Automated segmentation of electron tomograms for a quantitative description of actin filament networks

Cryo-electron tomography allows to visualize individual actin filaments and to describe the three-dimensional organization of actin networks in the context of unperturbed cellular environments. For a quantitative characterization of actin filament networks, the tomograms must be segmented in a reproducible manner. Here, we describe an automated procedure for the segmentation of actin filaments, which combines template matching with a new tracing algorithm. The result is a set of lines, each one representing the central line of a filament. As demonstrated with cryo-tomograms of cellular actin networks, these line sets can be used to characterize filament networks in terms of filament length, orientation, density, stiffness (persistence length), or the occurrence of branching points.     

In situ electron microscopic observation of negatively stained tissue culture cells contaminated with mycoplasmas

A simple, fast, and in situ method of detecting the inapparent infection of cultured cells with mycoplasmas is reported. Animal cells grown on Formvar-coated electron microscopic grids were directly fixed with glutaraldehyde, negatively stained with phosphotungstic acid and examined by transmission electron microscopy. Cells contaminated with mycoplasmas could be discriminated from uncontaminated cells. The micro-organisms in the negatively stained preparations corresponded with those revealed by thin sectioning, and the distribution of mycoplasmas in cultured cells coincided with those revealed by the Hoechst staining method. Most of the highly resolved mycoplasmas were polymorphic, and closely associated with host cells; often more than 500 organisms per host cell were seen.     

Actin filament labels for localizing protein components in large complexes viewed by electron microscopy

Localizing specific components in three-dimensional reconstructions of protein complexes visualized in an electron microscope increases the scientific value of those structures. Subunits are often identified within the complex by labeling; however, unless the label produces directly visible features, it must be detected by computational comparison with unlabeled complex. To bypass this step, we generated a cloneable tag from the actin-nucleating protein Spire that produces a directly visible “pointer” to the subunit after actin polymerization. We have used this new label to identify the intron of the C complex spliceosome to its small domain by fusing the 10 kDa Spire moiety to the affinity label that binds recombinant stem loops in the pre-mRNA substrate and assembling an actin filament on the particle.     

Actin filament organization in the fish keratocyte lamellipodium

From recent studies of locomoting fish keratocytes it was proposed that the dynamic turnover of actin filaments takes place by a nucleation- release mechanism, which predicts the existence of short (less than 0.5 microns) filaments throughout the lamellipodium (Theriot, J. A., and T. J. Mitchison. 1991. Nature (Lond.). 352:126-131). We have tested this model by investigating the structure of whole mount keratocyte cytoskeletons in the electron microscope and phalloidin-labeled cells, after various fixations, in the light microscope. Micrographs of negatively stained keratocyte cytoskeletons produced by Triton extraction showed that the actin filaments of the lamellipodium are organized to a first approximation in a two-dimensional orthogonal network with the filaments subtending an angle of around 45 degrees to the cell front. Actin filament fringes grown onto the front edge of keratocyte cytoskeletons by the addition of exogenous actin showed a uniform polarity when decorated with myosin subfragment-1, consistent with the fast growing ends of the actin filaments abutting the anterior edge. A steady drop in filament density was observed from the mid- region of the lamellipodium to the perinuclear zone and in images of the more posterior regions of lower filament density many of the actin filaments could be seen to be at least several microns in length. Quantitative analysis of the intensity distribution of fluorescent phalloidin staining across the lamellipodium revealed that the gradient of filament density as well as the absolute content of F-actin was dependent on the fixation method. In cells first fixed and then extracted with Triton, a steep gradient of phalloidin staining was observed from the front to the rear of the lamellipodium. With the protocol required to obtain the electron microscope images, namely Triton extraction followed by fixation, phalloidin staining was, significantly and preferentially reduced in the anterior part of the lamellipodium. This resulted in a lower gradient of filament density, consistent with that seen in the electron microscope, and indicated a loss of around 45% of the filamentous actin during Triton extraction. We conclude, first that the filament organization and length distribution does not support a nucleation release model, but is more consistent with a treadmilling-type mechanism of locomotion featuring actin filaments of graded length. Second, we suggest that two layers of filaments make up the lamellipodium; a lower, stabilized layer associated with the ventral membrane and an upper layer associated with the dorsal membrane that is composed of filaments of a shorter range of lengths than the lower layer and which is mainly lost in Triton.     

