Specific organization of Golgi apparatus in plant cells

Microtubules, actin filaments, and Golgi apparatus are connected both directly and indirectly, but it is manifested differently depending on the cell organization and specialization, and these connections are considered in many original studies and reviews. In this review we would like to discuss what underlies differences in the structural organization of the Golgi apparatus in animal and plant cells: specific features of the microtubule cytoskeleton organization, the use of different cytoskeleton components for Golgi apparatus movement and maintenance of its integrity, or specific features of synthetic and secretory processes. We suppose that a dispersed state of the Golgi apparatus in higher plant cells cannot be explained only by specific features of the microtubule system organization and by the absence of centrosome as an active center of their organization because the Golgi apparatus is organized similarly in the cells of other organisms that possess the centrosome and centrosomal microtubules. One of the key factors determining the Golgi apparatus state in plant cells is the functional uniformity or functional specialization of stacks. The functional specialization does not suggest the joining of the stacks to form a ribbon; therefore, the disperse state of the Golgi apparatus needs to be supported, but it also can exist “by default”. We believe that the dispersed state of the Golgi apparatus in plants is supported, on one hand, by dynamic connections of the Golgi apparatus stacks with the actin filament system and, on the other hand, with the endoplasmic reticulum exit sites distributed throughout the endoplasmic reticulum.     

Engineering the robustness of industrial microbes through synthetic biology

Microbial fermentations and bioconversions play a central role in the production of pharmaceuticals, enzymes and chemicals. To meet the demands of industrial production, it is desirable that microbes maintain a maximized carbon flux towards target metabolites regardless of fluctuations in intracellular or extracellular environments. This requires cellular systems that maintain functional stability and dynamic homeostasis in a given physiological state, or manipulate transitions between different physiological states. Stable maintenance or smooth transition can be achieved through engineering of dynamic controllability, modular and hierarchical organization, or functional redundancy, three key features of biological robustness in a cellular system. This review summarizes how synthetic biology can be used to improve the robustness of industrial microbes.     

The cognitive neuroscience of sleep: neuronal systems,consciousness and learning

Sleep can be addressed across the entire hierarchy of biological organization. We discuss neuronal-network and regional forebrain activity during sleep, and its consequences for consciousness and cognition. Complex interactions in thalamocortical circuits maintain the electroencephalographic oscillations of non-rapid eye movement (NREM) sleep. Functional neuroimaging affords views of the human brain in both NREM and REM sleep, and has informed new concepts of the neural basis of dreaming during REM sleep -- a state that is characterized by illogic, hallucinosis and emotionality compared with waking. Replay of waking neuronal activity during sleep in the rodent hippocampus and in functional images of human brains indicates possible roles for sleep in neuroplasticity. Different forms and stages of learning and memory might benefit from different stages of sleep and be subserved by different forebrain regions.     

Probing the role of water in protein conformation and function

Life began in a bath of water and has never escaped it. Cellular function has forced the evolution of many mechanisms ensuring that cellular water concentration has never changed significantly. To free oneself of any conceptual distinction among all small molecules, solutes and solvents, means that experiments to probe water's specific role in molecular function can be designed like any classical chemical reaction. Such an 'osmotic stress' strategy will be described in general and for an enzyme, hexokinase. Water behaves like a reactant that competes with glucose in binding to hexokinase, and modulates its conformational change and activity. This 'osmotic stress' strategy, now applied to many very different systems, shows that water plays a significant role, energetically, in most macromolecular reactions. It can be required to fill obligatory space, it dominates nearest non-specific interactions between large surfaces, it can be a reactant modulating conformational change; all this in addition to its more commonly perceived static role as an integral part of stereospecific intramolecular structure.     

Natural foci of diseases: the development of the concept at the close of the century

E. N. Pavlovski?'s concept of natural focality of diseases and the development of general knowledge about natural foci and their structural (components), functional (mechanisms of pathogen maintenance), and ecosystem-related organization (assortment and interrelations of ecosystems) are reviewed from principal (in authors' opinion) aspects. The 60-year history of this theory includes three stages at which its scope and contents differed. At the first stage, it concerned transmissible zoonoses. It had been assumed that structurally, natural foci necessarily include the pathogen-vector-host triad, and the functioning of the focus is provided for by only pathogen circulation in terrestrial ecosystems. At the second stage, it became clear that vector is not a necessary structural component of any focus (an example of nontransmissible diseases), although the functioning of foci remained to be unequivocally attributed to the continuous pathogen circulation among animals of terrestrial ecosystems. The third stage is characterized by an understanding that, in general, the presence of a warm-blooded host in the focus is also unnecessary for pathogen survival, and natural foci can be represented by soil and aquatic ecosystems. The only necessary and specific component of any natural focus is the pathogen population. In this context, modern views on natural focality of diseases are reviewed, and the essence of the terms "natural focus" and "epizootic process" is defined. It is proposed to distinguish the phases of pathogen reservation and epizootic spread (circulation) in ecosystems of any type. The current state of this concept provides evidence that, in general biological terms, studies on natural focality of diseases belong to one of the fields of symbiotology.     

