The primary cilium, a solitary non-motile structure projecting from the centriole of mammalian cells, has been a subject of interest of anatomists since 1898. Surprisingly, the function of the primary cilium in mammalian cells is completely unknown. Virtually all of the epithelial cells of the mammalian kidney, with the exception of the intercalated cells of the collecting duct, express a single primary cilium on their apical (lumenal) surface. These structures were ignored by physiologists until recently when the mechanical properties of the primary cilia of cultured cells of renal origin were measured and it was proposed that they could serve as flow sensors. The proposal stemmed from the observation that flow rates comparable to those observed in renal tubules resulted in a deflection of the cilium of a few microns and that the stiffness of the cilium was commensurate with mechanosensing.

The primary cilia of renal tubular cells are generally about 2 - 3 μm long whereas those of cultured renal cells become much longer as the cells age and may extend 50 μm or more into the medium. MDCK cells, a cultured cell line derived from the collecting duct of the canine kidney, exhibit two cell types analogous to the principal and intercalated cells of the collecting duct. MDCK principal cells express a primary cilium that is visible by high-resolution DIC microscopy. About one week after splitting, the primary cilium of MDCK principal cells is about 8 μm long and is well suited for testing the hypothesis that the cilium serves as a mechanosensor of fluid flow.

We have discovered a new method, Fluorescent Speckle Microscopy (FSM), for analyzing the dynamic movement and turnover of macromolecular protein assemblies, such as the cytoskeleton, in living cells (Waterman-Storer et al., 1998). FSM compliments or replaces the techniques of fluorescence recovery after photobleaching or photoactivation of fluorescence for measuring protein dynamics in vivo. For FSM, cells are microinjected with a very low fraction of fluorescently labeled subunits that co-assemble with unlabeled subunits to give a structure with a fluorescent speckled appearance in diffraction-limited wide-field or confocal digital fluorescence images. At low fractions of fluorescent subunits relative to unlabeled subunits, fluorescent speckles vary randomly in intensity according to the number of fluorescent subunits within a diffraction-limited region. in time-lapse FSM image series, movement of the fluorescent speckle pattern indicates translocation of structures, while changes in speckle intensity indicate subunit turnover. We have used FSM to study microtubule and actin behavior in interphase and mitotic cells. We use kymograph analysis to quantitate the movement of speckled structures (Fig 1) and are currently developing analysis procedures to quantify subunit turnover in structures.

We have applied these methods to the study of microtubule and actin cytoskeletal dynamics in migrating vertebrate cells in culture. Interactions between the microtubule and actin cytoskeletons underlie fundamental cellular processes such as cytokinesis and cell locomotion, but are poorly understood.

High resolution fluorescent speckle microscopy (FSM) and green fluorescent protein (GFP) imaging in living cells can require image recording at low densities of fluorophores (10 or less/resolvable unit) with low light excitation to prevent photobleaching. This needs efficient optical components, a high quantum efficiency detector, and a digital image acquisition and display system for time-lapse recording of multiple channels. Recently, Shinya and Ted Inoue have described the advantages of the Yokogawa CSU-10 spinning-disk confocal scanning unit for obtaining high quality fluorescent images with brief exposures and low fluorescence bleaching. Based on their findings, we have combined the CSU-10 unit with a high sensitivity pan-chromatic CCD camera to facilitate high spatial and temporal resolution imaging of fluorescence in living cells. in addition, the high signal-to-noise in images obtained with this instrument provides the opportunity to obtain 3-D views of extraordinary resolution and image quality after iterative constrained de-convolution.

Our imaging system is constructed around a Nikon TE300 inverted microscope equipped with either a 60X or 100X Plan Apochromat objective, and standard epi-fluorescence optics for visual inspection of the specimen to locate cells for recording.

