Light Sheet Fluorescence Microscopy: A Review

Light sheet fluorescence microscopy (LSFM) functions as a non-destructive microtome and microscope that uses a plane of light to optically section and view tissues with subcellular resolution. This method is well suited for imaging deep within transparent tissues or within whole organisms, and because tissues are exposed to only a thin plane of light, specimen photobleaching and phototoxicity are minimized compared to wide-field fluorescence, confocal, or multiphoton microscopy. LSFMs produce well-registered serial sections that are suitable for three-dimensional reconstruction of tissue structures. Because of a lack of a commercial LSFM microscope, numerous versions of light sheet microscopes have been constructed by different investigators. This review describes development of the technology, reviews existing devices, provides details of one LSFM device, and shows examples of images and three-dimensional reconstructions of tissues that were produced by LSFM.     

A Modification of the Tannic Acid Phosphomolybdic Acid-Dye Stain for Demonstrating Myoepithelial Cells in Formalin Fixed Tissue

A modified tannic acid-phosphomolybdic acid-dye procedure is used for staining myoepithelial cells in formalin fixed surgical and autopsy material. Paraffin section are brought to water, mordanted for 1 hr in Bouin's fixative previously heated to 56 C, cooled while still in Bouin's, rinsed in tap water until sections are colorless, rinsed in distilled water, treated with 5% aqueous tannic acid 5-20 min, rinsed in distilled water 30 sec or less, treated with 1% aqueous phosphomolybdic acid 10-15 min, rinsed 30 sec in distilled water, rinsed in methanol, stained 1 hr in a saturated solution of amido black or phloxine B in 9:l methanol:acetic acid, rinsed in 9:l methanol:acetic acid, dehydrated, cleared and mounted. Myoepithelial cells of sweat, lacrimal, salivary, bronchial, and mammary glands are blue-green with amido black or pink with phloxine B. Fine processes of myoepithelial cells are well delineated. Background staining is minimal and the procedure is highly reproducible.     

A Self-Limiting, Highly Selective Chromium-Hematoxylin Stain

A compound, which is probably a cationic chelate, can be isolated as a dry powder from a hematoxylin-chrome alum lake. In aqueous acid solution this compound is an excellent nuclear stain which is extremely selective, very resistant to acids and alcohols, and self-limiting. Staining time may vary from 20 min to 16 hr without causing significant differences in staining intensity. To prepare the dry stain, dissolve 10 gm of hematoxylin, 10 gm of NaOH and 70 gm of chrome alum in 600 ml of distilled water, boil 20 min, cool and filter, allowing the filtrate to drop into 3.5 liters of absolute alcohol. Filter off the precipitate formed in the alcohol, and air dry it at room temperature. The staining solution is prepared by dissolving 3 gm of the dried precipitate in 100 ml of 3% HCl.     

Basic Fuchsin and Picro-Indigo Carmine: A Selective Stain for Cells in Mitosis and for Autoradiography

Selective staining of dividing nuclei is accomplished as follows: paraffin sections, after hydration, are stained 15 min in a saturated aqueous solution of basic fuchsin, washed, then stained 1.5 min in an equal-volumes mixture of indigo carmine saturated in 70% alcohol, and saturated aqueous picric acid. Removal of excess dye with 3 changes of 70% alcohol, dehydration, clearing and covering in a resinous medium completes the process. Nuclei of dividing cells are stained red; cytoplasm and interphase nuclei, light green. This method has been used successfully for determining the mitotic activity of skin, kidney, liver and other rabbit and mouse tissues. Tissue sections previously prepared as autoradiographs may be stained by this method to facilitate the determination of radioactive labeling of mitotic cells.     

