Publications

Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100-to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diame-ter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman et al., eLife 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.

Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).

We present here a novel multi-parametric approach for the characterization of multiple cellular features, using images acquiredby high-throughput and high-definition light microscopy. We specifically used this approach for deep and unbiased analysis of the effects of a drug library on five cultured cell lines. The presented method enables the acquisition and analysis of millions of images, of treated and control cells, followed by an automated identification of drugs inducing strong responses, evaluating the median effect concentrations and those cellular properties that are most highly affected by the drug. The tools described here provide standardized quantification of multiple attributes for systems level dissection of complex functions in normal and diseased cells, using multiple perturbations. Such analysis of cells, derived from pathological samples, may help in the diagnosis and follow-up of treatment in patients.

We present here a novel multi-parametric approach for the characterization of multiple cellular features, using images acquired by high-throughput and high-definition light microscopy. We specifically used this approach for deep and unbiased analysis of the effects of a drug library on five cultured cell lines. The presented method enables the acquisition and analysis of millions of images, of treated and control cells, followed by an automated identification of drugs inducing strong responses, evaluating the median effect concentrations and those cellular properties that are most highly affected by the drug. The tools described here provide standardized quantification of multiple attributes for systems level dissection of complex functions in normal and diseased cells, using multiple perturbations. Such analysis of cells, derived from pathological samples, may help in the diagnosis and follow-up of treatment in patients.

The complex environment of biological cells and tissues has motivated development of three-dimensional (3D) imaging in both light and electron microscopies. To this end, one of the primary tools in fluorescence microscopy is that of computational deconvolution. Wide-field fluorescence images are often corrupted by haze due to out-of-focus light, i.e., to cross-talk between different object planes as represented in the 3D image. Using prior understanding of the image formation mechanism, it is possible to suppress the cross-talk and reassign the unfocused light to its proper source post facto. Electron tomography based on tilted projections also exhibits a cross-talk between distant planes due to the discrete angular sampling and limited tilt range. By use of a suitably synthesized 3D point spread function, we show here that deconvolution leads to similar improvements in volume data reconstructed from cryoscanning transmission electron tomography (CSTET), namely a dramatic in-plane noise reduction and improved representation of features in the axial dimension. Contrast enhancement is demonstrated first with colloidal gold particles and then in representative cryotomograms of intact cells. Deconvolution of CSTET data collected from the periphery of an intact nucleus revealed partially condensed, extended structures in interphase chromatin.

Focal adhesions (FAs) are multi-protein complexes that connect the actin cytoskeleton to the extracellular matrix, via integrin receptors. The growth, stability and adhesive functionality of these structures are tightly regulated by mechanical stress, yet, despite the extensive characterization of the integrin adhesome, the detailed molecular mechanisms underlying FA mechanosensitivity are still unclear. Besides talin, another key candidate for regulating FA-associated mechanosensing, is vinculin, a prominent FA component, which possesses either closed ("auto-inhibited") or open ("active") conformation. A direct experimental demonstration, however, of the conformational transition between the two states is still absent. In this study, we combined multiple structural and biological approaches to probe the transition from the auto-inhibited to the active conformation, and determine its effects on FA structure and dynamics. We further show that the transition from a closed to an open conformation requires two sequential steps that can differentially regulate FA growth and stability.

Adhesion of epithelial cell to each other and to extracellular matrix, as well as cell migration ability and cytoskeleton organization undergo significant alterations in the course of neoplastic transformation, but regulatory mechanisms involved in these processes are not fully understood. Here, we studied the role of a Rho GAP protein GRAF1 (GTPase Regulator Associated with Focal adhesion kinase-1) in the regulation of the epithelial phenotype in cells of breast derived, non-malignant, MCF10A cell line. GRAF1 was shown to be localized to cell-cell junctions, and its depletion resulted in accelerated cell migration velocity, elongation of the cells and cell colonies, impaired monolayer integrity and significant disruption of desmosomes with a loss of associated keratin filaments. These processes were accompanied by formation of larger focal adhesions, an increased number of contractile actin stress fibers, reduction in epithelial markers and increase in mesenchymal markers such as epithelial-mesenchymal transition (EMT)-specific transcription factors Snail-1 and Snail-2, as well as N-cadherin, and vimentin. Moreover, unlike control cells, GRAF1 knocked-down cells demonstrated anchorage-independent growth in soft agar. GRAF1 expression in several highly invasive breast cancer cell lines was low, as compared to the non-malignant MCF10A cells, while overexpressing of GRAF1 in the malignant BT-549 cell line led to a decrease of mesenchymal markers, especially the Snail-1 and 2. Altogether, our analysis suggests that GRAF1 plays a role in the maintenance of normal epithelial phenotype and its depletion leads to an EMT-like process that might be involved in neoplastic transformation.

Cellular stress and proinflammatory cytokines induce phosphorylation of insulin receptor substrate (IRS) proteins at Ser sites that inhibit insulin and IGF-I signaling. We therefore examined the effects of mutation of five "inhibitory" Ser phosphorylation sites on IRS2 function in transgenic mice that overexpress, selectively in pancreatic beta;-cells, either wild-type (WT) or a mutated IRS2 protein (IRS2^5A). Islets size, number, and mRNA levels of catalase and superoxide dismutase were increased, whereas those of nitric oxide synthase were decreased, in 7- to 10-week-old IRS2^5A-β mice compared with IRS2_WT-β mice. However, glucose homeostasis and insulin secretion in IRS2^5A-β mice were impaired when compared with IRS2^WT-β mice or to nontransgenic mice. This was associated with reduced mRNA levels of Glut2 and islet beta;-cell transcription factors such as Nkx6.1 and MafA. Similarly, components mediating the unfolded protein response were decreased in islets of IRS2^5A-β mice in accordance with their decreased insulin secretion. The beneficial effects of IRS2^5A on beta;-cell proliferation and beta;-cell transcription factors were evident only in 5- to 8-day-old mice. These findings suggest that elimination of inhibitory Ser phosphorylation sites of IRS2 exerts short-term beneficial effects in vivo; however, their sustained elimination leads to impaired beta;-cell function.

Bone resorption by osteoclasts (OCs) depends on the formation and stability of the sealing zone (SZ), a peripheral belt of actin and integrin-based podosomes. Recent studies demonstrated that the SZ is a highly dynamic structure, undergoing cycles of assembly and disassembly. In this study, we explored the mechanisms underlying the regulation of SZ stability and reorganization in OCs cultured on glass slides, and forming an SZ-like podosome belt (SZL). By monitoring this belt in cultured RAW264.7 cells expressing GFP-tagged actin, we show here that SZL stability is usually locally regulated, and its dissociation, occurring mostly in concave segments, is manifested in the loss of both podosome coherence, and actin belt continuity. Double labeling of cells for actin and tubulin indicated that microtubules (MTs) are mostly confined by the inner aspect of the stable SZL-associated actin belt. However, in unstable regions of the SZL, MTs tend to extend radially, across the SZL, toward the cell edge. Disruption of MTs by nocodazole induces SZ disassembly, without affecting individual podosome stability. Inspection of the MT network indicates that it is enriched along stable SZL regions, while bypassing disorganized regions. These results suggest that the SZL is stabilized by MTs flanking its inner aspect, while disruption or misalignment of MTs leads to SZL destabilization. We further demonstrate that the MT-associated protein dynamin2 is involved in the regulation of SZL stability, and dynamin2 knockdown or inactivation cause SZL destabilization.

Osteoclasts are multinucleated, bone-resorbing cells formed via fusion of monocyte progenitors, a process triggered by prolonged stimulation with RANKL, the osteoclast master regulator cytokine. Monocyte fusion into osteoclasts has been shown to play a key role in bone remodeling and homeostasis; therefore, aberrant fusion may be involved in a variety of bone diseases. Indeed, research in the last decade has led to the discovery of genes regulating osteoclast fusion; yet the basic cellular regulatory mechanism underlying the fusion process is poorly understood.Here, we applied a novel approach for tracking the fusion processes, using live-cell imaging of RANKL-stimulated and non-stimulated progenitor monocytes differentially expressing dsRED or GFP, respectively. We show that osteoclast fusion is initiated by a small (~. 2.4%) subset of precursors, termed "fusion founders", capable of fusing either with other founders or with non-stimulated progenitors (fusion followers), which alone, are unable to initiate fusion. Careful examination indicates that the fusion between a founder and a follower cell consists of two distinct phases: an initial pairing of the two cells, typically lasting 5-35. min, during which the cells nevertheless maintain their initial morphology; and the fusion event itself. Interestingly, during the initial pre-fusion phase, a transfer of the fluorescent reporter proteins from nucleus to nucleus was noticed, suggesting crosstalk between the founder and follower progenitors via the cytoplasm that might directly affect the fusion process, as well as overall transcriptional regulation in the developing heterokaryon.

Treatment of cultured cells with inhibitors of actomyosin contractility induces rapid deterioration of stress fibers, and disassembly of the associated focal adhesions (FAs). In this study, we show that treatment with the Rho kinase inhibitor Y-27632, which blocks actomyosin contractility, induces disarray in the FA-associated actin bundles, followed by the differential dissociation of eight FA components from the adhesion sites. Live-cell microscopy indicated that the drug triggers rapid dissociation of VASP and zyxin from FAs (τ values of 7-8 min), followed by talin, paxillin and ILK (τ ~16 min), and then by FAK, vinculin and kindlin-2 (τ = 25-28 min). Examination of the molecular kinetics of the various FA constituents, using Fluorescence Recovery After Photobleaching (FRAP), in the absence of or following short-term treatment with the drug, revealed major changes in the k_on and k_off values of the different proteins tested, which are in close agreement with their differential dissociation rates from the adhesion sites. These findings indicate that mechanical, actomyosin-generated forces differentially regulate the molecular kinetics of individual FA-associated molecules, and thereby modulate FA composition and stability.

In this article, we characterize the lateral field distortions in a low numerical aperture and large field-of-view (FOV) fluorescence imaging system. To this end, we study a commercial fluorescence MACROscope setup, which is a zooming microscope. The versatility of this system lies in its ability to image at different zoom ranges, so that sample preparations can be examined in three-dimensions, at cellular, organ and whole body levels. Yet, we found that the imaging system's optics are optimized only for high magnifications where the observed FOV is small. When we studied the point-spread function (PSF) by using fluorescent polystyrene beads as "guide-stars", we noticed that the PSF is spatially varying due to field distortions. This variation was found to be laterally symmetrical and the distortions were found to increase with the distance from the center of the FOV. In this communication, we investigate the idea of using the field at the back focal plane of an optical system for characterizing distortions. As this field is unknown, we develop a theoretical framework to retrieve the amplitude and phase of the field at the back focal pupil plane, from the empirical bead images. By using the retrieved amplitude, we can understand and characterize the underlying cause of these distortions. We also propose a few approaches, before acquisition, to either avoid it or correct it at the optical design level.

