Isolation of extrachromosomal elements by histone immunoprecipitation

Here, we describe a gentle and effective method for the rapid and reproducible isolation of histone-bound extrachromosomal DNA molecules called extrachromosomal elements (EEs). This method facilitates the harvest of a specific population of EEs following their isolation from cultured cells, primary tissues, and tumor cells. Active EEs are bound to histone proteins, and these histone-bound EEs carry actively transcribing genes such as c-myc. Our method exploits the presence of histones on EEs and serves as a first-step purification procedure, allowing for the cloning or multivariant analysis of an immunopurified sample of EEs. We isolated EEs from 4-hydroxytamoxifen (4-HT)-activated Myc-ER-regulatable Pre-B ABM cells. Following one round of immunoprecipitation, we demonstrate the purification of histone-bound EEs. We confirmed that our purification enriched for EEs that carry genes by fluorescent in situ hybridization of EEs (FISH-EEs), and we probed non-enriched and immunopurified EEs with a dihydrofolate reductase (DHFR) cDNA probe that is known to detect extrachromosomal amplification in Myc-activated cells. We demonstrate the enrichment of immunoprecipitated DHFR-containing extrachromosomal DNA molecules.     

Annexin A2 facilitates endocytic trafficking of antisense oligonucleotides

Chemically modified antisense oligonucleotides (ASOs) designed to mediate site-specific cleavage of RNA by RNase H1 are used as research tools and as therapeutics. ASOs modified with phosphorothioate (PS) linkages enter cells via endocytotic pathways. The mechanisms by which PS-ASOs are released from membrane-enclosed endocytotic organelles to reach target RNAs remain largely unknown. We recently found that annexin A2 (ANXA2) co-localizes with PS-ASOs in late endosomes (LEs) and enhances ASO activity. Here, we show that co-localization of ANXA2 with PS-ASO is not dependent on their direct interactions or mediated by ANXA2 partner protein S100A10. Instead, ANXA2 accompanies the transport of PS-ASOs to LEs, as ANXA2/PS-ASO co-localization was observed inside LEs. Although ANXA2 appears not to affect levels of PS-ASO internalization, ANXA2 reduction caused significant accumulation of ASOs in early endosomes (EEs) and reduced localization in LEs and decreased PS-ASO activity. Importantly, the kinetics of PS-ASO activity upon free uptake show that target mRNA reduction occurs at least 4 hrs after PS-ASOs exit from EEs and is coincident with release from LEs. Taken together, our results indicate that ANXA2 facilitates PS-ASO trafficking from early to late endosomes where it may also contribute to PS-ASO release.     

Rate of excitation propagation in a reduced Hodgkins-Huxley model. II. Slow relaxation of the sodium current]

The influence of sodium current activation on the value of nerve excitation conduction velocity is investigated on the basis of Hodgkin-Huxley model. The potassium activation and sodium inactivation are considered as slow processes which do not develop to an appreciable extent in the region of conduction velocity formation. The system of equations was derived and solved analytically after neglecting the dependency of sodium relaxation time on potential; the approximation of steady-state sodium activation was also used with the help of Hevyside function. The algebraic equation for conduction velocity was obtained; its solution has a simple analytical form in two limits of rapid and slow sodium current relaxation. The comparison with the experimental data has shown that at not very high temperatures the slow (compared to the potential dynamics) sodium current relaxation approximation is more appropriate. The dependency of impulse velocity on capacitance and conductance of the fiber was analyzed.     

How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study

Phosphorylation mediates the function of many proteins and enzymes. In the catalytic subunit of cAMP-dependent protein kinase, phosphorylation of Thr 197 in the activation loop strongly influences its catalytic activity. In order to provide theoretical understanding about this important regulatory process, classical molecular dynamics simulations and ab initio QM/MM calculations have been carried out on the wild-type PKA-Mg(2) ATP-substrate complex and its dephosphorylated mutant, T197A. It was found that pThr 197 not only facilitates the phosphoryl transfer reaction by stabilizing the transition state through electrostatic interactions but also strongly affects its essential protein dynamics as well as the active site conformation.     