A Fluorescent Gram Stain for Flow Cytometry and Epifluorescence Microscopy

The fluorescent nucleic acid binding dyes hexidium iodide (HI) and SYTO 13 were used in combination as a Gram stain for unfixed organisms in suspension. HI penetrated gram-positive but not gram-negative organisms, whereas SYTO 13 penetrated both. When the dyes were used together, gram-negative organisms were rendered green fluorescent by SYTO 13; conversely, gram-positive organisms were rendered red-orange fluorescent by HI, which simultaneously quenched SYTO 13 green fluorescence. The technique correctly predicted the Gram status of 45 strains of clinically relevant organisms, including several known to be gram variable. In addition, representative strains of gram-positive anaerobic organisms, normally decolorized during the traditional Gram stain procedure, were classified correctly by this method.Gram’s staining method is considered fundamental in bacterial taxonomy. The outcome of the Gram reaction reflects major differences in the chemical composition and ultrastructure of bacterial cell walls. The Gram stain involves staining a heat-fixed smear of cells with a rosaniline dye such as crystal or methyl violet in the presence of iodine, with subsequent exposure to alcohol or acetone. Organisms that are decolorized by the alcohol or acetone are designated gram negative.Alternative Gram staining techniques have recently been proposed. Sizemore et al. (19) reported on the use of fluorescently labeled wheat germ agglutinin. This lectin binds specifically to N-acetylglucosamine in the peptidoglycan layer of gram-positive bacteria, whereas gram-negative organisms contain an outer membrane that prevents lectin binding. Although simpler and faster than the traditional Gram stain, this method requires heat fixation of organisms.Other Gram stain techniques suitable for live bacteria in suspension have been described. Allman et al. (1) demonstrated that rhodamine 123 (a lipophilic cationic dye) rendered gram-positive bacteria fluorescent, but its uptake by gram-negative organisms was poor. This reduced uptake by gram-negative bacteria was attributed to their outer membranes. The outer membrane can be made more permeable to lipophilic cations by exposure to the chelator EDTA (4). Shapiro (18) took advantage of this fact to form the basis of another Gram stain, one which involved comparing the uptake of a carbocyanine dye before and after permeabilizing organisms with EDTA. All of these methods, however, rely on one-color fluorescence, making analysis of mixed bacterial populations difficult.An alternative to the use of stains is the potassium hydroxide (KOH) test. The method categorizes organisms on the basis of differences in KOH solubility. After exposure to KOH, gram-negative bacteria are more easily disrupted than gram-positive organisms. This technique has been used to classify both aerobic and facultatively anaerobic bacteria, including gram-variable organisms (8). In a study by Halebian et al. (9), however, this technique incorrectly classified several anaerobic strains, giving rise to the recommendation that the method should only be used in conjunction with the traditional Gram stain.In this study we demonstrate a Gram staining technique for unfixed organisms in suspension, by using clinically relevant bacterial strains and organisms notorious for their gram variability. The method uses two fluorescent nucleic acid binding dyes, hexidium iodide (HI) and SYTO 13. Sales literature (11) published by the manufacturers of HI (Molecular Probes, Inc., Eugene, Oreg.), which displays a red fluorescence, suggests that the dye selectively stains gram-positive bacteria. SYTO 13 is one of a group of cell-permeating nucleic acid stains and fluoresces green (11). These dyes have been found to stain DNA and RNA in live or dead eukaryotic cells (16). Both dyes are excited at 490 nm, permitting their use in fluorescence instruments equipped with the most commonly available light sources. We reasoned that a combination of these two dyes applied to mixed bacterial populations would result in all bacteria being labeled, with differential labeling of gram-positive bacteria (HI and SYTO 13) and gram-negative bacteria (SYTO 13 only). The different fluorescence emission wavelengths of the two dyes would ensure differentiation of gram-positive from gram-negative bacteria by either epifluorescence microscopy or flow cytometry when equipped with the appropriate excitation and emission filters. While a commercial Gram stain kit produced by Molecular Probes includes HI and an alternative SYTO dye, SYTO 9, we are unaware of any peer-reviewed publications regarding either its use or its effectiveness with traditionally gram-variable organisms.     

A Selective Stain for Renal Basement Membranes

Paraffin sections from human kidneys fixed in Carnoy's fluid No. 2 were treated consecutively with periodic acid-sodium bisulfite and stained with resorcin-fuchsin. Basement membranes were colored black in cross sections, dark gray in tangential sections. Cytoplasm, nuclei, reticulin and collagen fibers remained unstained or were only lightly colored, depending on duration of fixation. Elastic fibers were colored black. In sections counterstained with Kernechtrot, the sharp black coloration of basement membranes and the pink staining of nuclei facilitated the study of glomerular lesions. After counterstaining with Van Gieson's picro-fuchsin, the black basement membranes contrasted well with the red reticulin and collagen fibers. Because this method does not require differentiation, it gave uniform results in the hands of different users. No fading was observed in section stored for 3 yr.     

