Correlated fluorescence and 3D electron microscopy with high sensitivity and spatial precision

Correlative electron and fluorescence microscopy has the potential to elucidate the ultrastructural details of dynamic and rare cellular events, but has been limited by low precision and sensitivity. Here we present a method for direct mapping of signals originating from ～20 fluorescent protein molecules to 3D electron tomograms with a precision of less than 100 nm. We demonstrate that this method can be used to identify individual HIV particles bound to mammalian cell surfaces. We also apply the method to image microtubule end structures bound to mal3p in fission yeast, and demonstrate that growing microtubule plus-ends are flared in vivo. We localize Rvs167 to endocytic sites in budding yeast, and show that scission takes place halfway through a 10-s time period during which amphiphysins are bound to the vesicle neck. This new technique opens the door for direct correlation of fluorescence and electron microscopy to visualize cellular processes at the ultrastructural scale.     

On the involvement of electron transfer reactions in the fluorescence decay kinetics heterogeneity of proteins

Time-resolved fluorescence study of single tryptophan-containing proteins, nuclease, ribonuclease T1, protein G, glucagon, and mastoparan, has been carried out. Three different methods were used for the analysis of fluorescence decays: the iterative reconvolution method, as reviewed and developed in our laboratory, the maximum entropy method, and the recent method that we called "energy transfer" method. All the proteins show heterogeneous fluorescence kinetics (multiexponential decay). The origin of this heterogeneity is interpreted in terms of current theories of electron transfer process, which treat the electron transfer process as a radiationless transition. The theoretical electron transfer rate was calculated assuming the peptide bond carbonyl as the acceptor site. The good agreement between experimental and theoretical electron-transfer rates leads us to suggest that the electron-transfer process is the principal quenching mechanism of Trp fluorescence in proteins, resulting in heterogeneous fluorescence kinetics. Furthermore, the origin of apparent homogeneous fluorescence kinetics (monoexponential decay) in some proteins also can be explained on the basis of electron-transfer mechanism.     

Calcium-mediated fusion to produce ultra large osmotically active mitochondrial inner membranes of controlled protein density

We have developed a new membrane fusion method which produces ultra large, spherical mitochondrial inner membranes attached to microscope slides. The fused inner membranes measured up to 200 microns in diameter. The technique fuses native inner membranes as well as inner membranes in which the protein density has been varied by enriching with exogenous phospholipid. The fusion process is accomplished through the use of calcium, low pH and elevated temperature. Characterization of the fused membranes was carried out using phase, fluorescence, and freeze-fracture electron microscopy. These ultra large, fused inner membranes were found to model the inner membranes from which they were formed. The fused inner membranes were found to be osmotically active and are large enough for measuring the lateral diffusion of membrane components by fluorescence recovery after photobleaching and are large enough for microelectrode impalement.     

Serial block face scanning electron microscopy—the future of cell ultrastructure imaging

One of the major drawbacks in transmission electron microscopy has been the production of three-dimensional views of cells and tissues. Currently, there is no one suitable 3D microscopy technique that answers all questions and serial block face scanning electron microscopy (SEM) fills the gap between 3D imaging using high-end fluorescence microscopy and the high resolution offered by electron tomography. In this review, we discuss the potential of the serial block face SEM technique for studying the three-dimensional organisation of animal, plant and microbial cells.     

Visualizing Endocytotic Pathways at Transmission Electron Microscopy via Diaminobenzidine Photo-Oxidation by a Fluorescent Cell-Membrane Dye

The endocytotic pathway involves a complex, dynamic and interacting system of intracellular compartments. PKH26 is a fluorescent dye specific for long-lasting cell membrane labelling which has been successfully used for investigating cell internalization processes, at either flow cytometry or fluorescence microscopy. In the present work, diaminobenzidine photo-oxidation was tested as a procedure to detect PKH26 dye at transmission electron microscopy. Our results demonstrated that DAB photo-oxidation is a suitable technique to specifically visualise this fluorescent dye at the ultrastructural level: the distribution of the granular dark reaction product perfectly matches the pattern of the fluorescence staining, and the electron density of the fine precipitates makes the signal evident and precisely detectable on the different subcellular compartments involved in the plasma membrane internalization routes.Key words: Endocytosis, PKH26 dye, diaminobenzidine photo-oxidation, transmission electron microscopy     

