An optical imaging chamber for viewing living plant cells and tissues at high resolution for extended periods

Multifunction fluorescence open source in vivo/in vitro imaging system (openIVIS)

The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study, we designed and built a multifunction fluorescent open source in vivo/in vitro imaging system (openIVIS) system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the potential applications of our system, we tested its performance against a diverse set of experiments including laboratory assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of ten days. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.

Noninvasive Long-Term Imaging of the Cytoskeleton in Arabidopsis Seedlings

The preparation of biological samples, especially for live-cell microscopy, remains a major experimental challenge in the lab despite technological advances. In addition, high-resolution microscopy techniques require higher sample quality and uniformity, which is difficult to ensure during manual preparation while maintaining "ideal" growth conditions. In this protocol, we provide a way out by growing Arabidopsis thaliana seedlings directly in an imaging chamber, which eliminates invasive sample preparation directly before imaging. This method hinges on the precise placement of seeds into imaging chambers, which can be grown in conventional climate chambers. We detail three methods to grow hypocotyls, cotyledons, leaves, and roots for high-resolution and long-term imaging of the plant cytoskeleton. Furthermore, we show that the growth and development of seedlings inside the chambers can be externally manipulated by the addition of chemicals.

An optimized pipeline for live imaging whole Arabidopsis leaves at cellular resolution

BACKGROUND

Live imaging is the gold standard for determining how cells give rise to organs. However, tracking many cells across whole organs over large developmental time windows is extremely challenging. In this work, we provide a comparably simple method for confocal live imaging entire Arabidopsis thaliana first leaves across early development. Our imaging method works for both wild-type leaves and the complex curved leaves of the jaw-1D mutant.

RESULTS

We find that dissecting the cotyledons, affixing a coverslip above the samples and mounting samples with perfluorodecalin yields optimal imaging series for robust cellular and organ level analysis. We provide details of our complementary image processing steps in MorphoGraphX software for segmenting, tracking lineages, and measuring a suite of cellular properties. We also provide MorphoGraphX image processing scripts we developed to automate analysis of segmented images and data presentation.

CONCLUSIONS

Our imaging techniques and processing steps combine into a robust imaging pipeline. With this pipeline we are able to examine important nuances in the cellular growth and differentiation of jaw-D versus WT leaves that have not been demonstrated before. Our pipeline is approachable and easy to use for leaf development live imaging.

Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy

Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin.

Live imaging of microtubule organization, cell expansion, and intercellular space formation in Arabidopsis leaf spongy mesophyll cells

Leaf spongy mesophyll cells form an interconnected network of branched cells and intercellular spaces to maximize the surface area available for light capture and photosynthetic gas exchange. To investigate the morphogenetic events leading to cell separation and branching in Arabidopsis thaliana, we used mesophyll-specific promoters to facilitate imaging of mesophyll cell shape and microtubule (MT) organization over multiple spatiotemporal scales without interference from the overlying epidermal cells. We show that cells enlarge by selective expansion of cell wall regions in contact with intercellular spaces. Cell-cell contacts remain relatively fixed in size, forming the termini of interconnecting branches. Surprisingly, classic schizogeny (de-adhesion of neighboring cells) is relatively infrequent, being related to the local topology of cell junctions during early expansion. Intercellular spaces cue the position of stable MT bundles, which in turn promote efficient dilation of intercellular spaces and cell branching. Our data provide insights into mesophyll morphogenesis and MT organization and lay the groundwork for future investigations.

