Multi-Annual Fluctuations in Reconstructed Historical Time-Series of a European Lobster (Homarus gammarus) Population Disappear at Increased Exploitation Levels

Through the history of ecology, fluctuations of populations have been a dominating topic, and endogenous causes of fluctuations and oscillations have been recognized and studied for more than 80 years. Here we analyzed an historical dataset, covering more than 130 years, of European lobster (Homarus gammarus) catches. The data shows periodic fluctuations, which are first dampened and then disappear over time. The disappearance of the periodicity coincided with a substantial increase in fishing effort and the oscillations have not reappeared in the time series. The shifting baseline syndrome has changed our perception of not only the status of the stock, but also the regulating pressures. We describe the transition of a naturally regulated lobster population into a heavily exploited fisheries controlled stock. This is shown by the incorporation of environmental and endogenous processes in generalized additive models, autocorrelation functions and periodicity analyses of time-series.     

Ultradian biorhythms in mouse bone marrow

Ultradian oscillations in the number of karyocytes isolated from the femoral bone of intact ACR mice have been demonstrated. The periodicity of oscillations did not depend on the season or the site of mice breeding. The bone marrow also showed ultradian oscillations in relative and absolute amount of lymphoid, myeloid and mitotic cells. It is postulated that differentiation and migration of bone marrow cells might have ultradian biorhythms.     

Geographical variation in the periodicity of gypsy moth outbreaks

The existence of periodic oscillations in populations of forest Lepidoptera is well known. While information exists on how the periods of oscillations vary among different species, there is little prior evidence of variation in periodicity within the range of a single Lepidopteran species. The exotic gypsy moth is an introduced foliage-feeding insect in North America. Its populations are characterized by high amplitude oscillations between innocuously low densities and outbreak levels during which large regions of forests are defoliated. These outbreaks are recognized to arise periodically with considerable synchrony across much of the gypsy moth's North American range. Our analysis indicates that gypsy moth outbreaks in North America are periodic but they exhibit two dominant periodicities: a primary period of 8–10 yr (as previously reported) and a secondary period of 4–5 yr (a new finding in this study). The outbreak periodicity varied geographically and this variation was associated with forest type. We found that in the most susceptible forest types, those on xeric sites where oak is often mixed with pines, outbreak periodicity had a more dominant 5-yr period while in forest types characteristic of more mesic sites where oak was mixed with maples and other species, cycles were clearly operating on a 10-yr period.     

Dickkopf1--a new player in modelling the Wnt pathway

The Wnt signaling pathway transducing the stabilization of β-catenin is essential for metazoan embryo development and is misregulated in many diseases such as cancers. In recent years models have been proposed for the Wnt signaling pathway during the segmentation process in developing embryos. Many of these include negative feedback loops where Axin2 plays a key role. However, Axin2 null mice show no segmentation phenotype. We therefore propose a new model where the negative feedback involves Dkk1 rather than Axin2. We show that this model can exhibit the same type of oscillations as the previous models with Axin2 and as observed in experiments. We show that a spatial Wnt gradient can consistently convert this temporal periodicity into the spatial periodicity of somites, provided the oscillations in new cells arising in the presomitic mesoderm are synchronized with the oscillations of older cells. We further investigate the hypothesis that a change in the Wnt level in the tail bud during the later stages of somitogenesis can lengthen the time period of the oscillations and hence the size and separation of the later somites.     

How is bursting mode maintained under the action of exo- and endogenous factors?

The investigation is concerned with slow oscillations of the intracellular calcium concentration, fast oscillations of the membrane potential, and their interactions during bursting generation. The question associated with functioning of the bursting mode is considered: how is the condition of simultaneous existence of the slow and fast membrane potential oscillations (necessary for the bursting mode) realized under exo- and endogenous actions that result in changes in the neuron membrane parameters? To answer the question the regions of existence of fast, slow and bursting oscillations have been constructed on different parameter planes. The study has revealed that in spite of the fact the regions of the existence of the slow and fast oscillations are sensitive to parameter variations, the condition of the bursting mode existence remains due to invariance of the spatial vicinity of these regions. Furthermore, it has been demonstrated that there exists the possibility to enhance the maximal conductances of the calcium-dependent currents simultaneously such that even strong variations of their values do not induce changes of the oscillations mode (i.e. it remains bursting).     