Quantum dot based immunosensor using 3D circular microchannels fabricated in PDMS

Microchannel is basic functional component of microfluidic chip and every step-forward of its construction technique has been receiving concern all over the world. The present work describes a novel, rapid and simple fabrication technique for building 3D microchannels in poly(dimethyl siloxane) (PDMS) elastomer. These microchannels were used for rapid detection of antigens (E. coli) by quantum dot (QD) based approach. Luminescent QD (CdTe) were synthesized by aqueous method and characterized using high resolution transmission electron microscopy (HRTEM), fluorescence spectroscopy and X-ray diffraction (XRD). The QDs were functionalized with anti-E. coli antibodies for immuno-detection. The reported process allowed easier and faster method of fabrication of circular 3D micochannels and demonstrated their potential use in an immuno-biosensor device.     

Studies of the distribution of proteins bound to CNBr-activated Sepharose 6B at the electron-microscopic level.

Proteins were covalently attached to Sepharose by the CNBr method. Their distribution across the carrier beads was studied at the electron microscopic level. The approach has been to ferritinstain and to section the gel beads. Ferritin was either coupled directly to the polysaccharide backbone of the carrier or conjugated with pure rabbit anti-aminopeptidase in order to visualize covalently bound leucine aminopeptidase by the immunferritin technique. The results corroborate earlier fluorescence microscopic findings of a uniform protein distribution, provided that a number of conditions are fulfilled.     

Possibilities and limitations of the smearing technique for cellular studies in compact tissues: a transmission electron microscopic analysis of liver smears

During the last decade a sophisticated biophysical technique called fluorescence recovery after photobleaching (FRAP) has become available for the measurement of lateral diffusion constants of lipids and proteins in the cell membrane. The information obtainable by this method is of great importance; however, the applicability of this method is seriously hindered by the fact that it has been elaborated mostly for isolated, individual cells. On the other hand, the use of freshly prepared cells from compact tissues for such studies is highly desirable. Therefore, a special smearing method was devised (using liver cells) for this purpose. The present paper describes (i) the method of standardization of the smearing technique, (ii) the ultrastructural features of the liver cells when studying the liver smears by means of transmission electron microscopy. The possibilities and limitations of this method are discussed. According to the observations, under well-defined conditions the structural integrity of hepatocytes is maintained in the liver smears to such an extent that they are suitable for FRAP experiments.     

Gas exchange measurements, what can they tell us about the underlying limitations to photosynthesis? Procedures and sources of error

The principles, equipment and procedures for measuring leaf and canopy gas exchange have been described previously as has chlorophyll fluorescence. Simultaneous measurement of the responses of leaf gas exchange and modulated chlorophyll fluorescence to light and CO2 concentration now provide a means to determine a wide range of key biochemical and biophysical limitations on photo synthesis in vivo. Here the mathematical frameworks and practical procedures for determining these parameters in vivo are consolidated. Leaf CO2 uptake (A) versus intercellular CO2 concentration (Ci) curves may now be routinely obtained from commercial gas exchange systems. The potential pitfalls, and means to avoid these, are examined. Calculation of in vivo maximum rates of ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) carboxylation (Vc,max), electron transport driving regeneration of RuBP (Jmax), and triose-phosphate utilization (VTPU) are explained; these three parameters are now widely assumed to represent the major limitations to light-saturated photosynthesis. Precision in determining these in intact leaves is improved by the simultaneous measurement of electron transport via modulated chlorophyll fluorescence. The A/Ci response also provides a simple practical method for quantifying the limitation that stomata impose on CO2 assimilation. Determining the rate of photorespiratory release of oxygen (Rl) has previously only been possible by isotopic methods, now, by combining gas exchange and fluorescence measurements, Rl may be determined simply and routinely in the field. The physical diffusion of CO2 from the intercellular air space to the site of Rubisco in C3 leaves has long been suspected of being a limitation on photosynthesis, but it has commonly been ignored because of the lack of a practical method for its determination. Again combining gas exchange and fluorescence provides a means to determine mesophyll conductance. This method is described and provides insights into the magnitude and basis of this limitation.     