Exposure of live cells to shear flow induces major changes in cell shape, adhesion to the extracellular matrix, and migration. In the present study, we show that exposure of cultured multiple myeloma (MM) cells to shear flow of 4-36dynes/cm² triggers the extension of long tubular protrusions (denoted flow-induced protrusions, or FLIPs) in the direction of the flow. These FLIPs were found to be rich in actin, contain few or no microtubules and, apart from endoplasmic reticulum (ER)-like membranal structures, are devoid of organelles. Studying the dynamics of this process revealed that FLIPs elongate at their tips in a shear force-dependent manner, and retract at their bases. Examination of this force dependence revealed considerable heterogeneity in the mechanosensitivity of individual cells, most likely reflecting the diversity of the malignant B cell population. The mechanisms underlying FLIP formation following mechanical perturbation, and their relevance to the cellular trafficking of MM cells, are discussed.

Cell elongation and polarization are basic morphogenetic responses to extracellular matrix adhesion. We demonstrate here that human cultured fibroblasts readily polarize when plated on rigid, but not on compliant, substrates. On rigid surfaces, large and uniformly oriented focal adhesions are formed, whereas cells plated on compliant substrates form numerous small and radially oriented adhesions. Live-cell monitoring showed that focal adhesion alignment precedes the overall elongation of the cell, indicating that focal adhesion orientation may direct cell polarization. siRNA-mediated knockdown of 85 human protein tyrosine kinases (PTKs) induced distinct alterations in the cell polarization response, as well as diverse changes in cell traction force generation and focal adhesion formation. Remarkably, changes in rigidity-dependent traction force development, or focal adhesion mechanosensing, were consistently accompanied by abnormalities in the cell polarization response. We propose that the different stages of cell polarization are regulated by multiple, PTK-dependent molecular checkpoints that jointly control cell contractility and focal-adhesion-mediated mechanosensing.

Sufficient vascularization in engineered tissues can be achieved through coordinated application of improved biomaterial systems with proper cell types. In this study, we employed 3D fibrin gels alone or in combination with the synthetic poly(l-lactic acid) (PLLA)/polylactic-glycolic acid (PLGA) sponges to support in-vitro construct vascularization and to enhance neovascularization upon implantation. Two multicellular assays were embedded in these constructs: (a) co-culture of endothelial (EC) and fibroblast cells, and (b) a tri-culture combination of ECs, fibroblasts and tissue specific skeletal myoblast cells. In-vitro vessel network formation was examined under advanced confocal microscopy in various time points from cell seeding. Vessel network maturity levels and morphology were found to be highly regulated by fibrinogen concentrations in-vitro. Combination of PLLA/PLGA sponges with fibrin matrices provided added mechanical strength and featured highly mature vessels-like networks. Implantation studies revealed that the implanted ECs developed into 3D interconnected vessel-like networks in-vivo. The PLLA/PLGA scaffold proved to be a key stimulator of neovascularization and perfusion of implanted grafts. Our findings demonstrate that complex biomaterial platform involving fibrin and PLLA/PLGA synthetic scaffold provide a way to enhancing vascularization in-vitro and in-vivo.

In mammalian cells, the Golgi apparatus is a ribbon-like, compact structure composed of multiple membrane stacks connected by tubular bridges. Microtubules are known to be important to Golgi integrity, but the role of the actin cytoskeleton in the maintenance of Golgi architecture remains unclear. Here we show that an increase in Rho activity, either by treatment of cells with lysophosphatidic acid or by expression of constitutively active mutants, resulted in pronounced fragmentation of the Golgi complex into ministacks. Golgi dispersion required the involvement of mDia1 formin, a downstream target of Rho and a potent activator of actin polymerization; moreover, constitutively active mDia1, in and of itself, was sufficient for Golgi dispersion. The dispersion process was accompanied by formation of dynamic F-actin patches in the Golgi area. Experiments with cytoskeletal inhibitors (e.g., latrunculin B, blebbistatin, and Taxol) revealed that actin polymerization, myosin-II-driven contractility, and microtubule-based intracellular movement were all involved in the process of Golgi dispersion induced by Rho-mDia1 activation. Live imaging of Golgi recovery revealed that fusion of the small Golgi stacks into larger compartments was repressed in cells with active mDia1. Furthermore, the formation of Rab6-positive transport vesicles derived from the Golgi complex was enhanced upon activation of the Rho-mDia1 pathway. Transient localization of mDia1 to Rab6-positive vesicles was detected in cells expressing active RhoA. Thus, the Rho-mDia1 pathway is involved in regulation of the Golgi structure, affecting remodeling of Golgi membranes.

Monoclonal antibodies (mAbs) to HER2 are currently used to treat breast cancer, but low clinical efficacy, along with primary and acquired resistance to therapy, commonly limit clinical applications. We previously reported that combinations of antibodies directed at non-overlapping epitopes of HER2 are endowed with enhanced antitumor effects, probably due to accelerated receptor degradation. Here, we extend these observations to three-dimensional mammary cell models, and compare the effects of single mAbs with the effects of antibody combinations. Collectively, our in vitro assays and computational image analyses indicate that combining mAbs against different epitopes of HER2 better inhibits invasive growth. Importantly, while growth factors are able to reduce intraluminal apoptosis and induce an invasive phenotype, combinations of mAbs better than single mAbs can reverse the growth factor-induced phenotypes of HER2-overexpressing spheroids. In conclusion, our studies propose that mAb combinations negate the biological effects of growth factors on invasive growth of HER2-overexpressing cells. Hence, combining mAbs offers a therapeutic strategy, potentially able to enhance clinical efficacy of existing antireceptor immunotherapeutics.

Three-dimensional live imaging in cell biology is hindered by optical aberrations which degrade the resolution and signal-to-noise ratio as the focal plane is moved deeper into the sample. The solution to this problem is to use adaptive optics to correct the aberrations. In this paper, we discuss our work on applying adaptive optics to wide-field fluorescence microscopy. We demonstrate correction of depth-aberrations and focusing using a deformable mirror in open-loop operation. We then discuss the use of phase retrieval and phase diversity in adaptive optics.

Live fluorescence microscopy has the unique capability to probe dynamic processes, linking molecular components and their localization with function. A key goal of microscopy is to increase spatial and temporal resolution while simultaneously permitting identification of multiple specific components. We demonstrate a new microscope platform, OMX, that enables subsecond, multicolor four-dimensional data acquisition and also provides access to subdiffraction structured illumination imaging. Using this platform to image chromosome movement during a complete yeast cell cycle at one 3D image stack per second reveals an unexpected degree of photosensitivity of fluorophore-containing cells. To avoid perturbation of cell division, excitation levels had to be attenuated between 100 and 10,000x below the level normally used for imaging. We show that an image denoising algorithm that exploits redundancy in the image sequence over space and time allows recovery of biological information from the low light level noisy images while maintaining full cell viability with no fading.

Live imaging in cell biology requires three-dimensional data acquisition with the best resolution and signal-to-noise ratio possible. Depth aberrations are a major source of image degradation in three-dimensional microscopy, causing a significant loss of resolution and intensity deep into the sample. These aberrations occur because of the mismatch between the sample refractive index and the immersion medium index. We have built a wide-field fluorescence microscope that incorporates a large-throw deformable mirror to simultaneously focus and correct for depth aberration in three-dimensional imaging. Imaging fluorescent beads in water and glycerol with an oil immersion lens we demonstrate a corrected point spread function and a 2-fold improvement in signal intensity. We apply this new microscope to imaging biological samples, and show sharper images and improved deconvolution.

In this paper, we model the point-spread function (PSF) of a fluorescence MACROscope with a field aberration. The MACROscope is an imaging arrangement that is designed to directly study small and large specimen preparations without physically sectioning them. However, due to the different optical components of the MACROscope, it cannot achieve the condition of lateral spatial invariance for all magnifications. For example, under low zoom settings, this field aberration becomes prominent, the PSF varies in the lateral field, and is proportional to the distance from the center of the field. On the other hand, for larger zooms, these aberrations become gradually absent. A computational approach to correct this aberration often relies on an accurate knowledge of the PSF. The PSF can be defined either theoretically using a scalar diffraction model or empirically by acquiring a three-dimensional image of a fluorescent bead that approximates a point source. The experimental PSF is difficult to obtain and can change with slight deviations from the physical conditions. In this paper, we model the PSF using the scalar diffraction approach, and the pupil function is modeled by chopping it. By comparing our modeled PSF with an experimentally obtained PSF, we validate our hypothesis that the spatial variance is caused by two limiting optical apertures brought together on different conjugate planes.

In this work, we propose a novel method for the regularization of blind deconvolution algorithms. The proposed method employs example-based machine learning techniques for modeling the space of point spread functions. During an iterative blind deconvolution process, a prior term attracts the point spread function estimates to the learned point spread function space. We demonstrate the usage of this regularizer within a Bayesian blind deconvolution framework and also integrate into the latter a method for noise reduction, thus creating a complete blind deconvolution method. The application of the proposed algorithm is demonstrated on synthetic and real-world three-dimensional images acquired by a wide-field fluorescence microscope, where the need for blind deconvolution algorithms is indispensable, yielding excellent results.

Cell adhesion to the extracellular matrix is mediated by elaborate networks of multiprotein complexes consisting of adhesion receptors, cytoskeletal components, signaling molecules, and diverse adaptor proteins. To explore how specific molecular pathways function in the assembly of focal adhesions (FAs), we performed a highthroughput, high-resolution, microscopy-based screen. We used small interfering RNAs (siRNAs) to target human kinases, phosphatases, and migration- and adhesionrelated genes. Multiparametric image analysis of control and of siRNA-treated cells revealed major correlations between distinct morphological FA features. Clustering analysis identified different gene families whose perturbation induced similar effects, some of which uncoupled the interfeature correlations. Based on these findings, we propose a model for the molecular hierarchy of FA formation, and tested its validity by dynamic analysis of FA formation and turnover. This study provides a comprehensive information resource on the molecular regulation of multiple cell adhesion features, and sheds light on signaling mechanisms regulating the formation of integrin adhesions.

We propose an alternate minimization algorithm for estimating the point-spread function (PSF) of a con-focal laser scanning microscope and the specimen fluorescence distribution. A three-dimensional separable Gaussian model is used to restrict the PSF solution space and a constrainton the specimen isused so as to favor the stabilization and convergence of the algorithm. The results obtained from the simulation show that the PSF can be estimated to a high degree of accuracy, and those on real data show better deconvolution as compared to a full theoretical PSF model.

In this paper we propose a method for retrieving the Point Spread Function (PSF) of an imaging system given the observed image sections of a fluorescent microsphere. Theoretically calculated PSFs often lack the experimental or microscope specific signatures while empirically obtained data are either over sized or (and) too noisy. The effect of noise and the influence of the microsphere size can be mitigated from the experimental data by using a Maximum Likelihood Expectation Maximization (MLEM) algorithm. The true experimental parameters can then be estimated by fitting the result to a model based on the scalar diffraction theory with lower order Spherical Aberration (SA). The algorithm was tested on some simulated data and the results obtained validate the usefulness of the approach for retrieving the PSF from measured data.