Oscillatory signaling processes: the how, the why and the where

Oscillatory processes in biological signal transduction have come under progressively increasing scrutiny in terms of their functional significance and mechanisms of emergence and regulation. Since oscillatory processes can be a by-product of rapid adaptation and can also easily emerge if the feedback underlying adaptive processes is inadvertently artificially enhanced, one needs to exercise caution in both claiming the existence of in vivo oscillations and seeking to assign to them a specific functional significance. Nevertheless, oscillations can be a powerful means of encoding and transferring information both in time and in space, thus possessing important potential advantages for evolutionary selection and stabilization. Thus periodicity in the cell responses to diverse persistent external stimuli might become a more recognized and even expected feature of signaling processes.     

Method revealing latent periodicity of the nucleotide sequences modified for a case of small samples.

An earlier reported method for revealing latent periodicity of the nucleotide sequences has been considerably modified in a case of small samples, by applying a Monte Carlo method. This improved method has been used to search for the latent periodicity of some nucleotide sequences of the EMBL data bank. The existence of the nucleotide sequences' latent periodicity has been shown for some genes. The results obtained have implied that periodicity of gene structure is projected onto the periodicity of primary amino acid sequences and, further, onto spatial protein conformation. Even though the periodic structure of gene sequences has been eroded, it is still retained in primary and/or spatial structures of corresponding proteins. Furthermore, in a few cases the study of genes' periodicity has suggested their possible evolutionary origin by multifold duplications of some gene's fragments.     

Spontaneously active cells induce state transitions in a model of olfactory cortex

The existence of neurons with intrinsic oscillations does not in itself explain the synchronization of local populations of neurons, but it is likely to pace population rhythms when the neurons are suitably coupled by chemical and/or electrical synapses. In the present study, we have investigated the role of spontaneously active cells as noisy or pacemaker units in setting global oscillations in a three-layered cortical model. The presence of a small number of noisy (spontaneously active) units induce oscillations at the network level in the range of the gamma rhythm. The number of noisy units in the network and their type (excitatory or inhibitory or excitatory and inhibitory together) determines the emergence of regular oscillations or aperiodic (chaotic) behaviour. It also determines the onset of the global behaviour. On replacing a noisy unit by a pacemaker unit, similar gamma oscillations were generated. With both noisy and pacemaker units, we found that certain characteristics of the spontaneous activity determine the delay period for the onset of global activity. Preliminary studies have been carried out with spontaneously active units having a chaotic dynamics but the results are much similar to that with a noisy burst. Different functional roles have been suggested for cortical oscillations, such as determining global functional states and specifying connectivity during development. Oscillations at different frequency bands, in particular in the gamma band (around 40 Hz), have also been associated with memory and attention. The presence of spontaneously active neurons, either with noisy or oscillatory activity, could be responsible for global oscillations in the absence of external stimuli in certain cortical areas in the mature brain.     

Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose

We report that autonomous oscillations, which usually happen in aerobic glucose-limited continuous cultures of yeast at low dilution rate, were also observed in trehalose discontinuous cultures of Saccharomyces cerevisiae. This unexpected oscillatory behaviour was therefore examined using fast Fourier transformation of online gas measurements. This robust mathematical analysis underlined the existence of two types of oscillation. The first was found to be linked to the cell cycle because (a) the periodicity corresponded to a fraction of the generation time and (b) the oscillations were accompanied by a transient increase in the budding index, mobilization of storage carbohydrates, and fermentative activity. Moreover, these oscillations occurred in a range of specific growth rates between 0.04 and 0.15 h(-1). All these criteria were consistent with the cell-cycle-related metabolic oscillations observed in the same range of growth rates in glucose-limited continuous cultures. The second type were short-period respiratory oscillations, independent of the specific growth rate. Both types of oscillation were found to take place consecutively and/or simultaneously during batch culture on trehalose. In addition, mobilization of intracellular trehalose emerged as a key parameter for the sustainability of these autonomous oscillations as they were no longer observed in a mutant defective in neutral trehalase activity. We propose that batch culture on trehalose may be an excellent device for further investigation of the molecular mechanisms that underlie autonomous oscillations in yeast.     

