The cytomatrix: a short history of its study

Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix

Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.

Physical aspects of sensory transduction on seeing, hearing and smelling

What is the general principle of sensory transduction? Sensory transduction is defined as energy transformation from the external world to the internal world. The energy of the external world, such as thermal energy (heat), electro-magnetic energy (light), mechanical energy (sound) and the energy from molecules (chemicals), is converted into electrochemical events in the animal nervous system. The following five classes of special sense receptors are utilized for energy conversion: vision (photo); audition (sound); taste and smell (chemo); and tactile (mechano). There are also other special sense receptors, including thermo and noxious receptors. The focus of this study is on photoreceptors, sound-receptors and odorant-receptors because the transduction mechanisms of these receptors are explained biochemically and understood by a common physical principle; these biochemical models are well known in neuroscience. The following notable problems are inherent in these biochemical models: the cGMP ionophore model of the vertebrate photoreceptor cannot explain the fast photo-response (∼msec); the tip links connection model of stereocilia in the basilar membrane for opening the K(+) channel on the tip of a hair has difficulty explaining the high frequency vibration of hair cells without a damping of the oscillation, and the odorant shape-specific receptor model for olfactory transduction has difficulty in discriminating the minute differences among similar fragrant smells of essential oils with different molecular shapes. These difficulties might arise from a lack of the physical sense when the transduction models were proposed. This article will reconsider these problems and propose rational models for visual, olfactory and auditory transduction.

Advantages of embedment-free section transmission electron microscopy

The usefulness of embedment-free section transmission electron microscopy (TEM) is stressed for present and future morphological analyses, and several examples are demonstrated which are revealed in sections for the first time by this method: en-face views of slit diaphragm of renal glomerulus and fenestrated diaphragm of capillary endothelium, transparency of neural myelin, attenuated endothelium and some basement laminae, labyrinth architecture of vacuoles within lipid droplets, and enhanced 3D effect of ultrastructures, the latter of which is the case in electron tomography. In addition, the biological significance of structured appearance (microtrabecular lattices) of the cytoplasmic matrix, which is disclosed by this method, are briefly reviewed in relation to the sol-gel transition of cytoplasmic heterogenous proteins. Since the ultrastructures of various cells and tissues in this method are confirmed to be well correspondent to those in conventional epoxy section TEM except for isotropic dimensional changes, and because there is no necessity for any special expensive equipments other than those for the conventional TEM, the embedment-free section TEM method with these advantages, deserves much more wide application to the morphological research including electron tomography.

Coherent Behavior and the Bound State of Water and K(+) Imply Another Model of Bioenergetics: Negative Entropy Instead of High-energy Bonds

Observations of coherent cellular behavior cannot be integrated into widely accepted membrane (pump) theory (MT) and its steady state energetics because of the thermal noise of assumed ordinary cell water and freely soluble cytoplasmic K(+). However, Ling disproved MT and proposed an alternative based on coherence, showing that rest (R) and action (A) are two different phases of protoplasm with different energy levels. The R-state is a coherent metastable low-entropy state as water and K(+) are bound to unfolded proteins. The A-state is the higher-entropy state because water and K(+) are free. The R-to-A phase transition is regarded as a mechanism to release energy for biological work, replacing the classical concept of high-energy bonds. Subsequent inactivation during the endergonic A-to-R phase transition needs an input of metabolic energy to restore the low entropy R-state. Matveev's native aggregation hypothesis allows to integrate the energetic details of globular proteins into this view.

Water in the orchestration of the cell machinery. Some misunderstandings: a short review

Nowadays, biologists can explore the cell at the nanometre level. They discover an unsuspected world, amazingly overcrowded, complex and heterogeneous, in which water, also, is complex and heterogeneous. In the cell, statistical phenomena, such as diffusion, long considered as the main transport for water soluble substances, must be henceforth considered as inoperative to orchestrate cell activity. Results at this level are not yet numerous enough to give an exact representation of the cell machinery; however, they are sufficient to cease reasoning in terms of statistics (diffusion, law of mass action, pH, etc.) and encourage cytologists and biochemists to prospect thoroughly the huge panoply of the biophysical properties of macromolecule-water associations at the nanometre level. Our main purpose, here, is to discuss some of the more common misinterpretations due to the ignorance of these properties, and expose briefly the bases for a better approach of the cell machinery. Giorgio Careri, who demonstrated the correlation between proton currents at the surface of lysozyme and activity of this enzyme was one of the pioneers of this approach.

Ultrastructural consideration on the nature, sol and gel, of the aqueous cytoplasm in embedment-free section electron microscopy

TEM of any in situ cells in embedment-free sections--regardless of specimen-fixation methods--clearly shows strand-lattices occupying the cytoplasmic matrix. The cytoplasmic matrix is assumed to be a site of soluble proteins; however, it appears indistinct as conventional TEM cannot target it. Strand-lattices similar to the cytoplasmic ones are duplicated in bovine serum albumin as well as solated gelatin fixed at warm temperatures and at appropriate concentrations, while lattices from gelatin gelated by cooling before fixation are much more compact than those from solated gelatin at a given concentration. Based on the finding of the in vitro proteins, a new interpretation of cell ultrastructures in embedment-free section TEM is proposed: first, differences in the compactness of cytoplasmic lattices represent those in the protein concentration in the cytoplasmic matrix; second, when loose and compact lattices are contiguous within a cell, the cytoplasmic matrix domain occupied by the compact lattice is in a gel state while the remaining domain of the same cell is in a sol state. The explanation for the states of the gel and sol based on the lattice-compactness is applicable to changes in the lattice-compactness of the cytoplasmic matrix of neurohypophyseal axons under intense secretion.

Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations

According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity.

"One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity."

Josiah Willard Gibbs (1839-1903)

From protoplasmic theory to cellular systems biology: a 150-year reflection

Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, "system" character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The origin of the "system" view of the cell dates to the birth of the protoplasm concept. The 150-year history of the role of "protoplasm" in cell biology is traced. It is found that the "protoplasmic theory," not the "cell theory," was the key 19th-century construct that drove the study of the structure-and-function of living cells and set the course for the development of modern cell biology. The evolution of the "protoplasm" picture into the 20th century is examined by looking at controversial issues along the way and culminating in the current views on the role of cytological organization in cellular activities. The relevance of the "protoplasmic theory" to 21st-century cellular systems biology is considered.

