Hallucinogen persisting perception disorder in neuronal networks with adaptation

We study the spatiotemporal dynamics of neuronal networks with spike frequency adaptation. In particular, we compare the effects of adaptation being either a linear or nonlinear function of neural activity. We find that altering parameters controlling the strength of synaptic connections in the network can lead to spatially structured activity suggestive of symptoms of hallucinogen persisting perception disorder (HPPD). First, we study how both networks track spatially homogeneous flickering stimuli, and find input is encoded as continuous at lower flicker frequencies when the network??s synapses exhibit more net excitation. Mainly, we study instabilities of stimulus-driven traveling pulse solutions, representative of visual trailing phenomena common to HPPD patients. Visual trails are reported as discrete afterimages in the wake of a moving input. Thus, we analyze several solutions arising in response to moving inputs in both networks: an ON state, stimulus-locked pulses, and traveling breathers. We find traveling breathers can arise in both networks when an input moves beyond a critical speed. These possible neural substrates of visual trails occur at slower speeds when the modulation of synaptic connectivity is increased.     

Discrete breathers in a realistic coarse-grained model of proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin, discrete breathers (DBs), emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. DBs are time-periodic, space-localized vibrational modes that exist generically in nonlinear discrete systems and are known for their resilience and ability to concentrate energy for long times. In the case of the small β-barrel structure that we consider, DB-mediated localization occurs on the turns connecting the strands. At high energies, DBs stabilize the structure by concentrating energy on a few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of these two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.     

Ion acoustic envelope solitons in explosive ionospheric experiments

The conditions are studied under which stable ion acoustic envelope solitons propagating perpendicular to the magnetic field lines can exist in the ionospheric plasma. The amplitudes, frequencies, and lengths of the waves are determined. The results obtained are compared with the experimental data. It is suggested that such solitons play an important role in both the formation of an ionization front and its motion across the magnetic field and also give rise to a fluctuation precursor in explosive ionospheric experiments.     

Nonlinear mechanism for weak photon emission from biosystems

The nonlinear mechanism for the origin of the weak biophoton emission from biological systems is suggested. The mechanism is based on the properties of solitons that provide energy transfer and charge transport in metabolic processes. Such soliton states are formed in alpha-helical proteins. Account of the electron-phonon interaction in macromolecules results in the self-trapping of electrons in a localized soliton-like state, known as Davydov's solitons. The important role of the helical symmetry of macromolecules is elucidated for the formation, stability and dynamical properties of solitons. It is shown that the soliton with the lowest energy has an inner structure with the many-hump envelope. The total probability of the excitation in the helix is characterized by interspine oscillations with the frequency of oscillations, proportional to the soliton velocity. The radiative life-time of a soliton is calculated and shown to exceed the life-time of an excitation on an isolated peptide group by several orders of magnitude.     

Structures of the fluctuation precursor in an active explosive ionospheric experiment

Results are presented from processing the measurement data on low-frequency fluctuations from the North Star active explosive ionospheric experiment. The fluctuation precursor signal was processed by the wavelet analysis method. The structures revealed are identified as ion acoustic envelope solitons.     

Discrete breathers in protein structures

Recently, using a numerical surface cooling approach, we have shown that highly energetic discrete breathers (DBs) can form in the stiffest parts of nonlinear network models of large protein structures. In the present study, using an analytical approach, we extend our previous results to low-energy discrete breathers as well as to smaller proteins. We confirm and further scrutinize the striking site selectiveness of energy localization in the presence of spatial disorder. In particular, we find that, as a sheer consequence of disorder, a non-zero energy gap for exciting a DB at a given site either exists or not. Remarkably, in the former case, the gaps arise as a result of the impossibility of exciting small-amplitude modes in the first place. In contrast, in the latter case, a small subset of linear edge modes acts as accumulation points, whereby DBs can be continued to arbitrary small energies, while unavoidably approaching one of such normal modes. In particular, the case of the edge mode seems peculiar, its dispersion relation being simple and little system dependent. Concerning the structure-dynamics relationship, we find that the regions of protein structures where DBs form easily (zero or small gaps) are unfailingly the most highly connected ones, also characterized by weak local clustering. Remarkably, a systematic analysis on a large database of enzyme structures reveals that amino-acid residues involved in catalysis tend to be located in such regions. This finding reinforces the idea that localized modes of nonlinear origin may play an important biological role, e.g., by providing a ready channel for energy storage and/or contributing to lower energy barriers of chemical reactions.     

Hydrogen shuttles in air versus water breathing fishes.

