The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree

Lineage analysis of Caenorhabditis elegans is a powerful tool for characterizing developmental phenotypes and embryonic gene-expression patterns. We present a detailed protocol for the lineaging of embryos by computational analysis of 4D images of embryos that ubiquitously express histone-GFP (green fluorescent protein) fusion proteins through the 350 cell stage followed by manual editing. We describe how to optimize imaging settings for this purpose, the use of the lineage-extraction software, StarryNite, and the lineage-editing software, AceTree. In addition, we describe a useful polymer bead mounting technique for C. elegans embryos that has several advantages compared with the standard agar pad mounting technique. The protocol requires about 1 h of user time spread over 2 days to generate the raw lineage, and an additional 2 or 4 h to edit the lineage to the 194- or 350-cell stage, respectively.     

Studies in the electron microscope of the adoral zone of membranelles of the rumen ciliate entodinium caudatum using the technique of negative staining

The structure of the organelles situated beneath the kinetosomes in the adoral zone of membranelles of the rumen ciliate Entodinium caudatum have been investigated in the electron microscope using the technique of negative staining. Each kinetosome was joined to a sub-kinetosomal plate and these plates were joined together in rows which in turn were more loosely linked to form a sheet. The structure or these plates is described and their relationship to similar structures in other protozoa is discussed. The nature of the argentophilic structures observed in the light microscope at the anterior end of Entodinium caudatum has also been investigated in the electron microscope.     

Practical Image Restoration of Thick Biological Specimens Using Multiple Focus Levels in Transmission Electron Microscopy

Three-dimensional electron tomographic studies of thick specimens such as cellular organelles or supramolecular structures require accurate interpretations of transmission electron micrograph intensities. In addition to microscope lens aberrations, thick specimen imaging is complicated by additional distortions resulting from multiple elastic and inelastic scattering. Extensive analysis of the mechanism of image formation using electron energy-loss spectroscopy and imaging as well as exit wavefront reconstruction demonstrated that multiple scattering does not contribute to the coherent component of the exit wave (Hanet al.,1996, 1995). Although exit wavefront restored images showed enhanced contrast and resolution, that technique, which requires the collection of more than 30 images at different focus levels, is not practical for routine data collection in 3D electron tomography, where usually over 100 projection views are required for each reconstruction. Using a 0.7-μm-thick specimen imaged at 200 keV, the accuracy of reconstructions using small numbers of defocused images and a simple linear filter (Schiske, 1968) was assessed by comparison to the complete exit wave restoration. We demonstrate that only four optimal focus levels are required to effectively restore the coherent component (deviation 5.1%). By contrast, the optimal single image (zero defocus) shows a 25.5% deviation to the exit wave restoration. Two pairs of under- and over-defocus images should be taken: one pair at quite high defocus (>10 μm) to differentiate the coherent (single elastic scattering) from the incoherent (multiple elastic and inelastic scattering) components, and the second pair to optimize information content at the highest desired resolution (e.g., 5 μm for (2.5 nm)⁻¹resolution). We also propose a new interpretation of the restored amplitude and phase components where the specimen mass-density is proportional to the logarithm of the amplitude component and linearly related to the phase component. This approach should greatly facilitate the collection of high resolution tomographic data from thick samples.     

CHARGE CONTRAST IMAGING OF EXCEPTIONALLY-PRESERVED FOSSILS

Abstract:  Charge contrast images are a variant of secondary electron images acquired by operating a variable pressure scanning electron microscope in low vacuum mode; i.e. a gas is present in the specimen chamber. Spatial variation in the amount of charge that accumulates on the surface of the specimen is expressed as differences in greyscale tone; areas that are charging less are darker in tone. The precise mechanisms by which charge contrast images are generated are not known fully. Various different properties of a mineral may create a charge contrast; electrical conductivity is known to be one potentially important variable. As carbon is highly conductive but typical host lithologies (carbonates, silicates) less so or dielectric, the technique is potentially very suitable for imaging organically preserved fossils such as those from the Solite and Jehol biotas. It can also be applied to Burgess Shale fossils: complex films comprising 'aluminosilicates' with or without carbonaceous remains. Charge contrast images reveal anatomical detail not visible using either optical or other scanning electron microscope-based imaging methods.     