The actin cytoskeleton in whole mount preparations and sections

In non-muscle cells, the actin cytoskeleton plays a key role by providing a scaffold contributing to the definition of cell shape, force for driving cell motility, cytokinesis, endocytosis, and propulsion of pathogens, as well as tracks for intracellular transport. A thorough understanding of these processes requires insight into the spatial and temporal organisation of actin filaments into diverse higher-order structures, such as networks, parallel bundles, and contractile arrays. Transmission and scanning electron microscopy can be used to visualise the actin cytoskeleton, but due to the delicate nature of actin filaments, they are easily affected by standard preparation protocols, yielding variable degrees of ultrastructural preservation. In this chapter, we describe different conventional and cryo-approaches to visualise the actin cytoskeleton using transmission electron microscopy and discuss their specific advantages and drawbacks. In the first part, we present three different whole mount techniques, which allow visualisation of actin in the peripheral, thinly spread parts of cells grown in monolayers. In the second part, we describe specific issues concerning the visualisation of actin in thin sections. Techniques for three-dimensional visualisation of actin, protein localisation, and correlative light and electron microscopy are also included.

Scale-free flow of life: on the biology, economics, and physics of the cell

The present work is intended to demonstrate that most of the paradoxes, controversies, and contradictions accumulated in molecular and cell biology over many years of research can be readily resolved if the cell and living systems in general are re-interpreted within an alternative paradigm of biological organization that is based on the concepts and empirical laws of nonequilibrium thermodynamics. In addition to resolving paradoxes and controversies, the proposed re-conceptualization of the cell and biological organization reveals hitherto unappreciated connections among many seemingly disparate phenomena and observations, and provides new and powerful insights into the universal principles governing the emergence and organizational dynamics of living systems on each and every scale of biological organizational hierarchy, from proteins and cells to economies and ecologies.

First disclosure of lipid droplet substructure and myelin translucency in embedment-free section electron microscopy

In conventional transmission electron microscopy (EM), thinly sectioned specimens embedded in epoxy resin are observed. However, because of a substantial level of electron density of epoxy resin, the possibility cannot be ruled out that bio-structures having electron density similar to that of epoxy resin are not clearly recognized and thus are neglected or misinterpreted in conventional EM. This was the reason to require for embedment-free EM. Embedment-free sections have already been made available reliably by transient embedding in polyethylene glycol (PEG) and subsequent de-embedding through immersion in water, and further by critical-point drying, and this embedment-free EM is thus termed PEG-EM. However, this PEG-EM has not been successful to attract reasonable attention from electron microscopists and instead been misunderstood as a non-reliable method. In this paper, the remarkably enhanced contrast and electron translucency of any observation targets in PEG-EM are clearly demonstrated by comparing with images in conventional EM of adipocytes and neural myelin as examples. These features of PEG-EM, together with faithful correspondence in EM images of any individual substructures between the two methods, confirm the reliability of PEG-EM. Furthermore, the much higher thickness of embedment-free sections together with these features makes the PEG-EM more advantageous than the conventional EM for three-dimensional appreciation of structural elements, which is made by stereo-viewing of sections or by EM tomography. Therefore, the PEG-EM is regarded as an important adjunct to the conventional EM for histological studies and wide application of this method may unravel a new level of histology.

Ultrastructural visualization of the transmembranous and cytomatrix-related part of nicotinic acetylcholine receptor of frog motor endplate by means of an immunochemical avidity of IgG for d-tubocurarine

In the present study, a fine ultrastructural localization of nicotinic acetylcholine receptor (nAChR) was attempted, using d-tubocurarine (d-TC), a quaternary ammonium compound binding to nAChR. The localization was based on the binding avidity of immunoglobulin G (IgG) for acetylcholine (ACh) and other quaternary ammonium compounds, such as d-TC. d-TC was applied to the frog neuromuscular preparation and caused a blockade of neuromuscular transmission. Then, d-TC was rendered insoluble in situ by silicotungstic acid (STA), a precipitating agent of soluble proteins and quaternary ammonium compounds. After tissue fixation, a normal rabbit serum was applied to the fine precipitate of the insoluble salt of d-TC silicotungstate (quaternary ammonium radical of d-TC) to form the immunochemical complex d-TC- rabbit IgG at ACh binding sites. The IgG of the complex was revealed by means of the conventional immunoperoxidase procedure used for ultrastructural localization. Under the electron microscope, fine diaminobenzidine (DAB) precipitates appeared as regular rod-like structures oriented to cytoplasmic side of the horizontal part (crest) of the postsynaptic membrane (between the junctional folds) which is known to be endowed with nAChR. The rod-like precipitates were not observed in the postsynaptic junctional folds which are devoid of nAChR. The distance separating the rods each other was rather constant (12 - 15 nm), while the length of the rods was variable and exceeded the usual length of nAChR. The present work indicates that the rod-like structures, already observed in association with sarcoplasmic side of the postsynaptic membrane, did correspond to the intramembranous and intracytoplasmic part of nAChR and related proteins. These cytochemical results confirm that d-TC binds to ACh binding sites in the pore of nAChR, and raise the question of DAB staining of cytoskeletal proteins related to the nAChR complex.

What we have learned and will learn from cell ultrastructure in embedment-free section electron microscopy

The limitations inherent in conventional electron microscopy (EM) using epoxy ultrathin sections for a clear recognition of biological entities having electron densities similar to or lower than that of epoxy resin have led to the development of embedment-free sectioning for EM. Embedment-free section EM is reliably performed using water-soluble polyethylene glycol (PEG) as a transient embedding medium, with subsequent de-embedment of PEG by immersion into water, followed by critical point-drying (CPD) of the embedment-free section. The present author has stressed that this approach clearly discloses structures whose contours and/or appearance are accordingly vague and/or fuzzy in conventional EM, but does not reveal any new structures. Based on embedment-free electron microscopy (PEG-EM), this article presents five major findings regarding strand- or microtrabecular lattices which have been clearly revealed to occur in the cytoplasmic matrix-an impossibility with conventional EM. These are (1) the appearance of lattices of different compactness in various cells and in intracellular domains of a given cell; (2) the faithful reproduction from an albumin solution in vitro of strand-lattices with correspondingly increasing compactness following increasing concentrations; (3) the appearance of more compact lattices from gelated gelatin than from solated gelatin at a given concentration in vitro; (4) the appearance of either greater or less lattice-compactness by hyper- or hypotonic pretreatments of cells; and (5) the appearance of certain intracellular proteins confined to the centripetal demilune-domain of centrifuged ganglion cells which is occupied with strand-lattices of a substantial compactness. From these findings, questions now arise as to the biological significance of the individual strand itself in the microtrabecular lattices in PEG-EM. In addition, it may be that the appearance of strand-lattices in a given biological domain represents the presence of soluble proteins; the lattice-compactness indicates the concentration of soluble proteins in the domain, and the aqueous cytoplasm is equivalent to the aqueous solution. Further, the appearance of two contiguous lattice domains exhibiting differing degrees of compactness in a given cell indicates that cytoplasmic proteins are solated in a domain with less compact lattices, whereas they are gelated in the other domain. These proposed interpretations need to be confirmed by further studies. If confirmed, the control mechanisms of the localization and movement of intracellular organelles could then be understood on the basis not only of information about the cytoskeletons but also of cell ultrastructure-related information on the concentration and sol-gel states of intracellular proteins. In addition, possible interpretations of the significance of strand-lattices in PEG-EM are also applicable to the nucleoplasm, especially extra-heterochromatin (euchromatin) areas. Finally, several potential uses/advantages of PEG-EM in the cell-ultrastructure have also been demonstrated, especially in three-dimensional reconstructions of nonmembranous structures including stereo-viewing using a pair of EM images with appropriate tilting as well as electron microscopic tomography.

Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

A large body of experimental evidence indicates that the specific molecular interactions and/or chemical conversions depicted as links in the conventional diagrams of cellular signal transduction and metabolic pathways are inherently probabilistic, ambiguous and context-dependent. Being the inevitable consequence of the dynamic nature of protein structure in solution, the ambiguity of protein-mediated interactions and conversions challenges the conceptual adequacy and practical usefulness of the mechanistic assumptions and inferences embodied in the design charts of cellular circuitry. It is argued that the reconceptualization of molecular recognition and cellular organization within the emerging interpretational framework of self-organization, which is expanded here to include such concepts as bounded stochasticity, evolutionary memory, and adaptive plasticity offers a significantly more adequate representation of experimental reality than conventional mechanistic conceptions do. Importantly, the expanded framework of self-organization appears to be universal and scale-invariant, providing conceptual continuity across multiple scales of biological organization, from molecules to societies. This new conceptualization of biological phenomena suggests that such attributes of intelligence as adaptive plasticity, decision-making, and memory are enforced by evolution at different scales of biological organization and may represent inherent properties of living matter.

The Cytomatrix as a Cooperative System of Macromolecular and Water Networks

Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.

Intracellular trafficking of nucleic acids

Until recently, the attention of most researchers has focused on the first and last steps of gene transfer, namely delivery to the cell and transcription, in order to optimise transfection and gene therapy. However, over the past few years, researchers have realised that the intracellular trafficking of plasmids is more than just a "black box" and is actually one of the major barriers to effective gene delivery. After entering the cytoplasm, following direct delivery or endocytosis, plasmids or other vectors must travel relatively long distances through the mesh of cytoskeletal networks before reaching the nuclear envelope. Once at the nuclear envelope, the DNA must either wait until cell division, or be specifically transported through the nuclear pore complex, in order to reach the nucleoplasm where it can be transcribed. This review focuses on recent developments in the understanding of these intracellular trafficking events as they relate to gene delivery. Hopefully, by continuing to unravel the mechanisms by which plasmids and other gene delivery vectors move throughout the cell, and by understanding the cell biology of gene transfer, superior methods of transfection and gene therapy can be developed.

Mechanics of crawling cells

Crawling of keratocytes derived from aquatic vertebrates represents a very useful model system for the investigation of cell locomotion because of its ease of handling and the clear structural separation of a thin cytoplasmic layer, the lamella, from the cell body containing the nucleus and other organelles. Spreading of spherical keratocytes results in fried egg shaped cells, which on withdrawing their lamella at one side become polarized and start moving. Hydrostatic pressure, tension at the cortex, traction forces exerted on the adhesion sites and inside the cells along filamentous structures are required to gain a certain shape. Traction forces have been made visible using scanning acoustic microscopy. This method also allowed for the demonstration of cytoplasmic fluxes inside a moving keratocyte and changes of forces while a migrating cell is changing its direction of locomotion. The pros and cons for actin polymerization at the leading front providing the driving force for crawling are discussed on the basis of structural and experimental results: do they stringently identify polymerization of actin as the only driving machinery. Such a mechanism not only should explain the advancement of the leading edge but also the movement of the whole cell, i.e. the material flux taking place from the cell body to the periphery. Even if the lamella periphery itself may be motile by actin turnover this scheme may represent an oversimplification if applied to the whole cell. Considering the complexity of a whole cell simplifying model systems may not lead to adequate descriptions of the mechanisms as they occur within cells with a highly complex structure, although the model might be consistent and sufficient to describe, i.e. crawling in general.

Mechanistic model of cardiac energy metabolism predicts localization of glycolysis to cytosolic subdomain during ischemia

A new multidomain mathematical model of cardiac cellular metabolism was developed to simulate metabolic responses to reduced myocardial blood flow. The model is based on mass balances and reaction kinetics that describe transport and metabolic processes of 31 key chemical species in cardiac tissue. The model has three distinct domains (blood, cytosol, and mitochondria) with interdomain transport of chemical species. In addition to distinguishing between cytosol and mitochondria, the model includes a subdomain in the cytosol to account for glycolytic metabolic channeling. Myocardial ischemia was induced by a 60% reduction in coronary blood flow, and model simulations were compared with experimental data from anesthetized pigs. Simulations with a previous model without compartmentation showed a slow activation of glycogen breakdown and delayed lactate production compared with experimental results. The addition of a subdomain for glycolysis resulted in simulations showing faster rates of glycogen breakdown and lactate production that closely matched in vivo experimental data. The dynamics of redox (NADH/NAD+) and phosphorylation (ADP/ATP) states were also simulated. These controllers are coupled to energy transfer reactions and play key regulatory roles in the cytosol and mitochondria. Simulations showed a similar dynamic response of the mitochondrial redox state and the rate of pyruvate oxidation during ischemia. In contrast, the cytosolic redox state displayed a time response similar to that of lactate production. In conclusion, this novel mechanistic model effectively predicted the rapid activation of glycogen breakdown and lactate production at the onset of ischemia and supports the concept of localization of glycolysis to a subdomain of the cytosol.

Cytomechanical properties of papaver pollen tubes are altered after self-incompatibility challenge

Self-incompatibility (SI) in Papaver rhoeas triggers a ligand-mediated signal transduction cascade, resulting in the inhibition of incompatible pollen tube growth. Using a cytomechanical approach we have demonstrated that dramatic changes to the mechanical properties of incompatible pollen tubes are stimulated by SI induction. Microindentation revealed that SI resulted in a reduction of cellular stiffness and an increase in cytoplasmic viscosity. Whereas the former cellular response is likely to be the result of a drop in cellular turgor, we hypothesize that the latter is caused by as yet unidentified cross-linking events. F-actin rearrangements, a characteristic phenomenon for SI challenge in Papaver, displayed a spatiotemporal gradient along the pollen tube; this suggests that signal propagation occurs in a basipetal direction. However, unexpectedly, local application of SI inducing S-protein did not reveal any evidence for localized signal perception in the apical or subapical regions of the pollen tube. To our knowledge this represents the first mechanospatial approach to study signal propagation and cellular responses in a well-characterized plant cell system. Our data provide the first evidence for mechanical changes induced in the cytoplasm of a plant cell stimulated by a defined ligand.

