Plant array chip for the germination and growth screening of Arabidopsis thaliana

Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity

BACKGROUND

Arabidopsis thaliana primary root growth has become a model for evo-devo studies due to its simplicity and facility to record cell proliferation and differentiation. To identify new genetic components relevant to primary root growth, we used a Genome-Wide Association Studies (GWAS) meta-analysis approach using data published in the last decade. In this work, we performed intra and inter-studies analyses to discover new genetic components that could participate in primary root growth.

METHODS AND RESULTS

We used 639 accessions from nine different studies under control conditions and performed different GWAS tests. We found that primary root growth changes were associated with 41 genes, of which six (14.6%) have been previously described as inhibitors or promoters of primary root growth. The knockdown lines of two genes, Suppressor of Gene Silencing (SGS3), involved in tasiRNA processing, and a gene with a Sterile Alpha Motif (SAM) motif named NOJOCH MOOTS (NOJO), confirmed their role as repressors of primary root growth, none has been shown to participate in this developmental process before.

CONCLUSIONS

In summary, our GWAS analysis of different available studies identified new genes that participate in primary root growth; two of them were identified as repressors of primary root growth.

Model-Based Analysis of Lactuca sativa Root Growth under the Action of Herbicides in Milli-Channel Arrays with In Situ Imaging

Extracting practical information from the large amounts of data gathered during the live imaging analysis of plant organs is a challenging issue. The present work investigates the use of the logistic growth model to analyze experimental data from root elongation assays performed in milli-fluidic devices with in situ imaging. Lactuca sativa was used as a bioindicator and was subjected to wide concentration ranges of four different herbicides: 2,4-D, atrazine, glyphosate, and paraquat. The model parameters were directly connected to standard indicators of toxicity and plant development, such as the LD50 and the absolute growth rate, respectively. In addition, it was found that realistic predictions of the maximum root length can be achieved about 60 h before the bioassay end point, which could significantly shorten the turnaround time. The combination of milli-fluidic devices, real-time imaging, and model-based data analysis becomes a powerful tool for environmental studies and ecotoxicity testing.

Studying root-environment interactions in structured microdevices

In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.

RAV1 mediates cytokinin signaling for regulating primary root growth in Arabidopsis

Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size, for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signaling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contains higher cell numbers, compared with wild-type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signaling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1, another member of the AP2/ERF family implicated in cytokinin signaling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further associating RAV1 with cytokinin signaling, our results demonstrate that cytokinin upregulates RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signaling. To conclude, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development in Arabidopsis.

Light Gradient-Based Screening of Arabidopsis thaliana on a 384-Well Type Plant Array Chip

Arabidopsis thaliana (Arabidopsis), as a model for plant research, is widely used for various aspects of plant science. To provide a more sophisticated and microscopic environment for the germination and growth of Arabidopsis, we report a 384-well type plant array chip in which each Arabidopsis seed is independently seeded in a solid medium. The plant array chip is made of a poly(methyl methacrylate) (PMMA) acrylic material and is assembled with a home-made light gradient module to investigate the light effects that significantly affect the germination and growth of Arabidopsis. The light gradient module was used to observe the growth pattern of seedlings according to the intensity of the white light and to efficiently screen for the influence of the white light. To investigate the response to red light (600 nm), which stimulates seed germination, the light gradient module was also applied to the germination test. As a result, the germination results showed that the plant array chip can be used to simultaneously screen wild type seeds and phytochrome B mutant seeds on a single array chip according to the eight red light intensities.

Hydrophilic Porous Polydimethysiloxane Sponge as a Novel 3D Matrix Mimicking Heterogeneous Pores in Soil for Plant Cultivation

In this work, a citric acid monohydrate (CAM)-templated polydimethylsiloxane (PDMS) sponge was proposed to mimic heterogeneous pore structures in the soil for plant cultivation. The porosity of the PDMS sponges was tuned by adjusting the CAM template. The water intake capability of the sponge was improved by (3-Aminopropyl) triethoxysilane (APTES) functionalization. The pore size and pore distribution were characterized by SEM and micro-computed tomography (micro-CT). The effect of pore structures on Oryzasativa (O. sativa) growth was investigated. Also, a 3D multi-layer PDMS sponge assembling was proposed to mimic the heterogeneous pore distribution at the different soil depth. The different growth rates of O. sativa and Nicotiana tabacum L. (N. tabacum) seeds on porous PDMS sponge indicated the impact of physical obstacles (pores) and chemical (water content) conditions on plant development. It is anticipated that this PDMS sponge could serve as a 3D matrix to mimic soil and provide a new idea for plant cultivation.

A Foldable Chip Array for the Continuous Investigation of Seed Germination and the Subsequent Root Development of Seedlings

Seed germination and seedling root development are important indicators of plant development. This work designed and fabricated a foldable microfluidic chip array for conducting nondestructive and continuous evaluation of seed germination and subsequent seedling development in situ. Each plant chamber has two functional units: seed germination part and root-growth part. The root-growth parts are themselves connected to a single channel designed to provide a uniform culture medium for plant growth. The individual chips are connected into an array using elastic hinges that facilitate the folding and unfolding of the array to accommodate different viewing purposes. In the folded state, the seed germination chambers form a closely spaced array platform to facilitate the comparison of seed germination and plant development characteristics. Unfolding the array facilitates a clear examination of root development within the root-growth parts. The observation window of an individual chip facilitates either the direct examination of the developing seedling (e.g., stems and leaves) or the use of a microscope for examining microscale features (e.g., root tips and root hairs). The potential of the proposed foldable chip array as a new cultivation platform for botanic studies is demonstrated by examining the seed germination and seedling development of tobacco (Nicotiana tabacum) under different cultivation conditions.