Role of lipoxygenase in the determination of wheat grain quality

Analysis of the correlation between endogenous lipoxygenase activity and 15 wheat grain quality parameters in three bread wheat populations has shown that enzyme activity influences the weight of 1000 grains, dough deformation energy, dough tenacity, and mixing properties. The correlations between the enzyme activity and the basic quality parameters are negative at high activity levels. The optimum values of specific lipoxygenase activity at which all quality parameters studied have the maximum values range from 108.5 ± 1.2 to 126.4 ± 1.9. It has been found that the ability of lipoxygenase to strengthen gluten is related to the lowering of dough extensibility.     

PxdA interacts with the DipA phosphatase to regulate peroxisome hitchhiking on early endosomes

In canonical microtubule-based transport, adaptor proteins link cargoes to dynein and kinesin motors. Recently, an alternative mode of transport known as “hitchhiking” was discovered, where cargoes achieve motility by hitching a ride on already-motile cargoes, rather than attaching to a motor protein. Hitchhiking has been best studied in two filamentous fungi, Aspergillus nidulans and Ustilago maydis. In U. maydis, ribonucleoprotein complexes, peroxisomes, lipid droplets (LDs), and endoplasmic reticulum hitchhike on early endosomes (EEs). In A. nidulans, peroxisomes hitchhike using a putative molecular linker, peroxisome distribution mutant A (PxdA), which associates with EEs. However, whether other organelles use PxdA to hitchhike on EEs is unclear, as are the molecular mechanisms that regulate hitchhiking. Here we find that the proper distribution of LDs, mitochondria, and preautophagosomes do not require PxdA, suggesting that PxdA is a peroxisome-specific molecular linker. We identify two new pxdA alleles, including a point mutation (R2044P) that disrupts PxdA’s ability to associate with EEs and reduces peroxisome movement. We also identify a novel regulator of peroxisome hitchhiking, the phosphatase DipA. DipA colocalizes with EEs and its association with EEs relies on PxdA. Together, our data suggest that PxdA and the DipA phosphatase are specific regulators of peroxisome hitchhiking on EEs.     

Latent foci of excitation and the unpredictability of behavioral reactions

As a model for studying of "subconsciousness" mechanisms, latent foci of excitation may serve formed in animals under different influences on the brain: direct current, endogenous shifts and also under trace excitation after suprathreshold activity. It is experimentally shown that latent foci of excitation can intensify at activation of other CNS areas; as a result externally unmotivated "unpredictable" behavioural reaction arises. Between two latent foci of excitation associative connection can be established. The latent foci of excitation in the human CNS are also able to be activated under the influence of sensory stimuli, and behavioural reaction arising as a result of summation has no reflection in consciousness. Conclusion is made: it is rightful to consider the dominant foci of excitation formed at the level of subconsciousness as one of possible mechanisms of "unpredictability" of behaviour.     

Simulation analysis of conduction of excitation in the atrioventricular node

The excitation conduction in the atrioventricular node was simulated based on the spatially discrete model of the heart proposed in an earlier paper (Kawato et al., 1986). We constructed a model system composed of the atrium, the atrioventricular node and the Purkinje fiber. Coupling coefficients between these tissues were quantitatively estimated from experimental data on size and membrane capacitance of the three kinds of cardiac cells. We found the following three important features in the simulated excitation conduction along the atrioventricular node. First, shape of action potential was found to be different at different locations of the atrioventricular node although the membrane properties were assumed uniform through the atrioventricular node. Our analysis suggests that the difference in the action potential waveforms observed by Paes de Carvalho & De Almedia (1960) can be ascribed to the electrical influences of the atrium and the His bundle on the atrioventricular node. Second, when the excitation wavefront invaded the atrioventricular node from the atrium, a step was observed in the depolarization phase of the action potential at the atrioventricular node neighboring with the atrium. Janse found a similar step in the real experiment (1969). It is revealed that this step is caused by termination of the junctional current which flows from the atrium to the atrioventricular node. Finally, we found that the conduction velocity measured near the boundary between the atrium and the atrioventricular node was lower than that in the middle part of the atrioventricular node, which is in accordance with the experimental observation by Scher et al. (1959).     