Comparative vibrational spectroscopy of intracellular tau and extracellular collagen I reveals parallels of gelation and fibrillar structure

The N-terminal tau 2-19 peptide undergoes gelation, syneresis, and aggregation over a period of years. These changes may be approximated on a shorter time scale by agitation and partial dehydration. The anomalously enhanced (229 nm) ultraviolet resonance Raman (UVRR) imide II band reveals a common structural feature for gels of nondehydrated tau 2-19 and collagen I and insoluble paired helical filaments (PHFs) and collagen I of weak hydrogen bonding at proline carbonyls. Anomalous UVRR enhancement of amide bands at 229 nm results from gel structure, as demonstrated by increased amide absorption at the red edge for tau 2-19 gel and implies the involvement of water in gel structure. In aged, dehydrated tau 2-19 gel, proline carbonyls lose their bonds to water and tyrosine becomes deprotonated, as demonstrated by UVRR spectroscopy. The Fourier transform infrared (FTIR) amide I band shows that antiparallel beta-sheet structure increases with syneresis in the tau 2-19 hydrogel. The comparison of FTIR results for PHFs with collagen I gel and polyproline demonstrates that the secondary structure of PHFs is polyproline II. One implication of this assignment is that the fibrillation of hydrophilic tau is thermodynamically driven by the entropy gained as hydrogen-bonded water is freed, as for collagen I. The FTIR results also show that peptide domains culled from a longer protein do not necessarily fold into identical secondary structures. A pathological, sequential mechanism of gelation, syneresis, and fibrillation for tau in AD is suggested and is supported by the observation of amorphous neurofibrillary tangle development and fibrillation in vivo.

Diffusion, perfusion and the exclusion principles in the structural and functional organization of the living cell: reappraisal of the properties of the 'ground substance'

The thesis is presented that only within very small microdomains of the cell internum might diffusion operate in the sorting of molecular affinities. Much of cell metabolism is guided and controlled in rate by the speed with which molecules that have to interact encounter one another. What is clear, however, is that the cell does not have a single 'modus operandi' but has the choice of many different strategies, each of which can contribute in different proportion to the rate of ongoing activity. It is probably our own desire to simplify things and use the most (or more) probable strategy that confines our appreciation of the overall robustness of the cell as a 'survival machine'. The main operative process at any given time (perfusion, diffusion or whatever) has always to be considered very carefully in relation to the organisational structure of the cell, which can be transient and fickle but nevertheless has been seen as involving an extensive cytomatrix, a ground substance, within an aqueous environment in which the degree of water structuring is even more fickle.

Morphological studies on the mechanisms of pigmentary organelle transport in fish xanthophores and melanophores

Pigmentary organelle translocations within fish chromatophores undergo physiological color changes when exposed to external signals. Chromatophores can be isolated in high yields, and their pigmentary organelles can be tracked readily by microscopy. The combined efforts of morphology and biomolecular chemistry have led to the identification of and determination of the interrelationships between cytoskeletal elements and accessory proteins, motor molecules, cytomatrix, and pigmentary organelles of various sizes. Fish chromatophores have been classified as fast, intermediate, and slow translocators, based on the relative numbers of microtubules. Studies on cultured goldfish (Carassius auratus L.) xanthophores for over 20 years have demonstrated that in this slow translocator, tubulovesicular structures of the smooth endoplasmic reticular (SER) cisternae are involved in the disperson and aggregation of associated carotenoid droplets (CD) with some involvement of cytoskeletal elements. Killifish (Fundulus heteroclitus L.) melanophore, a fast translocator, was also examined. Recent work demonstrates a bright fluorescent "starburst"-like spot that we call an actin filament-organizing center (AFOC) with radiating microfilaments, akin to the microtubule-organizing center (MTOC) with radiating microtubules. Melanosomes translocate single-file on microtubules and are not associated with SER cisternae. Slower CD dispersion or aggregation in goldfish xanthophores seems to be predominantly microfilament-based transport, or microfilament- and microtubule-based transport, respectively. Faster melanosome translocations in killifish melanophores are based on microtubules, with our evidence indicating microfilament involvement. Neural crest-derived chromatophores are models for vesicular transport in axons, and immunocytochemical and imaging technologies may help to elucidate the cellular transport mechanisms.

Femtosecond dynamics of intracellular water probed with nonlinear optical Kerr effect microspectroscopy

A nonlinear optical Kerr effect (OKE) microscope was developed and used to elucidate the ultra-fast diffusive motions of intracellular water molecules. In the OKE microscope, a pump-induced birefringence is sensed by a delayed probe pulse within a spatially confined volume that measures 0.5 microm in the lateral direction and 4.0 microm along the axial coordinate. This microscope allows the recording of time-resolved Kerr signals, which reflect the ultra-fast structural relaxation of the liquid, exclusively from intracellular aqueous domains. Because relaxation occurs on a picosecond time scale, only local diffusive motions are probed. The microscopic OKE signal is therefore insensitive to long-time-scale hindered translational motions enforced by intracellular mechanical barriers but probes the intrinsic orientational mobility of water molecules in cells instead. The Kerr response as determined from single intact mammalian cells under physiological conditions shows a structural relaxation time of 1.35 ps, which is 1.7 times slower than the Kerr decay observed in pure water. The data indicate that the mobility of water molecules in cellular domains is moderately restricted due to the high intracellular content of proteins and solutes.

Recurring views on the structure and function of the cytoskeleton: a 300-year epic

Some unnoticed or seldom remembered precedents of current views on biological motion and its structural bases are briefly outlined, followed by a concise recapitulation of how the present theory has been constructed in the last few decades. It is shown that the evolution of the concept of fibers as main constituents of living matter led to hypothesizing microscopic structures closely resembling microtubules in the 18th century. At the beginning of this period, fibers sliding over each other and driven by interposed moving elements were envisioned as the cause of muscle contraction. In the following century, an account of the mechanism of myofibril contraction visualized longitudinal displacements of myosin-containing submicroscopic rodlets. The existence of fibrils in the protoplasm of non-muscle cells, a subject of long debate in the second half of the 19th century, was virtually discarded as irrelevant or fallacious 100 years ago. The issue resurfaced in the early 1930s as a theoretical notion--the cytosquelette--nearly two decades before intracellular filamentous structures were first observed with electron microscopy. The role originally assumed for such fibrils as signal conductors is nowadays being reappraised, although under new interpretations with a much wider significance including modulation of gene expression, morphogenesis, and even consciousness. Since all of the above ancestral conceptions were eventually abandoned, the corresponding current views are, to a certain extent, recurrent.