The regulated degradation of damaged or misfolded proteins, as well as down-regulation of key signaling proteins, within eukaryotic and bacterial cells is catalyzed primarily by large, ATP-dependent multimeric proteolytic complexes, termed proteasomes. Inhibition of proteasomal activity affects a wide variety of physiological and pathological processes, and was found to be particularly effective for cancer therapy. We report here on the development of a novel high throughput assay for proteasome inhibition using a unique, highly sensitive live-cell screening, based on the cytoplasm-to-nucleus translocation of a fluorescent proteasome inhibition reporter (PIR) protein, consisting of nuclear localization signal-deficient p53 derivative. We further show here that mdm2, a key negative regulator of p53 plays a key role in the accumulation of PIR in the nucleus upon proteasome inhibition. Using this assay, we have screened the NCI Diversity Set library, containing 1,992 low molecular weight synthetic compounds, and identified four proteasome inhibitors. The special features of the current screen, compared to those of other approaches are discussed.

In a functional genomic screen performed by combining an Arabidopsis-yellow fluorescent protein (YFP)-fused complementary DNA (cDNA) library, rat fibroblasts as host and automatic microscopy, we found a short protein with a predictable trans-membrane domain encoded on chromosome 2. In rat fibroblasts, its pattern of distribution was to various organelle-like structures. From the databases, we learned that it has another family member in Arabidopsis and homologs in several other plants, Chlamydomonas and fungi, with a highly conserved N-terminal region. We named this protein from Arabidopsis short membrane protein (SMP) 2. No SMP homologs were found in mammalian sequence databases. When the full-length cDNAs of SMP2 was fused to YFP under the 35S promoter, comparable distribution was observed in Nicotiana benthamiana leaves, suggesting an unknown, evolutionarily conserved localization signal. Similar localization was observed when SMP2 was expressed in N. benthamiana leaves under the control of its own 5 regulatory sequences. Colocalization studies with green fluorescent protein and red fluorescent protein chimeras revealed its colocalization with chloroplasts, peroxisomes, and mitochondria. No localization of SMP2 was observed in the Golgi. Immunostaining with specific antibodies corroborated the SMP2 localization to the three organelles.

Why do seemingly identical cells respond differently to a drug? To address this, we studied the dynamics and variability of the protein response of human cancer cells to a chemotherapy drug, camptothecin. We present a dynamic-proteomics approach that measures the levels and locations of nearly 1000 different endogenously tagged proteins in individual living cells at high temporal resolution. All cells show rapid translocation of proteins specific to the drug mechanism, including the drug target (topoisomerase-1), and slower, wide-ranging temporal waves of protein degradation and accumulation. However, the cells differ in the behavior of a subset of proteins. We identify proteins whose dynamics differ widely between cells, in a way that corresponds to the outcomes - cell death or survival. This opens the way to understanding molecular responses to drugs in individual cells.

Centrosomes control microtubule dynamics in many cell types, and their removal from the cytoplasm leads to a shift from dynamic instability to treadmilling behavior and to a dramatic decrease of microtubule mass (Rodionov et al., 1999; PNAS 96: 115). In cadherin-expressing cells, these effects can be reversed: non-centrosomal cytoplasts that form cadherin-mediated adherens junctions display dense arrays of microtubules (Chausovsky et al., 2000; Nature Cell Biol 2: 797). In adherens junctions, cadherin's cytoplasmic domain binds p120 catenin and beta-catenin, which in turn binds beta-catenin. To elucidate the roles of the cadherin-associated proteins in regulating microtubule dynamics, we prepared GFP-tagged, plasma membrane targeted or untargeted p120 catenin, alpha-catenin and beta-catenin and tested their ability to rescue the loss of microtubule mass caused by centrosomal removal in the poorly adhesive cell line CHO-K1. Only membrane targeting of alpha-catenin led to a significant increase in microtubule length and density in centrosome-free cytoplasts. Expression of non-membrane-targeted alpha-catenin produced only a slight effect, while both membrane-targeted and non-targeted p120 and beta-catenin were ineffective in this assay. Together, these findings suggest that alpha-catenin is able to regulate microtubule dynamics in a centrosome-independent manner.

Background: Cellular processes occur within dynamic and multi-molecular compartments whose characterization requires analysis at high spatio-temporal resolution. Notable examples for such complexes are cell-matrix adhesion sites, consisting of numerous cytoskeletal and signaling proteins. These adhesions are highly variable in their morphology, dynamics, and apparent function, yet their molecular diversity is poorly defined. Methodology/Principal Findings: We present here a compositional imaging approach for the analysi5 and display of multi-component compositions. This methodology is based on microscopy-acquired multicolor data, multi-dimensional clustering of pixels according to their composition similarity and display of the cellular distribution of these composition clusters. We apply this approach for resolving the molecular complexes associated with focal-adhesions, and the time-dependent effects of Rho-kinase inhibition. We show here compositional variations between adhesion sites, as well as ordered variations along the axis of individual focal-adhesions. The multicolor clustering approach also reveals distinct sensitivities of different focal-adhesion-associated complexes to Rho-kinase inhibition. Conclusions/Significance: Multicolor compositional imaging resolves "molecular signatures" characteristic to focal-adhesions and related structures, as well as sub-domains within these adhesion sites. This analysis enhances the spatial information with additional "contents-resolved" dimensions. We propose that compositional imaging can serve as a powerful tool for studying complex multi-molecular assemblies in cells and for mapping their distribution at sub-micron resolution.

Background. Cell migration is a highly complex process, regulated by multiple genes, signaling pathways and external stimuli. To discover genes or pharmacological agents that can modulate the migratory activity of cells, screening strategies that enable the monitoring of diverse migratory parameters in a large number of samples are necessary. Methodology. In the present study, we describe the development of a quantitative, high-throughput cell migration assay, based on a modified phagokinetic tracks (PKT) procedure, and apply it for identifying novel pro-migratory genes in a cancer-related gene library. In brief, cells are seeded on fibronectin-coated 96-well plates, covered with a monolayer of carboxylated latex beads. Motile cells clear the beads, located along their migratory paths, forming tracks that are visualized using an automated, transmitted-light screening microscope. The tracks are then segmented and characterized by multi-parametric, morphometric analysis, resolving a variety of morphological and kinetic features. Conclusions. In this screen we identified 4 novel genes derived from breast carcinoma related cDNA library, whose over-expression induces major alteration in the migration of the stationary MCF7 cells. This approach can serve for high throughput screening for novel ways to modulate cellular migration in pathological states such as tumor metastasis and invasion.

Optical Sections of biological samples obtained from a fluorescence Confocal Laser Scanning Microscopes (CLSM) are often degraded by out-of-focus blur and photon counting noise. Such physical constraints on the observation are a result of the diffraction-limited nature of the optical system, and the reduced amount of light detected by the photomultiplier respectively. Hence, the image stacks can benefit from post-processing restoration methods based on deconvolution. The parameters of the acquisition system's Point Spread Function (PSF) may vary during the course of experimentation, and so they have to be estimated directly from the observation data. We describe here an alternate minimization algorithm for the simultaneous blind estimation of the specimen 3D distribution of fluorescent sources and the PSF. Experimental results on real data show that the algorithm provides very good deconvolution results in comparison to theoretical microscope PSF models.

Depth aberrations are a major source of image degradation in three-dimensional microscopy, causing a significant loss of resolution and intensity deep into the sample. These aberrations occur because of an inevitable mismatch between the sample refractive index and the immersion medium index. We have built a wide-field fluorescence microscope that incorporates a large-throw deformable mirror to correct for depth aberrations in 3D imaging. We demonstrate a corrected point spread function imaging beads in water with an oil immersion lens and a twofold improvement in peak signal intensity. We apply this new microscope to imaging biological samples, and show sharper images and improved deconvolution.

Background: Telomeres cap chromosome ends and protect the genome. We studied individual telomeres in live human cancer cells. In capturing telomere motions using quantitative imaging to acquire complete high-resolution three-dimensional datasets every second for 200 seconds, telomere dynamics were systematically analyzed. Results: The motility of individual telomeres within the same cancer cell nucleus was widely heterogeneous. One class of internal heterochromatic regions of chromosomes analyzed moved more uniformly and showed less motion and heterogeneity than telomeres. The single telomere analyses in cancer cells revealed that shorter telomeres showed more motion, and the more rapid telomere motions were energy dependent. Experimentally increasing bulk telomere length dampened telomere motion. In contrast, telomere uncapping, but not a DNA damaging agent, methyl methanesulfonate, significantly increased telomere motion. Conclusion: New methods for seconds-scale, four-dimensional, live cell microscopic imaging and data analysis, allowing systematic tracking of individual telomeres in live cells, have defined a previously undescribed form of telomere behavior in human cells, in which the degree of telomere motion was dependent upon telomere length and functionality.

Quantitative interpretation of microscope images is more challenging the higher the resolution of the images is. The reward is rich multi-parametric characterization of subcellular structures and detailed description of cell responses to perturbations. This information is the basis of high-throughput cell-based screening, searching to discover new drugs and understand molecular mechanisms at the cell level. We have developed a fast screening microscope acquiring high-resolution images from cells cultured in plastic-bottom multi-well plates, [1-4] and are writing an automated pipeline for the analysis of Tera Bytes of images from high throughput screens. The platform includes database for storage and retrieval of images, visualization with easy linkage of the analyzed results to the original multi-color images, segmentation of objects in images (including cells, nuclei, cytoskeletal fibers and sub-cellular organelles), multi-parametric quantification of morphological and multicolor fluorescence intensities, and statistical comparisons to control wells displayed in color coded scores on the plate graphics. This system was successfully employed for screening of the effect of drugs, gene over-expression and siRNA of diverse cellular properties, including cell adhesion, migration, survival and cytoskeletal organization.

High-resolution light-microscopy and high-throughput screening are two essential methodologies for characterizing cellular phenotypes. Optimally combining these methodologies in cell-based screening to test detailed molecular and cellular responses to multiple perturbations constitutes a major challenge. Here we describe the development and application of a screening microscope platform that automatically acquires and interprets sub-micron resolution images at fast rates. The analysis pipeline is based on the quantification of multiple subcellular features and statistical comparisons of their distributions in treated vs. control cells. Using this platform, we screened 2200 natural extracts for their effects on the fine structure and organization of focal adhesions. This screen identified 15 effective extracts whose fractionation and characterization were further analyzed using the same microscope system. The significance of combining resolution, throughput and multi-parametric analyses for biomedical research and drug discovery is discussed.

Wide-field fluorescence microscopy is an essential tool in modern cell biology. Unfortunately the image quality of fluorescence microscopes is often significantly degraded due to aberrations that occur under normal imaging conditions. In this article, we examine the use of adaptive optics technology to dynamically correct these problems to achieve close to ideal diffraction limited performance. Simultaneously, this technology also allows ultra-rapid focusing without having to move either the stage or the objective lens. We perform optical simulations to demonstrate the degree of correction that can be achieved.