1. The malate-aspartate cycle was demonstrable in subcellular preparations of hearts from Arapaima, Lepidosiren, and Synbranchus (obligate air breathers), Hoplerythriunus (facultative air breather), and Osteoglossum and Hoplias (obligate water breathers). 2. Although no respiratory evidence for significant alpha-glycerophosphate cycle participation could be shown in the air breathers, this cycle was demonstrable in hearts of water breathers. 3. In agreement with the O2 uptake studies, it was possible to reconstruct the malate-aspartate, but not the alpha-glycerophosphate cycle, in isolated mitochondria from air breathers, while both shuttles could be reconstructed with heart mitochondria in the case of water breathing fishes.     

Large-amplitude ion acoustic solitons in a bi-ion plasma

A gas-dynamic model is used to study the conditions for the existence of large-amplitude ion acoustic solitons in a plasma with negative ions. It is shown that the limiting Mach number—the upper boundary of the region of existence of compression solitons—depends nonmonotonically on the temperature of the positive ions. The result is that, for certain fixed densities of the negative ions, there are one or two temperature boundaries between the regions where solitons can and cannot exist. It is found that, for rarefaction solitons, it is fundamentally important to take into account electron inertia and that the Mach number of such solitary waves is restricted not by the complete decompression of electrons within the wave (as thought previously), but by the fact that the electrons at the center of the wave reach the acoustic speed, above which the thermal-pressure-induced action cannot be transferred back to the electron flow and smooth continuous solutions are impossible.     

Envelope synthesis during the cell cycle in Escherichia coli B/r

The rate of synthesis of envelope proteins and phospholipids during the cell cycle of Escherichia coli B/r has been studied using both synchronous cultures and random cultures, first labelled and then subsequently fractionated on an age basis by the membrane elution technique. The rate of total protein synthesis and of phospholipid synthesis, measured by incorporation of [2-³H]glycerol into whole cells, was found to increase exponentially throughout the cell cycle. Total envelope protein was also synthesized continuously throughout the cycle, but the rate of synthesis showed a stepwise pattern with a discrete doubling in rate in the first half of the cycle. Analysis of the pattern of synthesis of about 29 individual envelope polypeptides by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and autoradiography revealed that the great majority followed the pattern of the bulk measurements, with a discrete increase in rate of synthesis early in the cycle. One envelope polypeptide, molecular weight 76,000, was, however, only synthesized during a brief period, near the time of division of the bacteria. Pulse-chase studies of envelope polypeptide synthesis in synchronous cultures demonstrated that (1) synthesis and insertion of polypeptide into the envelope was always completed within the pulse period; (2) no post-synthetic modification of polypeptides was detected; (3) one group of polypeptides, including a major outer membrane protein, maintained a stable association with the envelope, whilst a second group displayed considerable “turnover”; (4) about 70% of newly synthesized 76,000 molecular weight protein was lost from the envelope during the succeeding generation.     

The Escherichia coli cell cycle

This review summarizes present knowledge of the bacterial cell cycle with particular emphasis on Escherichia coli. We discuss data coming from three different types of approaches to the study of cell extension and division: The search for discrete events occurring once per division cycle. It is generally agreed that the initiation and termination of DNA replication and cell septation are discrete events; there is less agreement on the sudden doubling in rate of cell surface extension, murein biosynthesis and the synthesis of membrane proteins and phospholipids. We discuss what is known about the temporal relationship amongst the various cyclic events studied. The search for discrete growth zones in the cell envelope layers. We discuss conflicting reports on the existence of murein growth zones and protein insertion sites in the inner and outer membranes. Elucidation of the mechanism regulating the initiation of DNA replication. The concept of "critical initiation mass" is examined. We review data suggesting that the DNA is attached to the envelope and discuss the role of the latter in the initiation of DNA replication.     

Rogue Waves: From Nonlinear Schr?dinger Breather Solutions to Sea-Keeping Test

Under suitable assumptions, the nonlinear dynamics of surface gravity waves can be modeled by the one-dimensional nonlinear Schrödinger equation. Besides traveling wave solutions like solitons, this model admits also breather solutions that are now considered as prototypes of rogue waves in ocean. We propose a novel technique to study the interaction between waves and ships/structures during extreme ocean conditions using such breather solutions. In particular, we discuss a state of the art sea-keeping test in a 90-meter long wave tank by creating a Peregrine breather solution hitting a scaled chemical tanker and we discuss its potential devastating effects on the ship.     

Life at the edge: the nuclear envelope and human disease

A group of human diseases, known as 'laminopathies', are associated with defects in proteins of the nuclear envelope. Most laminopathy mutations have been mapped to the A-type lamin gene, which is expressed in most adult cell types. So, why should different mutations in a near-ubiquitously expressed gene be associated with various discrete tissue-restricted diseases? Attempts to resolve this paradox are uncovering new molecular interactions #151; both inside the nucleus and at its periphery -- which indicate that the nuclear envelope has functions that go beyond mere housekeeping.     