Comparative electron microscopic studies of partially negatively stained, freeze-dried and freeze-fractured cytochrome reductase membrane crystals

Membrane crystals of ubiquinol: cytochrome c reductase have been studied by electron microscopy of one-sided negatively stained, freeze-dried and freeze-fractured specimens. The results confirm the unequal distribution of protein on both membrane surfaces which was found by three-dimensional image reconstruction. During freeze-drying, however, a considerable change in the lattice constants occurred. Furthermore, the apparent position of protein relative to the bilayer was changed by interaction with the support. The freeze-fracture plane was found to lie within the hydrophobic middle of the bilayer, splitting the membrane crystal into two equal leaflets.     

Filament arrangements in negatively stained cultured cells: the organization of actin

Treatment of spread, cultured cells with Triton X-100 followed by negative staining reveals the organization of the unextracted intracellular filamentous elements: actin, microtubules and the 100 angstrom filaments. The present report describes the organization of the actin-like filaments in human skin fibroblasts and mouse 3 T 3 cells. As shown in earlier studies, the cytoplasmic stress fibres were seen to be composed of bundles of colinear actin-like filaments. In addition to these large stress fibres much smaller bundles of thin filaments as well as randomly oriented thin filaments were also observed. A thick bundle of thin filaments, 0.2 microm to 0.5 microm in diameter, was found to delimit the concave cell edges most prominent in well-spread stationary cells. The leading edge and ruffled border of human skin fibroblasts appeared as a broad web, of meshwork of diagonally oriented thin filaments interconnecting radiating, linear bundles of thin filaments about 0.1 microm in diameter. These bundles corresponding to the microspikes described earlier ranged from about 1.5 microm in length and were separated by 1 microm to 3 microm laterally. The leading edge of 3 T 3 cells showed a similar organization but with fewer radiating thin filament bundles. Both the filaments in the bundles and in the meshwork formed arrowhead complexes with smooth muscle myosin subfragment - 1 which were unipolar and directed towards the main body of the cell. The findings are discussed in relation to the mechanisms of non-muscle cell motility.     

Attempted direct visualization of negatively stained amplified immune complex of synaptic acetylcholinesterase using cryoultramicrotomy sections

Summary An immunocytochemical method is proposed for the localization of synaptic acetylcholinesterase (AChE) on ultrathin frozen sections of the electric organ of the electric eel. The immune complex formed is amplified by a non-specific sandwich technique and visualized by negative staining. Definite white spots on synaptic cleft seem to correspond to basal lamina AChE molecules.     

Ultrastructure of the eukaryotic aminoacyl-tRNA synthetase complex derived from two dimensional averaging and classification of negatively stained electron microscopic images

Several aminoacyl-tRNA synthetases in higher eukaryotes are consistently isolated as a multi-enzyme complex for which little structural information is yet known. This study uses computational methods for analysis of electron microscopic images of the particle. A data set of almost 2000 negatively stained images was processed through reference-free alignment and multivariate statistical analysis. Interpretable structural information was evident in five eigenvectors. Hierarchical ascendant classification extracted clusters corresponding to distinct image orientations. The class averages are consistent with rotations around and orthogonal to a central particle axis and provide particle measurements: approximately 25 nm in height, 30 nm at the widest point and 23 nm thick. The results also provide objective evidence in support of the working structural model and demonstrate the feasibility of obtaining the three dimensional structure of the multisynthetase complex by single particle reconstruction methods.     

Actin filament organization of foot processes in rat podocytes.

The foot processes of podocytes possess abundant microfilaments and modulate glomerular filtration. We investigated the actin filament organization of foot processes in adult rat podocytes and the formation of the actin cytoskeletal system of immature podocytes during glomerulogenesis. Electron microscopy revealed two populations of actin cytoskeletons in foot processes of adult podocytes. One is the actin bundle running above the level of slit diaphragms and the other is the cortical actin network located beneath the plasmalemma. Immunogold labeling for actin-binding proteins demonstrated that alpha-actinin and synaptopodin were localized in the actin bundle, whereas cortactin was in the cortical actin network. Immunofluorescence labeling for actin-binding proteins in immature podocyte showed that alpha-actinin was localized at the level of the junctional complex, whereas cortactin was distributed beneath the entire plasmalemma. Synaptopodin was first observed along the basal plasmalemma from the advanced S-shaped body to the capillary loop stage. We conclude that foot processes have specialized actin filamentous organization and that its establishment is associated with the expression and redistribution of actin-binding proteins during development.     

