Spinal pattern generation and sensory gating mechanisms

Sensory gating mechanisms are deployed during vertebrate locomotion to ensure that adaptive and appropriate motor responses to afferent input occur during all phases of the movement cycle. Recent animal studies on the integration of cutaneous information have investigated the roles of interneurones in sensory gating. Premotor interneurones, rhythmically active during locomotion, as well as 'sensory' interneurones appear to be intimately involved in sensory gating, receiving synaptic inputs from the spinal rhythm generator to gate the flow of sensory information in the spinal cord.     

Synaptic mechanisms in invertebrate pattern generation

Although individual neurons can be intrinsically oscillatory and can be network pacemakers, motor patterns are often generated in a more distributed manner. Synaptic connections with other neurons are important because they either modify the rhythm of the pacemaker cell or are essential for pattern generation in the first place. Computational studies of half-center oscillators have made much progress in describing how neurons make transitions between active and inactive phases in these simple networks. In addition to characterizing phase transitions, recent studies have described the synaptic mechanisms that are important for the initiation and maintenance of activity in half-center oscillators.     

A model for basic pattern generating mechanisms in the lobster stomatogastric ganglion

The stomatogastric ganglion of the lobster contains three central pattern generators-the pyloric, lateral gastric and medial gastric systems. These networks are modelled using a simple neural model in which the only variable parameters are the synaptic potentials and thresholds for each cell. In each case a model network with the appropriate synaptic connections reproduces the main features of the observed output patterns. The basic pattern generating mechanisms are quite different for each of these model networks. For the pyloric and lateral gastric systems our results confirm previously suggested mechanisms. For the medial gastric system we have determined a network which explains pattern generation; no satisfactory mechanism was previously known.     

Neural circuit mechanisms for pattern detection and feature combination in olfactory cortex

Odors are initially encoded in the brain as a set of distinct physicochemical characteristics but are ultimately perceived as a unified sensory object--a "smell." It remains unclear how chemical features encoded by diverse odorant receptors and segregated glomeruli in the main olfactory bulb (MOB) are assembled into integrated cortical representations. Combining patterned optical microstimulation of MOB with in vivo electrophysiological recordings in anterior piriform cortex (PCx), we assessed how cortical neurons decode complex activity patterns distributed across MOB glomeruli. PCx firing was insensitive to single-glomerulus photostimulation. Instead, individual cells reported higher-order combinations of coactive glomeruli resembling odor-evoked sensory maps. Intracellular recordings revealed a corresponding circuit architecture providing each cortical neuron with weak synaptic input from a distinct subpopulation of MOB glomeruli. PCx neurons thus detect specific glomerular ensembles, providing an explicit neural representation of chemical feature combinations that are the hallmark of complex odor stimuli.     

Dynamics and mechanisms of oscillatory photosynthesis

We classify mathematical models that can be used to describe photosynthetic oscillations using ideas from nonlinear dynamics, and discuss potential mechanisms for photosynthetic oscillations in the context of this classification. We then turn our attention to recent experiments with leaves transferred to a low CO₂ atmosphere which revealed stochastic oscillations with a period of a few seconds. Rubisco is the enzyme that takes both CO₂ and O₂ as substrates correspondingly for photosynthetic assimilation and for photorespiration. Photosynthesis depletes CO₂ and produces O₂ while respiration and photorespiration work in the opposite direction, so the product of one process becomes the reactant of the other coupled process. We examine the possibility of oscillations of CO₂ and O₂ in the leaf in relation to photorespiration. We suggest that in the cell, oscillations with a period of a few seconds, corresponding to the time between photosynthetic CO₂ fixation and photorespiratory CO₂ release, underlie the dynamics of metabolism in C₃ plants.     

Central nervous mechanisms in the generation of the pattern of breathing

The role of the B?tzinger complex (B?tC) and the pre-B?tzinger complex (pre-B?tC) in the genesis of the breathing pattern was investigated in anesthetized, vagotomized, paralysed and artificially ventilated rabbits making use of bilateral microinjections of kainic acid (KA) and excitatory amino acid (EAA) receptor antagonists. KA microinjections into either the B?tC or the pre-B?tC transiently eliminated respiratory rhythmicity in the presence of tonic phrenic activity (tonic apnea). Rhythmic activity resumed as low-amplitude, high-frequency irregular oscillations, superimposed on tonic inspiratory activity and displayed a progressive, although incomplete recovery. Microinjections of kynurenic acid (KYN) and D(-)-2-amino-5-phosphonopentanoic acid (D-AP5) into the B?tC caused a pattern of breathing characterized by low-amplitude, high-frequency irregular oscillations and subsequently tonic apnea. Responses to KYN and D-AP5 in the pre-B?tC were similar, although less pronounced than those elicited by these drugs in the B?tC and never characterized by tonic apnea. Microinjections of 6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) into the B?tC and the pre-B?tC induced much less intense responses mainly consisting of increases in respiratory frequency. The results show that the investigated medullary regions play a prominent role in the genesis of the normal pattern of breathing through the endogenous activation of EAA receptors.     