Reciprocal actions between sensory signals and sleep

To the best of our knowledge, there is no simple way to induce neural networks to shift from waking mode into sleeping mode. Our best guess is that a whole group of neurons would be involved and that the process would develop in a period of time and a sequence which are mostly unknown. The quasi-total sensory deprivation elicits a new behavioral state called somnolence. Auditory stimulation as well as total auditory deprivation alter sleep architecture. Auditory units exhibiting firing shifts on passing to sleep (augmenting or diminishing) are postulated to be locked to sleep-related networks. Those ( approximately 50%) that did not change during sleep are postulated to continue informing the brain as in wakefulness. A rhythmic functional plasticity of involved networks is postulated. A number of auditory and visual cells have demonstrated a firing phase locking to the hippocampal theta rhythm. This phase locking occurs both during wakefulness and sleep phases. The theta rhythm may act as an organizer of sensory information in visual and auditory systems, in all behavioral states adding a temporal dimension to the sensory processing. Sensory information from the environment and body continuously modulates the central nervous system activity, over which sleep phenomenology must develop. It also produces a basal tonus during wakefulness and sleep, determining changes in the networks that contribute to sleep development and maintenance and, eventually, it also leads to sleep interruption.     

NREM2 and Sleep Spindles Are Instrumental to the Consolidation of Motor Sequence Memories

Although numerous studies have convincingly demonstrated that sleep plays a critical role in motor sequence learning (MSL) consolidation, the specific contribution of the different sleep stages in this type of memory consolidation is still contentious. To probe the role of stage 2 non-REM sleep (NREM2) in this process, we used a conditioning protocol in three different groups of participants who either received an odor during initial training on a motor sequence learning task and were re-exposed to this odor during different sleep stages of the post-training night (i.e., NREM2 sleep [Cond-NREM2], REM sleep [Cond-REM], or were not conditioned during learning but exposed to the odor during NREM2 [NoCond]). Results show that the Cond-NREM2 group had significantly higher gains in performance at retest than both the Cond-REM and NoCond groups. Also, only the Cond-NREM2 group yielded significant changes in sleep spindle characteristics during cueing. Finally, we found that a change in frequency of sleep spindles during cued-memory reactivation mediated the relationship between the experimental groups and gains in performance the next day. These findings strongly suggest that cued-memory reactivation during NREM2 sleep triggers an increase in sleep spindle activity that is then related to the consolidation of motor sequence memories.     

Cortical-subcortical Interactions in the Development of the Emotions

In contrast to the cerebral systems regulating the level of activation, the dynamics of sleep, the organization of sensory functions, and the construction of movements, the structures responsible for emotional responses in humans and higher mammals remain a subject of bitter debate. Although modern physiology of the brain has accumulated much data indicating the functional specialization of cerebral structures classified as emotion-producing, these results have as yet defied attempts to fit them into a relatively coherent system that would clarify the specific contribution made by each particular formation to the development of a particular emotional state.     

Ventilatory and arousal patterns during sleep in normal young and elderly subjects

Since elderly subjects have lower chemosensitivity, we postulated that ventilation might be more state dependent in the elderly. To address this we investigated the changes in ventilation, measured by respiratory inductive plethysmography, with sleep in 12 healthy young (19-29 yr) and 13 elderly (greater than 65 yr) subjects. Ventilation was measured in representative periods in each sleep state. These data showed that there is no difference between the elderly and the young either in mean ventilation or in the variability of ventilation awake or in the different states of sleep. In both groups ventilation was variable in stage 1-2 sleep and least variable in stage 3-4 sleep. The variability in stage 1-2 sleep was due to periodic breathing (cycle time approximately 45 s) in both age groups. Although within a sleep state no differences were observed, over the night of study the elderly behaved differently from the young. Apneas occurred more frequently in the elderly, and 5 of 13 elderly met the criteria for sleep apnea syndrome compared with 1 of 12 young subjects. Apneas tended to occur predominantly in stage 1-2 sleep and seem to be an exaggeration of the periodicity that is typical of this state. Four of the elderly with apnea remained in this stage of sleep throughout the night of study. The apneic episodes usually terminated with an electroencephalogram arousal that occurred prior to or simultaneously with the onset of ventilation.(ABSTRACT TRUNCATED AT 250 WORDS)     