Diverse cellular processes are carried out by distinct integrin-mediated adhesions. Cell spreading and migration are driven by focal complexes; robust adhesion to the extracellular matrix by focal adhesions; and matrix remodeling by fibrillar adhesions. The mechanism(s) regulating the spatio-temporal distribution and dynamics of the three types of adhesion are unknown. Here, we combine live-cell imaging, labeling with phosphospecific-antibodies and overexpression of a novel tyrosine phosphomimetic mutant of paxillin, to demonstrate that the modulation of tyrosine phosphorylation of paxillin regulates both the assembly and turnover of adhesion sites. Moreover, phosphorylated paxillin enhanced lamellipodial protrusions, whereas non-phosphorylated paxillin was essential for fibrillar adhesion formation and for fibronectin fibrillogenesis. We further show that focal adhesion kinase preferentially interacted with the tyrosine phosphomimetic paxillin and its recruitment is implicated in high turnover of focal complexes and translocation of focal adhesions. We created a mathematical model that recapitulates the salient features of the measured dynamics, and conclude that tyrosine phosphorylation of the adaptor protein paxillin functions as a major switch, regulating the adhesive phenotype of cells.

In this paper, we propose a method for the iterative restoration of fluorescence Confocal Laser Scanning Microscopic (CLSM) images and parametric estimation of the acquisition system's Point Spread Function (PSF). The CLSM is an optical fluorescence microscope that scans a specimen in 3D and uses a pinhole to reject most of the out-of-focus light. However, the quality of the images suffers from two basic physical limitations. The diffraction-limited nature of the optical system, and the reduced amount of light detected by the photomultiplier cause blur and photon counting noise respectively. These images can hence benefit from post-processing restoration methods based on deconvolution. An efficient method for parametric blind image deconvolution involves the simultaneous estimation of the specimen 3D distribution of fluorescent sources and the microscope PSF. By using a model for the microscope image acquisition physical process, we reduce the number of free parameters describing the PSF and introduce constraints. The parameters of the PSF may vary during the course of experimentation, and so they have to be estimated directly from the observed data. A priori model of the specimen is further applied to stabilize the alternate minimization algorithm and to converge to the solutions.

We describe the design and utilization of a deformable membrane to minimize the negative spherical aberration that occurs when a standard water-dipping objective is used to focus within a higher-index sample. In connection with two-photon laser scanning microscopy, we demonstrate twofold improved axial resolution of structures as deep as 1 mm in gels and brain tissue. In conjunction with plasma-mediated ablation, we demonstrate enhanced production of optical damage deep within a glass substrate. The present method provides a simple and inexpensive correction for a limited yet important class of optical aberrations.

Taking advantage of the high conservation of the cytoskeleton building blocks actin and tubulin between plant and animal kingdoms, we developed a functional genomic screen for the isolation of new plant cytoskeleton-binding proteins that uses a mammalian cell expression system. A yellow fluorescent protein (YFP)-fusion cDNA library from Arabidopsis was inserted into rat fibroblasts and screened for fluorescent chimeras localizing to cytoskeletal structures. The high-throughput screen was performed by an automated microscope. An initial set of candidate genes identified in the screen was isolated, sequenced, the full-length cDNAs were synthesized by RT-PCR and tested by biochemical approaches to verify the ability of the genes to bind actin directly. Alternatively, indirect binding via interaction with other actin-binding proteins was studied. The full-length cDNAs were transferred back to plants as YFP chimeras behind the CAMV-35S promoter. We give here two examples of new plant cytoskeletal proteins identified in the pilot screen. ERD10, a member of the dehydrin family of proteins, was localized to actin stress fibers in rat fibroblasts. Its direct binding to actin filaments was confirmed by several biochemical approaches. Touch-induced calmodulin-like protein, TCH2, was also localized to actin stress fibers in fibroblasts, but was unable to bind actin filaments directly in vitro. Nevertheless, it did bind to the IQ domains of Arabidopsis myosin VIII in a calcium-dependent manner. Further evidence for a cytoskeletal function of ERD10 was obtained in planta; GFP-ERD10 was able to protect the actin cytoskeleton from latrunculin-mediated disruption in Nicotiana benthamiana leaves.

Confocal laser scanning microscopy is a powerful and popular technique for 3D imaging of biological specimens. Although confocal microscopy images are much sharper than standard epifluorescence ones, they are still degraded by residual out-of-focus light and by Poisson noise due to photon-limited detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy iterative algorithm, which computes maximum likelihood estimation adapted to Poisson statistics. As this algorithm tends to amplify noise, regularization constraints based on some prior knowledge on the data have to be applied to stabilize the solution. Here, we propose to combine the Richardson-Lucy algorithm with a regularization constraint based on Total Variation, which suppresses unstable oscillations while preserving object edges. We show on simulated and real images that this constraint improves the deconvolution results as compared with the unregularized Richardson-Lucy algorithm, both visually and quantitatively.

Microscopy-based fluorescence resonance energy transfer (FRET) provides an opportunity to monitor molecular processes in the natural environment in live cells. Here we studied molecular interactions and tyrosine phosphorylation of paxillin, Crk-associated substrate (CAS), and focal adhesion kinase (FAK) in focal adhesions. For that purpose, these focal adhesion phosphoproteins, fused to cyan or yellow fluorescent proteins (CFP or YFP) were expressed in cultured fibroblasts. To assess the dynamics of tyrosine phosphorylation we used YFP- or CFP-tagged SH2 domain of pp60^src (dSH2), which specifically binds to phosphotyrosine residues. FRET measurements, combined with immunolabeling with phosphospecific antibodies revealed that FAK, CAS and paxillin are tyrosine phosphorylated in early matrix adhesions and that FAK is in FRET proximity to CAS and paxillin in focal complexes and focal adhesions. Data suggest that paxillin incorporation into nascent focal complexes precedes its tyrosine phosphorylation, which then gradually increases. In cells treated with Rho-kinase inhibitors or expressing constitutively active Rac, focal complexes showed similar levels of paxillin tyrosine phosphorylation as seen in mature focal adhesions. Dynamic FRET-based examination indicated that paxillin phosphorylation occurs in specific areas (hotspots) within focal adhesions, whereas FAK phosphorylation is broadly distributed.

Automated acquisition of high resolution, light microscope images of cells is becoming a common requirement in modern proteomic and cellomic research. A prerequisite for such microscopy is fine focus tuning, commonly optimized by multiple exposures, followed by image sharpness analysis. We describe here an extremely fast and accurate laser autofocusing system with distinct advantages for large-scale cell-based screening.

Membrane-bound hyaluronan mediates the initial adhesive interactions between many cell types and external surfaces. In RCJ-P chondrocytes, such early contacts are mediated through a thick hyaluronidase-sensitive coat. The early adhesion is followed by integrin-mediated interactions and the formation of stable focal adhesions. During this process, the distance between the cell membrane and the surface is reduced from micrometers to few tens of nanometers. The transition from hyaluronan- to integrin-mediated adhesion was studied on glass surfaces by total internal reflection fluorescence microscopy. Hyaluronan-mediated adhesion precedes focal adhesions formation by 2-10 min. After these initial interactions, the pericellular hyaluronan remains sequestered into discrete pockets between the cell and the surface, which are a few hundreds nanometers thick and a few micrometers wide, and are flanked by focal adhesions. The hyaluronan coat facilitates the nucleation of small paxillin-rich contacts, which later mature into focal adhesions. These dynamic studies demonstrate that pericellular hyaluronan mediates initial cell-surface adhesion, and regulates the formation of focal adhesions.

Large-scale microscopy-based screens offer compelling advantages for assessing the effects of genetic and pharmacological modulations on a wide variety of cellular features. However, development of such assays is often confronted by an apparent conflict between the need for high throughput, which usually provides limited information on a large number of samples, and a high-content approach, providing detailed information on each sample. This chapter describes a novel high-resolution screening (HRS) platform that is able to acquire large sets of data at a high rate and light microscope resolution using specific "reporter cells," cultured in multiwell plates. To harvest extensive morphological and molecular information in these automated screens, we have constructed a general analysis pipeline that is capable of assigning scores to multiparameter-based comparisons between treated cells and controls. This chapter demonstrates the structure of this system and its application for several research projects, including screening of chemical compound libraries for their effect on cell adhesion, discovery of novel cytoskeletal genes, discovery of cell migration-related genes, and a siRNA screen for perturbation of cell adhesion.

Exposure of sparsely plated endothelial cells or a wounded monolayer to shear flow induces an instantaneous inhibition of 'upstream' lamellipodial protrusion and suppresses cell migration against the flow. This phenomenon is caused by the inhibition of Rac1 activity in the upstream lamellae, as demonstrated by fluorescence resonance energy transfer experiments, and by the capacity of constitutively active Rac1 to abolish flow-induced cell polarization. The local inactivation of Rac1 coincides with rapid dephosphorylation of paxillin and the adapter protein p130^CAS, which, in their phosphorylated state, participate in the activation of the Rac1 exchange factor complex DOCK180/ELMO. Indeed, overexpression of DOCK180 and ELMO rescue upstream protrusion in cells exposed to flow. Searching for the mechanosensors responsible for the polarized p130^CAS dephosphorylation, we discovered that shear stress stimulates the turnover and overall growth of upstream focal adhesions, whereas downstream adhesions tend to shrink. We propose that polarized, shear stress-induced signaling from focal adhesions at the upstream lamellae, leads to the local inactivation of Rac1 by inhibiting paxillin and p130^CAS phosphorylation, and consequently blocking the DOCK180/ELMO pathway.

The study of normal or malignant haematopoiesis requires the analysis of heterogeneous cell populations using multiple morphological and molecular criteria. Flow cytometry has the capacity to acquire multi-parameter information of large haematopoietic cell populations, utilizing various combinations of >200 molecular markers (clusters of differentiation, CD). However, current flow cytometry analyses are based on serial gating of two-parametric scatter plots - a process that is inherently incapable to discriminate all subgroups of cells in the data. Here we studied the cellular diversity of normal bone marrows (BM) using multi-dimensional cluster analysis of six-parametric flow cytometry data (four CD, forward scatter and side scatter), focusing mainly on the myeloid lineage. Twenty-three subclasses of cells were resolved, many of them inseparable even when examined in all possible two-parametric scatter plots. The multi-dimensional analysis could distinguish the haematopoietic progenitors according to International Society of Haematotherapy and Graft Engineering criteria from other types of immature cells. Based on the defined clusters, we designed a classifier that assigns BM cells in samples to subclasses based on robust six-dimensional position and extended shape. The analysis presented here can manage successfully both the increasing numbers of haematopoietic cellular markers and sample heterogeneity. This should enhance the ability to study normal haematopoiesis, and to identify and monitor haematopoietic disorders.

Confocal laser scanning microscopy is a powerful and increasingly popular technique for 3D imaging of biological specimens. However the acquired images are degraded by blur from out-of-focus light and Poisson noise due to photon-limited detection. Several deconvolution methods have been proposed to reduce these degradations, including the Richardson-Lucy algorithm, which computes a maximum likelihood estimation adapted to Poisson statistics. However this method tends to amplify noise if used without regularizing constraint. Here, we propose to combine the Richardson-Lucy algorithm with a regularizing constraint based on total variation, whose smoothing avoids oscillations while preserving edges. We show on simulated images that this constraint improves the deconvolution result both visually and using quantitative measures.