Building a dendritic actin filament network branch by branch: models of filament orientation pattern and force generation in lamellipodia

We review mathematical and computational models of the structure, dynamics, and force generation properties of dendritic actin networks. These models have been motivated by the dendritic nucleation model, which provided a mechanistic picture of how the actin cytoskeleton system powers cell motility. We describe how they aimed to explain the self-organization of the branched network into a bimodal distribution of filament orientations peaked at 35° and ??35° with respect to the direction of membrane protrusion, as well as other patterns. Concave and convex force–velocity relationships were derived, depending on network organization, filament, and membrane elasticity and accounting for actin polymerization at the barbed end as a Brownian ratchet. This review also describes models that considered the kinetics and transport of actin and diffuse regulators and mechanical coupling to a substrate, together with explicit modeling of dendritic networks.     

Electron tomography of negatively stained complex viruses: application in their diagnosis

Pattern recognition receptors are a key component of the first line host defense against infection, recognizing specific microbial products. We hypothesize that monocyte hyporesponsiveness in human sepsis is associated with a downregulation of the pattern recognition receptors Toll-like receptor (TLR)-2 and TLR4. Protein expression of CD14, TLR2 and TLR4 on blood monocytes was examined using flow cytometry from 29 patients with sepsis and 14 healthy controls. In addition LPS stimulated TNF-α and IL-10 production was studied in a 24 hour whole blood assay. We found an increased expression of CD14, TLR2 and TLR4 in patients with sepsis compared to controls (p < 0.01). In patients with sepsis, death was associated with significant lower CD14 and TLR2 expression at admission (CD14: 25.7 +- 19.1 vs 39.1 +- 17.3 mean fluorescence intensity [MFI], p = 0.02; TLR2: 21.8 +- 9.4 vs. 30.9 +- 9.6, p = 0.01). At 72 hours the TLR2 expression on monocytes was associated with the IL-10 inducibility after LPS stimulation (r = 0.52, p = 0.02) and the CD14 expression with the IL-6, IL-10 and TNF inducibility. We conclude that septic patients are characterized by an increased expression of CD14, TLR2 and TLR4 on monocytes compared to controls. Death is associated with downregulation of TLR2 and CD14 expression on monocytes correlating with reduced cytokine inducibility. We suggest that CD14 and TLR2 are a key factor in monocyte hyporesponsibility during severe sepsis.     

Actin dynamics in lamellipodia of migrating border cells in the Drosophila ovary revealed by a GFP-actin fusion protein

Directional migration of border cells in the Drosophila egg chambers is a developmentally regulated event that requires dynamic cellular functions. In this study, the electron microscopic observation of migrating border cells revealed loose actin bundles in forepart lamellipodia and numerous microvilli extending from nurse cells and providing multiple adhesive contacts with border cells. To analyze the dynamics of actin in migrating border cells in vivo, we constructed a green fluorescent protein-actin fusion protein and induced its expression in Drosophila using the GAL4/UAS system. The green fluorescent protein-actin was incorporated into the actin bundles and it enabled visualization of the rapid cytoskeletal changes in border cell lamellipodia. During the growth of the lamellipodia, the actin bundles that increased in number and size radiated from the bundle-organizing center. Quantification of the fluorescence intensity showed that an accumulation of bundle-associated and spotted green fluorescent protein-actin signals took place during their centripetal movement. Our results favored a treadmilling model for actin behavior in border cell lamellipodia.     

Strain field in actin filament network in lamellipodia of migrating cells: Implication for network reorganization

Cell motility is spatiotemporally regulated by interactions among mechanical and biochemical factors involved in the regulation of cytoskeletal actin structure reorganization. Although the molecular mechanisms underlying cell motility have been well investigated, the contributions of mechanical factors such as strain in the network reorganization remain unclear. In this study, we have quantitatively evaluated the strain field in the actin filament network forming the lamellipodia of migrating fish keratocytes to elucidate the mechanism by which actin filament network reorganization is regulated by biomechanical factors. The results highlight the existence of a negative (compressive) strain in the lamellipodia whose direction is parallel to that of cell movement. A close correlation was found between the distributions of the strain and the actin filament density in the lamellipodia, suggesting that negative strain may be involved in filament depolymerization. Based on this result, we propose a selective depolymerization model which suggests that negative strain may couple with biomechanical factors such as ADF/cofilin to promote selective depolymerization of filaments oriented in the direction of the deformation because such filaments experience relatively higher levels of the deformation. This model, in conjunction with others, may explain the observed reduction in filament density and the reorganization of actin filament network at the back of the lamellipodia of migrating fish keratocytes. Thus, we suggest that by coupling with biochemical factors, mechanical factors are involved in the regulation of actin filament depolymerization, thereby contributing to the regulation of cell motility.