Electroencephalographic characteristics of sleep in subjects with paleo and neocerebellar lesions

The research was performed in order to study: 1) paleo and neocerebellar contributions in the sleep organization and 2) the electrical sleep activities at different time intervals during the functional compensation which follows the cerebellar lesion. Polygraphic sleep records (EEG, EMG, EOG) were performed on four subjects with surgical lesions more than 6 months old in cerebellar cortex (two subjects in paleo and two in neocerebellum). Another subject was studied before a surgical paleocerebellar lesion and at different time intervals after that (8th, 30th, 60th, and 90th day). Paleo and neocerebellar lesions showed different sleep abnormalities. The former induced both quantitative and qualitative alterations in the cyclic sleep organization, the latter did not show significant alterations in this organization but rather in transition between sleeping and waking and in sleep maintenance. The acute paleocerebellar lesion showed at the 8th and 30th day a strong reduction of the synchronized sleep (SS) and an increase of the desynchronized one (DS). In the successive records, 30th and 90th day, the SS/DS ratio increased to the values observed in the chronic paleocerebellar lesioned subjects.     

Hyperquenching and cold equilibration strategies for the study of liquid--liquid and protein folding transitions

In this paper we consider the extension of the recent quantitative studies of hyperquenched glassformers to include (1). systems that exhibit first order liquid-liquid phase transitions, and (2). systems that contain molecules, which, during normal cooling, undergo internal structural changes above the glass temperature. The general aim of these studies is to trap-in a high enthalpy, high entropy, state of the system and then observe it evolving in time at low temperatures during a controlled annealing procedure. In this manner events that normally occur during change of temperature may be observed occurring during passage of time, at much lower temperatures. At such low temperatures the smearing effects of vibrations are greatly reduced. While the case of most interest in the second class is the refolding of thermally denatured protein molecules, any reconstructive molecular or chemical exchange process is a potential subject for investigation. Processes that occur in stages can be studied in greater detail, and any stage of interest can be frozen when desired, by drop of temperature, for more detailed spectroscopic examination. We review an electrospray method for hyperquenching liquids at approximately 10(5) K/s, and discuss some results of such experiments in order to illustrate a calorimetric approach to exploiting the hyperquenching-and- cold-equilibration strategy. To apply the idea to the study of proteins, the following protein solvent requirements must be met: (1). the solvents must not crystallize ice on cooling or heating, yet must not denature the proteins; (2). the solvents must support thermally denatured molecules without permitting aggregation. We describe two solvent systems, the first of which meets the first requirement, but the second only partially. The second solvent system apparently meets both. Preliminary results, only at the proof of concept stage, are reported for cold refolding of lysozyme, which, it seems, can be trapped in our solvent in the unfolded but refoldable state, with only moderate (approx. 120 K/s) quenching rates.     

Early Closure of a Long Loop in the Refolding of Adenylate Kinase: A Possible Key Role of Non-Local Interactions in the Initial Folding Steps

Most globular protein chains, when transferred from high to low denaturant concentrations, collapse instantly before they refold to their native state. The initial compaction of the protein molecule is assumed to have a key effect on the folding pathway, but it is not known whether the earliest structures formed during or instantly after collapse are defined by local or by non-local interactions—that is, by secondary structural elements or by loop closure of long segments of the protein chain. Stable closure of one or several long loops can reduce the chain entropy at a very early stage and can prevent the protein from following non-productive pathways whose number grows exponentially with the length of the protein chain. In Escherichia coli adenylate kinase (AK), about seven long loops define the topology of the native structure. We selected four loop-forming sections of the chain and probed the time course of loop formation during refolding of AK. We labeled the termini of the loop segments with tryptophan and cysteine-5-amidosalicylic acid. This donor-acceptor pair of probes used with fluorescence resonance excitation energy transfer spectroscopy (FRET) is suitable for detecting very short distances and thus is able to distinguish between random and specific compactions. Refolding of AK was initiated by stopped-flow mixing, followed simultaneously by donor and acceptor fluorescence, and analyzed in terms of energy transfer efficiency and distance. In the collapsed state of AK, observed after the 5-ms dead time of the instrument, one of the selected segments shows a native-like separation of its termini; it forms a loop already in the collapsed state. A second segment that includes the first but is longer by 15 residues shows an almost native-like separation of its termini. In contrast, a segment that is shorter but part of the second segment shows a distance separation of its termini as high as a segment that spans almost the whole protein chain. We conclude that a specific network of non-local interactions, the closure of one or several loops, can play an important role in determining the protein folding pathway at its early phases.     