Sequence specific transcription factors are the predominant regulators of animal gene expression controlling nearly all biological processes. We are developing novel quantitative optical imaging techniques to map gene expression levels at cellular and sub-cellular resolution within an entire organism. Pregastrula Drosophila embryos have been chosen because these embryos allow high resolution 3D optical imaging since they comprise a single layer of dividing cells surrounding a yolk sac. in addition, the transcription network controlling gene expression is well characterized in early Drosophila embryos[1], and is being further dissected by a multi-laboratory collaboration, the Berkeley Collaboration in Drosophila Genomics, which encompasses this work.

Embryos at different stages of development are labeled for total DNA and specific gene products using different fluorophors and imaged in 3D with confocal microscopy (Figure 1). Intensity-based segmentation of the total DNA image[2] produces a nuclear mask which defines the nuclear boundaries, their location and the number of cells within the embryo (Figure 2). Presently, dilation of the nuclear volumes into their nearest-neighbours[3] is used to estimate the boundary of the cell (Figure 3) and superposition of these images produces a morphological mask defining each cell and its nucleus.

Autofluorescence, also known as adventitious fluorescence or background fluorescence, often poses a significant problem in many applications of fluorescence microscopy. It contributes to unwanted noise and can overwhelm the desired signal. Particularly difficult samples to image include many pathology specimens that have been processed using crosslinking fixatives (typically formaldehyde). This procedure dramatically increase the autofluorescence level, leading to bright, broad spectrum emissions, particularly from connective tissue components. Unprocessed plant tissue and neuronal tissue also have extremely high levels of endogenous autofluorescence that can make many convenient labeling strategies, including most green fluorescent protein (GFP) labels, extremely problematic. Various solutions have been proposed for the reduction or elimination of autofluorescence. These include using narrow bandpass emission filters to try to isolate the desired fluorescence signal, the use of labels that can be excited at wavelengths that are much less likely to induce autofluorescence (moving the excitation towards the NIR is effective), and post-processing aldehyde-fixed samples with such reagents as sodium borohydride or toluidine blue to chemically suppress the autofluorescence signal. However, in many cases, these approaches are either infeasible or ineffective. Spectral imaging, that is, the acquisition of a high-resolution optical spectrum at every pixel of an image, offers another approach to elimination of the contribution of autofluorescence. This has recently become possible due to the development of a number of technologies that allow the collection of spectral datasets from fluorescently labeled samples using fluorescence microscopy. Such technologies include liquid crystal tunable filters (LCTFs) and Fourier transform imaging spectrometers, both of which are now commercially available.

A high performance hyperspectral imager with high light throughput suitable for microscopy and analytical imaging was built and tested. The imager utilizes phenomenon of optical activity. The new technique provides a continuous spectral range of several hundreds of nanometers starting in deep UV. Similar spectral range starting in the near IR is also achievable.

A performance of a low cost implementation of the new technology is presented. The imager has a form of a microscope adaptor, which is inserted between the microscope and a low-cost 8-bit CCD camera. The resulting instrument is simple, robust, and highly compact. The imager module is placed in-line to the microscope imaging system and does not introduce observable image aberrations. Advantageously, the imager is transparent to conventional imaging operations, thus with the imager in-place there is no need for reconfiguration of the microscope to switch between conventional and hyperspectral video/digital imaging modes.

The presented spectral imager answers the need for a practical, sensitive, compact, and affordable imaging spectrometer. The instrument is well suited for a broad range of applications requiring rapid parallel acquisition of highly resolved concurrent spatial and spectral information such as high throughput screening, biochip analysis, remote sensing or nondestructive semiconductor testing.