HIGH-RESOLUTION LEAF X-RADIOGRAPHY IN SYSTEMATICS AND PALEOBOTANY

The foliar vein nets of many seed plants and ferns display systematically informative characters. These venation characters traditionally have been observed by chemically clearing and staining leaves, a process that is slow, involves toxic chemicals, and yields delicate, glass-mounted specimens that require long-term maintenance to prevent or correct bubbling or crystallization of the mounting medium. A technique that uses X-rays and photographic film to produce images of leaf venation consistently shows veins that are 50–100 μm thick. Although the X-ray images are slightly less detailed than the best cleared and stained leaves, the images can be made much more quickly, are more easily stored and reproduced, and do not require permanent alteration of the original herbarium specimen. The technique should facilitate the use of vein characters in systematics, and the identification and systematic analysis of fossil leaves.     

Computer-Assisted Laser Scanning and Video Microscopy for Analysis of Cryptosporidium parvum Oocysts in Soil, Sediment, and Feces

A computer-assisted laser scanning microscope equipped for confocal laser scanning and color video microscopy was used to examine Cryptosporidium parvum oocysts in two agricultural soils, a barnyard sediment, and calf fecal samples. An agar smear technique was developed for enumerating oocysts in soil and barnyard sediment samples. Enhanced counting efficiency and sensitivity (detection limit, 5.2 x 10(sup2) oocysts(middot)g [dry weight](sup-1)) were achieved by using a semiautomatic counting procedure and confocal laser scanning microscopy to enumerate immunostained oocysts and fragments of oocysts in the barnyard sediment. An agarose-acridine orange mounting procedure was developed for high-resolution confocal optical sectioning of oocysts in soil. Stereo images of serial optical sections revealed the three-dimensional spatial relationships between immunostained oocysts and the acridine orange-stained soil matrix material. In these hydrated, pyrophosphate-dispersed soil preparations, oocysts were not found to be attached to soil particles. A fluorogenic dye permeability assay for oocyst viability (A. T. Campbell, L. J. Robertson, and H. V. Smith, Appl. Environ. Microbiol. 58:3488-3493, 1992) was modified by adding an immunostaining step after application of the fluorogenic dyes propidium iodide and 4(prm1),6-diamidino-2-phenylindole. Comparison of conventional color epifluorescence and differential interference contrast images on one video monitor with comparable black-and-white laser-scanned confocal images on a second monitor allowed for efficient location and interpretation of fluorescently stained oocysts in the soil matrix. This multi-imaging procedure facilitated the interpretation of the viability assay results by overcoming the uncertainties caused by matrix interference and background fluorescence.     

A Method for Embedding Thin Membranes in Historesin

A method is described for flat-embedding thin membranous tissues in Historesin. It allows easy orientation for sectioning large areas parallel to the surface. Selected fields can be monitored from the unfixed specimen, throughout preparation, to mounting on the microscope slide. For cross-sectioning, the flat-embedded tissue can be stacked and re-embedded to increase the amount of material examined per section.     

Scanning Electron Microscopy of Bacterial Colonies

A technique is described for observing bacterial colony growth. Bacillus cereus, B. subtilis, and B. cereus var. mycoides were grown on strips of dialysis membrane layered on nutrient agar. Microcolonies of the organisms on strips were fixed in Formalin vapor in situ; the strips then were removed from the agar and secured to scanning microscope specimen stubs without markedly disturbing the cellular arrangement. Scanning electron micrographs clearly depict morphology of individual cells, as well as the spatial orientation of cells within the colony. This technique is reproducible, adaptable, and simple.     

