A three-dimensional study of organelle interrelationships in regenerating rat liver. 4. Multivesicular bodies.

Double-membraned plasma-membrane-loops are formed from the plasma membrane and released into the cytoplasm. The vesiculation of mainly their inner membrane may transform them into MVB. The so-formed internal vesicles contain cytosol. In many MVB the surface of all their internal vesicles to gether corresponds well with the surface of their bordering membrane. This correlation may be the result of a dynamic equilibrium whereby degradation (and partial recyclage) of internal vesicles is compensated for by the formation of new internal vesicles. When this equilibrium becomes disturbed, MVB may show much less internal vesicles. Such 'depleted' MVB are often producing peribiliary vesicles and may themselves transform into lacunate emptying into the bile canaliculi.     

Identification of protein latent periodicities using recurrent correlation analysis

Many large proteins have evolved by internal duplication and fusion. For proteins with internal structural symmetry, this means that their sequences should be made up of identical repeats. However, many of these repeat signals can only be seen at the structural level yet. We suggested a method of recurrent correlation analysis to detect the sequence repeats of proteins directly from their sequences. It showed that the internal repetitions of the representative proteins in six folds of mainly beta class could be identified directly at the sequence level.     

Effect of the shear flow in the generation and self-organization of internal gravity wave structures in the dissipative ionosphere

A linear mechanism for the generation and amplification of internal gravity waves and their further nonlinear dynamics in the stably stratified dissipative ionosphere in the presence of an inhomogeneous zonal wind (shear flow) is studied. For shear flows, the operators of linear problems are non-self-conjugate and the corresponding eigenfunctions are nonorthogonal. Therefore, the canonical modal approach is poorly applicable to study such motions. In this case, the so-called nonmodal mathematical analysis is more adequate. Dynamic equations and equations for the energy transport of internal gravity perturbations in the ionosphere with shear flows are derived on the basis of the nonmodal approach. Exact analytic solutions of linear and nonlinear equations are found. The growth rate of the shear instability of internal gravity waves is determined. It is revealed that perturbations grow in time according to a power law, rather than exponentially. The frequency and wavenumber of the generated internal gravity modes depend on time; hence, a wide spectrum of wave perturbations caused by linear effects (rather than nonlinear turbulent ones) forms in the ionosphere with shear flows. The efficiency of the linear mechanism for the amplification of internal gravity waves during their interaction with the inhomogeneous zonal wind is analyzed. A criterion for the development of the shear instability of such waves in the ionospheric plasma is obtained. It is shown that, in the presence of shear instability, internal gravity waves extract the shear flow energy in the initial (linear) stage of their evolution, due to which their amplitude and, accordingly, energy increase substantially (by an order of magnitude). As the amplitude increases, the mechanism of nonlinear self-localization comes into play and the process terminates with the self-organization of strongly localized solitary nonlinear internal gravity vortex structures. As a result, a new degree of freedom of the system and a new way of the evolution of perturbations in a medium with a shear flow appear. Inductive and viscous dampings limit the lifetime of vortex internal gravity structures in the ionosphere; nevertheless, their lifetime is long enough for them to strongly affect the dynamic properties of the medium. It is revealed on the basis of the analytic solution of a set of time-independent nonlinear dynamic equations that, depending on the velocity profile of the shear flow, the nonlinear internal gravity structures can take the form of a purely monopole vortex, a dipole cyclone-anticyclone pair, a transverse vortex chain, or a longitudinal vortex path against the background of the inhomogeneous zonal wind. The accumulation of such vortices in the ionosphere can result in a strongly turbulent state.     

Membrane-assisted viral DNA ejection

Genome packaging and delivery are fundamental steps in the replication cycle of all viruses. Icosahedral viruses with linear double-stranded DNA (dsDNA) usually package their genome into a preformed, rigid procapsid using the power generated by a virus-encoded packaging ATPase. The pressure and stored energy due to this confinement of DNA at a high density is assumed to drive the initial stages of genome ejection. Membrane-containing icosahedral viruses, such as bacteriophage PRD1, present an additional architectural complexity by enclosing their genome within an internal membrane vesicle. Upon adsorption to a host cell, the PRD1 membrane remodels into a proteo-lipidic tube that provides a conduit for passage of the ejected linear dsDNA through the cell envelope. Based on volume analyses of PRD1 membrane vesicles captured by cryo-electron tomography and modeling of the elastic properties of the vesicle, we propose that the internal membrane makes a crucial and active contribution during infection by maintaining the driving force for DNA ejection and countering the internal turgor pressure of the host. These novel functions extend the role of the PRD1 viral membrane beyond tube formation or the mere physical confinement of the genome. The presence and assistance of an internal membrane might constitute a biological advantage that extends also to other viruses that package their linear dsDNA to high density within an internal vesicle.     