Plants as competing populations of redundant organs

At any given time, a vascular or land plant may be a colony of functional sectors, each consisting of a shoot and its associated roots. In most plants, however, the activity of the cambium can change the relative vascular contacts of neighbouring shoots. Vascular tissues can even differentiate along new orientations, forming contacts that change the sectorial structure of the plant. Such reoriented differentiation is induced by the same auxin from developing leaves as are other types of vascular differentiation. The occurrence of vascular reorientation is determined by two criteria: the presence of an auxin flow that exceeds the transport capacity of the tissues that follow the previous, established orientation and the availability of nearby channels that are not fully occupied, not‘protected’ by their own flow of auxin. These controls of vascular orientation suggest that neighbouring shoots (and neighbouring roots) compete with one another, by means of signals indicating their state and their environment, for vascular contacts with the rest of the plant. Such internal competition between genetically equivalent shoots is an adaptation to heterogeneous environments: it is the shoots in the best conditions available to the plant that receive the support of a greater part of the root system. The potential for changes of vascular contacts points to open problems and to neglected aspects of the role of the cambium in plant organization.     

Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics

The three-dimensional (3D) organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state—accessibility and amount of gene expression—of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs, but not on the interaction strength that leads to these contact counts. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In this work, a novel inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the α-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. The results presented for multiple normalization methods suggest that all measurable quantities may crucially depend on the nature of normalization. We argue that by experimentally measuring predicted quantities, one may infer the appropriate form of normalization.     

A microcomputer system for monitoring and analysing oxyhemoglobin saturation during sleep

A computerized data acquisition and analysis routine was developed to quantitate respiratory disturbances in sleeping patients. Polysomnographic recordings of patients consisted of electroencephalograms, electro-occulograms, submental electromyograms, air flow at the nose and mouth, esophageal pressure, and oxyhemoglobin saturation (SaO2). SaO2, a physiological effect of ventilatory airflow, was sampled every two seconds and stored on disk during the night's study for subsequent analysis. Wild points in the data file can be marked so that they will be skipped during analysis. Patient polysomnographs were scored manually for sleep stage by a sleep technician. A file was then created containing the scored sleep information with time marks corresponding to each change in sleep stage during the study. An analysis routine used this file to develop indices of sleep apnea, severity for combinations or specific stages of sleep. These indices were: (A) number of oxyhemoglobin desaturation episodes per hour; (B) average maximum desaturation per episode; and (C) desaturation index, the product of (A) and (B). A graph was plotted showing cumulative sleep time at given SaO2 values. The degree of sleep apnea can be determined using these indices.     

Effect of gamma-aminobutyric acid derivatives on sleep disorders in neuroses

Electropolygraphic studies showed that under gamma-amino-butyric acid (GABA) derivatives various neurotic patients with sleep disorders had a tendency towards an increase in total sleep duration due to an accretion of basic sleep stages (the 2nd stage, delta-sleep, and rapid sleep), a statistically significant reduction in the number of spontaneous wake-ups, time of awakedness during night and the movements activation index. A detailed analysis of some electrographic data within the sleep stages revealed a tendency towards an increase in number of the 2nd stage sleep spindles, of delta-index in the 3rd and 4th sleep stages, as well as an increase in the average readings of rapid eye movements in the absence of any marked changes in their specific occurrence per time unit. GABA derivatives in the used dosage caused similar changes in the sleep patterns in case of its disturbances, with a relatively more pronounced action of sodium oxybutyrate.     

Respiratory instability during sleep onset.

It has been hypothesized that regulatory control in the respiratory system is state dependent. According to this view respiratory instability during sleep onset is a consequence of repeated fluctuations in arousal state. However, these speculations are based primarily on measurements during stable sleep, not during sleep onset itself. The aim of the present study was to assess changes in ventilation and gas tensions during sleep onset as a function of arousal state. Twenty-one subjects (12 males and 9 females, mean age 20 yr) were assessed over an average of 11.3 sleep onsets. The subject's state was classified as alpha, theta, body movement, or stage 2 sleep, and expiratory tidal volume, minute ventilation, respiratory rate, and end-tidal CO2 and O2 were measured by means of a face mask, valve, and pneumotachograph on a breath-by-breath basis. Respiratory instability during sleep onset was found to be a result of two factors. The first factor was a between-state effect in which transitions from alpha to theta were associated with falls, and from theta to alpha with increases, in ventilation. The magnitude of the change was a positive function of metabolic drive at the time of the state change (as indicated by alveolar PCO2 and PO2 levels). The second was a within-state effect in which ventilation fell during consecutive alpha breaths and increased during consecutive theta breaths. These changes were due to the influence of the relative hyperventilation of the alpha state and the relative hypoventilation of the theta state on metabolic drive.