Supersonic Vibron Solitons and Their Possible Existence in Polypeptides

Nonlinear interactions of vibrons with lattice solitons due to the soft cubic nonlinearity in a quasi-one-dimensional lattice yield supersonic vibron solitons. Their binding energy is larger than those of the conventional Davydov solitons and vibron solitons, and their propagation velocity is uniquely determined in contrast to the latter two. Examination of parameters in the model Hamiltonian for polypeptides leads to the result that the supersonic vibron solitons obtained here are more likely to be realizable than the Davydov solitons and the conventional vibron solitons in alpha-helical proteins.     

Soliton behaviour in a bistable reaction diffusion model

We analyze a generic reaction-diffusion model that contains the important features of Turing systems and that has been extensively used in the past to model biological interesting patterns. This model presents various fixed points. Analysis of this model has been made in the past only in the case when there is only a single fixed point, and a phase diagram of all the possible instabilities shows that there is a place where a Turing-Hopf bifurcation occurs producing oscillating Turing patterns. In here we focus on the interesting situation of having several fixed points, particularly when one unstable point is in between two equally stable points. We show that the solutions of this bistable system are traveling front waves, or solitons. The predictions and results are tested by performing extensive numerical calculations in one and two dimensions. The dynamics of these solitons is governed by a well defined spatial scale, and collisions and interactions between solitons depend on this scale. In certain regions of parameter space the wave fronts can be stationary, forming a pattern resembling spatial chaos. The patterns in two dimensions are particularly interesting because they can present a coherent dynamics with pseudo spiral rotations that simulate the myocardial beat quite closely. We show that our simple model can produce complicated spatial patterns with many different properties, and could be used in applications in many different fields.      

Differential localization of 5- and 15-lipoxygenases to the nuclear envelope in RAW macrophages.

Leukotriene formation is initiated in myeloid cells by an increase in intracellular calcium and translocation of 5-lipoxygenase from the cytoplasm to the nuclear envelope where it can utilize arachidonic acid. Monocyte- macrophages and eosinophils also express 15-lipoxygenase, which converts arachidonic acid to 15(S)-hydroxyeicosatetraenoic acid. Enhanced green fluorescent 5-lipoxygenase (5-LO) and 15-lipoxygenase (15-LO) fusion proteins were expressed in the cytoplasm of RAW 264.7 macrophages. Only 5-lipoxygenase translocated to the nuclear envelope after cell stimulation, suggesting that differential subcellular compartmentalization can regulate the generation of leukotrienes versus 15(S)-hydroxyeicosatetraenoic acid in cells that possess both lipoxygenases. A series of truncation mutants of 5-LO were created to identify putative targeting domains; none of these mutants localized to the nuclear envelope. The lack of targeting of 15-LO was then exploited to search for specific targeting motifs in 5-LO, by creating 5-LO/15-LO chimeric molecules. The only chimera that could sustain nuclear envelope translocation was one which involved replacement of the N-terminal 237 amino acids with the corresponding segment of 15-LO. Significantly, no discrete targeting domain could be identified in 5-LO, suggesting that sequences throughout the molecule are required for nuclear envelope localization.     

Respiratory Control in the Transition from Water to Air Breathing in Vertebrates

SYNOPSIS. Studies on extant bimodally breathing vertebratesoffer us a chance to gain insight into the changes in respiratorycontrol during the evolutionary transition from water to airbreathing. In primitive Actinopterygian air-breathingfishes(Lepisosteus and Amid), gill ventilation is driven by an endogenouslyactive central rhythm generator that is powerfully modulatedby afferent input from internally and externally oriented branchialchemoreceptors, as it is in water-breathing Actinopterygians.The effects of internal or external chemoreceptor stimulationon water and air breathing vary substantially in these aquaticair breathers, suggesting that their roles are evolutionarilymalleable. Air breathing in these bimodal breathers usuallyoccurs as single breaths taken at irregular intervals and isan on-demand phenomenon activated primarily by afferent inputfrom the branchial chemoreceptors. There is no evidence forcentral CO₂/pH sensitive chemoreceptors and air-breathing organmechanoreceptors have little influence over branchial- or air-breathingpatterns in Actinopterygian air breathers. In the Sarcopterygianlungfish Lepidosiren and Protopterus, ventilation of the highlyreduced gills is relatively unresponsive to chemoreceptor ormechanoreceptor input. The branchial chemoreceptors of the anteriorarches appear to monitor arterialized blood, while chemoreceptorsin the posterior arches may monitor venous blood. Lungfish respondvigorously to hypercapnia, but it is not known whether theseresponses are mediated by central or peripheral chemoreceptors.A major difference between the Sarcopterygian and Actinopterygianbimodal breathers is that lungfish can inflate their lungs usingrhythmic bouts of air breathing, and lung mechanoreceptors influencethe onset and termination of these lung inflation cycles. Thecontrol of breathing in amphibians appears similar to that oflungfish. Branchial ventilation may persist as rhythmic buccaloscillations in most adults, and stimulation of peripheral chemoreceptorsin the aortic arch or carotid labyrinths initiates short boutsof breathing. Ventilation is much more responsive to hypercapniain adult amphibians than in Actinopterygian fishes because ofcentral CO₂/pH sensitive chemoreceptors that act to convertperiodic to more continuous breathing patterns when stimulated.     

