Multiple steady states and oscillatory behavior of a compartmentalized phosphofructokinase system

MitomiRs, chloromiRs and modelling of the microRNA inhibition

MicroRNAs are non-coding parts of nuclear and mitochondrial genomes, preventing the weakest part of the genetic regulatory networks from being expressed and preventing the appearance of a too many attractors in these networks. They have also a great influence on the chromatin clock, which ensures the updating of the genetic regulatory networks. The post-transcriptional inhibitory activity by the microRNAs, which is partly unspecific, is due firstly to their possibly direct negative action during translation by hybridizing tRNAs, especially those inside the mitochondrion, hence slowing mitochondrial respiration, and secondly to their action on a large number of putative m-RNA targets like those involved in immunetworks; We show that the circuits in the core of the interaction graphs are responsible for the small number of dedicated attractors that correspond to genetically controlled functions, partly due to a general filtering by the microRNAs. We analyze this influence as well as their impact on important functions like the control by the p53 network over the apoptosis/proliferation system and the homeostasis of the energy metabolism. In this last case, we show the role of two kinds of microRNAs, both involved in the control of the mitochondrial genome: (1) nuclear microRNAs, called mitoMirs, inhibiting mitochondrial genes and (2) putative mitochondrial microRNAs inhibiting the tRNAs functioning.

Neurophysiologic responses of peripheral nerve to repeated episodes of anoxia

OBJECTIVE

Determine the effects of serial episodes of anoxia in an in vitro peripheral nerve preparation.

METHODS

The nerve action potential (NAP) from rat sciatic nerve was recorded during 5 cycles of anoxia and reperfusion. Multiple NAP parameters were analyzed as well as stimulus response curves.

RESULTS

The amplitude of the NAP declined to half baseline in 865 s on the first cycle of anoxia and recovered to half baseline during recovery in 470 s. These times increased with successive cycles of anoxia. The current required to produce a half maximal NAP showed a variable initial decrease before increasing with anoxia. The paired-pulse response showed a decline at 2-3 ms interstimulus interval during anoxia but was less dependent of interstimulus interval during recovery. NAP amplitude and velocity decrease over successive cycles of anoxia at a rate greater than in the absence of anoxia.

CONCLUSIONS

The NAP declines slowly when peripheral nerve is exposed to anoxia but returns at least twice as quickly when re-exposed to oxygen. Short periods of anoxia produce long lasting changes in the nerve suggesting greater resistance to anoxia. With serial episodes of anoxia there is gradual NAP amplitude reduction and increase in duration and latency.

SIGNIFICANCE

Anoxic-preconditioning appears in isolated peripheral nerve.

Robustness in regulatory interaction networks. A generic approach with applications at different levels: physiologic, metabolic and genetic

Regulatory interaction networks are often studied on their dynamical side (existence of attractors, study of their stability). We focus here also on their robustness, that is their ability to offer the same spatiotemporal patterns and to resist to external perturbations such as losses of nodes or edges in the networks interactions architecture, changes in their environmental boundary conditions as well as changes in the update schedule (or updating mode) of the states of their elements (e.g., if these elements are genes, their synchronous coexpression mode versus their sequential expression). We define the generic notions of boundary, core, and critical vertex or edge of the underlying interaction graph of the regulatory network, whose disappearance causes dramatic changes in the number and nature of attractors (e.g., passage from a bistable behaviour to a unique periodic regime) or in the range of their basins of stability. The dynamic transition of states will be presented in the framework of threshold Boolean automata rules. A panorama of applications at different levels will be given: brain and plant morphogenesis, bulbar cardio-respiratory regulation, glycolytic/oxidative metabolic coupling, and eventually cell cycle and feather morphogenesis genetic control.

Patterns of spatiotemporal organization in an "ambiquitous" enzyme model

Many enzymes in pathways such as glycolysis associate reversibly with cellular substructures. The spatiotemporal behavior of a "limit-cycle" oscillation model is studied under the condition that the "ambiquitous" oscillophor, phosphofructokinase, is partitioned between "bulk-phase" and "bound" forms in a heterogeneous system. Computer simulation demonstrates the occurrence of sustained, wave-like spatiotemporal patterns of chemical concentration in the bulk medium. Kinetic dissimilarity among the localized populations of bound enzyme leads to a "polarity" effect in the wave phenomenon. It is suggested that a key physiological role of the limit-cycle regime is to engender a rapid, site-to-site, signal-transmission modality in large eukaryotic (e.g., mammalian) cells.