Milli-channel array for direct and quick reading of root elongation bioassays

A novel platform to perform systematic analysis and direct reading of root elongation bioassays is presented. The device was designed to include multiplexed microenvironments for the germination and growth of individual seeds, which allows observation by the naked eye or by optical systems, notably cellphone cameras. Prototypes were fabricated by laser micromachining on a highly transparent material that is fully compatible with biological systems. The effectiveness of the milli-channel array was verified against the conventional system (Petri dish). Lactuca sativa was chosen as a model species and glyphosate as a typical toxic agent. All tests were run according to standardized procedures and data analysis was carried out through different statistical indicators such as the root elongation and germination indexes. Results attained in the milli-channel array were identical to those in Petri dish, with the remarkable benefit that several steps required in the conventional system were avoided, which enormously decreases the operation time and the possibility of experimental errors. Further advantages of the milli-channel array are also reported, such as the capability to achieve live imaging of plant organs growth through a simple experiment. The developed device has been proven to be effective, versatile, easy-to-use, and integrable to cellphones, which naturally provide facilities for data recording, analysis, and networking. These improvements open the route to novel applications of bioassays in the wide field of ecotoxicology and environmental studies.

Multi-chamber petaloid root-growth chip for the non-destructive study of the development and physiology of the fibrous root system of Oryza sativa

The root system of plants is a major component of their bodies in terms of both function and bulk. The investigation of root system development is greatly assisted by microfluidic devices, which improve the spatial and temporal resolution of observations without destroying tissue. In the present study, a multi-chamber petaloid root-growth chip was developed for studying the development and physiology of root systems that have thin branching structures (i.e., fibrous root systems). The petaloid root-growth chip includes a central seed germination chamber and five root-growth chambers for observing the development of fibrous roots. The proposed device was applied for investigating the root system development of Oryza sativa. The phenotype and growth kinetics of O. sativa root systems grown in the proposed device were compared with those obtained during growth in a conventional conical flask with agar-based medium, and the results indicated that cultivation in the miniaturized device did not delay root system growth in the early stage (≤2 weeks). In addition, the transparent device enabled the non-destructive observation of the developmental and microstructural characteristics of the roots, such as the root caps, root border cells, and root hairs. Moreover, the ability to control the microenvironment in each of the five root-growth chambers individually facilitated the investigation of specific adaptations in the fibrous root growth of single O. sativa seedlings to different drought stresses. Accordingly, five polyethylene glycol (PEG)6000-induced drought stress conditions were established in the five root-growth chambers to investigate the root development of a single O. sativa seedling in the central germination chamber. In situ observations demonstrated that the different PEG6000-induced conditions affected the root growth responses and root microstructural adaptations of the single seedlings in each root-growth chamber. Therefore, the petaloid root-growth microfluidic chip can eliminate the effects of variations in different plant seeds to reveal the responses of plants to different environmental conditions more objectively while concurrently allowing for non-destructive observations at very high spatial and temporal resolution.

Design of a comprehensive microfluidic and microscopic toolbox for the ultra-wide spatio-temporal study of plant protoplasts development and physiology

BACKGROUND

Plant protoplasts are basic plant cells units in which the pecto-cellulosic cell wall has been removed, but the plasma membrane is intact. One of the main features of plant cells is their strong plasticity, and their propensity to regenerate an organism from a single cell. Methods and differentiation protocols used in plant physiology and biology usually involve macroscopic vessels and containers that make difficult, for example, to follow the fate of the same protoplast all along its full development cycle, but also to perform continuous studies of the influence of various gradients in this context. These limits have hampered the precise study of regeneration processes.

RESULTS

Herein, we present the design of a comprehensive, physiologically relevant, easy-to-use and low-cost microfluidic and microscopic setup for the monitoring of Physcomitrella patens (P. patens) growth and development on a long-term basis. The experimental solution we developed is made of two parts (i) a microfluidic chip composed of a single layer of about a hundred flow-through microfluidic traps for the immobilization of protoplasts, and (ii) a low-cost, light-controlled, custom-made microscope allowing the continuous recording of the moss development in physiological conditions. We validated the experimental setup with three proofs of concepts: (i) the kinetic monitoring of first division steps and cell wall regeneration, (ii) the influence of the photoperiod on growth of the protonemata, and (iii) finally the induction of leafy buds using a phytohormone, cytokinin.

CONCLUSIONS

We developed the design of a comprehensive, physiologically relevant, easy-to-use and low-cost experimental setup for the study of P. patens development in a microfluidic environment. This setup allows imaging of P. patens development at high resolution and over long time periods.

3D-Printed seed planter and well array for high-throughput seed germination screening

A 3D-printed miniaturized well array and seed planter have been developed for in-field studies of seed quality and screening of conditions for seedlings.