The fluorescence lidar technique for the remote sensing of photoautotrophic biodeteriogens in the outdoor cultural heritage: A decade of in situ experiments

Fluorescence lidar is a non-invasive, remote sensing technique that makes it possible to extend the application of the laser-induced fluorescence technique to the outdoor environment, where uncontrolled external conditions must be met. Although initially developed for the investigation of marine environment and vegetation, in the past decade this technique has been successfully applied to the field of the cultural heritage. Among other applications, the detection and characterisation of photoautotrophic biodeteriogens has become very promising: the method is based on the detection of chlorophyll a fluorescence, while fluorescent accessory pigments can be exploited for a rough classification of the biodeteriogens present on the surface. Early experiments on monuments date back to the mid 1990s, when fluorescence lidar point measurements were conducted on the Cathedral and Baptistery of Parma, Italy. Subsequently, the technique has taken further advantage of the introduction of imaging capabilities in lidar instrumentation and this has led to the acquisition of hyperspectral fluorescence maps over extended areas of several monuments from distances as great as 80 m. Here, we present the main achievements obtained in the outdoor cultural heritage so far and the latest developments in the technique.     

Fluorescent properties of c-type cytochromes reveal their potential role as an extracytoplasmic electron sink in Geobacter sulfurreducens

A novel fluorescence technique for monitoring the redox status of c-type cytochromes in Geobacter sulfurreducens was developed in order to evaluate the capacity of these extracytoplasmic cytochromes to store electrons during periods in which an external electron acceptor is not available. When intact cells in which the cytochromes were in a reduced state were excited at a wavelength of 350 nm, they fluoresced with maxima at 402 and 437 nm. Oxidation of the cytochromes resulted in a loss of fluorescence. This method was much more sensitive than the traditional approach of detecting c-type cytochromes via visible light absorbance. Furthermore, fluorescence of reduced cytochromes in individual cells could be detected via fluorescence microscopy, and the cytochromes in a G. sulfurreducens biofilm, remotely excited with an optical fibre, could be detected at distances as far as 5 cm. Fluorescence analysis of cytochrome oxidation and reduction of the external electron acceptor, anthraquinone-2,6-disulfonate, suggested that the extracytoplasmic cytochromes of G. sulfurreducens could store approximately 10(7) electrons per cell. Independent analysis of the haem content of the cells determined from analysis of incorporation of (55)Fe into cytochromes provided a similar estimate of cytochrome electron-storage capacity. This electron-storage capacity could, in the absence of an external electron acceptor, permit continued electron transfer across the inner membrane sufficient to supply the maintenance energy requirements for G. sulfurreducens for up to 8 min or enough proton motive force to power flagella motors for G. sulfurreducens motility. The fluorescence approach described here provides a sensitive method for evaluating the redox status of Geobacter species in culture and/or its environments. Furthermore, these results suggest that the periplasmic and outer-membrane cytochromes of Geobacter species act as capacitors, allowing continued electron transport, and thus viability and motility, for Geobacter species as they move between heterogeneously dispersed Fe(III) oxides during growth in the subsurface.     

Single molecule FRET for the study on structural dynamics of biomolecules

Single molecule fluorescence resonance energy transfer (FRET) is the technique that has been developed by combining FRET measurement and single molecule fluorescence imaging. This technique allows us to measure the dynamic changes of the interaction and structures of biomolecules. In this study, the validity of the method was tested using fluorescence dyes on double stranded DNA molecules as a rigid spacer. FRET signals from double stranded DNA molecules were stable and their average FRET values provided the distance between the donor and acceptor in agreement with B-DNA type helix model. Next, the single molecule FRET method was applied to the studies on the dynamic structure of Ras, a signaling protein. The data showed that Ras has multiple conformational states and undergoes transition between them. This study on the dynamic conformation of Ras provided a clue for understanding the molecular mechanism of cell signaling switches.     

