Biology subjects

Kashkan, I.

Publications and source records attributed to Kashkan, I..

3 recordsLinked to original sources

bioRxiv2024

Dynamic Dark Root Chamber: Advancing non-invasive phenotyping of roots kept in darkness using infrared imaging

Root phenotyping is a challenging task that would require monitoring root growth in soil under dark conditions to mimic natural conditions, while allowing the shoot to grow in light. Most existing methods involve exposing the roots to light, which substantially alters their growth and function. In this paper, we present an improved imaging system that can overcome this limitation of experiments performed in laboratories. The Dynamic Dark Root imaging Chamber (DDrC) enables continuous monitoring and image acquisition to track the dynamic development of root architecture under controlled growth conditions. Our imaging system is based on a Raspberry Pi camera module and infrared LEDs, which do not induce any stress responses in the roots. The DDrC setup is simple, affordable, and suitable for dynamic phenotyping experiments. We provide a detailed tutorial for the assembly and adjustment of the imaging chamber. We conclude that our system is a valuable tool for studying the genetic and environmental factors that affect the root system architecture and development, and for identifying the root traits that are related to plant adaptation and performance.

plant biology↗

bioRxiv2022

RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level

Plants rely on fine-tuning organ movement to ensure their survival and productivity. Even subtle loss of directional growth orchestration can result in a huge impact when the plant is impaired to adapt to an ever-changing environment, where it is exposed to manifold exogenous stimuli simultaneously. We present a newly designed chamber to obtain live images to track organ growth and movement differences, called RaspberyPi Dark Chambers (RaPiD-chamber). The RaPiD-chamber is easy to self-assemble and cost-efficient and allows to monitor the continuous growth of etiolated seedlings, as well as their response to light of different wavelengths and from chosen positions. We tested the advice by comparing hypocotyl elongation rate and response to unilateral white and blue light exposure of Arabidopsis thaliana Col0. Additionally, we compared the elongation rate of etiolated hypocotyls between Col0 and kin10, a mutant lacking the catalytic subunit of the cellular signaling hub SUCROSE NON-FERMENTING RELATED KINASE 1 (SnRK1). kin10 is known for its diminished ability to control hypocotyl elongation. As a case study, we compared the growth dynamics of etiolated Col0 versus kin10. Without further energy source supplementation to the growth medium, the mutant cannot keep up with hypocotyl elongation. Additionally, continuous observation of the dark-grown seedlings allowed us to determine a shift in the dynamics of apical hook angle formation for the mutant.

plant biology↗

bioRxiv2020

Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Here we reveal, in the plant model Arabidopsis thaliana, that the PIN7 gene, which encodes a polarly localized transporter for the phytohormone auxin, produces two evolutionary-conserved transcripts. These isoforms PIN7a and PIN7b, differing in a 4 amino acid motif, are present at nearly equal levels in most cells. Although both variants do not differ in the subcellular localization and transport auxin with similar capacity, they closely associate and mutually influence their stability within the plasma membrane. Phenotypic complementation tests reveal that the functional contribution of PIN7b per se is minor but it markedly attenuates the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. These results establish alternative splicing of the PIN family as a conserved, functionally-relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.

plant biology↗