Superresolution microscopy for microbiology

This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of superresolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission‐depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate superresolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments.     

Correlative fluorescence and electron microscopy on ultrathin cryosections: bridging the resolution gap.

Microscopy has become increasingly important for analysis of cells and cell function in recent years. This is due in large part to advances in light microscopy that facilitate quantitative studies and improve imaging of living cells. Analysis of fluorescence signals has often been a key feature in these advances. Such studies involve a number of techniques, including imaging of fluorescently labeled proteins in living cells, single-cell physiological experiments using fluorescent indicator probes, and immunofluorescence localization. The importance of fluorescence microscopy notwithstanding, there are instances in which electron microscopy provides unique information about cell structure and function. Correlative microscopy in which a fluorescence signal is reconciled with a signal from the electron microscope is an additional tool that can provide powerful information for cellular analysis. Here we review two different methodologies for correlative fluorescence and electron microscopy using ultrathin cryosections and the advantages attendant on this approach. (J Histochem Cytochem 49:803-808, 2001)     

High-throughput fluorescence microscopy for systems biology

In this post-genomic era, we need to define gene function on a genome-wide scale for model organisms and humans. The fundamental unit of biological processes is the cell. Among the most powerful tools to assay such processes in the physiological context of intact living cells are fluorescence microscopy and related imaging techniques. To enable these techniques to be applied to functional genomics experiments, fluorescence microscopy is making the transition to a quantitative and high-throughput technology.     

Combining multiple fluorescence imaging techniques in biology: when one microscope is not enough

While fluorescence microscopy has proven to be an exceedingly useful tool in bioscience, it is difficult to offer simultaneous high resolution, fast speed, large volume, and good biocompatibility in a single imaging technique. Thus, when determining the image data required to quantitatively test a complex biological hypothesis, it often becomes evident that multiple imaging techniques are necessary. Recent years have seen an explosion in development of novel fluorescence microscopy techniques, each of which features a unique suite of capabilities. In this Technical Perspective, we highlight recent studies to illustrate the benefits, and often the necessity, of combining multiple fluorescence microscopy modalities. We provide guidance in choosing optimal technique combinations to effectively address a biological question. Ultimately, we aim to promote a more well-rounded approach in designing fluorescence microscopy experiments, leading to more robust quantitative insight.     

Quantitating the concentration of Py-Im polyamide-fluorescein conjugates in live cells

Quantitative fluorescence-based methods have been developed to determine the nuclear concentration of polyamide-fluorescein conjugates in cell culture. Confocal laser scanning microscopy and flow cytometry techniques are utilized to plot calibration curves, from which the nuclear concentration can be interpolated. Upon treatment with polyamide, the concentration in the nucleus of live HeLa cells is calculated to be between 0.1 and 0.5microM, which is significantly lower than the 2microM dosage concentration. In contrast, the observed nuclear concentration in U251 cells is closer to the dosage concentration, indicating a cell line-specific increase in uptake for this class of compounds. Although confocal microscopy and flow cytometry generate disparate values, taken together these experiments suggest that the polyamide concentration inside the cell nucleus is lower than it is outside the cell.     

Flow cytometry, microscopy, and DNA analysis as complementary phytoplankton screening methods in ballast water treatment studies

Ballast water is the main vector for marine invasions. To minimize the spread of invasive species, the International Maritime Organization (IMO) has adopted the Ballast Water Management Convention which requires the installation of shipboard ballast water treatment systems (BWTS). During BWTS tests, the phytoplankton abundance and species composition were followed after treatment with both filtration and ultraviolet radiation. Although the installation fulfilled the IMO criteria after a 5-day holding time in a model ballast tank, the ultimate effectiveness of the treatment was further tested in long-term (20 days) incubation experiments under optimal phytoplankton growth conditions. Application of flow cytometry, microscopy, and DNA sequencing to these incubation samples gave an indication of the phytoplankton species that might be introduced by ballast water discharge—despite treatment. Phytoplankton was reliably quantified using flow cytometry, while fast identification was best done using microscopy. Some groups that contained potentially toxic species could not be identified at species level using microscopy; for these species, identification using genetic techniques was necessary. It is concluded that if long-term incubation experiments are used as an additional tool in testing BWTS effectiveness, a combination of phytoplankton screening methods can be applied depending on the detail of information that is required.     