A hysteretic cycle in glucose 6-phosphate metabolism observed in a cell-free yeast extract

The dynamics of a partial glycolytic reaction sequence which converts glucose 6-phosphate to triose phosphates is described. The study was performed with cell-free extracts from baker's yeast harvested in the logarithmic and stationary growth phases. The experiments are based on a flow-through reactor supplied with the desalted cell-free extract as well as glucose 6-phosphate, ATP and phosphoenolpyruvate. In the reaction system the quasi-irreversible reactions catalyzed by 6-phosphofructo-1-kinase, pyruvate kinase, and fructose-1,6-bisphosphatase are involved. When substrate is supplied continuously, only stable stationary states can be observed. With transient perturbations of the substrate supply, multiple stationary states appear. Cyclic transitions between unique stable stationary states were induced by appropriate changes of the rate of substrate supply. A hysteretic cycle could then be demonstrated when, during reverse transitions, a parameter region of multistability was passed. The presence (in resting yeast) or absence (in growing yeast) of fructose-1,6-bisphosphatase did not significantly influence the dynamic capabilities of the investigated reaction sequence. The kinetic properties of the cell-free extracts fit mathematical models developed for in vitro systems reconstituted from purified enzymes.

Predictions of thermodynamic efficiency in a pumped biochemical reaction

We propose and analyze a possible experimental system for the investigation of the thermodynamic efficiency of generating biochemical gradients. We investigate the efficiency of a model pump that uses 6-phosphofructokinase (EC 2.7.1.11, an enzyme that exhibits highly nonlinear kinetics), chromatophores from Rhodobacter sphaeroides, and light to generate a biochemical gradient. We analyze the experimental system and an equivalent alternative configuration and show that the establishment and maintenance of a concentration gradient across a membrane is thermodynamically equivalent to the establishment and maintenance of a stationary state in a single-phase, isothermal, open, homogeneous reaction system. With a constant input of light, the system can exist in a stable node (a stable steady state), a stable focus (upon perturbation from its steady state, the system returns to its steady state with an oscillatory component), and a stable limit cycle (at steady state the system exhibits stable oscillations). We investigate the efficiency of the system with both steady and oscillatory light input and observe efficiency changes that depend upon the autonomous state of the system and the frequency and amplitude of the periodic light input. When the system is in a stable focus, an efficiency maximum is seen when the system is perturbed at its resonant frequency. When the system is in a stable limit cycle, efficiency increases are seen near the 1:3, 1:2, and 2:1 entrainment regions and an efficiency decrease is seen near the 1:1 entrainment region. We further calculate various contributions to the efficiency: the phase shift of the force and flux, the magnitude of the response to the perturbation, and changes in the average values of the force and flux during a perturbation. We show that all three changes contribute to the overall changes in efficiency, but increases and decreases in the average force make the largest contributions.

Threshold for repetitive activity for a slow stimulus ramp: a memory effect and its dependence on fluctuations

We have obtained new insights into the behavior of a class of excitable systems when a stimulus, or parameter, is slowly tuned through a threshold value. Such systems do not accommodate no matter how slowly a stimulus ramp is applied, and the stimulus value at onset of repetitive activity shows a curious, nonmonotonic dependence on ramp speed. (Jakobsson, E. and R. Guttman. Biophys. J. 1980. 31:293-298.) demonstrated this for squid axon and for the Hodgkin-Huxley (HH) model. Furthermore, they showed theoretically that for moderately slow ramps the threshold increases as the ramp speed decreases, but for much slower ramp speeds threshold decreases as the ramp speed decreases. This latter feature was found surprising and it was suggested that the HH model, and squid axon in low calcium, exhibits reverse accommodation. We have found that reverse accommodation reflects the influence of persistent random fluctuations, and is a feature of all such excitable systems. We have derived an analytic condition which yields an approximation for threshold in the case of a slow ramp when the effect of fluctuations are negligible. This condition predicts, and numerical calculations confirm, that the onset of oscillations occurs beyond the critical stimulus value which is predicted by treating the stimulus intensity as a static parameter, i.e., the dynamic aspect of a ramp leads to a delay in the onset. The condition further demonstrates a memory effect, i.e., firing threshold is dependent on the initial state of the system. For very slow ramps then, fluctuations diminish both the delay and memory effects. We characterize the class of excitable systems for which these behaviors are expected, and we illustrate the phenomena for the HH model and for a model of cAMP-receptor dynamics in Dictyostelium discoideum.

Plasmid stability in immobilized and free recombinant Escherichia coli JM105(pKK223-200): importance of oxygen diffusion, growth rate, and plasmid copy number

Stability of the plasmid pKK223-200 in Escherichia coli JM105 was studied for both free and immobilized cells during continuous culture. The relationship between plasmid copy number, xylanase activity, which was coded for by the plasmid, and growth rate and culture conditions involved complex interactions which determined the plasmid stability. Generally, the plasmid stability was enhanced in cultured immobilized cells compared with free-cell cultures. This stability was associated with modified plasmid copy number, depending on the media used. Hypotheses are presented concerning the different plasmid instability kinetics observed in free-cell cultures which involve the antagonistic effects of plasmid copy number and plasmid presence on the plasmid-bearing/plasmid-free cell growth rate ratio. Both diffusional limitation in carrageenan gel beads, which is described in Theoretical Analysis of Immobilized-Cell Growth, and compartmentalized growth of immobilized cells are proposed to explain plasmid stability in immobilized cells.