The metabolic "switch" AMPK regulates cardiac heparin-releasable lipoprotein lipase

The "fuel gauge" AMP-activated protein kinase (AMPK) facilitates ATP production to meet energy demands during metabolic stress. Given the importance of lipoprotein lipase (LPL) in providing hearts with fatty acids (FA), the preferred substrate consumed by the heart, the objective of the present study was to investigate whether activation of AMPK influences LPL at its functionally relevant location, the coronary lumen. Hearts from overnight-fasted rats were first perfused with heparin to release LPL, and homogenates from these hearts were then used to measure total and phospho-AMPK-alpha by Western blotting. Manipulation of AMPK activity [with drugs like adenine 9-beta-D-arabinofuranoside (Ara-A) and insulin (that inhibit) or perhexiline and oligomycin (that stimulate)] and its influence on LPL was also determined. Fasting augmented the activity of both AMPK and luminal LPL on immediate removal of hearts, effects that still remained even after in vitro perfusion of hearts for 1 h. Inhibition of AMPK in fasted hearts using an inhibitor like Ara-A or through provision of insulin markedly lowered the enhanced luminal LPL activity. In contrast, AMPK activators, like perhexiline and oligomycin, produced a significant elevation in heparin-releasable LPL activity. Thus, with fasting or drugs that influence AMPK, a strong correlation between this metabolic switch and cardiac LPL activity was established. Our data suggest that, in addition to its direct role in promoting FA oxidation, AMPK-mediated recruitment of LPL to the coronary lumen could represent an immediate compensatory response by the heart to guarantee FA supply.     

Characterization of the role of COP9 signalosome in regulating cullin E3 ubiquitin ligase activity

Cullin RING ligases (CRLs) are the largest family of cellular E3 ubiquitin ligases and mediate polyubiquitination of a number of cellular substrates. CRLs are activated via the covalent modification of the cullin protein with the ubiquitin-like protein Nedd8. This results in a conformational change in the cullin carboxy terminus that facilitates the ubiquitin transfer onto the substrate. COP9 signalosome (CSN)-mediated cullin deneddylation is essential for CRL activity in vivo. However, the mechanism through which CSN promotes CRL activity in vivo is currently unclear. In this paper, we provide evidence that cullin deneddylation is not intrinsically coupled to substrate polyubiquitination as part of the CRL activation cycle. Furthermore, inhibiting substrate-receptor autoubiquitination is unlikely to account for the major mechanism through which CSN regulates CRL activity. CSN also did not affect recruitment of the substrate-receptor SPOP to Cul3, suggesting it may not function to facilitate the exchange of Cul3 substrate receptors. Our results indicate that CSN binds preferentially to CRLs in the neddylation-induced, active conformation. Binding of the CSN complex to active CRLs may recruit CSN-associated proteins important for CRL regulation. The deneddylating activity of CSN would subsequently promote its own dissociation to allow progression through the CRL activation cycle.     

OCRL controls trafficking through early endosomes via PtdIns4,5P₂-dependent regulation of endosomal actin

Mutations in the phosphatidylinositol 4,5-bisphosphate (PtdIns4,5P(2)) 5-phosphatase OCRL cause Lowe syndrome, which is characterised by congenital cataracts, central hypotonia, and renal proximal tubular dysfunction. Previous studies have shown that OCRL interacts with components of the endosomal machinery; however, its role in endocytosis, and thus the pathogenic mechanisms of Lowe syndrome, have remained elusive. Here, we show that via its 5-phosphatase activity, OCRL controls early endosome (EE) function. OCRL depletion impairs the recycling of multiple classes of receptors, including megalin (which mediates protein reabsorption in the kidney) that are retained in engorged EEs. These trafficking defects are caused by ectopic accumulation of PtdIns4,5P(2) in EEs, which in turn induces an N-WASP-dependent increase in endosomal F-actin. Our data provide a molecular explanation for renal proximal tubular dysfunction in Lowe syndrome and highlight that tight control of PtdIns4,5P(2) and F-actin at the EEs is essential for exporting cargoes that transit this compartment.     

Some mechanisms of frontal cortical participation in afferent integration

Experiments on dogs anesthetized with chloralose showed that lowering the level of activity of the frontal cortex (area F₂) by cooling leads to an increase in the negative phase of the primary response of all primary projection areas of exteroceptive stimuli (somatosensory, auditory, visual). Activation of the frontal cortex (by strychninization) increases the amplitude of the positive phase of the primary response. The same treatment applied to the frontal cortex of a cerveau isolé preparation leads to similar changes but only in the positive phase of this response. It can be concluded from the results that the frontal cortex may exert tonic effects of two types on afferent channels. One effect is indirect, through the reticular formation, by inhibition of its activating influence on the afferent channel responsible for the formation of the primary response. The other, activating effect, is aimed at the afferent channel forming the positive phase of the primary response. Under natural conditions the frontal cortex, when activated at the stage of afferent integration, evidently weakens the tone of the brain stem reticular formation and its influences, but facilitates the conduction of afferent volleys through the specific pathways, thus improving the perception of the trigger stimulus.     