Biomass recycling and the origin of phenotype in fungal mycelia

Fungi are one of the most important and widespread components of the biosphere, and are essential for the growth of over 90% of all vascular plants. Although they are a separate kingdom of life, we know relatively little about the origins of their ubiquitous existence. This reflects a wider ignorance arising from their status as indeterminate organisms epitomized by extreme phenotypic plasticity that is essential for survival in complex environments. Here we show that the fungal phenotype may have its origins in the defining characteristic of indeterminate organisms, namely their ability to recycle locally immobilized internal resources into a mobilized form capable of being directed to new internal sinks. We show that phenotype can be modelled as an emergent phenomenon resulting from the interplay between simple local processes governing uptake and remobilization of internal resources, and macroscopic processes associated with their transport. Observed complex growth forms are reproduced and the sensitive dependence of phenotype on environmental context may be understood in terms of nonlinearities associated with regulation of the recycling apparatus.     

MITOCHONDRIAL STRUCTURE IN SITES OF STEROID SECRETION

1. Mitochondria of the adrenal gland, corpus luteum, theca interna and granulosa of the graafian follicle, interstitial cells of the testis, and placenta of the rat have been studied with the electron microscope. 2. In most sites of steroid secretion, the internal structure of the mitochondria is in the form of tubular reflections of the internal mitochondrial membrane, rather than plate-like cristae. 3. The mitochondria of the adrenal gland have a highly variable size, even within a single cell; they may reach 2 to 3 µ in diameter, and are nearly filled with tubules. 4. It is suggested that while mitochondria in many places have a tubular component, those in the adrenal gland are highly specialized by virtue of their giant size and their internal structure.     

Evolution of a predictive internal model in an embodied and situated agent

We show how simulated robots evolved for the ability to display a context-dependent periodic behavior can spontaneously develop an internal model and rely on it to fulfill their task when sensory stimulation is temporarily unavailable. The analysis of some of the best evolved agents indicates that their internal model operates by anticipating sensory stimuli. More precisely, it anticipates functional properties of the next sensory state rather than the exact state that sensors will assume. The characteristics of the states that are anticipated and of the sensorimotor rules that determine how the agents react to the experienced states, however, ensure that they produce very similar behaviour during normal and blind phases in which sensory stimulation is available or is self-generated by the agent, respectively. Agents’ internal models also ensure an effective transition during the phases in which agents’ internal dynamics is decoupled and re-coupled with the sensorimotor flow. Our results suggest that internal models might have arisen for behavioral reasons and successively exapted for other cognitive functions. Moreover, the obtained results suggest that self-generated internal states should not necessarily match in detail the corresponding sensory states and might rather encode more abstract and motor-oriented information.     

Characterization of the interaction between Actinin-Associated LIM Protein (ALP) and the rod domain of α-actinin

Background  

The PDZ-LIM proteins are a family of signalling adaptors that interact with the actin cross-linking protein, α-actinin, via their PDZ domains or via internal regions between the PDZ and LIM domains. Three of the PDZ-LIM proteins have a conserved 26-residue ZM motif in the internal region, but the structure of the internal region is unknown.     

Osmoregulation in juvenile Rhabdosargus holubi (Steindachner) (Teleostei: Sparidae)

Juvenile Rhabdosargus holubi (Steindachner), one of the commonest teleosts in south east African estuaries, are strong osmoregulators, showing little change in their internal osmotic concentration over an extremely wide salinity range. In 35‰ seawater the internal osmotic concentration is held at 370 mosmol/1. At a salinity of 1‰ the internal osmotic concentration falls to 216 mosmol/1 and at a salinity of 65‰ rises to 381 mosmol/1. When exposed to a new salinity the internal osmotic concentration does not change until after 10 h; this may be of considerable importance to fish living in areas subject to short term changes of salinity.     

State Dependent Valuation: The Effect of Deprivation on Risk Preferences

The internal state of an organism affects its choices. Previous studies in various non-human animals have demonstrated a complex, and in some cases non-monotonic, interaction between internal state and risk preferences. Our aim was to examine the systematic effects of deprivation on human decision-making across various reward types. Using both a non-parametric approach and a classical economic analysis, we asked whether the risk attitudes of human subjects towards money, food and water rewards would change as a function of their internal metabolic state. Our findings replicate some previous work suggesting that, on average, humans become more risk tolerant in their monetary decisions, as they get hungry. However, our specific approach allowed us to make two novel observations about the complex interaction between internal state and risk preferences. First, we found that the change in risk attitude induced by food deprivation is a general phenomenon, affecting attitudes towards both monetary and consumable rewards. But much more importantly, our data indicate that rather than each subject becoming more risk tolerant as previously hypothesized based on averaging across subjects, we found that as a population of human subjects becomes food deprived the heterogeneity of their risk attitudes collapses towards a fixed point. Thus subjects who show high-risk aversion while satiated shift towards moderate risk aversion when deprived but subjects who are risk tolerant become more risk averse. These findings demonstrate a more complicated interaction between internal state and risk preferences and raise some interesting implications for both day-to-day decisions and financial market structures.     