Current and future advances in fluorescence-based visualization of plant cell wall components and cell wall biosynthetic machineries

Plant cell wall-derived biomass serves as a renewable source of energy and materials with increasing importance. The cell walls are biomacromolecular assemblies defined by a fine arrangement of different classes of polysaccharides, proteoglycans, and aromatic polymers and are one of the most complex structures in Nature. One of the most challenging tasks of cell biology and biomass biotechnology research is to image the structure and organization of this complex matrix, as well as to visualize the compartmentalized, multiplayer biosynthetic machineries that build the elaborate cell wall architecture. Better knowledge of the plant cells, cell walls, and whole tissue is essential for bioengineering efforts and for designing efficient strategies of industrial deconstruction of the cell wall-derived biomass and its saccharification. Cell wall-directed molecular probes and analysis by light microscopy, which is capable of imaging with a high level of specificity, little sample processing, and often in real time, are important tools to understand cell wall assemblies. This review provides a comprehensive overview about the possibilities for fluorescence label-based imaging techniques and a variety of probing methods, discussing both well-established and emerging tools. Examples of applications of these tools are provided. We also list and discuss the advantages and limitations of the methods. Specifically, we elaborate on what are the most important considerations when applying a particular technique for plants, the potential for future development, and how the plant cell wall field might be inspired by advances in the biomedical and general cell biology fields.

Intrinsic Cell Polarity Coupled to Growth Axis Formation in Tobacco BY-2 Cells

Several plant proteins are preferentially localized to one end of a cell, allowing a polarity to be assigned to the cell. These cell polarity proteins often exhibit coordinated patterns between neighboring cells, termed tissue cell polarity. Tissue cell polarity is widespread in plants and can influence how cells grow, divide, and differentiate [1-5]. However, it is unclear whether cell polarity is established through cell-intrinsic or -extrinsic mechanisms and how polarity is coupled to growth. To address these issues, we analyzed the behavior of a tissue cell polarity protein BASL (BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE) in the simplifying context of cultured cell filaments and in protoplasts before and during regeneration. We show that BASL is polarly localized when ectopically expressed in tobacco BY-2 cell cultures. Ectopic BASL is found preferentially at the developing tips of cell filaments, likely marking a polarized molecular address. Polarity can shift during the cell cycle and is resistant to treatment with microtubule, actin or auxin transport inhibitors. BASL also exhibits polar localization in spherical protoplasts, in contrast to other polarity proteins so far tested. BASL polarity within protoplasts is dynamic and resistant to auxin transport inhibitors. As protoplasts regenerate, polarity remains dynamic in isotropically growing cells but becomes fixed in anisotropic cells and aligns with the axis of cell growth. Our findings suggest that plant cells have an intrinsic ability to polarize and that environmental or developmental cues may act by biasing the direction of this polarity and thus the orientation of anisotropic growth.

Long-term live-cell imaging techniques for visualizing pavement cell morphogenesis

Recent advancements in microscopy and biological technologies have allowed scientists to study dynamic plant developmental processes with high temporal and spatial resolution. Pavement cells, epidermal cells found on leaf tissue, form complex shapes with alternating regions of indentations and outgrowths that are postulated to be driven by the microtubule cytoskeleton. Given their complex shapes, pavement cells and the microtubule contribution towards morphogenesis have been of great interest in the field of developmental biology. Here, we focus on two live-cell imaging methods that allow for early and long-term imaging of the cotyledon (embryonic leaf-like tissue) and leaf epidermis with minimal invasiveness in order to study microtubules throughout pavement cell morphogenesis. The methods described in this chapter can be applied to studying other developmental processes associated with cotyledon and leaf tissue.

Probing the 3D architecture of the plant nucleus with microscopy approaches: challenges and solutions