Confocal Laser Scanning Microscopy (CLSM) is being used to visualize folliculogenesis and presumed apoptotic events in whole neonatal mouse/rat ovaries. Our laboratory has previously demonstrated that apoptosis can be visualized in 8-9 day whole mouse embryos, 12 day fetal mouse eyes or 12-15 fetal rat limbs stained with the fluorescent lysosomal stain, LysoTracker Red (LT). The observed LT staining has been correlated with Nile blue staining (lysosomes and phagocytosis), TUNEL staining (DNA breaks) and apoptotic tissue morphology in rat and mouse developmental systems. This increased LT staining intensity appeared to be associated with acidic tissue, lysosomes, phagocytosis and dying cells. Here we describe recent progress using LT to evaluate the apoptotic process in whole ovaries. We are currently optimizing sample preparation and confocal machine operation to improve the image quality. to increase depth of visualization, ovaries derived from 10-45 day old mice/rats are fixed with an aldehyde and then made transparent by MEOH dehydration followed by benzyl alcohol/benzyl aldehyde (BABB) clearing. Such whole ovaries or tissue sections are viewed by CLSM using 568-wavelength laser light to obtain images of oocytes and follicles. Follicles showing gross morphologic changes typical of atresia were also characterized by intense LT staining of granulosa cells. This increased LT staining intensity appeared to be associated with acidic tissue and dying cells contained within the follicle.

Fluorescent recovery from photobleaching coupled with confocal microscopy was explored as a potential high-resolution method of imaging the distribution of enzyme activity in single living cardiac myocytes without relying on steady state measurements of fluorescence. On a fundamental level, much remains to be determined regarding how local conditions within a cell affect metabolism. Many studies have suggested that energy metabolism in muscle cells cannot be accurately described assuming a homogenous system of enzymatic reactions [1,2]. The autofluorescence of NADH has been used in many studies as a quantitative assay of mitochondrial energy metabolism [3,4], but studies of steady state fluorescence cannot distinguish between changes in energy production or utilization.

In this study conditions were created where the fluorescent recovery of a probe would be solely dependent on cellular enzymatic activity (Enzyme Dependent Fluorescence Recovery after Photobleaching (ED-FRAP)). Experiments examining the inherent fluorescence of NADH (351nm excitation, 450 nm emission) were conducted on small droplets (less than 325 μm diameter) containing NADH alone, in droplets containing an enzyme system capable of synthesis of NADH (Figure 1A) and on isolated rabbit cardiac myocytes (Figure 1D). Photobleaching of the entire cell or droplet eliminated diffusion or bulk transport of NADH from non-bleached regions. Droplets containing NADH alone did not recover, while droplets containing enzyme were shown to recover exponentially (Figure 1B) with a rate constant of fluorescent recovery (kf) that was proportional to enzyme concentration (Figure 1C).

Spectral imaging is a relatively new technique that provides images of a scene at multiple wavelengths and can generate precise optical spectra at every pixel. Mathematical approaches may then be used to extract the maximum information from the spectral image. Spectral imaging is routinely used in “remote sensing”, that is, the analysis of distant landscapes and structures from airplanes or satellites. Minor differences in spectra can be used to detect different crops, or mineral deposits, for example. Closer in, spectral imaging has uses in industrial process control, detection of otherwise invisible bruising in fruit, vascular integrity in transplanted organs, and so on. Finally, spectral imaging has newly been adapted for easy use in microscopy, with applications in surgical pathology, multicolor fluorescence and immunohistochemistry, and in DNA expression arrays, among others. A variety of technologies can be used to perform imaging spectroscopy, including Fourier transform interferometry, tunable filters, line-scanning prism or gratings-based devices, and others based on polarization effects. Recently, CRI has developed a novel approach for brightfield microscopy which uses a spectrally agile light source. The latter has a number of advantages over previous techniques.

For live-cell imaging, two-photon excitation microscopy (TPEM) is proving to be a significant technological advancement. The unique features offered by TPEM are the ability to image thick sections, excellent optical sectioning capabilities, low damage to living cells, and less out of focus fluorescence and out of focus photobleaching. of these features, the most useful for the biological microscopist, is optical sectioning. Optical sectioning is an intrinsic property of the two-photon process, whereby, two infrared (IR) photons are absorbed quickly to excite a single UV/blue transition. The probability for exciting a two photon transition is proportional to the instantaneous excitation intensity squared. Therefore, for a focused laser beam, only light at the focal point of the excitation beam excites a fluorescent transition. Thus, the need for confocal apertures and time consuming deconvolution algorithms are, for the most part, eliminated.