Diffusion theory in biology: a relic of mechanistic materialism

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metalbolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science.

Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area

Classical biochemistry is founded on several assumptions valid in dilute aqueous solutions that are often extended without question to the interior milieu of intact cells. In the first section of this chapter, we present these assumptions and briefly examine the ways in which the cell interior may depart from the conditions of an ideal solution. In the second section, we summarize experimental evidence regarding the physical properties of the cell cytoplasm and their effect on the diffusion and binding of macromolecules and vesicles. While many details remain to be worked out, it is clear that the aqueous phase of the cytoplasm is crowded rather than dilute, and that the diffusion and partitioning of macromolecules and vesicles in cytoplasm is highly restricted by steric hindrance as well as by unexpected binding interactions. Furthermore, the enzymes of several metabolic pathways are now known to be organized into structural and functional units with specific localizations in the solid phase, and as much as half the cellular protein content may also be in the solid phase.

The role of prestress and architecture of the cytoskeleton and deformability of cytoskeletal filaments in mechanics of adherent cells: a quantitative analysis

Mechanical properties of adherent cells were investigated using methods of engineering mechanics. The cytoskeleton (CSK) was modeled as a filamentous network and key mechanisms and corresponding molecular structures which determine cell elastic behavior were identified. Three models of the CSK were considered: open-cell foam networks, prestressed cable nets, and a tensegrity model as a special case of the latter. For each model, the modulus of elasticity (i.e. an index of resistance to small deformation) was given as a function of mechanical and geometrical properties of CSK filaments whose values were determined from the data in the literature. Quantitative predictions for the elastic modulus were compared with data obtained previously from mechanical tests on adherent cells. The open-cell foam model yielded the elastic modulus (10(3)-10(4)Pa) which was consistent with measurements which apply a large compressive stress to the cell. This suggests that bending of CSK filaments is the key mechanism for resisting large compression. The prestressed cable net and tensegrity model yielded much lower elastic moduli (10(1)-10(2)Pa) which were consistent with values determined from equilibrium measurements at low applied stress. This suggests that CSK prestress and architecture are the primary determinants of the cell elastic response. The tensegrity model revealed the possibility that buckling of microtubules of the CSK also contributed to cell elasticity.

Effects of stress on cellular infrastructure and metabolic organization in plant cells

Ample evidence shows the role of cytoskeleton mainly in cell division, cell form, and general orientation by the perception of physical forces such as gravity and mechanical ones in plant cells. However, the problem of how cytoskeleton organization and its dynamics at the cellular level in turn affects main metabolic pathways of gene expression and cellular energetics is yet unsolved. The response given by cells to environmental challenges such as stress responses is crucially dependent on the organization of their architecture. Drought, high salinity, and low temperature are sensed by plants as a water stress condition. The latter is known to entrain a series of physiological and metabolic changes at the cellular level. This review hypothesizes that the cytoskeletal network of plant cells and tissues may transduce environmental stress into changes in the organization and dynamics of metabolism and gene expression. Accordingly, experimental evidence concerning the current models of cytoplasmic architecture that have emerged in recent years and the effects of stress on the cytostructure are analyzed.

Regulatory roles of microtubule-associated proteins in neuronal morphogenesis. Involvement of the extracellular matrix

As a result of recent investigations, the cytoskeleton can be viewed as a cytoplasmic system of interconnected filaments with three major integrative levels: self-assembling macromolecules, filamentous polymers, e.g., microtubules, intermediate filaments and actin filaments, and supramolecular structures formed by bundles of these filaments or networks resulting from cross-bridges between these major cytoskeletal polymers. The organization of this biological structure appears to be sensitive to fine spatially and temporally dependent regulatory signals. In differentiating neurons, regulation of cytoskeleton organization is particularly relevant, and the microtubule-associated protein (MAP) tau appears to play roles in the extension of large neuritic processes and axons as well as in the stabilization of microtubular polymers along these processes. Within this context, tau is directly involved in defining neuronal polarity as well as in the generation of neuronal growth cones. There is increasing evidence that elements of the extracellular matrix contribute to the control of cytoskeleton organization in differentiating neurons, and that these regulations could be mediated by changes in MAP activity. In this brief review, we discuss the possible roles of tau in mediating the effects of extracellular matrix components on the internal cytoskeletal arrays and its organization in growing neurons.

Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus

Fluorescence recovery after photobleaching (FRAP) was used to quantify the translational diffusion of microinjected FITC-dextrans and Ficolls in the cytoplasm and nucleus of MDCK epithelial cells and Swiss 3T3 fibroblasts. Absolute diffusion coefficients (D) were measured using a microsecond-resolution FRAP apparatus and solution standards. In aqueous media (viscosity 1 cP), D for the FITC-dextrans decreased from 75 to 8.4 x 10(-7) cm2/s with increasing dextran size (4-2,000 kD). D in cytoplasm relative to that in water (D/Do) was 0.26 +/- 0.01 (MDCK) and 0.27 +/- 0.01 (fibroblasts), and independent of FITC-dextran and Ficoll size (gyration radii [RG] 40-300 A). The fraction of mobile FITC-dextran molecules (fmob), determined by the extent of fluorescence recovery after spot photobleaching, was >>0.75 for RG << 200 A, but decreased to <<0.5 for RG >> 300 A. The independence of D/Do on FITC-dextran and Ficoll size does not support the concept of solute "sieving" (size-dependent diffusion) in cytoplasm. Photobleaching measurements using different spot diameters (1.5-4 micron) gave similar D/Do, indicating that microcompartments, if present, are of submicron size. Measurements of D/Do and fmob in concentrated dextran solutions, as well as in swollen and shrunken cells, suggested that the low fmob for very large macromolecules might be related to restrictions imposed by immobile obstacles (such as microcompartments) or to anomalous diffusion (such as percolation). In nucleus, D/Do was 0.25 +/- 0.02 (MDCK) and 0.27 +/- 0.03 (fibroblasts), and independent of solute size (RG 40-300 A). Our results indicate relatively free and rapid diffusion of macromolecule-sized solutes up to approximately 500 kD in cytoplasm and nucleus.

