ePro-ClearSee: a simple immunohistochemical method that does not require sectioning of plant samples

Florigen-producing cells express FPF1-LIKE PROTEIN 1 to accelerate flowering and stem growth in Arabidopsis

Plants induce the expression of the florigen FLOWERING LOCUS T (FT) in response to seasonal changes. FT is expressed in a distinct subset of phloem companion cells in Arabidopsis. Using tissue-specific translatome analysis, we discovered that the FT-expressing cells also express FLOWERING PROMOTING FACTOR 1 (FPF1)-LIKE PROTEIN 1 (FLP1), specifically under long-day conditions with the red/far-red ratio of natural sunlight. The master regulator of FT, CONSTANS (CO), is essential for FLP1 expression, suggesting that FLP1 is involved in the photoperiod pathway. We show that FLP1 promotes early flowering independently of FT, is active in the shoot apical meristem, and induces the expression of SEPALLATA3 (SEP3), a key E-class homeotic gene. Unlike FT, FLP1 also facilitates inflorescence stem elongation. Our cumulative evidence suggests that the small FLP1 protein acts as a mobile signal like FT. Taken together, FLP1 accelerates flowering in parallel with FT and orchestrates flowering and stem elongation during the reproductive transition.

Delivery and kinetics of immersion optical clearing agents in tissues: Optical imaging from ex vivo to in vivo

Advanced optical imaging provides a powerful tool for the structural and functional analysis of tissues with high resolution and contrast, but the imaging performance decreases as light propagates deeper into the tissue. Tissue optical clearing technique demonstrates an innovative way to realize deep-tissue imaging and have emerged substantially in the last two decades. Here, we briefly reviewed the basic principles of tissue optical clearing techniques in the view of delivery strategies via either free diffusion or external forces-driven advection, and the commonly-used optical techniques for monitoring kinetics of clearing agents in tissue, as well as their ex vivo to in vivo applications in multiple biomedical research fields. With future efforts on the even distribution of both clearing agents and probes, excavation of more effective clearing agents, and automation of tissue clearing processes, tissue optical clearing should provide more insights into the fundamental questions in biological events clinical diagnostics.

CRISPR-FISH: A CRISPR/Cas9-Based In Situ Labeling Method

Fluorescence in situ hybridization (FISH) has been widely used to visualize target DNA sequences in fixed chromosome samples by denaturing the dsDNA to allow complementary probe hybridization, thus damaging the chromatin structure by harsh treatments. To overcome this limitation, a CRISPR/Cas9-based in situ labeling method was developed, termed CRISPR-FISH. This method is also known as RNA-guided endonuclease-in situ labeling (RGEN-ISL). Here we present different protocols for the application of CRISPR-FISH on acetic acid: ethanol or formaldehyde-fixed nuclei and chromosomes as well as tissue sections for labeling repetitive sequences in a range of plant species. In addition, methods on how immunostaining can be combined with CRISPR-FISH are provided.

3D multiple immunoimaging using whole male organs in rice

Spatiotemporal regulation of proteins and RNAs is essential for the precise development of reproductive tissues in many organisms. The anther, a prominent part of the male reproductive organ in plants, contains several somatic cell layers named the anther wall and, within it, the germ cells. Here, we successfully developed a simple 3D organ-immunoimaging technique for rice anthers, which distinguishes each individual cell from the four somatic cell layers and germ cells without the need for transformation, embedding, sectioning, or clearing. The 3D immunostaining method is also applicable to the intracellular localization of meiosis-specific proteins in meiocytes, as exemplified by MEL1, a germ cell-specific ARGONAUTE in the cytoplasm, and ZEP1, a pachytene marker on meiotic chromosomes. Our 3D multiple immunostaining method with single-cell and intracellular resolution will contribute to a comprehensive organ-level elucidation of molecular mechanisms and cellular connectivity.

Imaging plant tissues: advances and promising clearing practices

The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.

Advances in Two-Photon Imaging in Plants

Live and deep imaging play a significant role in the physiological and biological study of organisms. Two-photon excitation microscopy (2PEM), also known as multiphoton excitation microscopy, is a fluorescent imaging technique that allows deep imaging of living tissues. Two-photon lasers use near-infrared (NIR) pulse lasers that are less invasive and permit deep tissue penetration. In this review, recent advances in two-photon imaging and their applications in plant studies are discussed. Compared to confocal microscopy, NIR 2PEM exhibits reduced plant-specific autofluorescence, thereby achieving greater depth and high-resolution imaging in plant tissues. Fluorescent proteins with long emission wavelengths, such as orange-red fluorescent proteins, are particularly suitable for two-photon live imaging in plants. Furthermore, deep- and high-resolution imaging was achieved using plant-specific clearing methods. In addition to imaging, optical cell manipulations can be performed using femtosecond pulsed lasers at the single cell or organelle level. Optical surgery and manipulation can reveal cellular communication during development. Advances in in vivo imaging using 2PEM will greatly benefit biological studies in plant sciences.