We have continued to develop and enhance our ability to perform high-speed, two-photon excitation fluorescence microscopy. in 1998, we successfully deployed a prototype, video-rate twophoton laser scanning system (30 frames/sec or faster at reduced scan width) developed with support from Nikon Corporation. That system was built upon a Nikon RCM 8000 confocal microscope.

The muscle nicotinic acetylcholine receptor channel (AChR) is a cylindrical allosteric membrane protein (∼120 x 60 Å Fig. 1) that adopts alternative quaternary conformations (“open” and “closed”) with different functional properties (ion-conducting and ion-impermeable, respectively). We have characterized, residue-by-residue, the dynamics of the conformational change associated with gating using the framework of linear free energy relationships (LFER). The sequence of molecular events that underlies the closed-to-open gating transition was inferred from kinetic measurements of the receptor at the single molecule level.

Specific regions of the AChR were perturbed using site-directed mutagenesis, changes in the membrane potential, or different agonists. Single-channel currents were recorded from cell-attached patches (Fig. 2). For the gain-of-function mutations, choline was used as the agonist because of its low efficacy. The opening rate constant was determined at a saturating concentration of agonist (for choline, 20 mM) in order to isolate gating from binding steps. to avoid bias introduced by fast channel blockade, the closing rate constant was measured at a low concentration (for choline, 200 μM). The diliganded channel opening (β) and closing (α) rate constants were estimated using the QuB suite of kinetic analysis programs. in general, a plot of the log rate constant vs. log equilibrium constant was linear.

RNA molecules must fold into specific three-dimensional shapes to perform their structural and catalytic functions. Unlike proteins, RNAs secondary structural features are usually stable enough to form by themselves in solution. The reason is that in RNA, the stabilization energy gained from the formation of secondary structure is substantially larger than the energies involved in tertiary interactions. As a result, the formation of tertiary interactions is expected to alter only slightly the pre-existing secondary structural contacts. Moreover, secondary structure prediction is robust and can be made without taking into consideration tertiary folding. However, bulk studies of the energetics and kinetics of their secondary and tertiary folding are often frustrated by the presence of multiple species and multiple folding pathways in solution. These problems are circumvented in single-molecule studies in which the folding/unfolding trajectories of the individual molecules can be followed. The T. thermophila group I intron ribozyme is organized into several domains whose mechanical unfolding can be investigated independently, and whose tertiary contacts are stabilized by numerous Mg++ ions.

We have begun characterization of the ribozyme by analysis of the P5abc domain because:

Direct observation of single molecules and single molecular events inside living cells could dramatically improve our understanding of basic cellular processes (e.g., signal transduction and gene transcription) as well as improving our knowledge on the intracellular transport and fate of therapeutic agents (e.g., antisense RNA and gene therapy vectors). However, a key remaining question is whether single-molecule methodologies could be developed to study complex molecular processes in living cells. in contrast to clean and well-controlled conditions in-vitro, the intracellular environment contains a broad collection of biological macromolecules and fluorescent materials such as porphyrins and flavins. This complex environment is known to produce intense background fluorescence, commonly known as autofluorescence. Thus, a major concern is that this intracellular background could overwhelm the relatively weak signals arising from single molecules.

We demonstrate that fluorescence detection of single molecules can be achieved by tightly focusing a laser beam into a living cell (see Figure 1). The observed background fluorescence is indeed higher than that in-vitro (e.g., pure biological buffer), but this background is continuous and stable, and does not significantly interfere with the measurement of single-molecule photon bursts. Specifically, we report single-molecule results on three types of extrinsic fluorescent molecules in cultured human HeLa cells (a cervical cancer cell line).

Biological membranes are not just a passive component of the cells, they actively support their functioning as the imbedded protein machineries carry out a wide range of crucial biochemical processes. Although studies in vivo are becoming more and more accessible to single-molecule optical microscopy, in vitro studies are still very much informative for the understanding of individual biological machineries. One of the major goals is to define the minimum number of components of a machinery that is necessary for a particular step, thereby allowing detailed studies of the mechanism of action. Reconstitution of a transmembrane protein system in artificial membranes (liposomes) is the main method for such a strategy, which thus may provide the option to investigate the functioning of transport proteins, ion channels, fusion machineries, and signal transducers in relation to their environment.

