A feedback quenched oscillator produces turing patterning with one diffuser

Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the "activator-inhibitor" models of Meinhardt and Gierer. Systems based on this model are notoriously difficult to engineer. We present the first demonstration that Turing pattern formation can arise in a new family of oscillator-driven gene network topologies, specifically when a second feedback loop is introduced which quenches oscillations and incorporates a diffusible molecule. We provide an analysis of the system that predicts the range of kinetic parameters over which patterning should emerge and demonstrate the system's viability using stochastic simulations of a field of cells using realistic parameters. The primary goal of this paper is to provide a circuit architecture which can be implemented with relative ease by practitioners and which could serve as a model system for pattern generation in synthetic multicellular systems. Given the wide range of oscillatory circuits in natural systems, our system supports the tantalizing possibility that Turing pattern formation in natural multicellular systems can arise from oscillator-driven mechanisms.     

Fast and robust image segmentation by small-world neural oscillator networks

Inspired by the temporal correlation theory of brain functions, researchers have presented a number of neural oscillator networks to implement visual scene segmentation problems. Recently, it is shown that many biological neural networks are typical small-world networks. In this paper, we propose and investigate two small-world models derived from the well-known LEGION (locally excitatory and globally inhibitory oscillator network) model. To form a small-world network, we add a proper proportion of unidirectional shortcuts (random long-range connections) to the original LEGION model. With local connections and shortcuts, the neural oscillators can not only communicate with neighbors but also exchange phase information with remote partners. Model 1 introduces excitatory shortcuts to enhance the synchronization within an oscillator group representing the same object. Model 2 goes further to replace the global inhibitor with a sparse set of inhibitory shortcuts. Simulation results indicate that the proposed small-world models could achieve synchronization faster than the original LEGION model and are more likely to bind disconnected image regions belonging together. In addition, we argue that these two models are more biologically plausible.     

Regulation of circulating levels of the crustacean hyperglycemic hormone: evidence for a dual feedback control system

The effects of glutamate, aspartate, glycine, proline, alanine, taurine, glycerol, glucose and lactate injections on the haemolymph levels of the crustancean hyperglycemic hormone and/or glucose and lactate in the shore crab, Carcinus maenas, were investigated. Only glucose and lactate caused significant changes of hyperglycaemic hormone levels. Glucose injections resulted in a drop of both hormone and lactate, while lactate had an opposite effect, i.e. it raised both crustacean hormone and glucose levels. The results suggest that during increases in glycolytic flux, lactate may cause a release of hormone by a positive feedback mechanism. The hormone would then stimulate glycogenolysis, thus increasing glucose availability. If more glucose is released than is metabolized, excess glucose may leak from the cells and suppress crustancean hyperglycemic hormone release from the X-organ/sinus gland complex by negative feedback.Abbreviations ABTS 2,2-azino-bis (3-ethylbenzthiazoline sulphonic acid) - ANOVA one-way analysis of variance - BSA bovine serum albumin - BW body weight - CHH crustacean hyperglycemic hormone - ELISA cnzyme-liked immunosorbent assay - GIH gonadinhibiting hormone - IgG immunoglobin G - MIH moult-inhibiting hormone - MTGXO medulla terminalis X-organ - PB sodium phosphate buffer - PBS phosphate buffered saline - Pi inorganic phosphate - XO-SG X-organ-sinus gland complex     

Merging microarray data from separate breast cancer studies provides a robust prognostic test

Background  

There is an urgent need for new prognostic markers of breast cancer metastases to ensure that newly diagnosed patients receive appropriate therapy. Recent studies have demonstrated the potential value of gene expression signatures in assessing the risk of developing distant metastases. However, due to the small sample sizes of individual studies, the overlap among signatures is almost zero and their predictive power is often limited. Integrating microarray data from multiple studies in order to increase sample size is therefore a promising approach to the development of more robust prognostic tests.     

The parvocellular LGN provides a robust disynaptic input to the visual motion area MT

Dorsal visual cortical areas are thought to be dominated by input from the magnocellular (M) visual pathway, with little or no parvocellular (P) contribution. These relationships are supported by a close correlation between the functional properties of these areas and the M pathway and by a lack of anatomical evidence for P input. Here we use rabies virus as a retrograde transynaptic tracer to show that the dorsal area MT receives strong input, via a single relay, from both M and P cells of the lateral geniculate nucleus. This surprising P input, likely relayed via layer 6 Meynert cells in primary visual cortex, can provide MT with sensitivity to a more complete range of spatial, temporal, and chromatic cues than the M pathway alone. These observations provide definitive evidence for P pathway input to MT and show that convergence of parallel visual pathways occurs in the dorsal stream.     