Transferrin receptor recycling in the absence of perinuclear recycling endosomes

In mammalian cells, internalized receptors such as transferrin (Tfn) receptor are presumed to pass sequentially through early endosomes (EEs) and perinuclear recycling endosomes (REs) before returning to the plasma membrane. Whether passage through RE is obligatory, however, remains unclear. Kinetic analysis of endocytosis in CHO cells suggested that the majority of internalized Tfn bypassed REs returning to the surface from EEs. To determine directly if REs are dispensable for recycling, we studied Tfn recycling in cytoplasts microsurgically created to contain peripheral EEs but to exclude perinuclear REs. The cytoplasts actively internalized and recycled Tfn. Surprisingly, they also exhibited spatially and temporally distinct endosome populations. The first appeared to correspond to EEs, labeling initially with Tfn, being positive for early endosomal antigen 1 (EEA-1) and containing only small amounts of Rab11, an RE marker. The second was EEA-1 negative and with time recruited Rab11, suggesting that cytoplasts assembled functional REs. These results suggest that although perinuclear REs are not essential components of the Tfn recycling pathway, they are dynamic structures which preexist in the peripheral cytoplasm or can be regenerated from EE- and cytosol-derived components such as Rab11.     

Molecular restraints in the permeation pathway of ion channels

Ion channels assist and control the diffusion of ions through biological membranes. The conduction process depends on the structural characteristics of these nanopores, among which are the hydrophobicity and the afforded diameter of the conduction pathway. In this contribution, we use full atomistic free-energy molecular dynamics simulations to estimate the effect of such characteristics on the energetics of ion conduction through the activation gate of voltage-gated potassium (Kv) channels. We consider specifically the ionic translocation through three different permeation pathways, corresponding to the activation gate of an atomistic model of Shaker channels in closed and partially opened conformations, and that of the open conformation of the Kv1.2 channel. In agreement with experiments, we find that the region of Val(478) constitutes the main gate. The conduction is unfavorable through this gate when the constriction is smaller than an estimated threshold of 4.5-5.0 A, mainly due to incomplete coordination-hydration of the ion. Above this critical size, e.g., for the Kv1.2, the valine gate is wide enough to allow fully coordination of the ion and therefore its diffusion on a flat energy surface. Similar to other ion channels, Kv channels appear therefore to regulate diffusion by constricting hydrophobic regions of the permeation pathway.     

Effects of medium polarization and pre-existing field on activation energy of enzymatic charge-transfer reactions

The highly organized spatial structure of proteins' polar groups results in the existence of a permanent intraprotein electric field and in protein's weak dielectric response, i.e. its low dielectric constant. The first factor affects equilibrium free energy gap of a charge-transfer reaction, the second (medium polarization effect) influences both equilibrium and non-equilibrium (reorganization) energies, decreasing the latter substantially. In the framework of the rigorous 'fixed-charge-density' formalism, the medium polarization component of the reaction activation energy has been calculated, both for the activation energy of the elementary act proper, and the effective activation energy accounting for the charges' transfer from water into a low-dielectric structureless medium. In all typical cases of reactions, the energy spent for charge transfer from water into structureless 'protein' is larger than the gain in activation energy due to the protein's low reorganization energy. Therefore, the low dielectric constant of proteins is not sufficient to ensure their high catalytic activity, and an additional effect of the pre-existing intraprotein electric field, compensating for an excessive charging energy, is necessary. Only a combined action of low reorganization energy and pre-existing electric field provides proteins with their high catalytic activity. The dependence of activation energy on the globule geometry has been analyzed. It is shown that, for each reaction, an optimum set of geometric parameters exists. For five hydrolytic enzymes, the optimum globule radii have been calculated using the experimental geometry of their active sites. The calculated radii agree satisfactorily with the real sizes of these macromolecules, both by absolute and by relative values.     