Resinless section electron microscopy reveals the yeast cytoskeleton

The cytoskeleton of Saccharomyces cerevisiae is essentially invisible using conventional microscopy techniques. A similar problem was solved for the mammalian cell cytoskeleton using resinless section electron microscopy, a technique applied here to yeast. In the resinless image, soluble proteins are no longer cloaked by embedding medium and must be removed by selective detergent extraction. In yeast, this requires breaching the cell wall by digesting with Zymolyase sufficiently to allow detergent extraction of the plasma membrane lipids. Gel electropherograms show that the extracted or "soluble" proteins are distinct from the retained or "structural" proteins that presumably comprise the cytoskeleton. These putative cytoskeleton proteins include the major portions of a 43-kDa protein, which is presumably actin, and of proteins in a band appearing at 55 kDa, as well as numerous less abundant, nonactin proteins. Resinless section electron micrographs show a dense, three-dimensional web of anastomosing, polymorphic filaments bounded by the remnant cell wall. Although the filament network is very heterogenous, there appear to be two principal classes of filament diameters-5 nm and 15-20 nm-which may correspond to actin and intermediate filaments, respectively. A large oval region of lower filament density probably corresponds to the vacuole, and an electron dense spheroidal body, 300-500 nm in diameter, is likely the nucleus. The techniques detailed in this report afford new approaches to the study of yeast cytoarchitecture.

Covisualization in living onion cells of putative integrin, putative spectrin, actin, putative intermediate filaments, and other proteins at the cell membrane and in an endomembrane sheath

Covisualizations with wide-field computational optical-sectioning microscopy of living epidermal cells of the onion bulb scale have evidenced two major new cellular features. First, a sheath of cytoskeletal elements clads the endomembrane system. Similar elements clad the inner faces of punctate plasmalemmal sites interpreted as plasmalemmal control centers. One component of the endomembrane sheath and plasmalemmal control center cladding is anti-genicity-recognized by two injected antibodies against animal spectrin. Immunoblots of separated epidermal protein also showed bands recognized by these antibodies. Injected phalloidin identified F-actin with the same cellular distribution pattern, as did antibodies against intermediate-filament protein and other cytoskeletal elements known from animal cells. Injection of general protein stains demonstrated the abundance of endomembrane sheath protein. Second, the endomembrane system, like the plasmalemmal puncta, contains antigen recognized by an anti-beta 1 integrin injected into the cytoplasm. Previously, immunoblots of separated epidermal protein were shown to have a major band recognized both by this antibody prepared against a peptide representing the cytosolic region of beta 1 integrin and an antibody against the matrix region of beta 1 integrin. The latter antiboby also identified puncta at the external face of protoplasts. It is proposed that integrin and associated transmembrane proteins secure the endomembrane sheath and transmit signals between it and the lumen or matrix of the endoplasmic reticulum and organellar matrices. This function is comparable to that proposed for such transmembrane linkers in the plasmalemmal control centers, which also appear to bind cytoskeleton and a host of related molecules and transmit signals between them and the wall matrix. It is at the plasmalemmal control centers that the endoplasmic reticulum, a major component of the endomembrane system, attaches to the plasma membrane.

Structure within eukaryotic cytoplasm and its relationship to glycolytic metabolism

Taken together, the results reviewed here indicate that both structural proteins and enzymes exist in a relatively mobile, uncomplexed form and in a relatively immobile form, complexed with the matrix. The relative amounts of free and complexed forms of each protein are dependent upon the local concentrations of both small molecules and other macromolecules and hence may vary in time and space throughout the cell. Free and cytomatrix-bound enzymes exchange rapidly, while free and cytomatrix-bound structural proteins exchange more slowly. These two distinct time scales suggest that the slowly exchanging structural proteins form the core of fibrous structural elements--having many stabilizing intermolecular contacts with near neighbours--whereas the more rapidly exchanging enzymes adsorb to the surface of the structural elements and have fewer near neighbour contacts. The hierarchical nature of these associations is depicted schematically in Figure 3. Metabolism is proposed to proceed primarily via transport of small metabolites rather than by transport of enzymes, which may be organized in functional clusters to facilitate, metabolic regulation.

Cytoplasmic viscosity near the cell plasma membrane: translational diffusion of a small fluorescent solute measured by total internal reflection-fluorescence photobleaching recovery

Total internal reflection-fluorescence recovery after photobleaching (TIR-FRAP) was applied to measure solute translational diffusion in the aqueous phase of membrane-adjacent cytoplasm. TIR fluorescence excitation in aqueous solutions and fluorescently labeled cells was produced by laser illumination at a subcritical angle utilizing a quartz prism; microsecond-resolution FRAP was accomplished by acousto-optic modulators and electronic photomultiplier gating. A mathematical model was developed to determine solute diffusion coefficient from the time course of photobleaching recovery, bleach time, bleach intensity, and evanescent field penetration depth; the model included irreversible and reversible photobleaching processes, with triplet state diffusion. The validity and accuracy of TIR-FRAP measurements were first examined in aqueous fluorophore solutions. Diffusion coefficients for fluorescein isothiocyanate-dextrans (10-2000 kDa) determined by TIR-FRAP (recovery t1/2 0.5-2.2 ms) agreed with values measured by conventional spot photobleaching. Model predictions for the dependence of recovery curve shape on solution viscosity, bleach time, and bleach depth were validated experimentally using aqueous fluorescein solutions. To study solute diffusion in cytosol, MDCK epithelial cells were fluorescently labeled with the small solute 2',7'-bis-2-carboxyethyl-5-carboxyfluorescein-acetoxymethyl-ester (BCECF). A reversible photobleaching process (t1/2 approximately 0.5 ms) was identified that involved triplet-state relaxation and could be eliminated by triplet-state quenching with 100% oxygen. TIR-FRAP t1/2 values for irreversible BCECF bleaching, representing BCECF translational diffusion in the evanescent field, were in the range 2.2-4.8 ms (0.2-1 ms bleach times), yielding a BCECF diffusion coefficient 6-10-fold less than that in water. These results establish the theory and the first experimental application of TIR-FRAP to measure aqueous-phase solute diffusion, and indicate slowed translational diffusion of a small solute in membrane-adjacent cytosol.

The cytoskeleton and neurotransmitter receptors

The neuronal cytoskeleton consists of microtubules and microfilaments that can interact with membrane proteins including neurotransmitter receptors and ion channels. Ligand-gated ion channels, such as nicotinic acetylcholine receptors, glycine receptors, glutamate receptors and gamma-aminobutryic acidA (GABAA) receptors, are known to cluster in plasma membranes. Studies suggest that postsynaptic ligand-gated channels form clusters that are anchored in the plasma membrane by interacting with cytoskeletal components and these clusters may serve to optimize delivery of neurotransmitters to the channels. Other findings indicate that the interaction of clustered ligand-gated ion channels with cytoskeletal components may also play a role in channel function. For example, studies suggest that the interaction of microtubules with GABAA receptors regualtes GABA binding affinity. Regulation of neurotransmitter function may be significant in the study of neuropathological processes, such as Alzheimer's disease, neurotrauma, and experimental epilepsy, in which the cytoskeleton is vulnerable to disruption.