A scanning electron microscope technique for restoring deformed fossils

Deformed fossils which originally had a regular geometric outline, such as crinoid columnals, can be restored using a scanning electron microscope technique called tilt correction. This magnifies the specimen in one direction only. It is unsuitable for specimens where deformation has occurred unevenly and can also distort small structures while restoring the whole specimen. D Crinoid columnals, scanning electron microscope, tilt correction.     

The Processing of Mammalian Haemopoietic Cells in Thin Layer Agar Cultures for Electron Microscopy

Human and mouse haemopoietic cells cultured by the thin layer agar technique have been studied with the electron microscope. To process colonies of haemopoietic cells or individual cells which appeared in these colonies, a special technique had to be developed. The technique presented covers methods of selection, isolation, and sectioning that were devised for this purpose.

Haemopoietic cells are cultured in small plastic Petri dishes containing a culture system with 0.25% agar. Cell colonies and individual cells intended for light as well as for electron microscopic study are examined and selected microscopically with the aid of a numbered grid which is placed under the closed Petri dish.

Cells in the agar gel are fixed with glutaraldehyde which is pipetted directly onto the cultures. In order to facilitate their removal from the medium, the consistency of the agar solution is increased by evaporating liquid with controlled mild warming.

Pieces of agar containing colonies or single cells are cut out with a fine trephine and postfixed in osmium tetroxide. Agar pieces are embedded cell side up in a thin layer of Epon. After polymerization, the Epon-embedded pieces of agar are appropriately oriented at the head of flat embedding molds filled with fresh Epon. After another polymerization procedure, the top of the Epon blocks containing the cells are trimmed to a smooth surface with a glass knife.

The exact distance between the smooth surface of the blocks and the cells is measured by use of the vertical micrometer of a standard light microscope. The Epon layer around the specimen is trimmed away to expose selected cells for subsequent semi-thick and ultrathin sectioning. Sections are stained and examined microscopically.

With minor modifications the technique described also enables the processing of extremely small quantities of biological materials derived from other experiments for both light and electron microscopic observation.     

Determination of three-dimensional imaging properties of a light microscope system. Partial confocal behavior in epifluorescence microscopy.

We have determined the three-dimensional image-forming properties of an epifluorescence microscope for use in obtaining very high resolution three-dimensional images of biological structures by image processing methods. Three-dimensional microscopic data is collected as a series of two-dimensional images recorded at different focal planes. Each of these images contains not only in-focus information from the region around the focal plane, but also out-of-focus contributions from the remainder of the specimen. Once the imaging properties of the microscope system are characterized, powerful image processing methods can be utilized to remove the out-of-focus information and to correct for image distortions. Although theoretical calculations for the behavior of an aberration-free microscope system are available, the properties of real lenses under the conditions used for biological observation are often far from an ideal. For this reason, we have directly determined the image-forming properties of an epifluorescence microscope under conditions relevant to biological observations. Through-focus series of a point object (fluorescently-coated microspheres) were recorded on a charge-coupled device image detector. From these images, the three-dimensional point spread function and its Fourier transform, the optical transfer function, were derived. There were significant differences between the experimental results and the theoretical models which have important implications for image processing. The discrepancies can be explained by imperfections of the microscope system, nonideal observation conditions, and partial confocal effects found to occur with epifluorescence illumination. Understanding the optical behavior of the microscope system has indicated how to optimize specimen preparation, data collection, and processing protocols to obtain significantly improved images.     

Raster image correlation spectroscopy in live cells

Raster image correlation spectroscopy (RICS) is a noninvasive technique to detect and quantify events in a live cell, including concentration of molecules and diffusion coefficients of molecules; in addition, by measuring changes in diffusion coefficients, RICS can indirectly detect binding. Any specimen containing fluorophores that can be imaged with a laser scanning microscope can be analyzed using RICS. There are other techniques to measure diffusion coefficients and binding; however, RICS fills a unique niche. It provides spatial information and can be performed in live cells using a conventional confocal microscope. It can measure a range of diffusion coefficients that is not accessible with any other single optical correlation-based technique. In this article we describe a protocol to obtain raster scanned images with an Olympus FluoView FV1000 confocal laser scanning microscope using Olympus FluoView software to acquire data and SimFCS software to perform RICS analysis. Each RICS measurement takes several minutes. The entire procedure can be completed in ～2 h. This procedure includes focal volume calibration using a solution of fluorophores with a known diffusion coefficient and measurement of the diffusion coefficients of cytosolic enhanced green fluorescent protein (EGFP) and EGFP-paxillin.     