A Tri-Basic-Dye Stain for Nerve Cells

A new staining method has been developed for the study of nerve cells and Nissl granules which combines three basic dyes, cresylecht violet, toluidine blue and thionin. The use of this tri-basic-dye stain results in finished preparations that are critically stained and permanent. Paraffin sections (4 μ sections preferably) are mounted on slides by the starch medium, deparaffinized and stained by the tribasic staining solution. After differentiation in acidified distilled water, sections are dehydrated, returned to stain solution and again dehydrated, then cleared and mounted in Clarite. Various vertebrate material including normal and pathological human tissues have been stained with this triple dye solution. Especially for pathological material, re-immersion of slides in the staining and 80% alcohol solutions before mounting, differentially intensifies the staining reaction. Fixatives used were 10% formalin, 95% alcohol, Bouin and formalin-Bouin (10% formalin followed by Bouin).     

Unifying Fluorescence Microscopy and Mass Spectrometry for Studying Protein Complexes in Cells

We have developed and applied a method unifying fluorescence microscopy and mass spectrometry for studying spatial and temporal properties of proteins and protein complexes in yeast cells. To combine the techniques, first we produced a variety of DNA constructs that can be used for genomic tagging of proteins with modular fluorescent and affinity tags. The modular tag consists of one of the multiple versions of monomeric fluorescent proteins fused to a variety of small affinity epitopes. After this step we tested the constructs by tagging two yeast proteins, Pil1 and Lsp1, the core components of eisosomes, the large protein complexes involved in endocytosis in Saccharomyces cerevisiae, with a variety of fluorescent and affinity probes. Among the modular tags produced we found several combinations that were optimal for determining subcellular localization and for purifying the tagged proteins and protein complexes for the detailed analysis by mass spectrometry. And finally, we applied the designed method for finding the new protein components of eisosomes and for gaining new insights into molecular mechanisms regulating eisosome assembly and disassembly by reversible phosphorylation and dephosphorylation. Our results indicate that this approach combining fluorescence microscopy and mass spectrometry into a single method provides a unique perspective into molecular mechanisms regulating composition and dynamic properties of the protein complexes in living cells.Fluorescent proteins have become invaluable probes for studying molecular processes in living cells with light microscopy techniques (1–3). Proteins, organelles, and entire cells can be selectively visualized using a variety of fluorescent proteins fused to the proteins of interest (1–6). Combined with genetics and molecular biology techniques fluorescence microscopy provides an efficient tool for observing molecular phenotypes useful for dissecting the pathways of cell cycle progression and cell response to internal and external signals (7). However, understanding the mechanism controlling the properties of proteins in cells can be a challenging task, frequently requiring a comprehensive characterization of the proteins at the molecular level.The proteins tagged with green fluorescent protein (GFP)¹ can be also purified using GFP antibodies. Cheeseman and Desai (8) and Cristea et al. (9) have enriched GFP-tagged proteins and protein complexes for further detailed analysis by MS. The MS-based methods for protein analysis are fast, sensitive, and able to identify both proteins in complex protein mixtures and residues bearing post-translational modifications (10, 11). Thus, the addition of affinity purification and mass spectrometry steps enabled the researchers to study protein interactions and the post-translational modifications in the context of the protein subcellular localization. Juxtaposition of the protein localization, composition of the protein complexes, and post-translational modifications frequently yield a unique perspective of the cellular processes and the molecular mechanisms of their regulation (12, 13).Using fluorescent proteins also as affinity probes can be problematic in several instances. First of all, the good quality antibodies against the rapidly increasing number of fluorescent proteins (3, 6) are not yet readily available. Furthermore raising antibodies specifically recognizing fluorescent proteins originating from the same organism but fluorescing a different color can be difficult or even impossible because such proteins frequently differ by mutations of only a few amino acids (1–6). Thus, we seek an alternative approach to the design of tags suitable for subcellular localization and purification of proteins and protein complexes that is 1) independent of the availability of antibody to a specific form of a fluorescent protein, 2) suitable for multiplexing, i.e. simultaneous observation of subcellular localization of several proteins and affinity purification of the proteins and stably associated protein complexes, and 3) flexible and easy to modify to incorporate better versions of fluorescent proteins and affinity tags after they are discovered.One possible solution that satisfies the stated requirements is to use a modular tag containing a version of a fluorescent protein fused to an affinity epitope. In this case we can decouple requirements for both modules and optimize the performance of each one independently for fluorescence microscopy and affinity purification experiments. To our knowledge, this possibility was first realized by Thorn and co-worker (14) who have fused 3HA (three repeats of YPYDVPDYA epitope from hemagglutinin protein) and 13MYC (13 repeats of EQKLISEEDL epitope, corresponding to a stretch of the C-terminal amino acids of the human c-MYC protein) tags to several variants of fluorescent proteins. The authors have argued that the fusion of the fluorescent proteins to the affinity epitopes may enable fluorescence and immunochemical analysis but did not test this idea. Cheeseman and Desai (8) fused the S-peptide and hexahistidine epitopes to the GFP protein to enable additional tandem purification steps. Su and co-workers (15) also fused a hexahistidine tag (His₆) to GFP to purify recombinantly produced proteins. Although hexahistidine tag performs well for isolation of overexpressed recombinant proteins, it works poorly for affinity purification of low abundance, endogenously expressed proteins (16). A double affinity tag containing a single MYC epitope and hexahistidine was also used to purify recombinantly produced fluorescent proteins (6).Here we describe the design and implementation of the modular fluorescent and affinity tags. These tags contain a variety of fluorescent proteins, which can be used exclusively for obtaining subcellular visualization, and several small epitope tags that can be utilized to perform two-step affinity purification. To test the performance of the constructs produced, we tagged two yeast proteins, Pil1 and Lsp1, the core components of eisosomes, with a variety of modular tags.Eisosomes are large heterodimeric protein complexes recently discovered in Saccharomyces cerevisiae (17). There are ∼50–100 eisosomes in each mature yeast cell distributed uniformly in a characteristic dotted pattern at the cell surface periphery. Each eisosome contains ∼2000–5000 copies of Pil1 and Lsp1. It was shown that eisosomes serve as portals of endocytosis in yeast. The function of eisosomes is regulated by reversible phosphorylation (18, 19).Among the constructs tested, we found several combinations of fluorescent protein and affinity tags that were optimal for determining subcellular localization and purification of the proteins and protein complexes. We applied these tags to further investigate eisosomes and found several new protein components of the complexes and obtained new insights into molecular mechanisms regulating eisosome integrity by reversible phosphorylation and dephosphorylation. Our results indicate that an approach combining fluorescence microscopy and mass spectrometry into a single method provides a unique perspective into molecular mechanisms regulating composition and dynamic properties of the protein complexes in living cells.     