Emergent mechanisms in multiple pattern generation of the lobster pyloric network

By using a hard-wired oscillator network, multiple pattern generation of the lobster pyloric network is simulated. The network model is constructed using a relaxation oscillator representing an oscillatory or quiescent (i.e. steady-state) neuron. Modulatory inputs to the network are hypothesized to cause changes in the dynamical properties of each pyloric neuron: the oscillatory frequency, the postinhibitory rebound property, and the resting membrane potential. Changes in each of these properties are induced by changing appropriate parameters of the oscillator. By changing seven parameters of the network as a whole, modulatory input-dependent patterns are successfully simulated. Received: 13 July 1999 / Accepted in revised form: 17 December 1999     

Finding differentially expressed genes for pattern generation

MOTIVATION: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation. RESULTS: We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided. CONTACT: alhajj@cpsc.ucalgary.ca.     

Methods for iPS cell generation for basic research and clinical applications

The induction of pluripotency can be achieved by forced expression of defined factors in somatic cells. The established cells, termed induced pluripotent stem (iPS) cells, have pluripotency and an infinite capacity for self-renewal in common with embryonic stem (ES) cells. Patient-specific iPS cells could be a useful source for drug discovery and cell transplantation therapies; however, the original method for iPS cell generation had several issues that were obstacles to their clinical application. Recent studies have brought about various improvements for iPS cell generation and uncovered several characteristics of iPS cells. Here we summarize the current status of iPS cell studies, with a focus on the improved methods that can be used to generate iPS cells, and also refer to the future challenges.     

Developmental mechanisms for the generation of telencephalic interneurons

Interneurons, which release the neurotransmitter γ-aminobutyric acid (GABA), are the major inhibitory cells of the central nervous system (CNS). Despite comprising only 20-30% of the cerebral cortical neuronal population, these cells play an essential and powerful role in modulating the electrical activity of the excitatory pyramidal cells onto which they synapse. Although interneurons are present in all regions of the mature telencephalon, during embryogenesis these cells are generated in specific compartments of the ventral (subpallial) telencephalon known as ganglionic eminences. To reach their final destinations in the mature brain, immature interneurons migrate from the ganglionic eminences to developing telencephalic structures that are both near and far from their site of origin. The specification and migration of these cells is a complex but precisely orchestrated process that is regulated by a combination of intrinsic and extrinsic signals. The final outcome of which is the wiring together of excitatory and inhibitory neurons that were born in separate regions of the developing telencephalon. Disruption of any aspect of this sequence of events during development, either from an environmental insult or due to genetic mutations, can have devastating consequences on normal brain function.     

Biological timing and the clock metaphor: oscillatory and hourglass mechanisms

Living organisms have developed a multitude of timing mechanisms--"biological clocks." Their mechanisms are based on either oscillations (oscillatory clocks) or unidirectional processes (hourglass clocks). Oscillatory clocks comprise circatidal, circalunidian, circadian, circalunar, and circannual oscillations--which keep time with environmental periodicities--as well as ultradian oscillations, ovarian cycles, and oscillations in development and in the brain, which keep time with biological timescales. These clocks mainly determine time points at specific phases of their oscillations. Hourglass clocks are predominantly found in development and aging and also in the brain. They determine time intervals (duration). More complex timing systems combine oscillatory and hourglass mechanisms, such as the case for cell cycle, sleep initiation, or brain clocks, whereas others combine external and internal periodicities (photoperiodism, seasonal reproduction). A definition of a biological clock may be derived from its control of functions external to its own processes and its use in determining temporal order (sequences of events) or durations. Biological and chemical oscillators are characterized by positive and negative feedback (or feedforward) mechanisms. During evolution, living organisms made use of the many existing oscillations for signal transmission, movement, and pump mechanisms, as well as for clocks. Some clocks, such as the circadian clock, that time with environmental periodicities are usually compensated (stabilized) against temperature, whereas other clocks, such as the cell cycle, that keep time with an organismic timescale are not compensated. This difference may be related to the predominance of negative feedback in the first class of clocks and a predominance of positive feedback (autocatalytic amplification) in the second class. The present knowledge of a compensated clock (the circadian oscillator) and an uncompensated clock (the cell cycle), as well as relevant models, are briefly re viewed. Hourglass clocks are based on linear or exponential unidirectional processes that trigger events mainly in the course of development and aging. An important hourglass mechanism within the aging process is the limitation of cell division capacity by the length of telomeres. The mechanism of this clock is briefly reviewed. In all clock mechanisms, thresholds at which "dependent variables" are triggered play an important role.     