Model for energy oscillations in cells

Rapid periodic pulses have been observed in yeast cell walls and these pulsations must be accompanied by coherent oscillations of energy. Such energy oscillations are likely to be a common feature in cells and we explore other consequences, either known or unknown, that may originate from chemical oscillations of small amplitude. We do not consider specific mechanisms for the energy oscillations, but here we accept their existence as a fact following from the yeast experiments. Chemical oscillators are treated as generic quantum oscillators and this model predicts that observed frequencies should have a simple volume-dependence where smaller cells exhibit higher frequencies than their larger counterparts. An extension to multicellular organisms then affords a derivation of the celebrated Kleiber law that evaluates both the numerical coefficient and the 34 exponent of mass. Calculations of activation energies and efficiencies at experimental temperatures follow. Finally, the model is applied to derive established expressions for blood flow and pulse rate. We conclude that the model reflects some common metabolic process insofar as it agrees with diverse quantitative findings while using minimal input data and without introducing free parameters.     

Nonsynchronized Oscillations in Stomatal Resistance among Sclerophylls of Eucalyptus umbra

Oscillations in stomatal resistance to viscous air flow have been recorded in the juvenile and adult sclerophylls of Eucalyptus umbra R. T. Baker, in both controlled and natural environments. Under constant illumination, temperature, and humidity, irregular oscillations in stomatal resistance with a periodicity of approximately 20 to 30 minutes occurred spontaneously, when the soil water potential was approximately −0.2 bar. In the natural summer environment, similar stomatal oscillations developed with periods ranging from 60 to 100 minutes only after imposition of soil moisture stress equivalent to −2 to −3 bars water potential. These cycles in stomatal resistance were not synchronized among the leaves of a given plant in any of the experiments.     

A clock-work somite

Somites are transient structures which represent the most overt segmental feature of the vertebrate embryo. The strict temporal regulation of somitogenesis is of critical developmental importance since many segmental structures adopt a periodicity based on that of the somites. Until recently, the mechanisms underlying the periodicity of somitogenesis were largely unknown. Based on the oscillations of c-hairy1 and lunatic fringe RNA, we now have evidence for an intrinsic segmentation clock in presomitic cells. Translation of this temporal periodicity into a spatial periodicity, through somite formation, requires Notch signaling. While the Hox genes are certainly involved, it remains unknown how the metameric vertebrate axis becomes regionalized along the antero-posterior (AP) dimension into the occipital, cervical, thoracic, lumbar, and sacral domains. We discuss the implications of cell division as a clock mechanism underlying the regionalization of somites and their derivatives along the AP axis. Possible links between the segmentation clock and axial regionalization are also discussed. BioEssays 22:72-83, 2000.     

Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions

A mathematical method has been developed in order to search for latent periodicity in protein amino-acid and other symbolical sequences using dynamic programming and random matrices. The method allows the detection of the latent periodicity with insertions and deletions at positions that are unknown beforehand. The developed method has been applied to search for the periodicity in the amino-acid sequences of several proteins and in the euro/dollar exchange rate since 2001. The presence of a long period with insertions and deletions in amino-acid sequences is shown. The period length of seven amino acids is observed in the proteins that contain supercoiled regions (a coiled-coil structure) as well as of six, five, or more amino acids. The existence of the period length of 6 and 7 days, as well as 24 and 25 h in the analyzed financial time series is observed; note that this periodicity is detectable only for insertions and deletions. The causes that underlie the occurrence of the latent periodicity with insertions and deletions in amino-acid sequences and financial time series are discussed.     