Intestinal Enterochromaffin Cells in Branchiostoma lanceolatum,Studied by Fluorescence and Electron Microscopy

Using the Falck-Hillarp method for demonstration of biogenic amines, the presence of indole alkylamine (possibly 5-hydroxytryptamine) containing enterochromaffin cells in strongly ciliated areas of the lancelet intestine was confirmed. An electron microscopic investigation of these areas, i.e. the “lateral ciliated tract” and the “dorsal ciliated tract”, revealed two cell types. 1. Mucous cells, equipped with tall cilia and giant rootlets, constitute the dominating type. 2. Enterochromaffin cells, containing numerous electron dense granules, are sparsely scattered among the mucous cells. The intestinal indole alkylamine is believed to be involved in the regulation of ciliary activity.     

A Selective Stain for Mitotic Figures, Particularly in the Developing Brain

A selective stain for mitotic figures is valuable where autoradiographic counting is not required, especially in the developing brain. Most work in this field has been based on conventional nuclear stains which do not differentiate mitotic figures from resting cells by color. Hematoxylin, Feulgen, gallocyanin and Nissl methods have been used particularly. The method described uses a modified Bouin fixative, followed by hydrolysis in 1 N HCl. Mitotic figures are selectively stained using crystal violet, with nuclear fast red as the counterstain for resting cells. The method has been tested using material from postnatal and fetal sheep, guinea pig and rat. Using paraffin mounted serial sections it is applicable to all organs. The method was very successful on developing rat brain, particularly for detail and quantitative estimation in the early stages of prenatal development, which was of primary interest. Nucleated cells of the erythrocytic series, keratin and what appear to be mast cells were found to stain. When nuclear counting or cell recognition were required these did not cause any difficulty, except in prenatal liver. The highly selective method presented stains mitotic figures, in all tissue tested, an intense blue against a background of red resting cells.     

Luxol Fast Blue Mbs: A Stain for Phase Contrast Microscopy

A staining method to increase the contrast of sectioned material for phase contrast microscopy is described. Two stock solutions of the stain are required. The first is made by dissolving 2 gm of luxol fast blue MBS in 100 ml of 95% ethanol. The second solution is made up of 4 ml of a 29% aqueous solution of FeCl₃, 95 ml of 95% ethanol, and 1 ml of concentrated HCl. The staining solution is made by mixing equal parts of the two solutions. Sections are deparaffinized and taken to 70% alcohol, stained for 1.5 hr, dehydrated, cleared and covered as usual.     