Biological image analysis software packages offer tools to analyze microscope images of cells. Some of these tools allow quantitative analysis through interactive processing. High-throughput applications employing microscopy for cell-based assays require analysis of large number of images. We describe here acquisition and analysis of cell images in high throughput automated mode aiming to screen for effects in structure and molecular organization of cellular components recorded by high resolution cell images and in cell motility.

Cellular locomotion is driven by repeated cycles of protrusion of the leading edge, formation of new matrix adhesions and retraction of the trailing edge. In this study we addressed the molecular composition and dynamics of focal complexes, formed under the leading lamellae of motile cells, and their maturation into focal adhesions. We combined phase-contrast and fluorescence microscopy approaches to monitor the incorporation of phosphotyrosine and nine different focal adhesion proteins into focal complexes in endothelial cells, migrating into an in vitro 'wound'. We show that newly formed complexes are located posterior to an actin-, VASP- and α-actinin-rich region in the lammelipodium. They are highly tyrosine phosphorylated, contain β₃-integrin, talin, paxillin and low levels of vinculin and FAK, but are apparently devoid of zyxin and tensin. The recruitment of these proteins into focal complexes occurs sequentially, so that their specific protein composition depends on their age. Interestingly, double color, time-lapse movies visualizing both paxillin and zyxin, indicated that the transition from paxillin-rich focal complexes to definitive, zyxin-containing focal adhesions, takes place only after the leading edge stops advancing or retracts. These observations illuminate, for the first time, early stages in focal complex assembly and the dynamic process associated with its transformation into focal adhesion.

Background: The cytoskeleton consists of complex arrays of fibers that play indispensable roles in cell structure and function. The cytoskeletal fibers are concertedly involved in numerous cellular processes, including cell adhesion, locomotion, intracellular transport, and cell division. The organization of the cytoskeleton was extensively studied, mainly by immunofluorescence microscopy, yet these studies were mostly qualitative, and a reliable quantitative approach for determining fiber structure and distribution is still missing. Methods: In this study we developed algorithms for filament feature extraction, based on fluorescence microscopy. These algorithms are robust against blurring by slight defocus, high background, and noise, and are applicable to both fixed, immunolabeled cells and live cells expressing fluorescently tagged cytoskeletal proteins. The implemented FiberScore program is used in order to recognize, segment, and quantify various structural parameters of the cytoskeleton, including total fiber-associated fluorescence, as well as fiber length and orientation. Furthermore, these parameters can be determined for different cytoskeletal proteins in the same sample tagged with multiple-fluorescent labels, and the results can be correlated with other cellular parameters. Results: FiberScore was used here for the quantification of simultaneous changes in microtubule and actin filaments induced by the microtubule-disrupting drug nocodazole. Actin filaments, which are reported to respond reciprocally to microtubule disruption, are found to be affected by both immediate and delayed signals. Conclusions: Analysis of the organization of fibers by the FiberScore algorithm allows quantification of the cytoskeletal signature of cells and offers reliable multiparametric functional assays for effects of drugs and other perturbations evaluated on a cell-by-cell basis.

Tyrosine phosphorylation of focal adhesion components is involved in the regulation of focal adhesion formation and turnover, yet the underlying molecular mechanisms are still poorly defined. In the present study, we have used quantitative fluorescence microscopy to investigate the dynamic relationships between the incorporation of new components into growing focal adhesions and tyrosine phosphorylation of these sites. For this purpose, a new approach for monitoring phosphotyrosine levels in live cells was developed, based on a 'phosphotyrosine reporter' consisting of yellow fluorescent protein fused to two consecutive phosphotyrosine-binding Src-homology 2 (SH2)-domains derived from pp60^c-Src. This YFP-dSH2 localized to cell-matrix adhesions and its intensity was linearly correlated with that of an anti-phosphotyrosine antibody labeling. The differential increase in vinculin and phosphotyrosine levels was examined in live cells by two-color time-lapse movies of CFP-vinculin and YFP-dSH2. In this study, focal adhesion growth was triggered by microtubule disruption, which was previously shown to stimulate focal adhesion development by inducing cellular contraction. We show here that, 2 minutes after addition of the microtubule-disrupting drug nocodazole, the local densities of the focal adhesion-associated proteins vinculin, paxillin and focal adhesion kinase (FAK) are significantly elevated and the focal adhesion area is increased, whereas elevation in tyrosine phosphorylation inside the growing adhesions occurs only a few minutes later. Phosphotyrosine and FAK density reach their maximum levels after 10 minutes of treatment, whereas vinculin and paxillin levels as well as focal adhesion size continue to grow, reaching a plateau at about 30 minutes. Our findings suggest that protein recruitment and growth of focal adhesions are an immediate and direct result of increased contractility induced by microtubule disruption, whereas tyrosine phosphorylation is activated later.

A novel phosphorylation-specific antibody (αpβ-catenin) was generated against a peptide corresponding to amino acids 33-45 of human β-catenin, which contained phosphorylated serines at positions 33 and 37. This antibody is specific to phosphorylated β-catenin and reacts neither with the non-phosphorylated protein nor with phosphorylated or non-phosphorylated plakoglobin. It weakly interacts with S33Y β-catenin but not with the S37A mutant. pβ-catenin is hardly detectable in normal cultured cells and accumulates (up to 55% of total β-catenin) upon overexpression of the protein or after blocking its degradation by the proteasome. Inhibition of both GSK-3β and the proteasome resulted in a rapid (t_1/2=10 minutes) and reversible reduction in pβ-catenin levels, suggesting that the protein can undergo dephosphorylation in live cells, at a rate comparable to its phosphorylation by GSK-3β. pβ-catenin interacts with LEF-1, but fails to form a ternary complex with DNA, suggesting that it is transcriptionally inactive. Immunofluorescence microscopy indicated that pβ-catenin accumulates in the nuclei of MDCK and BCAP cells when overexpressed and is transiently associated with adherens junctions shortly after their formation. pβ-catenin only weakly interacts with co-transfected N-cadherin, although it forms a complex with the ubiquitin ligase component β-TrCP. SW480 colon cancer cells that express a truncated APC, at position 1338, contain high levels of pβ-catenin, whereas HT29 cells, expressing APC truncated at position 1555, accumulate non-phosphorylated β-catenin, suggesting that the 1338-1555 amino acid region of APC is involved in the differential regulation of the dephosphorylation and degradation of pβ-catenin.

Important biological mechanisms, such as signal transduction and gene expression, are mediated by numerous interacting multifunctional molecules, whose expression and activation are tightly regulated in space and time in response to stimuli. In order to describe the network of functional inter-relationships that govern such mechanisms, we use simple algorithms to interpret multiple variable measurements, identify the prominent participants, evaluate their interactions and obtain a 'functional fingerprint' of cell behaviour. Dynamic measurements of responses yield hierarchical information about causal relations in the underlying pathway. As a proof of principles we apply this approach to phosphorylation assays in protein gels, probing hormone and insulin signalling.

Modern light microscopy has become a most powerful analytical tool for studying molecular processes in live cells. Recent advances in sample preparation, microscope design and image processing allow the generation of 'multidimensional' data, simultaneously reporting the three-dimensional distribution and concentrations of several different molecules within cells and tissues at multiple time points with sub-micron spatial resolution and sub-second temporal resolution. Thus, molecular interactions and processes that were approached by biochemical analyses in vitro can now be directly monitored in live cells. Here, we address different aspects of multidimensional microscopy and, in particular, image quantification and the characterization of molecular dynamics, as applied to the study of cell adhesion.

The transition of cell-matrix adhesions from the initial punctate focal complexes into the mature elongated form, known as focal contacts, requires GTPase Rho activity. In particular, activation of myosin II-driven contractility by a Rho target known as Rho-associated kinase (ROCK) was shown to be essential for focal contact formation. To dissect the mechanism of Rho-dependent induction of focal contacts and to elucidate the role of cell contractility, we applied mechanical force to vinculin-containing dot-like adhesions at the cell edge using a micropipette. Local centripetal pulling led to local assembly and elongation of these structures and to their development into streak-like focal contacts, as revealed by the dynamics of green fluorescent protein-tagged vinculin or paxillin and interference reflection microscopy. Inhibition of Rho activity by C3 transferase suppressed this force-induced focal contact formation. However, constitutively active mutants of another Rho target, the formin homology protein mDia1 (Watanabe, N., T. Kato, A. Fujita, T. Ishizaki, and S. Narumiya. 1999. Nat. Cell Biol. 1:136-143), were sufficient to restore force-induced focal contact formation in C3 transferasetreated cells. Force-induced formation of the focal contacts still occurred in cells subjected to myosin II and ROCK inhibition. Thus, as long as mDia1 is active, external tension force bypasses the requirement for ROCK-mediated myosin II contractility in the induction of focal contacts. Our experiments show that integrin-containing focal complexes behave as individual mechanosensors exhibiting directional assembly in response to local force.

Light microscopy of thick biological samples, such as tissues, is often limited by aberrations caused by refractive index variations within the sample itself. This problem is particularly severe for live imaging, a field of great current excitement due to the development of inherently fluorescent proteins. We describe a method of removing such aberrations computationally by mapping the refractive index of the sample using differential interference contrast microscopy, modeling the aberrations by ray tracing through this index map, and using space-variant deconvolution to remove aberrations. This approach will open possibilities to study weakly labeled molecules in difficult-to-image live specimens.

This study establishes that the physical state of the extracellular matrix can regulate integrin-mediated cytoskeletal assembly and tyrosine phosphorylation to generate two distinct types of cell-matrix adhesions. In primary fibroblasts, α₅/β₁ integrin associates mainly with fibronectin fibrils and forms adhesions structurally distinct from focal contacts, independent of actomyosin-mediated cell contractility. These 'fibrillar adhesions' are enriched in tensin, but contain low levels of the typical focal contact components paxillin, vinculin, and tyrosine-phosphorylated proteins. However, when the fibronectin is covalently linked to the substrate, α₅/β₁ integrin forms highly tyrosine-phosphorylated, 'classical' focal contacts containing high levels of paxillin and vinculin. These experiments indicate that the physical state of the matrix, not just its molecular composition, is a critical factor in defining cytoskeletal organization and phosphorylation at adhesion sites. We propose that molecular organization of adhesion sites is controlled by at least two mechanisms: 1) specific integrins associate with their ligands in transmembrane complexes with appropriate cytoplasmic anchor proteins (e.g., fibronectin-α₅/β₁ integrin-tensin complexes), and 2) physical properties (e.g., rigidity) of the extracellular matrix regulate local tension at adhesion sites and activate local tyrosine phosphorylation, recruiting a variety of plaque molecules to these sites. These mechanisms generate structurally and functionally distinct types of matrix adhesions in fibroblasts.

Here we use time-lapse microscopy to analyse cell-matrix adhesions in cells expressing one of two different cytoskeletal proteins, paxillin or tensin, tagged with green fluorescent protein (GFP). Use of GFP-paxillin to analyse focal contacts and GFP-tensin to study fibrillar adhesions reveals that both types of major adhesion are highly dynamic. Small focal contacts often translocate, by extending centripetally and contracting peripherally, at a mean rate of 19 micrometres per hour. Fibrillar adhesions arise from the medial ends of stationary focal contacts, contain α₅β₁ integrin and tensin but not other focal-contact components, and associate with fibronectin fibrils. Fibrillar adhesions translocate centripetally at a mean rate of 18 micrometres per hour in an actomyosin-dependent manner. We propose a dynamic model for the regulation of cell-matrix adhesions and for transitions between focal contacts and fibrillar adhesions, with the ability of the matrix to deform functioning as a mechanical switch.