Rethinking cell structure

Cell structure, emerging from behind the veil of conventional electron microscopy, appears far more complex than formerly realized. The standard plastic-embedded, ultrathin section can image only what is on the section surface and masks the elaborate networks of the cytoplasm and nucleus. Embedment-free electron microscopy gives clear, high-contrast micrographs of cell structure when combined with removal of obscuring material such as soluble proteins. The resinless ultrathin section is the technique of choice; it is simple and inexpensive, and it uses ordinary electron microscopes. The resulting pictures reveal a world of complex cell structure and function. These images necessarily change our conception of the cytoskeleton, nuclear matrix, mitosis, and the relation of membranes to cytostructure.

Possible continuity of subplasmalemmal cytoplasmic network with basement membrane cord network: ultrastructural study

The ultrastructure of the subplasmalemmal cytoplasm of the cell and the associated basement membrane as well as the area of the cell-basement membrane border were observed with high resolution electron microscopy after preparation of the tissues with cryofixation or glutaraldehyde fixation followed by freeze substitution. The subplasmalemmal cytoplasm of the smooth muscle cells of rat epididymal tubules and the podocyte processes of the mouse glomerular visceral epithelium were found to be composed of a fine network of irregular anastomosing strands. This network closely resembled the previously characterized cord network of the basement membrane. The cords are known to be composed of a 1.5 to 3 nm thick core filament made up of type IV collagen which is surrounded by an irregular ‘sheath’ of other components. The strands in the subplasmalemmal network showed ultrastructural features similar to those of the cord network. Ribbon-like, 4.5 nm wide heparan sulfate proteoglycan ‘double tracks’ were previously reported to be associated with the cord network. Structures similar in size and appearance to the double tracks were also found in the subplasmalemmal network. At the cell-basement membrane border, the lamina densa of the basement membrane was in contact with the cell without the intervening space of a lamina lucida which was recently found to be an artefact caused by conventional tissue processing. Furthermore, the subplasmalemmal network appeared to be continuous through the plasma membrane, with the cord network of the basement membrane.(ABSTRACT TRUNCATED AT 250 WORDS)

Microcompartmentation, metabolic channelling and carbohydrate metabolism

The inter-organelle cytoplasm of eukaryotic cells was once considered to be a homogeneous solution in which many of the enzymes of intermediary metabolism are soluble; however, advances in cell biology have revealed an intricate picture at the microscopic level of cytoplasm structure. Consequently, a great deal of constraint is required when extrapolating to the intact cell from enzyme studies in vitro, a point made frequently in the literature of the last decade or so. The idea of spatial organization is now accepted and covers a wide variety of local microenvironments and possibly localized metabolic channelling. The latter, although accepted as a phenomenon, is controversial in terms of its physiological significance. This review covers evidences showing that both glycolytic and glycogenolytic enzymes are microcompartmentalized. The potential significance of this compartmentation appears to involve metabolic chanelling, a process by which rearrangement of enzymes on a dynamic cytomatrix leads to "channels" in which metabolic substrates are passed from one enzyme to the next. The combined effects of such enzyme proximity and their activation as a result of the altered kinetic properties conferred upon the enzymes by their cytoskeletal associations favours maximal rate of reaction. These and other aspects of microcompartmentation and metabolic channelling are discussed.

Visualization of the transverse cytoskeletal network in insect-flight muscle by scanning-electron microscopy

Located at the level of the Z-line, the transverse cytoskeletal network of insect-flight muscle interconnects adjacent myofibrils with one another, and interconnects peripheral myofibrils with the cell membrane. This network has been presumed to keep myofibrils in register, or to distribute tension laterally among myofibrils. In this study, we used scanning-electron microscopy to reveal details of the three-dimensional arrangement of this network. The network is seen to interconnect longitudinal elements of the cytoskeletal network which surround each myofibril. The arrangement is not unlike that seen in vertebrate skeletal muscle. Interestingly, the transverse network makes contact with cell components such as dense bodies and mitochondria. Such contacts imply potential roles over and above those noted above. The network may be involved not only in mechanical function, but possibly also in intracellular communication.

Immobilized enzymes as tools for the demonstration of metabolon formation. A short overview

In recent years it has become clear that a cell cannot be visualized as a 'bag' filled with enzymes dissolved in bulk water. The aqueous-phase properties in the interior of a cell are, indeed, essentially different from those of an ordinary aqueous solution. Large amounts of water are believed to be organized in layers at the surface of intracellular structural proteins and membranes. Such considerations prompt us to reconsider the operation and regulation of metabolic pathways. Enzymes of metabolic pathways are nowadays thought to be clustered and operate as 'metabolons'. Very often interactions between enzymes of a pathway can exclusively be evidenced in vitro in media which are known to reduce the water concentration in the vicinity of the proteins. Immobilized enzyme preparations have been shown to be excellent tools for this type of research. We describe here some recent studies where immobilized enzymes have been used in various applications to investigate associations among enzymes of a number of different metabolic pathways (glycolysis/gluconeogenesis, citric acid cycle and its connection to the electron transport chain, aspartate-malate shuttle, glyoxylate cycle). Advantages and disadvantages of the different techniques are also discussed.

Cytoplasmic viscosity near the cell plasma membrane: measurement by evanescent field frequency-domain microfluorimetry

The purpose of this study was to determine whether the unique physical milieu just beneath the cell plasma membrane influences the rheology of fluid-phase cytoplasm. Cytoplasmic viscosity was evaluated from the picosecond rotation of the small fluorophore 2',7'-bis-(2-carboxyethyl)-5-carboxyfluorescein (BCECF) by parallel-acquisition Fourier transform microfluorimetry (Fushimi and Verkman, 1991). Information about viscosity within < 200 nm of cell plasma membranes was obtained by selective excitation of fluorophores in an evanescent field created by total internal reflection (TIR) of impulse-modulated s-plane-polarized laser illumination (488 nm) at a glass-aqueous interface. Measurements of fluorescence lifetime and time-resolved anisotropy were carried out in solutions containing fluorescein or BCECF at known viscosities, and monolayers of BCECF-labeled Swiss 3T3 fibroblasts and Madin-Darby canine kidney (MDCK) cells. Specific concerns associated with time-resolved fluorescence measurements in the evanescent field were examined theoretically and/or experimentally, including variations in lifetime due to fluorophore proximity to the interface, and the use of the s and p polarized excitation. In fluorescein solutions excited with s-plane polarized light, there was a 5-10% decrease in fluorescein lifetime with TIR compared to trans (subcritical) illumination, but no change in rotational correlation time (approximately 98 ps/cP). Intracellular BCECF had a single lifetime of 3.7 +/- 0.1 ns near the cell plasma membrane. Apparent fluid-phase viscosity near the cell plasma membrane was 1.1 +/- 0.2 cP (fibroblast) and 1.0 +/- 0.2 cP (MDCK), not significantly different from the viscosity measured in bulk cytoplasm far from the plasma membrane. The results establish the methodology for time-resolved microfluorimetric measurement of polarization in the evanescent field and demonstrate that the cell plasma membrane has little effect on the fluid-phase viscosity of adjacent cytoplasm.