Models of a dual inheritance system

In higher plants, animals and fungi, there are two inheritance systems: the familiar system, depending on DNA sequence, used in transmitting information between sexual generations, and an epigenetic inheritance system, depending on gene activation, responsible for the transmission of states of differentiation during development. Occasionally, epigenetic changes are transmitted in sexual reproduction. A formal model of such a dual inheritance system is presented, and it is shown how the separation between the two systems can sometimes break down. The evolutionary significance of such breakdowns is discussed.     

A dual function of V0-ATPase a1 provides an endolysosomal degradation mechanism in Drosophila melanogaster photoreceptors

The vesicular adenosine triphosphatase (v-ATPase) is a proton pump that acidifies intracellular compartments. In addition, mutations in components of the membrane-bound v-ATPase V0 sector cause acidification-independent defects in yeast, worm, fly, zebrafish, and mouse. In this study, we present a dual function for the neuron-specific V0 subunit a1 orthologue v100 in Drosophila melanogaster. A v100 mutant that selectively disrupts proton translocation rescues a previously characterized synaptic vesicle fusion defect and vesicle fusion with early endosomes. Correspondingly, V100 selectively interacts with syntaxins on the respective target membranes, and neither synaptic vesicles nor early endosomes require v100 for their acidification. In contrast, V100 is required for acidification once endosomes mature into degradative compartments. As a consequence of the complete loss of this neuronal degradation mechanism, photoreceptors undergo slow neurodegeneration, whereas selective rescue of the acidification-independent function accelerates cell death by increasing accumulations in degradation-incompetent compartments. We propose that V100 exerts a temporally integrated dual function that increases neuronal degradative capacity.     

Plk1-dependent phosphorylation of optineurin provides a negative feedback mechanism for mitotic progression

Plk1 activation is required for progression through mitotic entry to cytokinesis. Here we show that at mitotic entry, Plk1 phosphorylates Optineurin (Optn) at serine 177 and that this dissociates Optn from the Golgi-localized GTPase Rab8, inducing its translocation into the nucleus. Mass spectrometry analysis revealed that Optn is associated with a myosin phosphatase complex (MP), which antagonizes the mitotic function of Plk1. Our data also indicate that Optn functionally connects this complex to Plk1 by promoting phosphorylation of the myosin phosphatase targeting subunit 1 (MYPT1). Accordingly, silencing Optn expression increases Plk1 activity and induces abscission failure and multinucleation, which were rescued upon expression of wild-type (WT) Optn, but not a phospho-deficient mutant (S177A) that cannot translocate into the nucleus during mitosis. Overall, these results highlight an important role of Optn in the spatial and temporal coordination of Plk1 activity.     

A robust orthogonal algorithm for system identification and time-series analysis

We describe and illustrate methods for obtaining a parsimonious sinusoidal series representation or model of biological time-series data. The methods are also used to identify nonlinear systems with unknown structure. A key aspect is a rapid search for significant terms to include in the model for the system or the time-series. For example, the methods use fast and robust orthogonal searches for significant frequencies in the time-series, and differ from conventional Fourier series analysis in several important respects. In particular, the frequencies in our resulting sinusoidal series need not be commensurate, nor integral multiples of the fundamental frequency corresponding to the record length. Freed of these restrictions, the methods produce a more economical sinusoidal series representation (than a Fourier series), finding the most significant frequencies first, and automatically determine model order. The methods are also capable of higher resolution than a conventional Fourier series analysis. In addition, the methods can cope with unequally-spaced or missing data, and are applicable to time-series corrupted by noise. Fially, we compare one of our methods with a wellknown technique for resolving sinusoidal signals in noise using published data for the test time-series.     