The inner nuclear membrane protein LAP1 forms a native complex with B-type lamins and partitions with spindle-associated mitotic vesicles.

We have examined the in situ organization and nearest neighbours of the 'lamina-associated polypeptide-1' (LAP1), a type II membrane protein and a major constituent of the mammalian nuclear envelope. We show here that, during interphase, LAP1 forms multimeric assemblies which are suspended in the inner nuclear membrane and are specifically associated with B-type lamins. The LAP1-lamin B complex is distinct from analogous complexes formed by the 'lamina-associated polypeptide-2' (LAP2), another inner nuclear membrane protein, and includes a protein kinase. Upon nuclear envelope breakdown, LAP1 partitions with mitotic vesicles which carry nuclear lamin B. The LAP1 vesicles can be distinguished from fragments of the nuclear envelope containing LAP2 and exhibit a striking co-alignment with spindle microtubules. These observations suggest that the inner nuclear membrane comprises discrete territories which accommodate specific integral membrane proteins and are differentially disassembled during mitosis.     

Ion-acoustic soliton in a plasma with finite-temperature ions

The influence of the ion temperature on the properties of ion-acoustic solitons is considered. The critical parameters, the role of reflected ions, and the soliton profile are analyzed. The soliton evolution is studied using numerical simulations. The stability of stationary solutions is demonstrated. The results obtained are compared with the Korteweg-de Vries soliton and available experimental data.     

Nonlinear ion acoustic waves in a quantum degenerate warm plasma with dust grains

A study is made of the propagation of ion acoustic waves in a collisionless unmagnetized dusty plasma containing degenerate ion and electron gases at nonzero temperatures. In linear theory, a dispersion relation for isothermal ion acoustic waves is derived and an exact expression for the linear ion acoustic velocity is obtained. The dependence of the linear ion acoustic velocity on the dust density in a plasma is calculated. An analysis of the dispersion relation reveals parameter ranges in which the problem has soliton solutions. In nonlinear theory, an exact solution to the basic equations is found and examined. The analysis is carried out by Bernoulli’s pseudopotential method. The ranges of the phase velocities of periodic ion acoustic waves and the velocities of solitons are determined. It is shown that these ranges do not overlap and that the soliton velocity cannot be lower than the linear ion acoustic velocity. The profiles of the physical quantities in a periodic wave and in a soliton are evaluated, as well as the dependence of the critical velocity of solitons on the dust density in a plasma.     

COMPARISON OF MITOTIC PHENOMENA AND EFFECTS INDUCED BY HYPERTONIC SOLUTIONS IN HELA CELLS

Interphase HeLa cells exposed to solutions that are 1.6 x isotonic manifest a series of morphological transformations, several of which grossly resemble those which occur when untreated cells enter prophase. These include chromosome condensation with preferential localization at the nuclear envelope and nucleolus, ruffling of the nuclear envelope, and polyribosome breakdown. The nucleolus loses its fibrous component and appears diffusely granular. At 2.8 x isotonicity the nuclear envelope is selectively dispersed although other membranes show morphological alterations also. The characteristic transitions of the lysosomes, Golgi complex, and microtubules seen in normal mitosis do not occur during hypertonic treatment. All the changes induced with hypertonic solutions are rapidly reversible, and the nucleus particularly goes through a recovery phase which bears some similarity to that of the telophase nucleus. The prophase-like condensation of the chromatin following exposure of the intact cell to hypertonic medium cannot be reproduced on an ultrastructural level in the isolated nucleus with any known variation in salt concentration, suggesting significant modifications of the nuclear contents during isolation. In addition to these morphological responses, hypertonic solutions also markedly and reversibly depress macromolecular synthesis. The polyribosome disaggregation that results from exposure to hypertonic solutions may be partially prevented by prior exposure to elevated Mg⁺⁺ concentrations; this same ion is also partially effective in preventing the polyribosome breakdown which normally occurs as cells enter mitosis.