Previously, it was implicated that p53 plays a role in spermatogenesis. Here we report that p53 knockout mice exhibit significantly less mature motile spermatozoa than their p53(+/+) counterparts. To better understand the role of p53 in spermatogenesis, we analyzed the response of spermatogenic cells to DNA insult during prophase. It was found that although low-level γ- irradiation activated a p53-dependent premeiotic delay, higher levels of γ- irradiation induced a p53-independent apoptosis during meiosis. Furthermore, p53 knockout mice exhibited reduced in vivo levels of unscheduled DNA synthesis, indicative of compromised DNA repair. Thus, p53 provides another level of stringency in addition to other spermatogenic 'quality control' mechanisms.

In this study the direct involvement of cadherins in adhesion-mediated growth inhibition was investigated. It is shown here that overexpression of N-cadherin in CHO cells significantly suppresses their growth rate. Interaction of these cells and two additional fibroblastic lines with synthetic beads coated with N-cadherin ligands (recombinant N-cadherin ectodomain or specific antibodies) leads to growth arrest at the G1 phase of the cell cycle. The cadherin-reactive beads inhibit the entry into S phase and the reduction in the levels of cyclin-dependent kinase (cdk) inhibitors p21 and p27, following serum-stimulation of starved cells. In exponentially growing cells these beads induce G1 arrest accompanied by elevation in p27 only. We propose that cadherin-mediated signaling is involved in contact inhibition of growth by inducing cell cycle arrest at the G1 phase and elevation of p27 levels.

As the zebrafish embryo undergoes gastrulation and epiboly, the cells of the enveloping layer (EVL) expand, covering the entire yolk cell. During the epiboly process, the EVL cells move as a coherent layer, remaining tightly attached to each other and to the underlying yolk syncytial layer (YSL). In view of the central role of the actin cytoskeleton, in both cell motility and cell-cell adhesion, we have labeled these cells in situ with fluorescent phalloidin and anti-actin antibodies. We show that, throughout their migration, the EVL cells retain a conspicuous cortical actin cytoskeletal belt coinciding with cell surface cadherins. At the margins approaching the YSL, the EVL cells extend, from their apicolateral domains, actin-rich filopodial protrusions devoid of detectable cadherin. We have studied the role of the actin cytoskeleton in the maintenance of EVL cohesion during epiboly. Cytochalasin treatment of embryos induces EVL dissociation accompanied by general detachment of the rest of the embryonic cells. In the dissociating EVL cells, the cortical actin belt undergoes fragmentation with the formation of actin aggregates; cadherins, on the other hand, remain evenly distributed at the junctional cell surface. Removal of Ca²⁺ by ethyleneglycolbis (amino-ethyl-ether)-tetraacetic acid (EGTA) treatment also induces cell dissociation without visible disruption of the cortical actin belt. The protein kinase inhibitor (1-isoquinolinylsulfonyl)-2-methyl- piperazine dihydrochloride (H-7), which blocks acto-myosin contractility and disrupts actin cables in cultured cells, also potentiates cytochalasin- induced dissociation and promotes the projection of numerous actin-rich lamellipodial extensions. The fact that EVL cells produce microspike-like structures towards the YSL and are capable of lamellipodial activity lend further support to the suggestion (R.W. Keller and J.P. Trinkaus. 1987. Dev. Biol. 120: 12-24) that the EVL cells are not passively mobilized on the expanding YSL but actively participate in epiboly.

In this study we have examined for molecular heterogeneity of cell-matrix adhesions and the involvement of actomyosin contractility in the selective recruitment of different plaque proteins. For this purpose, we have developed a novel microscopic approach for molecular morphometry, based on automatic identification of matrix adhesions, followed by quantitative immunofluorescence and morphometric analysis. Particularly informative was fluorescence ratio imaging, comparing the local labeling intensities of different plaque molecules, including vinculin, paxillin, tensin and phosphotyrosine-containing proteins. Ratio imaging revealed considerable molecular heterogeneity between and within adhesion sites. Most striking were the differences between focal contacts, which are vinculin- and paxillin-rich and contain high levels of phosphotyrosine, and fibrillar adhesions, which are tensin-rich and contain little or no phosphotyrosine. Ratio imaging also revealed considerable variability in the molecular substructure of individual focal contacts, pointing to a non-uniform distribution of phosphotyrosine and the different plaque constituents. Studying the quantitative relationships between the various components of the submembrane plaque indicated that the levels of vinculin, paxillin and phosphotyrosine in adhesion sites are positively correlated with each other and negatively correlated with the levels of tensin. Tyrosine phosphorylation of focal contacts was highly sensitive to cellular contractility, and was diminished within 5 minutes after treatment with the kinase inhibitor H-7, an inhibitor of actomyosin contractility. This was followed by the loss of paxillin and vinculin from the focal adhesions. Tensin-rich fibrillar adhesions were relatively insensitive to H-7 treatment. These findings suggest a role for contractility in the generation of matrix adhesion diversity.

Ligand-induced down-regulation of two growth factor receptors, EGF receptor (ErbB-1) and ErbB-3, correlates with differential ability to recruit c-Cb1, whose invertebrate orthologs are negative regulators of ErbB. We report that ligand-induced degradation of internalized ErbB-1, but not ErbB- 3, is mediated by transient mobilization of a minor fraction of c-Cb1 into ErbB-1-containing endosomes. This recruitment depends on the receptor's tyrosine kinase activity and an intact carboxy-terminal region. The alternative fate is recycling of internalized ErbBs to the cell surface. Cb1- mediated receptor sorting involves covalent attachment of ubiquitin molecules, and subsequent lysosomal and proteasomal degradation. The oncogenic vital form of Cbl inhibits down-regulation by shunting endocytosed receptors to the recycling pathway. These results reveal an endosomal sorting machinery capable of controlling the fate, and, hence, signaling potency, of growth factor receptors.

Neuregulin, or neu differentiation factor, induces cell proliferation or differentiation through interaction with members of the ErbB family of receptor tyrosine kinases. We report that neuregulin can also induce profound morphogenic responses in cultured epithelial cells of different origins. These effects include scattering of small epithelial islands and rearrangement of larger cell islands into ordered ring-shaped arrays with internal lumens. The ring-forming cells are interconnected by cadherin- and β-catenin-containing adherens junctions. In confluent cultures, neuregulin treatment induces formation of circular lumenlike gaps in the monolayer. Both cell scattering and ring formation are accompanied by a marked increase in cell motility that is independent of hepatocyte growth factor/scatter factor and its receptor (c-Met). Affinity-labeling experiments implied that a combination of ErbB-2 with ErbB-3 mediates the morphogenic signal of neuregulin in gastric cells. Indeed, a similar morphogenic effect could be reconstituted in nonresponsive cells by coexpression of ErbB-2 and -3. We conclude that a heterodimer between the kinase-defective neuregulin receptor, ErbB-3, and the coreceptor, ErbB-2, mediates the morphogenetic action of neuregulin.

Differential interference contrast (DIC) microscopy is the preferred imaging mode for studying live unstained cells and embryos. This is mainly attributed to the optical sectioning capability which makes DIC suitable for three-dimensional microscopy. However, DIC images are not convenient for standard computerized image interpretation. We present here a processing algorithm that converts DIC images into a form which is much more amenable for such analysis. The algorithm is based on computational inversion of the directional gradient performed optically by DIC, namely path integration (line integrated DIC, or LID). LID images relate to the refractive index of the specimen, and are inherently positive in value, thus many powerful algorithms developed for fluorescent images can be applied to them. The method is demonstrated here for identifying and tracking nuclei in developing zebrafish embryos, and for reconstructing the shape of live leukocytes.

A modified optical system for the light microscope has been devised in order to remotely shift the focal plane and to manipulate the point spread function for any given objective lens. An adjustable telescope system is inserted into the microscope tube so as to move the intermediate image position, thus achieving two goals of fundamental importance for the three- dimensional imaging of biological samples. First, it allows the focus to be rapidly varied without actually moving the objective lens. This permits high throughput three-dimensional microscopy of living specimens. Secondly, it makes possible the compensation of objective lens spherical aberration. This distortion is especially significant when high numerical aperture objectives are utilized to image deep into thick specimens.

The early development of the zebra fish (Danio rerio) embryo is characterized by a series of rapid and synchronous cell cycles with no detectable transcription. This period is followed by the midblastula transition (MBT), during which the cell cycle gradually lengthens, cell synchrony is lost, and zygotic transcription is initially detected. In this work, we examined the changes in the pattern of the cell cycle during MBT in zebra fish and whether these changes are dependent on the initiation of zygotic transcription. To characterize the pattern of the early zebra fish cell cycles, the embryonic DNA content was determined by flow cytometric analysis. We found that G₁ phase is below detection levels during the first 10 cleavages and can be initially detected at the onset of MBT. Inhibition of zygotic transcription, by microinjection of actinomycin D, abolished the appearance of G₁ phase at MBT. Premature activation of zygotic transcription, by microinjection of nonspecific DNA, induced G₁ phase before the onset of MBT, while coinjection of actinomycin D and nonspecific DNA abolished this early appearance of G₁ phase. We therefore suggest that during the early development of the zebra fish embryo, G₁ phase appears at the onset of MBT and that the activation of transcription at MBT is essential and sufficient for the G₁-phase induction.

The mucociliary system is one of the most important airway defense mechanisms, and knowledge of the mucociliary wave frequency (MWF) is important in the understanding of this system. Employing a laser light scattering technique and a thin, flexible fiberoptic probe, we developed and tested a simple and practical device for real-time in vivo measurements of mucociliary activity in the human nose. The laser instrument is user-friendly and does not produce any discomfort to the patient. The mean ± SE of MWF of 36 measurements in 16 normal subjects was 7.7 ± 0.5 Hz. The mean MWF of 17 measurements in 7 patients with allergic rhinitis was 5.5 ± 0.2 Hz (p < .005), and the mean MWF of 56 measurements in 17 patients with septum deviation was 5.8 ± 0.2 Hz (p < .001). The instrument presented in this study might provide a new and convenient method of studying the mucociliary activity in the respiratory tract.

Based on a laser light scattering technique and fibre optic probe, we have developed and tested a simple and practical device for real time measurements of ciliary activity in human Fallopian tubes during laparoscopy and laparotomy. A further aim was to investigate the relationship between the ciliary beat frequency (CBF) and the morphology of the ciliary epithelium. The mean ± SE of CBF in the fimbria and in the ampulla were 5.4 ± 0.3 Hz and 5.0 ± 0.1 Hz respectively. Small pieces of fimbria and ampulla epithelium were taken from the same sites at which the CBF was measured, and the percentage of ciliary cells was determined by scanning electron microscopy. A high positive correlation was found between CBF and the percentage of ciliary cells in the fimbria (r = 0.84) and in the ampulla (r = 0.88). The instrument presented in this study provided, for the first time, a quantitative examination of the CBF in intact human Fallopian tubes and may be used for the investigation of ciliary activity in patients with infertility.