Collective movement of ions in the cytoplasm

A theoretical model of propagation in the cytoplasm of self-consistent electromagnetic waves of the millimeter-infrared range has been developed, cytoplasmic ions surrounded by water ??coats?? being the main carriers of these waves. It has been discovered that not only own long-wavelength transverse oscillations, but also longitudinal waves that cannot leave the cytoplasm can exist in tissues of living organisms. Frequencies and logarithmic decrements of such perturbations have been found, and it is shown that these frequencies are close to those of ion oscillations inside the ??coats.?? Passage of laser radiation in bioobjects at the indicated frequencies has been analyzed, revealing bands of body impenetrability for waves. A new mechanism of swinging of cytoplasm own oscillations is proposed, based on the existence of an extreme border of the ion movement area. It has been shown that with this mechanism, the electric field amplitude for the longitudinal waves is six to seven orders of magnitude greater than the Planck fluctuation level.     

Late Miocene biogeography and paleoclimatology of the central North Atlantic

Quantitative analyses of planktonic foraminiferal assemblages from Deep Sea Drilling Project (DSDP) Holes 334 and 410 demonstrate that subpolar and subtropical faunal provinces existed in the North Atlantic during the late Miocene. Climatic oscillations are clearly recorded in Hole 410 by variations in abundance of the Neogloboquadrina subpolar assemblage. These climatic oscillations have a period of about 1 m.y. Higher frequency oscillations with a periodicity of one to several hundred thousand years are evident from about 6.5 to 7.5 m.y. and are probably present throughout the entire late Miocene.A revised age of 7.0 m.y. is proposed for the first occurrence of the calcareous nannofossil Amaurolithus primus (the Amaurolithus datum).     

Circadian photoreception in humans and mice

Circadian rhythms are the endogenous oscillations, occurring with a periodicity of approximately twenty-four hours, in the biochemical and behavioral functions of organisms. In mammals, the phase and period of the rhythm are synchronized to the daily light-dark cycle by light input through the eye. Certain retinal degenerative diseases affecting the photoreceptor cells, both rods and cones, in the outer retina reveal that classical opsins (i.e., rhodopsin and color opsins located in these cells) are essential for vision, but are not required for circadian photoreception. The mammalian cryptochromes and melanopsin (and possibly other opsin family pigments) have been proposed as circadian photoreceptor pigments that exist in the inner retina. Genetic analysis indicates that the cryptochromes, which contain flavin and folate as the light-absorbing cofactors, are the primary circadian photoreceptors. The classical photoreceptors in the outer retina, and melanopsin or other minor opsins in the inner retina, may perform redundant functions in circadian rhythmicity.     

On the dynamics of controlled metabolic network and cellular behavior

The existence of elaborate control mechanisms for the various biochemical processes inside and within living cells is responsible for the coherent behaviour observed in its spatio-temporal organisation. Stability and sensitivity are both necessary properties of living systems and these are achieved through negetive and positive feedback loops as in other control systems. We have studied a three-step reaction scheme involving a negative and a positive feedback loop in the form of end-product inhibition and allosteric activation. The variety of behaviour exhibited by this system, under different conditions, includes steady state, simple limit cycle oscillations, complex oscillations and period bifurcations leading to random oscillations or chaos. The system also shows the existence of two distinct chaotic regimes under the variation of a single parameter. These results, in comparison with single biochemical control loops, show that new behaviours can be exhibited in a more complex network which are not seen in the single control loops. The results are discussed in the light of a diverse variety of cellular functions in normal and altered cells indicating the role of controlled metabolic network as the underlying basis for cellular behaviour.     

Neuronal rebound spiking,resonance frequency and theta cycle skipping may contribute to grid cell firing in medial entorhinal cortex

Data show a relationship of cellular resonance and network oscillations in the entorhinal cortex to the spatial periodicity of grid cells. This paper presents a model that simulates the resonance and rebound spiking properties of entorhinal neurons to generate spatial periodicity dependent upon phasic input from medial septum. The model shows that a difference in spatial periodicity can result from a difference in neuronal resonance frequency that replicates data from several experiments. The model also demonstrates a functional role for the phenomenon of theta cycle skipping in the medial entorhinal cortex.     

Calcium Ion Binding Properties of Medicago truncatula Calcium/Calmodulin-Dependent Protein Kinase

A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (～125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.