A Simple Permanent Aceto-Orcein Stain for Free Cells, Cultures and Homogenates

A simplified technic for preparation of the aceto-orcein stain permits the storage of cells in the stain or squash preparations at room temperature for long periods without in* jury to or distortion of the cells and mitotic plates. Fresh cells from tumor ascites, tissue culture cells growing in free suspension or over cover slips, and homogenates of whole tissues are stained directly in a test tube in either (1) regular aceto-orcein and subsequently mounted in glycerol, or (2) aceto-orcein-glycerol mixture. These preparations are squashed for chromosome counts, and the permanent slides are kept from drying out by ringing the cover slip with Damar or Permount.     

Luxol Fast Blue Mbs: A Stain for Phase Contrast Microscopy

A staining method to increase the contrast of sectioned material for phase contrast microscopy is described. Two stock solutions of the stain are required. The first is made by dissolving 2 gm of luxol fast blue MBS in 100 ml of 95% ethanol. The second solution is made up of 4 ml of a 29% aqueous solution of FeCl₃, 95 ml of 95% ethanol, and 1 ml of concentrated HCl. The staining solution is made by mixing equal parts of the two solutions. Sections are deparaffinized and taken to 70% alcohol, stained for 1.5 hr, dehydrated, cleared and covered as usual.     

Pinacyanol Erythrosinate as A Stain for Mast Cells

An alcoholic solution of the compound dye, pina-cyanol erythrosinate when diluted to the optimum dissociation point is a differential tissue stain which, in addition, selectively stains and differentiates mast cells. It can be made up and used like any other compound dye (e.g., Bowie's stain, neutral gentian, etc. or like a blood stain). It can be used after any of the common fixatives and has the advantage of selectively staining all types of mast cells in their various functional phases, even in those species (notably rabbit and man) in which they may be difficult to demonstrate with other mast cell stains after aqueous fixatives.     

Pinacyanol Erythrosinate as A Stain for Mast Cells

An alcoholic solution of the compound dye, pina-cyanol erythrosinate when diluted to the optimum dissociation point is a differential tissue stain which, in addition, selectively stains and differentiates mast cells. It can be made up and used like any other compound dye (e.g., Bowie's stain, neutral gentian, etc. or like a blood stain). It can be used after any of the common fixatives and has the advantage of selectively staining all types of mast cells in their various functional phases, even in those species (notably rabbit and man) in which they may be difficult to demonstrate with other mast cell stains after aqueous fixatives.     

Phosphotungstic Acid-Chromic Acid as a Selective Electron-Dense Stain for Plasma Membranes of Plant Cells

A mixture consisting of 1% phosphotungstic acid (PTA) in 10% chromic acid (CrO₃) selectively stains the plasma membrane of plant cells. Whole tissue or pelleted cell fractions are prepared for electron microscopy using conventional methods including glutaraldehyde fixation and OsO₄ postfixation, dehydration in acetone and embedding in Epon. To stain the plasma membrane, thin sections are transferred with a plastic loop to the surface of a 1% aqueous solution of periodic acid for 30 min for destaining. Following transfer through 5 distilled water rinses, the sections are exposed to the PTA-CrO₃ mixture for 5 min, rinsed and mounted on grids for viewing with the electron microscope. The selectivity of the stain is retained in homogenates and serves to identify the plant plasma membrane in cell fractions.     

Video-Rate Confocal Microscopy for Single-Molecule Imaging in Live Cells and Superresolution Fluorescence Imaging

There is no confocal microscope optimized for single-molecule imaging in live cells and superresolution fluorescence imaging. By combining the swiftness of the line-scanning method and the high sensitivity of wide-field detection, we have developed a, to our knowledge, novel confocal fluorescence microscope with a good optical-sectioning capability (1.0 μm), fast frame rates (<33 fps), and superior fluorescence detection efficiency. Full compatibility of the microscope with conventional cell-imaging techniques allowed us to do single-molecule imaging with a great ease at arbitrary depths of live cells. With the new microscope, we monitored diffusion motion of fluorescently labeled cAMP receptors of Dictyostelium discoideum at both the basal and apical surfaces and obtained superresolution fluorescence images of microtubules of COS-7 cells at depths in the range 0–85 μm from the surface of a coverglass.