Ecology of nematophagous fungi: Methods of collection,isolation and maintenance of predatory and endoparasitic fungi

The methods employed in a recent investigation into the ecology of nematophagous fungi are examined in detail. The best sources from which fungi can be isolated are examined, and the main field collection and recovery techniques are compared and discussed. Other practical problems considered are the examination of plates, microscopy, identification, isolation and culture methods, maintenance of fungi, the production of nematodes as bait. A summary of the experimental techniques used is given.     

Behavior,activities, and effects of bacteria on synthetic quartz monocrystal surfaces

Two strains ofBacillus sp. and a strain ofBrevibacterium sp., originally isolated from a natural quartzite surface, were characterized and employed as test strains with several methods: acridine orange fluorochromation and epifluorescence microscopy were used for detection of individual cells; scanning and transmission microscopy for studying attachment behavior; replica techniques in combination with electron microscopy for following surface interaction effects; and chemical analysis of SiO₂ for detecting possible silica leaching activities. The experimental results clearly showed that the three test strains were able to attach to and grow on the precleaned quartz surfaces. Attachment modes were either by direct sorption mechanisms (Brevibacterium sp. S) or the production of adhesive polymers (Bacillus sp. U andBacillus sp. W). In short-term contact incubation experiments with rich media, neither quartz crystal surface structures nor bacterial cell surfaces appeared to be changed. Likewise, significant biochemical dissolution and mechanical dislocation of SiO₂ (which would have indicated rapid bacterial weathering activities) could not be detected. The importance of quartz purity and crystalline structure for the initiation of weathering processes is discussed.     

Visualisation studies and glomerular filtration in early diabetic rats

The purpose of this mini-review is to show that more modern multi-photon microscopy approaches allow quantitative glomerular filtration experiments. Modern science has now entered a transition period from light microscopy to multi-photon confocal microscopy. Since the late 20th century, multi-photon microscopy has been applied in the study of organ function. In keeping with observations made in renal physiology and other representative studies throughout this transition period, and in the context of advancing microscopy techniques, this review has been presented as a comment on the glomerular filtration barrier, with a focus on the early aetiopathogenesis of diabetes.     

Capturing the surface texture and shape of pollen: a comparison of microscopy techniques

Research on the comparative morphology of pollen grains depends crucially on the application of appropriate microscopy techniques. Information on the performance of microscopy techniques can be used to inform that choice. We compared the ability of several microscopy techniques to provide information on the shape and surface texture of three pollen types with differing morphologies. These techniques are: widefield, apotome, confocal and two-photon microscopy (reflected light techniques), and brightfield and differential interference contrast microscopy (DIC) (transmitted light techniques). We also provide a first view of pollen using super-resolution microscopy. The three pollen types used to contrast the performance of each technique are: Croton hirtus (Euphorbiaceae), Mabea occidentalis (Euphorbiaceae) and Agropyron repens (Poaceae). No single microscopy technique provided an adequate picture of both the shape and surface texture of any of the three pollen types investigated here. The wavelength of incident light, photon-collection ability of the optical technique, signal-to-noise ratio, and the thickness and light absorption characteristics of the exine profoundly affect the recovery of morphological information by a given optical microscopy technique. Reflected light techniques, particularly confocal and two-photon microscopy, best capture pollen shape but provide limited information on very fine surface texture. In contrast, transmitted light techniques, particularly differential interference contrast microscopy, can resolve very fine surface texture but provide limited information on shape. Texture comprising sculptural elements that are spaced near the diffraction limit of light (~250 nm; NDL) presents an acute challenge to optical microscopy. Super-resolution structured illumination microscopy provides data on the NDL texture of A. repens that is more comparable to textural data from scanning electron microscopy than any other optical microscopy technique investigated here. Maximizing the recovery of morphological information from pollen grains should lead to more robust classifications, and an increase in the taxonomic precision with which ancient vegetation can be reconstructed.     