Sensitivity of the gradient oscillatory number to flow input waveform shapes

The sensitivity of the gradient oscillatory number (GON), which is a potential hemodynamic indicator for cerebral aneurysm initiation, to flow input waveform shapes was examined by performing computational fluid dynamics (CFD) simulations of an anatomical model of a human internal carotid artery under three different waveform shape conditions. The local absolute variation (standard deviation) and relative variation (coefficient of variation) of the GON calculations for three waveform shapes were computed to quantify the variation in GON due to waveform shape changes. For all waveform shapes, an elevated GON was evident at a known aneurysm site, albeit occurring at additional sites. No significant differences were observed among the qualitative GON distributions derived using the three different waveform shapes. These results suggest that the GON is largely insensitive to the variability in flow input waveform shapes. The quantitative analysis revealed that GON displays an improved relative variation over a relatively high GON range. We therefore conclude that it is reasonable to use assumed flow input waveform shapes as a substitute for individual real waveform shapes for the detection of possible GON elevations of individual clinical cases in large-scale studies, where the higher values of GON are of primary interest.     

Neural mechanisms for entrainment and generation of mammalian circadian rhythms.

The identification of a direct retinohypothalamic tract (RHT) terminating in the supra-chiasmatic nuclei (SCN) has focused attention on the role of these structures in the entrainment and generation of circadian rhythms in mammals. Light effects on circadian rhythms are mediated by both the RHT and portions of the classical visual system. The complex interactions of these systems are reflected both in their direct anatomical connections and in the functional changes in entrainment produced by interruption of either set of projections. Destruction of the RHT/SCN eliminated both normal entrainment and normal free-running circadian rhythms. No circadian rhythms has survived SCN ablation in rodents, but a variety of non-circadian cycles can be generated by lesioned animals. The complex behavioral patterns produced by SCN-lesioned hamsters suggest that circadian oscillators continue to function in these animals, but that their activity is no longer integrated into a single circadian framework. The available evidence indicates that the mammalian pacemaking system comprises a set of independent oscillators normally regulated by the SCN and by light information that is transmitted via several retinofugal pathways.     

Direct measurement of oscillatory generation of superoxide anions by single phagocytes

Phagocytic cells such as neutrophils generate superoxide anions (O₂⁻) within phagocytic vacuoles for killing and digesting microorganisms. Here we report the simultaneous observation of morphological changes and O₂⁻ generation in single phagocytic cells during phagocytosis. Point stimulation of a cell by contact with an opsonized microelectrode at the cell surface induced significant deformation to engulf the electrode, and also induced the O₂⁻ generation which was measured by the electrode. Periodic fluctuations in the magnitude of the O₂⁻ generation were observed in the time course. These oscillations may be caused by metabolic regulation of the formation of NADPH, which is the substrate for the O₂⁻ generation.     

Physical mechanisms for chemotactic pattern formation by bacteria.

This paper formulates a theory for chemotactic pattern formation by the bacteria Escherichia coli in the presence of excreted attractant. In a chemotactically neutral background, through chemoattractant signaling, the bacteria organize into swarm rings and aggregates. The analysis invokes only those physical processes that are both justifiable by known biochemistry and necessary and sufficient for swarm ring migration and aggregate formation. Swarm rings migrate in the absence of an external chemoattractant gradient. The ring motion is caused by the depletion of a substrate that is necessary to produce attractant. Several scaling laws are proposed and are demonstrated to be consistent with experimental data. Aggregate formation corresponds to finite time singularities in which the bacterial density diverges at a point. Instabilities of swarm rings leading to aggregate formation occur via a mechanism similar to aggregate formation itself: when the mass density of the swarm ring exceeds a threshold, the ring collapses cylindrically and then destabilizes into aggregates. This sequence of events is demonstrated both in the theoretical model and in the experiments.     

'Generic' physical mechanisms of morphogenesis and pattern formation

The role of 'generic' physical mechanisms in morphogenesis and pattern formation of tissues is considered. Generic mechanisms are defined as those physical processes that are broadly applicable to living and non-living systems, such as adhesion, surface tension and gravitational effects, viscosity, phase separation, convection and reaction-diffusion coupling. They are contrasted with 'genetic' mechanisms, a term reserved for highly evolved, machine-like, biomolecular processes. Generic mechanisms acting upon living tissues are capable of giving rise to morphogenetic rearrangements of cytoplasmic, tissue and extracellular matrix components, sometimes leading to 'microfingers', and to chemical waves or stripes. We suggest that many morphogenetic and patterning effects are the inevitable outcome of recognized physical properties of tissues, and that generic physical mechanisms that act on these properties are complementary to, and interdependent with genetic mechanisms. We also suggest that major morphological reorganizations in phylogenetic lineages may arise by the action of generic physical mechanisms on developing embryos. Subsequent evolution of genetic mechanisms could stabilize and refine developmental outcomes originally guided by generic effects.