The assembly of focal adhesions was investigated in F9 embryonal carcinoma cells in which the expression of vinculin was eliminated by a targeted disruption of the vinculin gene. Vinculin-deficient F9 cells were capable of adhering to fibronectin-coated surfaces, though they displayed a reduced spreading compared to the parental cells. Transmission electron microscopy as well as interference reflection microscopy of live cells showed that vinculin-null F9 cells formed focal adhesions that were indistinguishable from those of the control cells. Fluorescent labeling for actin, talin, α-actinin, paxillin and phosphotyrosinated components indicated that the organization of all these focal contact-associated components was essentially identical in the vinculin-containing and vinculin-null cells. However, quantitative, digitized microscopy indicated that the intensity of fluorescence labeling in focal adhesions for α-actinin, talin and paxillin was significantly higher in cells lacking vinculin. The results suggest that there are multiple molecular mechanisms for the formation of focal adhesions in the absence of vinculin.

Quantitative microscopic imaging of resonance energy transfer (RET) was applied for immunological high resolution proximity mapping of several cytoskeletal components of cell adhesions. To conduct this analysis, a microscopic system was developed, consisting of a highly stable field illuminator, computer-controlled filter wheels for rapid multiple-color imaging and a sensitive, high resolution CCD camera, enabling quantitative data recording and processing. Using this system, we have investigated the spatial inter-relationships and organization of four adhesion-associated proteins, namely vinculin, talin, α-actinin and actin. Cultured chick lens cells were double labeled for each of the junctional molecules, using fluorescein- and rhodamine-conjugated antibodies or phalloidin. RET images were acquired with fluorescein excitation and rhodamine emission filter setting, corrected for fluorescein and rhodamine fluorescence, and normalized to the fluorescein image. The results pointed to high local densities of vinculin, talin and F-actin in focal adhesions, manifested by mean RET values of 15%, 12% and 10%, respectively. On the other hand, relatively low values (less than 1%) were observed following double immunofluorescence labeling of the same cells for α-actinin. Double indirect labeling for pairs of these four proteins (using fluorophore-conjugated antibodies or phalloidin) resulted in RET values of 5% or lower, except for the pair α-actinin and actin, which yielded significantly higher values (13-15%). These results suggest that despite their overlapping staining patterns, at the level of resolution of the light microscope, the plaque proteins vinculin and talin are not homogeneously interspersed at the molecular level but form segregated clusters. α-Actinin, on the other hand, does not appear to form such clusters but, rather, closely interacts with actin. We discuss here the conceptual and applicative aspects of RET measurements and the implications of the results on the subcellular molecular organization of adherens-type junctions.

Ncadherin cDNA was cloned from a zebrafish embryonic cDNA library. Analysis of the deduced amino acid sequence of this moleoule (ZNeadherin) revealed a high degree of homology to Ncadherins of other species, except that its presequence is considerably shorter. Nevertheless, following transfection into chinese hamster ovary (CHO) cells, the expressed protein was functionally active, namely participated in calciumdependent intercellular interactions. Moreover, ectopic overexpression of ZNcadherin, following mRNA microinjection into 24 cell embryos, caused microaggregation and uneven segregation of deep cells, resulting in distorted embryos. Developmental Northern and Western blot analyses indicated that both the mRNA and the protein first appear at gastrulation. Insitu hybridization showed that ZNcadherin mRNA was initially present in all deep cells, and later became restricted to various epithelial and neural tissues. Wholemount immunostaining indicated that while ZNcadherin was already present at 50% epiboly, it became associated with cell junctions only 45 h later. In developing somites ZNcadherin expression was prominent but transient. High levels of the protein were detected in epithelial somites and its expression was apparently down regulated concomitantly with the onset of myogenesis. © 1994 WileyLiss, Inc.

EXPRESSION OF G1 CYCLINS DURING EARLY DEVELOPMENT OF ZEBRAFISH EMBRYOS

The locomotion of human polymorphonuclear leukocytes (PMNs) was studied with two complementary methods: Threedimensional shapes were reconstructed from time series of optical sectioning microscopy using differential interference contrast (DIC) optics, and the diffusion of cytoplasm granules within individual cells was measured using quasielastic laser light scattering (QELS). The threedimensional cell edges outlined in the optical sections were analyzed qualitatively in timelapse film strips and quantitatively from morphometry. The fastest locomotion occurred in chemotactic gradient with cell velocity that oscillated between 10 and 30 μm/min with a period of 5055 seconds. Within the periodic bursts of speed, a fibroblastlike locomotory cycle was observed, with leading lamella extended and contacts formed with the substrate surface, followed by rapid motion of the cell body and nucleus over the immobile contacts. Consistent with this apparent staged motion, correlation analysis revealed a phase lag of 23 seconds in velocities between the bottom (ventral) and the top layers of the cell. In addition there was a tendency to a lower cell profile at times of higher velocity. The diffusion of natural cytoplasmic granules within resting PMNs was not affected by cytoskeleton disrupting drugs. During the stage of most rapid motion, when cytoplasmic streaming could be seen, diffusion of the granules decreased two to 2.5fold, and then returned to resting levels. These observations suggest that PMN locomotion consists of extensions near the surface to form forward contacts and then stiffening or possibly contraction of the cytoskeleton when the body of the cell is moved forward. Threedimensional movies of PMN cells are included in the video supplement. © 1994 WileyLiss, Inc.

A new modular transmission and fluorescence illumination system has been designed and built. The approach utilizes fiber optics to scramble the spatial intensity variations and digital monitoring of light intensity to allow accurate correction for inherent temporal instability. The illumination system has been characterized by a variety of methods and is shown to have an evenly filled objective back focal plane for maximal resolution in all three axes. The use of this illumination system in conjunction with a scientific grade CCD camera and pixelbypixel correction makes possible data of such high quality as to be only limited by the photon counting statistics. This illumination approach has proven to be particularly important for threedimensional imaging coupled with image processing to remove outoffocus information.

The distribution of adherens junction (AJ) components was investigated in cultured heart myocytes. These cells, derived from either newborn rats or chick embryos, develop elaborate arrays of myofibrils which become extensive and laterally aligned following several days in culture. The Z-disks in these cells, visualized by immunolabeling with antibodies to muscle-specific alpha-actinin, exhibit a characteristic periodicity of about 2-mu-m and are in register with those of neighboring myofibrils throughout the sarcoplasm. Vinculin, in these celts, associates with intercellular AJ and cell-matrix adhesions. In addition, this protein is detected in periodic bands located along the lateral cell membranes corresponding to "costamers" previously described by Pardo, J.V., Siliciano, J.D. and Craig, S.W. (Proc. Natn. Acad. Sci. USA, 80, 1008). Similarly, N-cadherin, which is predominantly associated with intercellular junctions, is also detected in periodic striations located mainly on the dorsal and lateral cell surfaces. Using computer-aided three-dimensional microscopy confirmed that these vinculin- and N-cadherin-containing structures are located in extrajunctional sites, apparently associated with Z-disks of peripheral myofibrils. Based on these findings an alternative pathway is proposed for the assembly of vinculin and N-cadherin, which is not triggered by adhesive interactions with extracellular surfaces but rather by interactions at the membrane-cytoplasm interphase with the periphery of the pre-assembled myofibrils. Moreover, we present evidence that antibodies to N-cadherin, which are capable of blocking AJ formation in culture, have an inhibitory effect also on the development and alignment of myofibrils. We discuss the functional significance of the "costameric" organization of vinculin and N-cadherin and consider its involvement both in the lateral alignment of neighboring muscle celts and in the stabilization of developing myofibrils.

The first event of Drosophila gastrulation is the formation of the ventral furrow. This process, which leads to the invagination of the mesoderm, is a classical example of epithelial folding. To understand better the cellular changes and dynamics of furrow formation, we examined living Drosophila embryos using three-dimensional time-lapse microscopy. By injecting fluorescent markers that visualize cell outlines and nuclei, we monitored changes in cell shapes and nuclear positions. We find that the ventral furrow invaginates in two phases. During the first 'preparatory' phase, many prospective furrow cells in apparently random positions gradually begin to change shape, but the curvature of the epithelium hardly changes. In the second phase, when a critical number of cells have begun to change shape, the furrow suddenly invaginates. Our results suggest that furrow formation does not result from an ordered wave of cell shape changes, contrary to a model for epithelial invagination in which a wave of apical contractions causes invagination. Instead, it appears that cells change their shape independently, in a stochastic manner, and the sum of these individual changes alters the curvature of the whole epithelium.

The first event of Drosophila gastrulation is the formation of the ventral furrow. This process, which leads to the invagination of the mesoderm, is a classical example of epithelial folding. To understand better the cellular changes and dynamics of furrow formation, we examined living Drosophila embryos using three-dimensional time-lapse microscopy. By injecting fluorescent markers that visualize cell outlines and nuclei, we monitored changes in cell shapes and nuclear positions. We find that the ventral furrow invaginates in two phases. During the first 'preparatory' phase, many prospective furrow cells in apparently random positions gradually begin to change shape, but the curvature of the epithelium hardly changes. In the second phase, when a critical number of cells have begun to change shape, the furrow suddenly invaginates. Our results suggest that furrow formation does not result from an ordered wave of cell shape changes, contrary to a model for epithelial invagination in which a wave of apical contractions causes invagination. Instead, it appears that cells change their shape independently, in a stochastic manner, and the sum of these individual changes alters the curvature of the whole epithelium.

The toxic lectin ricin has been covalently labelled with fluorescein isothiocyanate on the enzymatically active A chain. The fluorescein reacted toxin maintains its biological activity. The lateral diffusion coefficient of cell surface bound ricin, studied in two cell lines by fluorescence photobleaching recovery, is D = 1 - 2 × 10^-10 cm²/s. Fluorescence microscopy provides preliminary evidence for secondary endosomes in the cytoplasm.

Computerized image-intensified fluorescence microscopy has been used to quantify routing and subcellular concentrations of rhodaminated EGF (Rh-EGF) during its receptor-mediated endocytosis in two transfected NIH-3T3 cell lines expressing 2 x 10⁵ and 1.5 x 10⁶ receptors per cell, respectively. A series of images were digitized by focusing at different depths through the volume of a single cell. The digitized pictures were corrected for fluorescence photobleaching, and removal of out-of-focus fluorescence contributions by deconvolution using the point spread function of the microscope optics (Agard, D.A., and J.W. Sedat. 1980. Proc. Soc. Photo-Opt. Instr. Eng. 264:110-117) allowed automatic computer analysis of the time dependence of endosomal vesicle size and fluorescence intensity in a live cell and also enabled the study of isolated vesicles. An increase in the amount of fluorescence bound to the cell surface, either by increasing the number of receptors expressed per cell or the concentration of Rh-EGF in the incubation drop, yielded an increase in the total fluorescence of internalized vesicles without an increase in their number and area. The linear relation between fluorescence intensity and area for vesicles at different times indicates that EGF concentration is conserved. This is compatible with fusion of small vesicles to form larger ones. However, as endocytosis proceeds, a twofold increase in the slope of fluorescence vs. area plots is observed for larger vesicles, suggesting that active sorting causes the EGF to be concentrated. Alternatively, this factor could be produced by cumulative fluorescence contributions from stacked membranes. Since coated pits are internalized independent of their occupancy with EGF receptor, we propose that endocytosis does not involve a mechanism specifically recognizing occupied receptors but is rather triggered by a global intracellular event.