Effect of fengycin, a lipopeptide produced by Bacillus subtilis, on model biomembranes

Fengycin is a biologically active lipopeptide produced by several Bacillus subtilis strains. The lipopeptide is known to develop antifungal activity against filamentous fungi and to have hemolytic activity 40-fold lower than that of surfactin, another lipopeptide produced by B. subtilis. The aim of this work is to use complementary biophysical techniques to reveal the mechanism of membrane perturbation by fengycin. These include: 1), the Langmuir trough technique in combination with Brewster angle microscopy to study the lipopeptide penetration into monolayers; 2), ellipsometry to investigate the adsorption of fengycin onto supported lipid bilayers; 3), differential scanning calorimetry to determine the thermotropic properties of lipid bilayers in the presence of fengycin; and 4), cryogenic transmission electron microscopy, which provides information on the structural organization of the lipid/lipopeptide system. From these experiments, the mechanism of fengycin action appears to be based on a two-state transition controlled by the lipopeptide concentration. One state is the monomeric, not deeply anchored and nonperturbing lipopeptide, and the other state is a buried, aggregated form, which is responsible for membrane leakage and bioactivity. The mechanism, thus, appears to be driven mainly by the physicochemical properties of the lipopeptide, i.e., its amphiphilic character and affinity for lipid bilayers.     

Simplified preparation of mycoplasmas, an acholeplasma, and a spiroplasma for scanning electron microscopy.

A simple, effective procedure was developed for scanning electron microscopic examination of mycoplasmas and similar organisms. Cultivation of several mycoplasmal species, an acholeplasma, and a spiroplasma in broth media in Leighton tubes with cover slips resulted in attachment of the organisms to the cover slips. The attached cells were easily processed for either scanning electron microscopy or light microscopy. By eliminating the need for centrifugation, which was used in previously described techniques, physical stress on the cell is minimized. The effects of different preparative procedures on the morphology of Mycoplasma gallisepticum are described.     

Mechanoreceptor Cells on the Tertiary Pulvini of Mimosa pudica L.

Special red cells were found on the adaxial surface of tertiary pulvini of Mimosa pudica and experiments performed to determine the origin and function of these cells. Using anatomical (light, scanning electron and transmission electron microscopy) and electrophysiological techniques, we have demonstrated that these red cells are real mechanoreceptor cells. They can generate receptor potential following mechanical stimuli and they are in connection with excitable motor cells (through plasmodesmata). We also provide evidence that these red cells are derived from stomatal subsidiary cells and not guard cells. As histochemical studies show red cells contain tannin, which is important in development of action potentials and movements of plants. These cells could be one of unidentified mechanoreceptors of mimosa.Key Words: mimosa, mechanoreceptor cells, microscopy, electrophysiology, receptor potential     

Mouse satellite DNA, centromere structure, and sister chromatid pairing

The experiments described were directed toward understanding relationships between mouse satellite DNA, sister chromatid pairing, and centromere function. Electron microscopy of a large mouse L929 marker chromosome shows that each of its multiple constrictions is coincident with a site of sister chromatid contact and the presence of mouse satellite DNA. However, only one of these sites, the central one, possesses kinetochores. This observation suggests either that satellite DNA alone is not sufficient for kinetochore formation or that when one kinetochore forms, other potential sites are suppressed. In the second set of experiments, we show that highly extended chromosomes from Hoechst 33258-treated cells (Hilwig, I., and A. Gropp, 1973, Exp. Cell Res., 81:474-477) lack kinetochores. Kinetochores are not seen in Miller spreads of these chromosomes, and at least one kinetochore antigen is not associated with these chromosomes when they were subjected to immunofluorescent analysis using anti-kinetochore scleroderma serum. These data suggest that kinetochore formation at centromeric heterochromatin may require a higher order chromatin structure which is altered by Hoechst binding. Finally, when metaphase chromosomes are subjected to digestion by restriction enzymes that degrade the bulk of mouse satellite DNA, contact between sister chromatids appears to be disrupted. Electron microscopy of digested chromosomes shows that there is a significant loss of heterochromatin between the sister chromatids at paired sites. In addition, fluorescence microscopy using anti-kinetochore serum reveals a greater inter-kinetochore distance than in controls or chromosomes digested with enzymes that spare satellite. We conclude that the presence of mouse satellite DNA in these regions is necessary for maintenance of contact between the sister chromatids of mouse mitotic chromosomes.     