The eukaryotic cell nucleus is a central organelle whose architecture determines genome function at multiple levels. Deciphering nuclear organizing principles influencing cellular responses and identity is a timely challenge. Despite many similarities between plant and animal nuclei, plant nuclei present intriguing specificities. Complementary to molecular and biochemical approaches, 3D microscopy is indispensable for resolving nuclear architecture. However, novel solutions are required for capturing cell-specific, sub-nuclear and dynamic processes. We provide a pointer for utilising high-to-super-resolution microscopy and image processing to probe plant nuclear architecture in 3D at the best possible spatial and temporal resolution and at quantitative and cell-specific levels. High-end imaging and image-processing solutions allow the community now to transcend conventional practices and benefit from continuously improving approaches. These promise to deliver a comprehensive, 3D view of plant nuclear architecture and to capture spatial dynamics of the nuclear compartment in relation to cellular states and responses. Abbreviations: 3D and 4D: Three and Four dimensional; AI: Artificial Intelligence; ant: antipodal nuclei (ant); CLSM: Confocal Laser Scanning Microscopy; CTs: Chromosome Territories; DL: Deep Learning; DLIm: Dynamic Live Imaging; ecn: egg nucleus; FACS: Fluorescence-Activated Cell Sorting; FISH: Fluorescent In Situ Hybridization; FP: Fluorescent Proteins (GFP, RFP, CFP, YFP, mCherry); FRAP: Fluorescence Recovery After Photobleaching; GPU: Graphics Processing Unit; KEEs: KNOT Engaged Elements; INTACT: Isolation of Nuclei TAgged in specific Cell Types; LADs: Lamin-Associated Domains; ML: Machine Learning; NA: Numerical Aperture; NADs: Nucleolar Associated Domains; PALM: Photo-Activated Localization Microscopy; Pixel: Picture element; pn: polar nuclei; PSF: Point Spread Function; RHF: Relative Heterochromatin Fraction; SIM: Structured Illumination Microscopy; SLIm: Static Live Imaging; SMC: Spore Mother Cell; SNR: Signal to Noise Ratio; SRM: Super-Resolution Microscopy; STED: STimulated Emission Depletion; STORM: STochastic Optical Reconstruction Microscopy; syn: synergid nuclei; TADs: Topologically Associating Domains; Voxel: Volumetric pixel.

Spatiotemporal coordination of cell division and growth during organ morphogenesis

A developing plant organ exhibits complex spatiotemporal patterns of growth, cell division, cell size, cell shape, and organ shape. Explaining these patterns presents a challenge because of their dynamics and cross-correlations, which can make it difficult to disentangle causes from effects. To address these problems, we used live imaging to determine the spatiotemporal patterns of leaf growth and division in different genetic and tissue contexts. In the simplifying background of the speechless (spch) mutant, which lacks stomatal lineages, the epidermal cell layer exhibits defined patterns of division, cell size, cell shape, and growth along the proximodistal and mediolateral axes. The patterns and correlations are distinctive from those observed in the connected subepidermal layer and also different from the epidermal layer of wild type. Through computational modelling we show that the results can be accounted for by a dual control model in which spatiotemporal control operates on both growth and cell division, with cross-connections between them. The interactions between resulting growth and division patterns lead to a dynamic distributions of cell sizes and shapes within a deforming leaf. By modulating parameters of the model, we illustrate how phenotypes with correlated changes in cell size, cell number, and organ size may be generated. The model thus provides an integrated view of growth and division that can act as a framework for further experimental study.

Organ morphogenesis involves two coordinated processes: growth of tissue and increase in cell number through cell division. Both processes have been analysed individually in many systems and shown to exhibit complex patterns in space and time. However, it is unclear how these patterns of growth and cell division are coordinated in a growing leaf that is undergoing shape changes. We have addressed this problem using live imaging to track growth and cell division in the developing leaf of the mustard plant Arabidopsis thaliana. Using subsequent computational modelling, we propose an integrated model of leaf growth and cell division, which generates dynamic distributions of cell size and shape in different tissue layers, closely matching those observed experimentally. A key aspect of the model is dual control of spatiotemporal patterns of growth and cell division parameters. By modulating parameters in the model, we illustrate how phenotypes may correlate with changes in cell size, cell number, and organ size.

Ectopic BASL Reveals Tissue Cell Polarity throughout Leaf Development in Arabidopsis thaliana