Ventricular activation is impaired in aged rat hearts

Ventricular arrhythmias are frequently observed in the elderly population secondary to alterations of electrophysiological properties that occur with the normal aging process of the heart. However, the underlying mechanisms remain poorly understood. The aim of the present study was to determine specific age-related changes in electrophysiological properties and myocardial structure in the ventricles that can be related to a structural-functional arrhythmogenic substrate. Multiple unipolar electrograms were recorded in vivo on the anterior ventricular surface of four control and seven aged rats during normal sinus rhythm and ventricular pacing. Electrical data were related to morphometric and immunohistochemical parameters of the underlying ventricular myocardium. In aged hearts total ventricular activation time was significantly delayed (QRS duration: +69%), while ventricular conduction velocity did not change significantly compared with control hearts. Moreover, ventricular activation patterns displayed variable numbers of epicardial breakthrough points whose appearance could change with time. Morphological analysis in aged rats revealed that heart weight and myocyte transverse diameter increased significantly, scattered microfoci of interstitial fibrosis were mostly present in the ventricular subendocardium, and gap junction connexin expression decreased significantly in ventricular myocardium compared with control rats. Our results show that in aged hearts delayed total ventricular activation time and abnormal activation patterns are not due to delayed myocardial conduction and suggest the occurrence of impaired impulse propagation through the conduction system leading to uncoordinated myocardial excitation. Impaired interaction between the conduction system and ventricular myocardium might create a potential reentry substrate, contributing to a higher incidence of ventricular arrhythmias in the elderly population.     

Electric responses of the cerebral cortex to central excitation and inhibition

An attempt was made to evaluate critically the extent to which the background electrocorticogram, neuronal impulse activity, and evoked potentials reflect the state of cortical excitation and inhibition. It was shown that during electrocorticogram desynchronization, firing neurons predominated in the surface (mainly afferent) layers, while inhibited neurons were in the majority in the lower layers of the cortex. Consequently, desynchronization does not reflect diffuse excitation of the cortex and cannot be taken as an index of central excitation. Slow electrocortical waves cannot be used as indicators of an inhibitory state, even though they may be associated with processes leading to the development of inhibition. Under the effects of different stimuli, the number of neurons participating in impulse condition, and the number of neurons temporarily inhibiting impulse activity in the projection cortical area were stable (ratio 2:1). It was found that the correlation between impulse discharges of neuronal pairs increases during both central excitation and central inhibition. Nonetheless, differences between cortical excitation and inhibition were seen in the reorganization of neuronal columns. The use of evoked potentials to determine cortical excitation or inhibition is complicated by the fact that the amplitude of evoked-potential components reflects the divergent influences of many factors. It was shown that conditional excitation diminished the evoked potential to a light stimulus in the projection cortical area, but caused it to increase in the region of the motor analyzer. The elaboration of a conditional inhibition (extinction) is accompanied by the growth of an evoked potential to a stimulus in the primary cortical area, and by its repression in the region of the motor analyzer. In this case, a large delayed negative wave appears in the evoked potential.This report was presented at the All-Union Symposium on Electric Responses of the Cerebral Cortex to Afferent Stimuli, Kiev, October, 1969.Rostov-on-Don State University. Translated from Neirofiziologiya, Vol. 2, No. 2, pp. 140–154, March–April, 1970.     

Determination of the optimum proportion of saccharides in the diet of adult rats

SPF male Wistar rats weighing 250-260 g and aged 90 days were fed 14 days on diets with a constant 10% protein (casein) content, a constant 11% fat (margarine) content and mounting saccharide (rice starch: sugar: potato starch - 6.4: 1.2: 1) contents of 31, 36, 41, 46, 51, 56, 61 and 66%. Protein intake and the body and liver nitrogen values were used to determine the utilization parameters of protein biological value, i.e. NPU (body) and LPU (liver), for the individual diets. Liver gluconeogenesis was also studied by measuring specific phosphoenolpyruvate carboxykinase (PEPCK) and fructose-1.6-diphosphatase (FDP-ase) activity. On the basis of linearity between the growth parameter NPR and protein and saccharide intake we determined the reciprocal relationship of the intake of the two nutrients and used it to compute the optimum saccharide concentration for the diet. The 51% saccharide diet gave the best protein utilization (the maximum (net) protein utilization value) in the 90-day-old rat organism. This was confirmed by the course of gluconeogenesis, which was significantly activated in the presence of 31-46% saccharide diets. By substituting the optimum protein intake in the reciprocal saccharide-protein intake relationship we obtained the optimum saccharide intake, which corresponded to a 49% concentration in the diet. With its use of a biological, biochemical and computation method, the study is a contribution to the determination of optimum nutrient values.