Compartmentation of enzymes in the rabbit parotid salivary gland. A study by enzyme histochemical, tissue fractionation and morphometric techniques

Synopsis Rabbit parotid gland was chosen as a suitable model tissue for studying the role of membranes in enzyme secretion by acinar cells. The study was initiated using subcellular fractionation techniques. During these experiments the effects of various tissue disruption conditions such as the medium and the duration and vigour of homogenization were explored and the results assessed by enzyme and chemical assays and both quantitatively and qualitatively by electron microscopy. A series of basic fractions was isolated and marker enzyme or chemical assays selected for each of the relevant membrane types (rough endoplasmic reticulum, Golgi apparatus, zymogen granule, plasmalemma). A parallel study was effected using enzyme histochemical methods applied to frozen sections. Interesting comparisons could then be made between histochemical and biochemical methods of enzyme demonstration. These comparisons are discussed. the basic fractions provide the material from which specimens of purified membranes of the four species can be obtained. The isolation and characterization of such purified membranes is the subject of another report.     

The symbiotic chloroplasts in the sacoglossan Elysia clarki are from several algal species

Abstract. The sacoglossan sea slug Elysia clarki feeds on siphonaceous algae, and intracellularly sequesters chloroplasts, which actively photosynthesize for 4 months. We have determined the algal source of chloroplasts in adults of E. clarki from the Florida Keys, using molecular techniques, feeding experiments, and electron microscopy. Our results clearly demonstrate that specimens of E. clarki sequester chloroplasts from four different species of algae, representing two genera: Penicillus lamourouxii, P. capitatus, Halimeda incrassata , and H. monile. In addition, chloroplasts from more than one species of algae are sequestered simultaneously in the same digestive cell.     

Co-localization of PARP-1 and lamin B in the nuclear architecture: a halo-fluorescence- and confocal-microscopy study

A functional interaction between poly(ADP-ribose) polymerase-1 (PARP-1) and lamin B has recently been proposed by nuclear fractionation, crosslinking, and immunoprecipitation experiments. Here we use fluorescence microscopy to verify and extend these findings. We analyze nuclear halo preparations by fluorescence in situ immuno staining (FISIS), which shares attributes with traditional nuclear fractionation techniques, and by confocal laser scanning microscopy (CLSM). The results agree in that a major part of the enzyme co-localizes with lamin B under physiological conditions, where PARP-1 only has basal activity. After DNA damage and the associated activation of PARP-1, and during the subsequent entry into apoptosis, dramatic changes occur: a gradual release of the enzyme from the lamina, accompanied by its accumulation in nucleoli. Our observations are in line with biochemical evidence for lamin B-PARP-1 interactions under physiological conditions and suggest ways by which these interactions are modified to support PARP-functions in damage and its fate in apoptosis.     

Imaging living cells and tissues by two-photon excitation microscopy

Two-photon excitation microscopy provides attractive advantages over confocal microscopy for three-dimensionally resolved fluorescence imaging. Since two-photon excitation occurs only at the focal point of the microscope, it inherently provides three-dimensional resolution. This localization of excitation also minimizes photobleaching and photodamage, which are the ultimate limiting factors in imaging living cells. Furthermore, no pinhole is required to attain three-dimensional discrimination, so the efficiency of fluorescence collection is increased. These advantages allow experiments on thick living samples that would not be possible with other imaging techniques. The cost and complexity of the lasers required for two-photon excitation microscopy have limited its use, but appropriate turn-key lasers have now been introduced, and their cost should decrease. Finally, the recent introduction of commercial two-photon excitation laser-scanning microscope systems allows a much larger group of researchers access to this state-of-the-art methodology.