Tissue-wide polarity fields, in which cell polarity is coordinated across the tissue, have been described for planar organs such as the Drosophila wing and are considered important for coordinating growth and differentiation [1]. In planar plant organs, such as leaves, polarity fields have been identified for subgroups of cells, such as stomatal lineages [2], trichomes [3, 4], serrations [5], or early developmental stages [6]. Here, we show that ectopic induction of the stomatal protein BASL (BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE) reveals a tissue-wide epidermal polarity field in leaves throughout development. Ectopic GFP-BASL is typically localized toward the proximal end of cells and to one lobe of mature pavement cells, revealing a polarity field that aligns with the proximodistal axis of the leaf (base to tip). The polarity field is largely parallel to the midline of the leaf but diverges in more lateral positions, particularly at later stages in development, suggesting it may be deformed during growth. The polarity field is observed in the speechless mutant, showing that it is independent of stomatal lineages, and is observed in isotropic cells, showing that cell shape anisotropy is not required for orienting polarity. Ectopic BASL forms convergence and divergence points at serrations, mirroring epidermal PIN polarity patterns, suggesting a common underlying polarity mechanism. Thus, we show that similar to the situation in animals, planar plant organs have a tissue-wide cell polarity field, and this may provide a general cellular mechanism for guiding growth and differentiation.

•

Ectopic expression of BASL in Arabidopsis leaves reveals coordinated polarity

•

The ectopic BASL polarity field is independent of the stomatal lineage

•

The polarity field reorients around serrations, mirroring PIN1 polarity

Shoot regeneration: a journey from acquisition of competence to completion

Plants display an extraordinary ability to regenerate complete shoot systems from a tissue fragment or even from a single cell. Upregulation of the determinants of pluripotency during a precise window of time in response to external inductive cues is a key decisive factor for shoot regeneration. A burst of recent studies has begun to provide an understanding of signaling molecules that are instrumental in the making of the regenerative mass, as well as the developmental regulators that are seminal in shaping the pluripotent state. Here, we discuss how signaling molecules, waves of mutually exclusive stem cell regulators and epigenetic modifiers could contribute to cellular heterogeneity in an island of regenerative mass, thus leading to de novo shoot regeneration.

Pavement cells and the topology puzzle

D'Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is established early during leaf development, already before the typical pavement cell shapes emerge, with topological homeostasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw piece-like shape of the cells, but rather owes itself to a strongly life history-driven process, with limited impact from cell-surface mechanics.

The Application of Contrast Media for In Vivo Feature Enhancement in X-Ray Computed Tomography of Soil-Grown Plant Roots

The use of in vivo X-ray microcomputed tomography (μCT) to study plant root systems has become routine, but is often hampered by poor contrast between roots, soil, soil water, and soil organic matter. In clinical radiology, imaging of poorly contrasting regions is frequently aided by the use of radio-opaque contrast media. In this study, we present evidence for the utility of iodinated contrast media (ICM) in the study of plant root systems using μCT. Different dilutions of an ionic and nonionic ICM (Gastrografin 370 and Niopam 300) were perfused into the aerial vasculature of juvenile pea plants via a leaf flap (Pisum sativum). The root systems were imaged via μCT, and a variety of image-processing approaches used to quantify and compare the magnitude of the contrast enhancement between different regions. Though the treatment did not appear to significantly aid extraction of full root system architectures from the surrounding soil, it did allow the xylem and phloem units of seminal roots and the vascular morphology within rhizobial nodules to be clearly visualized. The nonionic, low-osmolality contrast agent Niopam appeared to be well tolerated by the plant, whereas Gastrografin showed evidence of toxicity. In summary, the use of iodine-based contrast media allows usually poorly contrasting root structures to be visualized nondestructively using X-ray μCT. In particular, the vascular structures of roots and rhizobial nodules can be clearly visualized in situ.

A Simple Chamber for Long-term Confocal Imaging of Root and Hypocotyl Development

Several aspects of plant development, such as lateral root morphogenesis, occur on time spans of several days. To study underlying cellular and subcellular processes, high resolution time-lapse microscopy strategies that preserve physiological conditions are required. Plant tissues must have adequate nutrient and water supply with sustained gaseous exchange but, when submerged and immobilized under a coverslip, they are particularly susceptible to anoxia. One strategy that has been successfully employed is the use of a perfusion system to maintain a constant supply of oxygen and nutrients. However, such arrangements can be complicated, cumbersome, and require specialized equipment. Presented here is an alternative strategy for a simple imaging system using perfluorodecalin as an immersion medium. This system is easy to set up, requires minimal equipment, and is easily mounted on a microscope stage, allowing several imaging chambers to be set up and imaged in parallel. In this system, lateral root growth rates are indistinguishable from growth rates under standard conditions on agar plates for the first two days, and lateral root growth continues at reduced rates for at least another day. Plant tissues are supplied with nutrients via an agar slab that can be used also to administer a range of pharmacological compounds. The system was established to monitor lateral root development but is readily adaptable to image other plant organs such as hypocotyls and primary roots.