We present a novel procedure in order to reconstitute transmembrane proteins in chemically well-defined and close-to-native lipid bilayers, providing an in vitro system for single-molecule optical microscopy. Furthermore, an application of this technique is shown in the case of a single-molecule study of protein-protein and protein-lipid interactions for the light-induced proton pump bacteriorhodopsin.

In this study, Giant Unilamellar Vesicles (GUV), 10-100 μm sized, are used as lipid bilayer models for several reasons.

The challenge of the post-genomic era is functional genomics, i.e. understanding how the genome is expressed to produce myriad cell phenotypes. A phenotype is the result of selective expression of the genome in response to the microenvironment. to use genomic information to understand the biology of complex organisms, the biological responses and signaling pathways in cells need to be studied in context, i.e. within the proper tissue structure. Nonetheless, most current biology is conducted using cells cultured in monolayers on traditional tissue culture plastic. These non-physiological models impede the ability to predict in vivo responses from model systems. The same cells cultured in 2-dimensions (i.e. monolayers) vs. 3-dimensions (e.g. multicellular tumor spheroids) differ in their responses to external stimuli such as ionizing radiation, viral infection, cytotoxic drugs, and chemotherapeutic agents. Our laboratory has led the way in promoting and developing 3-dimensional cell culture models that more accurately reflect in vivo biology, beginning with the establishment 15 years ago of physiologically functional reconstituted mammary acini in culture.

Quantitation of spatial and temporal concurrent behavior of multiple markers in these 3-dimensional cell cultures is hampered by the currently routine mode of sequential image acquisition, measurement and analysis of specific targets. This precludes the detailed analysis of multi-dimensional, time sequence responses and fails to relate features in novel and meaningful ways that will further our understanding of basic biology. Thus new methodology was needed for high-throughput, dynamic evaluations of large numbers of live multicellular specimens. Rather than using confocal microscopy methods, which interfere with live cell systems due to photo-damage, optical sectioning of the 3-dimensional structures is achieved with structured light illumination using the Wilson grating in an implementation described by Lanni.

Post-Golgi sorting of different classes of newly synthesized proteins and lipids is central to the generation and maintenance of cellular polarity. to directly visualize the dynamics and location of apical/basolateral sorting and trafficking we used fast time-lapse multicolor video microscopy in living cells. Specifically, green fluorescent protein color variants (cyan, CFP; yellow, YFP) of apical cargo (GPI-anchored) and basolateral cargo (vesicular stomatitis virus glycoprotein, VSVG) were generated; see FIG 1. Fast dual color fluorescence video microscopy allowed visualization with high temporal and spatial resolution. Our studies revealed that apical and basolateral cargo progressively segregated into large domains in Golgi/TGN structures, excluded resident proteins, and exited in separate transport containers. These carries remained distinct and did not merge with endocytic structures en route to the plasma membrane. Interestingly, our data suggest that the primary sorting occurs by lateral segregation in the Golgi, prior to budding (FIG 2). Further characterization of morphological differences of apical versus basolateral transport carriers was achieved using a specialized microscopy technique called total internal reflection (TIR) microscopy. with this approach only the bottom of the cell (<100 nm) was illuminated by an exponentially decaying evanescent “wave” of light. A series of images, taken at ∼1 second intervals, shows a bright “flash” of fluorescence when the vesicle fuse with the plasma membrane and the fluorophore diffuses into the plasma membrane (FIG 3).

We present a new method of fluorescence imaging, which yields an unprecedented nm scale vertical resolution. The method uses the unique spectral signature of the fluorescent emission intensity above a reflecting surface to determine vertical position unambiguously. Emission from several heights could be resolved by deconvoluting the spectrum, so that three dimensional imaging is possible. The related technique of standing wave microscopy uses the spatial intensity variation for increased resolution. Applications of this technique include intracellular imaging and screening for specific bacteria, virus or proteins, where discrimination between raised fluorescently labeled specifically bound markers from non-specific binding is crucial.