Physical and chemical mechanisms of tissue optical clearing

Advanced optical methods combined with various probes pave the way toward molecular imaging within living cells. However, major challenges are associated with the need to enhance the imaging resolution even further to the subcellular level for the imaging of larger tissues, as well as for in vivo studies. High scattering and absorption of opaque tissues limit the penetration of light into deep tissues and thus the optical imaging depth. Tissue optical clearing technique provides an innovative way to perform deep-tissue imaging. Recently, various optical clearing methods have been developed, which provide tissue clearing based on similar physical principles via different chemical approaches. Here, we introduce the mechanisms of the current clearing methods from fundamental physical and chemical perspectives, including the main physical principle, refractive index matching via various chemical approaches, such as dissociation of collagen, delipidation, decalcification, dehydration, and hyperhydration, to reduce scattering, as well as decolorization to reduce absorption.

Navigating across multi-dimensional space of tissue clearing parameters

Optical tissue clearing refers to physico-chemical treatments which make thick biological samples transparent by removal of refractive index gradients and light absorbing substances. Although tissue clearing was first reported in 1914, it was not widely used in light microscopy until 21th century, because instrumentation of that time did not permit to acquire and handle images of thick (mm to cm) samples as whole. Rapid progress in optical instrumentation, computers and software over the last decades made micrograph acquisition of centimeter-thick samples feasible. This boosted tissue clearing use and development. Numerous diverse protocols have been developed. They use organic solvents or water-miscible substances, such as detergents and chaotropic agents; some protocols require application of electric field or perfusion with special devices. There is no 'best-for-all' tissue clearing method. Depending on the case, one or another protocol is more suitable. Most of protocols require days or even weeks to complete, thus choosing an unsuitable protocol may cause an important waste of time. Several inter-dependent parameters should be taken into account to choose a tissue clearing protocol, such as: (1) required image quality (resolution, contrast, signal to noise ratio etc), (2) nature and size of the sample, (3) type of labels, (4) characteristics of the available instrumentation, (5) budget, (6) time budget, and (7) feasibility. Present review focusses on the practical aspects of various tissue clearing techniques. It is aimed to help non-experts to choose tissue clearing techniques which are optimal for their particular cases.

Decrosslinking enables visualization of RNA-guided endonuclease-in situ labeling signals for DNA sequences in plant tissues

Information about the positioning of individual loci in the nucleus and the status of epigenetic modifications at these loci in each cell contained in plant tissue increases our understanding of how cells in a tissue coordinate gene expression. To obtain such information, a less damaging method of visualizing DNA in tissue that can be used with immunohistochemistry is required. Recently, a less damaging DNA visualization method using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/associated caspase 9) system, named RNA-guided endonuclease-in situ labeling (RGEN-ISL), was reported. This system made it possible to visualize a target DNA locus in a nucleus fixed on a glass slide with a set of simple operations, but it could not be applied to cells in plant tissues. In this work, we have developed a modified RGEN-ISL method with decrosslinking that made it possible to simultaneously detect the DNA loci and immunohistochemistry signals, including histone modification, in various types of plant tissues and species.

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.

See-through observation of malaria parasite behaviors in the mosquito vector

Although it is known that malaria parasites proliferate in the midgut of mosquito vector, their detailed behaviors, from gamete maturation to formation of next generation sporozoite, have not been fully understood at cellular or molecular level. This is mainly attributed to technical difficulties of dissection and whole-mount observation, of delicate and opaque mosquito body contents. In addition, blood pigment surrounding parasites immediately after blood meal also complicates tracing mosquito-stage parasites. Recent revolutionary studies have overcome such negative factors in tissue observation by clearing organisms. CUBIC reagents succeeded to remove both light scattering and blood pigment from various mouse tissues, and to whole-organ image fluorescence-labeled cell structures. In this study, we utilized the advanced version of CUBIC technology and high sensitivity fluorescent markers for see-through observation of mosquito vector after engulfment of rodent malaria parasites to clarify their behaviors during mosquito stage. As a result, we succeeded to visualize oocysts, sporozoites, female gametes and ookinetes in the mosquito bodies without any dissection.

Three-Dimensional Multiphoton Imaging of Transcription Factor by ClearSee

In plants, transcription factors often act as cell-to-cell trafficking mobile proteins and specify cell fate. Thus, to visualize spatiotemporal expression pattern and localization of transcription factors are essential to understand their functions during development. Several protocols have been developed to observe fluorescent protein. However, plant-specific autofluorescent compounds and various tissue components with different refractive indexes interfere with detection of fluorescent signals of your interest. Furthermore, cell fate specification often occurs in a limited number of cells covered by lateral/layers of organs. To overcome those issues, the plant clearing method, ClearSee, was recently developed for high-resolution imaging inside tissues by making background transparent. In this chapter, we provide three-dimensional imaging of fluorescent-protein-fused transcription factors by two-photon excitation microscopy in Arabidopsis and rice. Complex cell patterning with gene expression could be observed from any direction three-dimensionally. This method could be applicable to visualize any protein of your interest or it can readily be adapted in various other plants.

Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

Tackling Plant Meiosis: From Model Research to Crop Improvement

Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.