growth chambers for confocal microscopes [1][2][3] . However, confocal microscopy introduces high light-intensity to the plant, which can cause stress responses and usually inhibits the growth 4 .…”