The emission spectrum of fluorescent markers is modified in the presence of a reflecting surface. Within the wavelength range of the fluorescent emission, the selfinterference of the emitted photons from the direct and reflected path results in enhanced or suppressed emission (constructive or destructive interference) depending on the height and wavelength.

Microscopy is an essential tool for developing strategies to use genetic therapy in the treatment of diseases. Negative staining (fig. 1) and cryo-electron microscopy are critical in understanding the structure of native and hybrid vectors to be used as transfer agents. Enzyme cytochemistry is widely used for the detection of markers that aid in determining the rate of gene transfer to cells and tissues. Immunocytochemistry is necessary to identify new gene products. Light, confocal and electron microscopy are used to evaluate pathogenesis, inflammation and cellular changes. For much of the past decade, we have been working to identify the specific gene and cell structure (chloride channel) that is compromised in Cystic Fibrosis patients. Subsequently, appropriate vectors had to be developed for treatment. A significant amount of time and effort has been expended to identify effective viral and other vectors to be used in the transfer of the normal gene construct.

In order to facilitate experimentation, we have developed a cell culture system utilizing normal and cystic fibrosis airway epithelia. These cultures are maintained at an air interface and the cells differentiate into the same types found in vivo.

The formation of memory and the process of learning are believed to be regulated, at least in part, by the expression, distribution, and redistribution of glutamate receptors. The expression of these receptors at synaptic sites has a major impact on the strength of synaptic connections, and the AMPA receptor subunit GluR1 appears to play a key role within this system. Increasing evidence suggests that previously silent synapses become activated through rapid AMPA receptor insertion upon appropriate stimulation, and thus the trafficking of this receptor subunit from cellular stores to the synapse is of prime interest.

We are using a transgenic mouse expressing a GFP-tagged form of GluR1 (GluR1-GFP) in order to study the dynamic changes in GluR1 expression and distribution occurring during brain development and following induction of long-term potentiation (LTP). The fusion protein is transcribed under the control of the CaMKIIα promoter, which restricts the localization to forebrain neurons and is coupled to a tetrepressible system, thus allowing for the control of transcription with doxycycline. The anatomical distribution of GluR1-GFP on the light level is consistent with that of wild-type GluR1 (Fig. 1).

We are combining molecular biology with quantitative 3D image analysis on the light and electron microscopic level. The highly fluorescent polar tracer Alexa Fluor 568 (Molecular Probes Inc.) is being used to fill GluR1-GFP expressing pyramidal neurons in tissue slices fixed with aldehydes

Cooling significantly affects cellular ultrastructure [1], as well as structural and functional state of histohematic barrier [2]. The aim of the given work was to study ultrastructural mechanisms of the permeability of brain cortex vascular endothelium under the effect of rhythmic hypothermia. Experiments were conducted on 180-220 g white males rats. Cooling of caudal part of animals was conducted in an automatic regimen by an ice water with 0.1 Hz frequency during 40 and 80 min. Experimental animals were narcotized by intraperitoneal injection of thiopenthal sodium and sodium hydroxybutyrate mixture in respect of 30mg/kg, 100 mg/kg of mass, correspondingly. Material from parietal lobe of brain cortex for electron-microscopic investigations was taken immediately after the effect finishing. Rectal temperature, which made 36-35C, was measured during the experiment. For electron microscopic investigations the samples were fixed by immerging into 4% glutar aldehyde on a phosphate buffer and were additionally fixed by 1% osmium fixative on a phosphate buffer. After dehydration in ethanol, samples were placed into the mixture of epoxy resins Epon-Araldit (Fluka, Sweden). Colloid carbon was used as a tracer for the estimation of permeability of brain capillary endothelium. with this aim 3-5 ml of 10% colloid carbon solution, prepared on 0,85% NaCl solution, were injected into a tail vein of the animals immediately after their decapitation. Preliminary estimation of the material quality was done on semi-fine tissue sections after the staining by toluidine blue.