Stimulation of microsecond-delayed fluorescence from spinach chloroplasts by uncouplers and by phosphorylation

Delayed fluorescence, as measured with a laser phosphoroscope, is stimulated not inhibited by uncouplers during the first 100 μs after the light is turned off. This is true only wen uncouplers cause an increase in the rate of electron transport. When ADP and P_i cause an increase in the electron transport rate, microsecond-delayed fluorescence is also increased. Indeed, there is a complex quantitative relationship between the rate of electron transport and the initial intensity of delayed fluorescence under a wide range of conditions.

Uncouplers or ADP and P_i also increase the rate of decay of delayed fluorescence so that after about 150 μs they become inhibitory, as already reported by many authors.

Microsecond-delayed fluorescence continues to rise with rising light intensities long after the rate of reduction of exogenous acceptor is light-saturated.

These observations suggest a correlation of the rate of electron transport both with the intensity of the 5–100 μs-delayed fluorescence and with the rate of decay in the intensity of delayed fluorescence. The data imply that the decrease in intensity of millisecond-delayed fluorescence which has often been noted with uncouplers is probably not due to the elimination of a membrane potential. It seems more likely that the decrease in millisecond-delayed fluorescence is a reflection of the rate of disappearance of some other electron transport-generated condition, a condition which is uncoupler-insensitive. Certainly stimulations of microsecond-delayed fluorescence by electron transport which has been uncoupled by gramicidin suggest that ion gradients are not an essential component of the conditions responsible for delayed fluorescence.     

Fluorescence polarization: analysis of carbohydrate-protein interaction.

Fluorescence polarization has been widely used for the studies on the molecular motion in solution and has been applied to immunoassays for proteins, therapeutic drug monitoring in clinical pharmacy, and assays for environmentally toxic compounds. Because fluorescence polarization is most readily applicable to the kinetic analysis of the binding reaction between a substance having small molecular mass and a receptor molecule, this method is easily applied to the analysis of carbohydrate-lectin binding. In this tutorial Thematic Review, we briefly introduce the principles of fluorescence polarization and some applications of fluorescence polarization technique to glycobiology.     

Binding of wheat germ agglutinin in the matrix of rat tracheal cartilage

Summary The binding of wheat germ agglutinin (WGA) to the extracellular matrix of rat tracheal cartilage was studied at both the light and electron microscopic levels. The detection of binding sites was accomplished by a postembedment method using the direct fluorescence technique for light microscopy and the avidin—biotin bridging system for electron microscopy. Distinct fluorescence was observed in the pericellular region of chondrocytes, and this fluorescence was completely removed after treatment with 4 M guanidine hydrochloride. By electron microscopy, the reaction products as found in the pericellular region were not observed in the interterritorial collagenous matrix, confirming a similar distribution as found by fluorescence microscopy. These results show that WGA-binding sites are present in pericellular matrical substances, which are known to be rich in proteoglycan and glycosaminoglycan complexes and which exhibit similar staining with antibodies to proteoglycans or with cationic dyes. As WGA binds toN-acetyl-glucosamine andN-acetyl-neuraminic acid residues, the pericellular matrix of rat tracheal cartilage appears to consist of proteoglycan having a high concentration of these saccharides.     

Enumerating viruses by using fluorescence and the nature of the nonviral background fraction

Bulk fluorescence measurements could be a faster and cheaper way of enumerating viruses than epifluorescence microscopy, flow cytometry, or transmission electron microscopy (TEM). However, since viruses are not imaged, the background fluorescence compromises the signal, and we know little about its nature. In this paper the size ranges of nucleotides that fluoresce in the presence of SYBR gold were determined for wastewater and a range of freshwater samples using a differential filtration method. Fluorescence excitation-emission matrices (FEEMs) showed that >70% of the SYBR fluorescence was in the <10-nm size fraction (background) and was not associated with intact viruses. This was confirmed using TEM. The use of FEEMs to develop a fluorescence-based method for counting viruses is an approach that is fundamentally different from the epifluorescence microscopy technique used for enumerating viruses. This high fluorescence background is currently overlooked, yet it has had a most pervasive influence on the development of a simple fluorescence-based method for quantifying viral abundance in water.     