Astrotactin provides a receptor system for CNS neuronal migration

CNS neuronal migration is a specialized form of cell motility that sets forth the laminar structure of cortical regions of brain. To define the neuronal receptor systems in glial-guided neuronal migration, an in vitro assay was developed for mouse cerebellar granule neurons, which provides simultaneous tracking of hundreds of migrating neurons. Three general classes of receptor systems were analyzed, the neuron-glial adhesion ligand astrotactin, the neural cell adhesion molecules of the IgG superfamily, N-CAM, L1 and TAG-1, and the beta 1 subunit of the integrin family. In the absence of immune activities, migrating cerebellar granule neurons had an average in vitro migration rate of 12 microns h-1, with individual neurons exhibiting migration rates over a range between 0 to 70 microns h-1. The addition of anti-astrotactin antibodies (or Fabs) significantly reduced the mean rate of neuronal migration by sixty-one percent, resulting in eighty percent of the neurons having migration rates below 8 microns h-1. By contrast, blocking antibodies (or Fabs) against L1, N-CAM, TAG-1 or beta 1 integrin, individually or in combination, did not reduce the rate of neuronal migration. By video-enhanced contrast differential interference contrast microscopy the effects of anti-astrotactin antibodies were seen to be rapid. Within fifteen minutes of antibody application, streaming of cytoplasmic organelles into the leading process arrested, the nucleus shifted from a caudal to a central position, and the extension of filopodia and lamellopodia along the leading process ceased. Correlated video and electron microscopy suggested that the mechanism of arrest by antiastrotactin antibodies involved the failure to form new adhesion sites along the leading process and the disorganization of cytoskeletal components. These results suggest astrotactin acts as a neuronal receptor for granule neuron migration along astroglial fibers.     

A robust system for production of minicircle DNA vectors

Minicircle DNA vectors allow sustained transgene expression in quiescent cells and tissues. To improve minicircle production, we genetically modified Escherichia coli to construct a producer strain that stably expresses a set of inducible minicircle-assembly enzymes, ΦC31 integrase and I-SceI homing endonuclease. This bacterial strain produces purified minicircles in a time frame and quantity similar to those of routine plasmid DNA preparation, making it feasible to use minicircles in place of plasmids in mammalian transgene expression studies.     

A physiological model of a circannual oscillator

Recent evidence based on studies in hypothalamo-pituitary disconnected Soay sheep suggests that the generation of circannual rhythms may be local to specific tissues or physiological systems. Now, the authors present a physiological model of a circannual rhythm generator centered in the pituitary gland based on the interaction between melatonin-responsive cells in the pars tuberalis that act to decode photoperiod, and lactotroph cells of the adjacent pars distalis that secrete prolactin. The model produces a self-sustained, circannual rhythm in endocrine output that the authors explore by mathematical modeling. The circannual oscillation requires a delayed negative feedback mechanism. The authors highlight specific features of the pituitary dynamics as a guide to future research on circannual rhythms.     

Optimal control mode of a biochemical feedback system

An optimal feedback system for constant-value control of biochemical reaction system was investigated by computer simulations. A feedback system containing a cyclic enzyme system where two enzyme types share a substrate in a cyclic manner, was found to be the most reliable one. This feedback system has a capability to keep the stationary value of the end product at a desired level against not only exogenous substrate supply but also endogenous parametric disturbances. The cyclic enzyme system installed as a control element of this feedback system played the role of comparator in this feedback system. The control mode of this feedback system was in good agreement with that of a system established by means of optimization technique based on the maximum principle. Also bang - bang control could be performed in this biochemical feedback system as well as in electrical one.     

Learning combined feedback and feedforward control of a musculoskeletal system

The goal of this paper is the learning of neuromuscular control, given the following necessary conditions: (1) time delays in the control loop, (2) non-linear muscle characteristics, (3) learning of feedforward and feedback control, (4) possibility of feedback gain modulation during a task. A control system and learning methodology that satisfy those conditions is given. The control system contains a neural network, comprising both feedforward and feedback control. The learning method is backpropagation through time with an explicit sensitivity model. Results will be given for a one degree of freedom arm with two muscles. Good control results are achieved which compare well with experimental data. Analysis of the controller shows that significant differences in controller characteristics are found if the loop delays are neglected. During a control task the system shows feedback gain modulation, similar to experimentally found reflex gain modulation during rapid voluntary contraction. If only limited feedback information is available to the controller the system learns to co-contract the antagonistic muscle pair. In this way joint stiffness increases and stable control is more easily maintained. Received: 7 November 1995 / Accepted in revised form: 13 February 1996