Measuring internal representations from behavioral and brain data

The study of internal knowledge representations is a cornerstone of the research agenda in the interdisciplinary study of cognition. An influential proposal assumes that the brain uses its internal knowledge of the external world to constrain, in a top-down manner, high-dimensional sensory data into a lower-dimensional representation that enables perceptual decisions and other higher-level cognitive functions [1-9]. This proposal relies on a precise formulation of the observer-specific internal knowledge (i.e., the internal representations, or models) that guides reduction of the high-dimensional retinal input onto a low-dimensional code. Here, we directly revealed the content of subjective internal representations by instructing five observers to detect a face in the presence of only white noise, to force a pure top-down, knowledge-based task. We used reverse correlation methods to visualize each observer's internal representation that supports detection of an illusory face. Using reverse correlation again, this time applied to observers' electroencephalogram activity, we established where and when in the brain specific internal knowledge conceptually interprets the input white noise as a face. We show that internal representations can be reconstructed experimentally from behavioral and brain data, and that their content drives neural activity first over frontal and then over occipitotemporal cortex.     

Quantitative determination of benazepril and benazeprilat in human plasma by gas chromatography-mass spectrometry using automated 96-well disk plate solid-phase extraction for sample preparation

An analytical method for the determination of benazepril and its active metabolite, benazeprilat, in human plasma by capillary gas chromatography-mass-selective detection, with their respective labelled internal standard, was developed and validated according to international regulatory requirements. After addition of the internal standards, the compounds were extracted from plasma by solid-phase extraction using automated 96-well plate technology. After elution, the compounds were converted into their methyl ester derivatives by means of a safe and stable diazomethane derivative. The methyl ester derivatives were determined by gas chromatography using a mass-selective detector at m/z 365 for benazepril and benazeprilat and m/z 370 for the internal standards. Intra- and inter-day accuracy and precision were found to be suitable over the range of concentrations between 2.50 and 1000 ng/mL.     

Microbial growth on the edge of desiccation

The availability of water, which can be expressed in terms of water activity (a(w)), is one of the most important determinants for microbial homeostasis and growth on surface to air interfaces. Here we show, using an environmental control chamber containing a precisely controlled temperature/a(w) gradient in combination with a mathematical approach, that the environmental a(w) growth limit of a microorganism can be lower than its intracellular a(w) limit. This internal limit represents the point at which microbial cells cannot lower their internal a(w) any further in response to low external a(w) values without interfering with essential intracellular processes. To grow at external a(w) values below their internal limit, microbes need to generate more water metabolically than they lose to their environment. This internal a(w) limit can be calculated by measuring the a(w) growth limit of an organism at different water vapour diffusivities using barometric pressure as a variable. Fascinating morphological changes, such as rope-like superstructures formed by B. subtilis, are furthermore observed in response to low external a(w) values in particular around the calculated intracellular a(w) limit. The intracellular a(w) limit of an organism is a decisive parameter for water limitation-induced adaptations in cellular hydrophilicity and morphogenesis.     

Internal proteins of bacteriophage T4D: Their characterization and relation to head structure and assembly

Three basic proteins of low molecular weight (about 8000, 10,000 and 18,000) were isolated from the T4D phage particle. Many molecules of each protein are located within the phage head, possibly in association with the DNA, and together with the proteins which form the head membrane comprise most of the head structural protein. The purified internal proteins were characterized by physicochemical and immunological techniques; a radio-immunoassay allowed measurement of their synthesis in phage infected bacteria. Each internal protein is synthesized at both early and late times after infection. Their structural genes are present in the phage genome, but do not appear to be among the known amber mutant-containing genes of T4D. No evidence was found to suggest that the internal proteins are formed from a common precursor molecule, nor are their origins related to those of the internal peptides; however, one of the internal proteins may be altered before its incorporation into the phage. Pulse-chase experiments with two of these proteins show that they are incorporated into certain defective T4D heads. Whether or not they are incorporated appears to depend on the degree of completion of these heads, perhaps with respect to DNA packaging.     

Levels of H+ and other monovalent cations in dormant and germinating spores of Bacillus megaterium.