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

One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions.

Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

Alfalfa Root Growth Rate Correlates with Progression of Microtubules during Mitosis and Cytokinesis as Revealed by Environmental Light-Sheet Microscopy

Cell division and expansion are two fundamental biological processes supporting indeterminate root growth and development of plants. Quantitative evaluations of cell divisions related to root growth analyses have been performed in several model crop and non-crop plant species, but not in important legume plant Medicago sativa. Light-sheet fluorescence microscopy (LSFM) is an advanced imaging technique widely used in animal developmental biology, providing efficient fast optical sectioning under physiological conditions with considerably reduced phototoxicity and photobleaching. Long-term 4D imaging of living plants offers advantages for developmental cell biology not available in other microscopy approaches. Recently, LSFM was implemented in plant developmental biology studies, however, it is largely restricted to the model plant Arabidopsis thaliana. Cellular and subcellular events in crop species and robust plant samples have not been studied by this method yet. Therefore we performed LSFM long-term live imaging of growing root tips of transgenic alfalfa plants expressing the fluorescent molecular marker for the microtubule-binding domain (GFP-MBD), in order to study dynamic patterns of microtubule arrays during mitotic cell division. Quantitative evaluations of cell division progress in the two root tissues (epidermis and cortex) clearly indicate that root growth rate is correlated with duration of cell division in alfalfa roots. Our results favor non-invasive environmental LSFM as one of the most suitable methods for qualitative and quantitative cellular and developmental imaging of living transgenic legume crops.

Formation of polarity convergences underlying shoot outgrowths

The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments.

DOI:http://dx.doi.org/10.7554/eLife.18165.001

Plants, unlike animals, are able to grow and develop throughout their lives. New leaves and flowers are made from outgrowths that constantly form at the tip of growing shoots. Groups of cells in the outer layer of the shoot tip arrange a protein called PIN1 so that it is more abundant on the cell surfaces that face towards the centre of the group. PIN1 transports a hormone called auxin out of plant cells and this “convergent” arrangement of PIN1 increases the levels of auxin in cells at the centre of the group, leading to the formation of a new outgrowth. However, it is not clear what causes these cells to position their PIN1 proteins in this way.

Several hypotheses have been proposed to explain how convergent patterns of PIN1 form. For example, according to the “up-the-gradient” hypothesis, PIN1 is allocated to the end of a cell that is next to a cell with a higher level of auxin. Abley et al. have now compared predictions from computer models with new experimental data from a plant called Arabidopsis to evaluate three hypotheses for how convergent PIN1 patterns form. A computer model based on the up-the-gradient hypothesis naturally creates convergent PIN1 patterns, even if each cell starts off with the same level of auxin. On the other hand, models based on two other hypotheses generate tandem alignments of PIN1 so that auxin is transported in the same direction along lines of cells.

Next, Abley et al. tested these models using mutant Arabidopsis plants that develop outgrowths from the lower surface of their leaves. These outgrowths form in a similar way to outgrowths at the growing shoot tip, but in a simpler context. The experiments show that the patterns of where auxin is produced in growing leaves were more compatible with the tandem alignment models than the up-the-gradient model. This suggests that plants use a tandem alignment mechanism to form convergences of PIN1 proteins that generate the local increases in auxin needed to make new outgrowths.

This study only examined a single layer of cells on the plant surface. Other cell layers also show highly organised patterns of PIN1 proteins, so a future challenge is to extend the approach to study the entire 3D structure of new shoot outgrowths.

DOI:http://dx.doi.org/10.7554/eLife.18165.002