Oriented Embedding of Single-Cell Organisms

The dexribed technique facilitates oriented embedding of individual cells in various media for both light and electron microscopy. A fixed Specimen is embedded in a small cube of 2% agar at 40 C and subsequently sealed in the desired orientation to a strip of black paper which then serves as a tab for transferring the specimen during dehydrating and embedding procedures. The beveled ends of the strip indicate the exact location of the specimen in the cube. This technique can be employed for the embedding media used in both light and electron microscopy. It ah permits photomicrographs of the whole specimen to be made which can be compared with photomicrographs of individual sections cut from the specimen in a selected plane.     

Performing and Processing FNA of Anterior Fat Pad for Amyloid

Historically, heart, liver, and kidney biopsies were performed to demonstrate amyloid deposits in amyloidosis. Since the clinical presentation of this disease is so variable and non-specific, the associated risks of these biopsies are too great for the diagnostic yield. Other sites that have a lower biopsy risk, such as skin or gingival, are also relatively invasive and expensive. In addition, these biopsies may not always have sufficient amyloid deposits to establish a diagnosis. Fat pad aspiration has demonstrated good clinical correlation with low cost and minimal morbidity. However, there are no standardized protocols for performing this procedure or processing the aspirated specimen, which leads to variable and nonreproducible results. The most frequently utilized modality for detecting amyloid in tissue is an apple-green birefringence on Congo red stained sections using a polarizing microscope. This technique requires cell block preparation of aspirated material. Unfortunately, patients presenting in early stage of amyloidosis have minimal amounts of amyloid which greatly reduces the sensitivity of Congo red stained cell block sections of fat pad aspirates. Therefore, ultrastructural evaluation of fat pad aspirates by electron microscopy should be utilized, given its increased sensitivity for amyloid detection. This article demonstrates a simple and reproducible procedure for performing anterior fat pad aspiration for the detection of amyloid utilizing both Congo red staining of cell block sections and electron microscopy for ultrastructural identification.     

Method for immobilizing microbial cells on gel surface for dynamic AFM studies.

The processes of cell growth and budding of the yeast cells Saccharomyces cerevisiae, which were gently immobilized on 3% agar and submerged in culture medium, were successfully imaged with an atomic force microscope for 6-7 h. Similar experiments on chemically fixed cells did not detect any appreciable change in their appearance except in a few scannings at the very beginning, indicating that the dissolution of agar and/or scraping of its surface by the scanning tip, if any, did not significantly interfere with the images taken thereafter. The increment in the height of many of the untreated cells, accompanied by their lateral enlargement, was taken as an indication of successful imaging of the growth process of yeast cells, together with an image of a growing daughter cell attached to its mother cell.     

Pathogenesis of Streptoverticillium albireticuli on Caenorhabditis elegans and its antagonism to soil-borne fungal pathogens

AIMS: To examine the biological activity of Streptoverticillium albireticuli. METHODS: Isolation of S. albireticuli was carried out using the dry-heat technique. Nematicidal and pathogenic activity on Caenorhabditis elegans was measured by mortality in metabolites and colonization rate on fishmeal extract agar. Antifungal and enzymatic activities of S. albireticuli were measured by the agar plate method and the semidefined solid media method, respectively. RESULTS: S. albireticuli showed strong nematicidal activity against C. elegans. Pathogenic activity was also evident with the colonized nematode by the isolate on fishmeal extract agar. It also showed antifungal activity against certain fungal pathogens such as Rhizoctonia solani, Phytophthora cinnamomi and Fusarium oxysporum. SIGNIFICANCE AND IMPACT OF THE STUDY: The discovery of an actinomycete showing pathogenic activity against the nematode may indicate the potential for it to be used as a biocontrol agent of parasitic nematodes, in addition to its ability to suppress fungal pathogens.     