Interactions between membrane proteins are believed to be important for the induction of transmembrane signaling. Endocytosis is one of the responses which is regulated by both intracellular and extracellular signals. To study such interactions, we have measured the lateral mobility and rate of endocytosis of epidermal growth factor receptor in three transfected NIH-3T3 cell lines (HER84, HER22, and HER82) expressing 2 x 10⁴, 2 x 10⁵ and 1.5 x 10⁶ EGF-receptors per cell, respectively. Using rhodamine-labeled EGF (Rh-EGF) and rhodamine-labeled monoclonal anti-EGF-receptor antibody (Rh-mAb-108), we measured twofold decreases in the lateral diffusion coefficients for each ~10-fold increase in EGF-receptor concentration. Since steric effects cannot account for such dependence, we propose that protein mobility within the membrane, which is determined by the rate of motion between immobile barriers, decreases due to aggregate formation. The rate of endocytosis also decreases twofold between the HER84 92 x 10⁴ receptors/cell) and HER22 (2 x 10⁵ receptors/cell) cell lines, suggesting that it is diffusion limited. The comparable rates of endocytosis of the HER82 and HER22 cell lines suggest that at high receptor density endocytosis may be limited by the total number of sites for receptors in coated-pits and by their rate of recycling.

Quasi-elastic light scattering has been used to examine solutions and gels of deoxyhemoglobin S. The autocorrelation function is found to decay with a characteristic exponential relaxation which can be ascribed to the diffusion of monomer (64,000 molecular weight) hemoglobin S molecules. In the absence of polymers, the relaxation time is in good agreement with previous measurements of the diffusion coefficient for solutions of normal human hemoglobin. In the presence of the polymer phase, a large (greater than 200-fold) increase in the scattered intensity is observed but no contribution to the decay of the autocorrelation function from the motion of the aligned polymer phase can be detected. Heterodyning between the time-independent scattering amplitude from the polymers and the time-dependent scattering of the diffusing monomers results in a twofold increase in the relaxation time arising from monomer diffusion.

Correlation averaging was used to enhance the three-dimensional spherical harmonic expansion of human wart virus particles from randomly-oriented negatively-stained electron microscopic images in holey grids. The reconstruction reveals the coat protein arrangement and variations in stain distribution inside the virus core. Selection rules imposed by the spherical symmetry on the harmonic expansion component are obtained indeed for angular momenta, l, lower than 11, but cannot be shown for l≥11, due to non-spherical distortions of about 1/11th of the radius of the virus. This prevents us from resolving fine details of packing of the protomers on the surface lattice. Distribution of stain inside the virus core, and its spherical symmetry, is reconstructed and may be related to nucleic acids and core protein structure.

The structure of spectrin dimers and tetramers in solution has been examined by light, low-angle X-ray and neutron scattering. The results show a good correspondence between the solution dimensions of these molecules and their appearance in the electron microscope after shadowing. The scattering profiles are not compatible with an extended rod-like character, but reflect the presence of a considerable degree of bending. The radii of gyration of the dimer and tetramer were determined to be 170 and 375 Å and the cross-section radii of gyration 14 and 12.3 Å. respectively. Both are thus long. thin. rather bent molecules, and the tetramer is twice the length of the dimer.

The analysis of particle images displaying the same orientation in the electron micrographs is carried out by enhancement of auto-correlations of image densities as a function of the spatial coordinates of single particle images. The averaging of the spatial correlations, which is "incoherent" since it does not require alignment of the individual images, is compared to existing coherent averaging methods of enhancement using lattices and single particle images aligned by cross correlations.

Cross-correlation between two detectors was applied to analyze laser light-scattering fluctuations. Laser scattering from random concentration fluctuations is spatially coherent over small angular areas that are inversely proportional in size to the dimension of the scattering volume. By cross-correlating scattering intensity fluctuations in different angles, the correlation due to relaxation of concentration fluctuations is practically eliminated, and correlations reflecting changes in the scattering from the individual particles can be enhanced. Rotational diffusion of assymetric particles, conformational relaxation of random coils, and association-dissociation dynamics are determined here using the above approach.

Malate dehydrogenase from the organism Halo-bacterium marismortui was studied in solutions of varying salt concentration by using a small-angle X-ray system employing a linear position sensitive detector. Considerations pertaining to the study of absorbing multicomponent solutions are presented. The radius of gyration of halophilic malate dehydrogenase was found to be 31.8 ± 0.6 Å and the shape of the molecule spheroidal. The scattering from prolate ellipsoids of eccentricity between 1 and 2 best fitted the data while for oblate ellipsoids the scattering was best fitted for eccentricities between 1 and 0.5. No significant change in the radius of gyration or anisotropy of halophilic malate dehydrogenase was found in the range of NaCl concentrations studied (14 M). The contrast matching electron density was found to be 0.407 ± 0.002 e/ų. A parallel study of bovine serum albumin yielded within experimental error a similar contrast matching electron density of 0.404 ± 0.006 e/ų. This information combined with the diffusion coefficient and the amount of water and salt associated with halophilic malate dehydrogenase renders the existence of an outer hydration shell unlikely. The data are rather consistent at low resolution with a spheroidal particle of uniform electron density.

We show that the persistence length a of DNA, derived from total intensity laser light scattering of linear Col E₁ DNA and corrected for excludedvolume effects, varies from about 68 nm in 0.005M NaCl to about 40 nm in 0.2M NaCl, leveling off to a constant value (about 27 nm) at high NaCl (14M) concentration. These observations do not agree with current views on the effect of electrostatic charge and ionic conditions on DNA dimensions. The apparent diffusion constant D_app, determined from laser light scattering autocorrelation as a function of scattering vector q, at NaCl concentrations 0.0054M, correctly yields the translational diffusion coefficient D_t at low values of q and scales with molecular dimensions rather than segment length at high values of q; thus, D_app/D_t yields a universal curve when plotted against q²Rg2, where R_g is the radius of the gyration. The sedimentation coefficients s at 0.1 and 0.2M NaCl concentration closely agree with the welltested empirical relations, and a combination of s, D_t, and the appropriate density increments yield correct molar masses over the whole salt concentration range. Approximate constancy of D_tR_g indicates limited draining in translational flow. We present some observations and thoughts on the regimes in which a dependence of the correlation decay times on q³ rather than q² applies. We conclude that quasielastic laser light scattering discloses little information about dynamics of internal motion of DNA chains.

We propose to use the sun as a bright incoherent light source to probe the rotational diffusion of asymmetric particles. Lateral (spatial) coherence of the sun can be adjusted by proper optics to be shorter than the interparticle distance. In contrast to laser light scattering, where translational diffusion contribution dominates the scattering fluctuations, this method may probe directly into the time course of particles rotation and internal motion.

For the study of DNA conformations, conformational transitions, and DNA-protein interactions, covalently closed supercoiled ColE₁-plasmid DNA has been purified from cultures of Escherichia coli harboring this plasmid and grown in the presence of chloramphenicol according to the method of D.B. Clewell [ J. Bact. 110 (1972) 667]. The open circular and linear forms of the plasmid were prepared by digestion of the covalently closed, supercoiled form with pancreatic deoxyribonuclease and EcoRI-restriction endonuclease, respectively. The linear form was found to be very homogeneous by electron microscopy and sedimenting boundary analysis. Its physical properties (s⁰_20,w = 16.3 S,D⁰_20,w = 1.98× l0^-8 cm²s^-1 and [η] = 2605 ml g^-1)have been carefully determined in 0.2 M NaCl, 0.002 M NaPO₄ pH 7.0,0.002 M EDTA, at 23°C. Combination of s⁰_20,w and D⁰_20,w (obtained by quasielastic laser light scattering) gave M_s,D= = 4.39 × 10⁶. This value is in reasonable agreement with the molecular weight from total intensity laser light scattering M = 4.30 × 10⁶. The covalently closed and open circular forms of the ColE₁-plasmid are less homogeneous due to slight cross-contamination and the presence of small amounts of dimers in these preparations. The weight fractions of the various components as determined by boundary analysis or electron microscopy are given together with the averaee quantities obtained in the same solvent for the supercoiled form(< s⁰_20,w>_ww = 25.4 S. _z = 2.89 × 10^-8cm²s^-1, [η] = 788 ml g^-1, M_s,D, = 4.69 × 10⁶ and M_w, = 4.59 × 10⁶) and the open circular form (s⁰_20,w>_w = 20.1 S, _z = 2.45 × 10^-8 cm²s^-1,[η]= 1421 ml g^-1, M_s,D = 4.37 × 10 and M_w= 4.15 × 10 ). Midpoint analysis of the sedimenting boundaries allows unambiguous determination of the sedimentation coefficients of these two forms: s⁰_20,w = 24.5 S and s⁰_20,w = 18.8 S, respectively. Also deduced from total intensity light scattering were radii of gyration R_g (103.5, 134.2 and 186 nm) and second virial coefficients A₂ (0.7,4.8 and 5.4 × 10^-4 mole ml g²) for the supercoiled, the open circular and linear forms, respectively. The data presented are discussed in relation to the confonnational parameters for the three forms in solution.

Human erythrocyte spectrin prepared from fresh blood is a mixture of different association states. Depending on the manner of preparation, the two-chain dimer or the tetramer predominates. These forms are not in rapid thermodynamic equilibrium. The molecular weight of the dimer by sedimentation and diffusion and by light scattering is about 5 × 10⁵. The frictional properties indicate a low or moderate asymmetry (axial ratio in the range 2-10), and from the angular dependence of light scattering intensity an upper limit of about 80 Å can be set for the radius of gyration. The tetramer similarly has a moderate asymmetry. Electron microscopy reveals that the dimer is a compact, slightly elongated molecule, and that the tetramer probably consists of two parallel dimers. On increasing the concentration of solutions containing spectrin dimers, oligomers are formed, which are not rapidly dissociated on dilution. At very low protein concentrations (below about 0.05 mg/mL) there is evidence of the onset of a rapid dissociation equilibrium between dimers and single chains. Other physical properties of the spectrin have been measured. The size and shape of the spectrin molecule would seem to rule out any major physical resemblance to myosin.

I propose a new type of scattering technique which includes measurements of scattering intensities at two angles and accumulates the spatial correlation of fluctuations of elastic scattering from solutions. A theoretical analysis of the proposed method shows that it contains structural information much more detailed than the classical diffuse, orientationally averaged scattering intensity pattern. In principle it approaches the information obtainable from difffraction studies of single crystals. A data acquisition and reduction scheme is described. It solves the coefficients of expansion in spherical harmonics that give the oriented, single-particle scattering intensity pattern. The experimental conditions required to perform the proposed measurements and the resolution limitations are discussed. A simple example is presented as an illustration.