有机荧光团及荧光标记细胞的阴极荧光成像研究

目的 阴极荧光（CL）成像是一种以电子束为激发源的高分辨荧光成像技术,但生物材料对电子束的敏感性限制了CL技术在生命科学中的广泛应用。为了研究和发展CL技术在生物样品中的应用,本文旨在通过探究电子辐照引起碳基材料的结构损伤、有机基团的降解及荧光猝灭等问题,深入理解电子源对有机荧光团的激发特性。方法 本研究应用扫描电镜（SEM）和阴极荧光谱仪系统（SEM-CL）,研究电子源对有机荧光团及荧光探针标记细胞的激发特性,观测了有机物的CL信号的发射特性、强度衰减、成像方式及特点。结果 实验结果显示,在低能量（2.5～5 keV）和低束流（～10 pA）电子辐照下,有机荧光微珠发射出较强的荧光,CL像分辨率达到～30 nm。荧光微珠经过12 min辐照,信号强度衰减了25%,CL像仍保持了可接受的发光强度和足够的信噪比。此外,还获得了从细胞表面到内部一定深度内,荧光标记的亚细胞结构信息。结论 在SEM-CL系统中,可以同时获得由电子束激发产生的电子像和CL像,实现阴极荧光与电子显微镜关联（CCLEM）成像。本实验的研究结果为CCLEM技术应用于生物结构研究提供了数据及技术支持。     

Technique for cultivation of transitional epithelium from mammalian urinary bladder.

A technique for initiating cultures of epithelial (urothelial) cells from mammalian urinary bladder has been described. Urothelial cells obtained by this method have been used to support replication of viruses and as controls for immunological, biochemical, chromosome, and electron microscopy studies. Both light and electron microscopic studies of cultured cells suggest that they are epithelial and not a mixed culture.     

In vivo measurement of pyridine nucleotide fluorescence from cat brain cortex.

A modification of the methods is described which makes it possible to measure pyridine nucleotide fluorescence from the brain cortex in vivo without interference from movement and hemodynamic artifacts. Movement artifacts were eliminated by the use of a window technique. Fluorescence changes due to changes in hemoglobin oxygenation have been eliminated by measuring fluorescence at an isobestic wavelength of the hemoglobin-oxyhemoglobin reaction. The interference due to changes in red blood cell concentration has been studied by simultaneous measurements of fluorescence and ultraviolet reflection. Hemodilution revealed a linear relationship between the fluorescence from the pyridine nucleotide and reflected ultraviolet light. The ratio between the light absorption changes was approximately unity under the particular optical geometry employed in this study. This method has been used to measure fluorescence changes produced by nitrogen anoxia. The technique is discussed in relation to previous methods and the effects of anoxia are compared to previous findings.     

Dual-color fluorescence cross-correlation spectroscopy for monitoring the kinetics of enzyme-catalyzed reactions

Dual-color fluorescence correlation spectroscopy is a biophysical technique that enables precise and sensitive analyzes of molecular interactions. It is unique in its ability to analyze reactions in real time at nanomolar substrate concentrations and below, especially when applied to the monitoring of enzyme-catalyzed reactions. Furthermore, it offers a wide range of accessible reactions, restricted only by the prerequisite that a chemical bond or a physical interaction between two spectrally distinguishable fluorophores is established or broken. Recently, the optical setup of dual-color fluorescence correlation spectroscopy has been extended toward two-photon excitation, resulting in several advantages compared with standard excitation, such as lower fluorescence background, an even larger spectrum of potential fluorescence dyes to be used, as well as a more stable and simplified optical setup. So far, the method has been successfully employed to analyze the kinetics of nucleic acid and peptide modifications catalyzed by nucleases, polymerases, and proteases.