Determinants of the translational mobility of a small solute in cell cytoplasm

The purposes of this study were: (a) to measure the translational mobility of a small solute in cell cytoplasm; (b) to define quantitatively the factors that determine solute translation; and (c) to compare and contrast solute rotation and translation. A small fluorescent probe, 2,7-bis-(2-carboxyethyl)-5-(and 6-)-carboxyfluorescein (BCECF), was introduced into the cytoplasm of Swiss 3T3 fibroblasts. BCECF translation was measured by fluorescence recovery after photo-bleaching; rotation was measured by Fourier transform polarization microscopy. Diffusion coefficients relative to those in water (D/D0) were determined by comparing mobility in cytoplasm with mobility in standard solutions of known viscosity. At isosmotic cell volume, the relative diffusion coefficients for BCECF translation and rotation in cytoplasm were 0.27 +/- 0.01 (SEM, n = 24, 23 degrees C) and 0.78 +/- 0.03 (n = 4), respectively. As cell volume increased from 0.33 to 2 times isosmotic volume, the relative translational diffusion coefficient increased from 0.047 to 0.32, while the relative rotational diffusion coefficient remained constant. The factors determining BCECF translation were evaluated by comparing rotation and translation in cytoplasm, and in artificial solutions containing dextrans (mobile barriers) and agarose gels (immobile barriers). It was concluded that the hindrance of BCECF translation in cytoplasm could be quantitatively attributed to three independent factors: (a) fluid-phase cytoplasmic viscosity is 28% greater than the viscosity of water (factor 1 = 0.78); (b) 19% of BCECF is transiently bound to intracellular components of low mobility (factor 2 = 0.81); and most importantly, (c) translation of unbound BCECF is hindered 2.5-fold by collisions with cell solids comprising 13% of isosmotic cell volume (factor 3 = 0.40). The product of the 3 factors is 0.25 +/- 0.03, in good agreement with the measured D/D0 of 0.27 +/- 0.01. These results provide the first measurement of the translational mobility of a small solute in cell cytoplasm and define quantitatively the factors that slow solute translation.

Patterns of spatiotemporal organization in an "ambiquitous" enzyme model

Many enzymes in pathways such as glycolysis associate reversibly with cellular substructures. The spatiotemporal behavior of a "limit-cycle" oscillation model is studied under the condition that the "ambiquitous" oscillophor, phosphofructokinase, is partitioned between "bulk-phase" and "bound" forms in a heterogeneous system. Computer simulation demonstrates the occurrence of sustained, wave-like spatiotemporal patterns of chemical concentration in the bulk medium. Kinetic dissimilarity among the localized populations of bound enzyme leads to a "polarity" effect in the wave phenomenon. It is suggested that a key physiological role of the limit-cycle regime is to engender a rapid, site-to-site, signal-transmission modality in large eukaryotic (e.g., mammalian) cells.

Organic osmolytes increase cytoplasmic viscosity in kidney cells

The hypothesis was tested that accumulation of osmolytes by kidney cells grown in hyperosmolar media decreases the rotational and translational mobilities of small polar solutes in the cytosolic compartment. Rotational mobility was measured by the picosecond rotational correlation times (tau c) of 2',7'-bis(2-carboxyethyl)-5(6)carboxylfluorescein (BCECF) by multiharmonic microfluorimetry. In isolated segments of rabbit proximal tubule, thick ascending limb, and cortical collecting duct that were perfused and bathed in 300 mosM media, tau c were in the range 180-250 ps, corresponding to apparent rotational viscosities (eta r) of 1.1-1.5 cP. In cortical collecting tubule, eta r was not influenced by serosal vasopressin. In Madin-Darby canine kidney (MDCK) cells grown in 300-1,200 mosM media, eta r increased progressively by up to a factor of 1.38 +/- 0.03; measurements of tau c and macroscopic viscosity in artificial solutions containing osmolytes supported the hypothesis that the increased eta r was due to accumulation of organic osmolytes. BCECF translational mobility was measured by fluorescence photobleaching recovery using a focused 1.2-microns diameter Ar laser beam at 488 nm. Recovery half-times were 36 +/- 3 (SE) ms (n = 10) in MDCK cells grown in 300 mosM media and 62 +/- 3 ms (n = 10) when grown in 1,200 mosM media. The results suggest that accumulation of osmolytes by renal cells is associated with significantly increased cytosolic viscosity. The increased viscosity would slow enzymatic and transport processes in the cytosolic compartment.

Preservation and visualization of molecular structure in detergent-extracted whole mounts of cultured cells

Today's electron microscopes have a resolution sufficient to resolve supramolecular structures. However, the methods used to prepare biological samples for electron microscopy often limit our ability to achieve the resolution that is theoretically possible. We use whole mounts of detergent-extracted cells grown on Formvar-coated gold grids as a model system to evaluate various steps in the preparation of biological samples for high resolution scanning electron microscopy (SEM). Factors that are important in determining the structure and composition of detergent-extracted cells include the nature of the detergent and the composition of the extraction vehicle. Chelation of calcium is extremely important to stabilize and preserve the cytoskeletal filaments. We have also demonstrated both morphologically and by gel electrophoresis that treatment of cells with bifunctional protein crosslinkers before or during extraction with detergent can significantly enhance the preservation of both proteins and supramolecular structures. The methods used to dry samples are a major determinant of the quality of structural preservation. For cytoskeletons freeze-drying (FD) is superior to critical point-drying (CPD), one reason being that CPD samples have to be dehydrated, thereby causing more shrinkage as compared to FD samples. The high pressures to which samples are exposed during CPD may also cause increased shrinkage, and water contamination during CPD causes severe structural damage. We have obtained the best structural preservation of detergent-extracted and fixed cells by manually plunging them into liquid propane and drying over night in a freeze-dryer. The factor that most limits achievement of high resolution in SEM is the metal coat, which has to be very thin, uniform, and free of grain in order not to hide structures or to create artifactual ones. We have found that sputter-coating with 1-3 nm of tungsten (W) or niobium (Nb) gives extremely fine-grained films as well as satisfactory emission of secondary electrons. These samples can also be examined at high resolution by transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). The best preservation and visualization of supramolecular structures have been obtained using cryosputtering, in which the samples are freeze-dried and then sputter-coated within the freeze-dryer while still frozen.