Previous investigators using the extent of uptake of the weak base methylamine to measure internal pH have shown that the pH in the core region of dormant spores of Bacillus megaterium is 6.3 to 6.5. Elevation of the internal pH of spores by 1.6 U had no significant effect on their degree of dormancy or their heat or ultraviolet light resistance. Surprisingly, the rate of methylamine uptake into dormant spores was slow (time for half-maximal uptake, 2.5 h at 24 degrees C). Most of the methylamine taken up by dormant spores was rapidly (time for half-maximal uptake, less than 3 min) released during spore germination as the internal pH of spores rose to approximately 7.5. This rise in internal spore pH took place before dipicolinic acid release, was not abolished by inhibition of energy metabolism, and during germination at pH 8.0 was accompanied by a decrease in the pH of the germination medium. Also accompanying the rise in internal spore pH during germination was the release of greater than 80% of the spores K+ and Na+. The K+ was subsequently reabsorbed in an energy-dependent process. These data indicate (i) that between pH 6.2 and 7.8 internal spore pH has little effect on dormant spore properties, (ii) that there is a strong permeability barrier in dormant spores to movement of charged molecules and small uncharged molecules, and (iii) that extremely early in spore germination this permeability barrier is breached, allowing rapid release of internal monovalent cations (H+, Na+, and K+).     

Traumatic ostial stenosis of internal mammary coronary graft

Because of the extensive use of arterial conduits for coronary surgery there is a growing interest in percutaneous intervention in these conduits. This kind of intervention presents a challenge for the interventional cardiologist owing to the anatomic and functional characteristics of this graft. In most cases significant internal mammary artery disease occurs at the distal anastomosis. Ostial stenoses are rare and their pathology uncertain. The authors report a case of an ostial graft lesion, most probably caused by repetitive ostial engagement of the left internal mammary artery in combination with atherosclerosis in the subclavian artery affecting the internal mammary artery.     

The DNA binding preference of RAD52 and RAD59 proteins: implications for RAD52 and RAD59 protein function in homologous recombination

We examined the double-stranded DNA (dsDNA) binding preference of the Saccharomyces cerevisiae Rad52 protein and its homologue, the Rad59 protein. In nuclease protection assays both proteins protected an internal sequence and the dsDNA ends equally well. Similarly, using electrophoretic mobility shift assays, we found the affinity of both Rad52 and Rad59 proteins for DNA ends to be comparable with their affinity for internal sequences. The protein-DNA complexes were also directly visualized using atomic force microscopy. Both proteins formed discrete complexes, which were primarily found (90-94%) at internal dsDNA sites. We also measured the DNA end binding behavior of human Rad52 protein and found a slight preference for dsDNA ends. Thus, these proteins have no strong preference for dsDNA ends over internal sites, which is inconsistent with their function at a step of dsDNA break repair that precedes DNA processing. Therefore, we conclude that S. cerevisiae Rad52 and Rad59 proteins and their eukaryotic counterparts function by binding to single-stranded DNA formed as intermediates of recombination rather than by binding to the unprocessed DNA double-strand break.     

Rapid method for the analysis of itraconazole and hydroxyitraconazole in serum by high-performance liquid chromatography

An assay for the determination of itraconazole and its active metabolite hydroxyitraconazole in serum has been developed, using ketoconazole as internal standard. The procedure involved a one-step liquid-liquid extraction of the drug, its metabolite and the internal standard, followed by their separation by reversed-phase HPLC. In this paper the validation of this method is described.     

Polarity Regulation in Migrating Neurons in the Cortex

The formation of the cerebral cortex requires migration of billions of cells from their birth position to their final destination. A motile cell must have internal polarity in order to move in a specified direction. Locomotory polarity requires the coordinated polymerization of cytoskeletal elements such as microtubules and actin combined with regulated activities of the associated molecular motors. This review is focused on migrating neurons in the developing cerebral cortex, which need to attain internal polarity in order to reach their proper target. The position and dynamics of the centrosome plays an important function in this directed motility. We highlight recent interesting findings connecting polarity proteins with neuronal migration events regulated by the microtubule-associated molecular motor, cytoplasmic dynein.     

Methods for monitoring signaling molecules in cellular compartments

Cells, irrespective of whether they are from multicellular or single-celled organisms, must communicate with the external environment through dynamic regulation of their internal metabolism, which are critical for their survival. Fluorescent and bioluminescent proteins, and related genetic engineering technologies, have provided new opportunities to investigate the molecular dynamics of cells and their internal compartments, with high spatio-temporal resolution. In this review article, since there is a sufficient number of previous reviews summarizing the history of their development and the techniques behind them, here we will focus on molecular features or technologies that have the potential to further open novel investigations of cellular and subcellular dynamics.