AN ELECTRON MICROSCOPE STUDY OF CALF THYMUS NUCLEAR PREPARATIONS ISOLATED IN SUCROSE SOLUTIONS

This work was carried out with the intent of developing a method capable of routinely evaluating calf thymus nuclear preparations with the electron microscope. Examination of small random samples, pre-embedded in agar after fixation with permanganate, were found to give results comparable to those obtained with much larger samples withdrawn randomly from pellets and embedded and sectioned conventionally. Results obtained by this pre-embedding technique with acrolein, osmium tetroxide, or permanganate fixations were equivalent. Calf thymus nuclear preparations isolated in sucrose by the method prevalently used (see 1) are contaminated only slightly with intact cells, to a degree which varies with each preparation. However, intact cells, damaged cells, or nuclei with some cytoplasm constitute together about 30 per cent of the preparation. Particles other than intact cells are not readily distinguishable from one another by light or phase microscope techniques. These preparations can be purified further by centrifuging through a dense sucrose layer. In our hands, however, contamination with some cytoplasm still remains in approximately 10 per cent of the particles. Incubation of the particles prepared without purification procedures, under conditions frequently used, results in the extensive breakdown of particles. Under at least one set of conditions, nuclei are selectively disrupted, leaving primarily damaged cells in the preparation.     

Sedimentation counting and morphology of Mycoplasma

Clark, Harold W. (The George Washington University School of Medicine, Washington, D.C.). Sedimentation counting and morphology of Mycoplasma. J. Bacteriol. 90:1373-1386. 1965.-The sedimentation technique for counting viral particles was applied to the quantitation and morphological identification of Mycoplasma in broth cultures. Mycoplasma, apparently in their native form, firmly adhered to the surface, when sedimented on glass cover slips or onto electron microscope grids. The sedimented cover slip preparations stained with crystal violet could be readily counted in the light microscope. The cultures sedimented onto electron microscope grids were readily counted at low magnification and provided excellent preparations for morphological examination at higher magnifications. It was found that air-dried Mycoplasma particles were enlarged considerably because of excessive flattening. Fixation of sedimented Mycoplasma particles in diluted OsO(4) prior to air drying yielded a more realistic morphology, with various sizes and shapes in the stages of the growth cycle exhibited. A new technique of differentially staining Mycoplasma colonies on agar plates was developed to facilitate the quantitation of viable colony-forming units for comparison with total counts. The use of plastic or Parafilm gaskets for dry mounting was developed to facilitate the handling and examination of the stained cover slip preparations. The results of this investigation indicated that the growth cycle of some Mycoplasma species includes a stage of hexadic fission with the cleavage of minimal reproductive units (less than 100 mmu) containing a limited deoxyribonucleic acid genetic coding molecule (approximately 4 x 10(6)).     

Three-dimensional structure of the crystalloid in the microbody of Kloeckera sp.: composite crystal model.

Electron microscopic investigations using the cryosectioning technique, together with electron diffraction, optical diffraction, and computer simulation, were carried out for the determination of the intrinsic structure of the crystalloid in the microbody of Kloeckera sp. The lattice images seen in the cryosections could be changed from one to another by tilting the specimen at an appropriate angle, the images obtained being well consistent with those obtained by computer simulation. The electron diffraction patterns also agreed with those obtained by optical diffraction. The results demonstrated that the crystalloid was composed of two different types of particles, large and small ones, arranged alternately and making up the composite crystal of rock salt structure. Large particles seemed to consist of alcohol oxidase molecules, while the small particles were presumably made up of catalase molecules.