Membrane Systems with Marked Membranes

AbstractMembrane computing is a biologically inspired computational paradigm. Motivated by brane calculi we investigate membrane systems which differ from conventional membrane systems by the following features: (1) biomolecules (proteins) can move through the regions of the systems, and can attach onto (and de-attach from) membranes, and (2) membranes can evolve depending on the attached molecules. The evolution of membranes is performed by using rules that are motivated by the operation of pinocytosis (the pino rule) and the operation of cellular dripping (the drip rule) that take place in living cells. We show that such membrane systems are computationally universal. We also show that if only the second feature is used then one can generate at least the family of Parikh images of the languages generated by programmed grammars without appearance checking (which contains non-semilinear sets of vectors). If, moreover, the use of pino/drip rules is non-cooperative (i.e., not dependent on the proteins attached to membranes), then one generates a family of sets of vectors that is strictly included in the family of semilinear sets of vectors. We also consider a number of decision problems concerning reachability of configurations and boundness

Mutual Mobile Membranes with Timers

A feature of current membrane systems is the fact that objects and membranes are persistent. However, this is not true in the real world. In fact, cells and intracellular proteins have a well-defined lifetime. Inspired from these biological facts, we define a model of systems of mobile membranes in which each membrane and each object has a timer representing their lifetime. We show that systems of mutual mobile membranes with and without timers have the same computational power. An encoding of timed safe mobile ambients into systems of mutual mobile membranes with timers offers a relationship between two formalisms used in describing biological systems

Genetic screen in Drosophila muscle identifies autophagy-mediated T-tubule remodeling and a Rab2 role in autophagy.

Transverse (T)-tubules make-up a specialized network of tubulated muscle cell membranes involved in excitation-contraction coupling for power of contraction. Little is known about how T-tubules maintain highly organized structures and contacts throughout the contractile system despite the ongoing muscle remodeling that occurs with muscle atrophy, damage and aging. We uncovered an essential role for autophagy in T-tubule remodeling with genetic screens of a developmentally regulated remodeling program in Drosophila abdominal muscles. Here, we show that autophagy is both upregulated with and required for progression through T-tubule disassembly stages. Along with known mediators of autophagosome-lysosome fusion, our screens uncovered an unexpected shared role for Rab2 with a broadly conserved function in autophagic clearance. Rab2 localizes to autophagosomes and binds to HOPS complex members, suggesting a direct role in autophagosome tethering/fusion. Together, the high membrane flux with muscle remodeling permits unprecedented analysis both of T-tubule dynamics and fundamental trafficking mechanisms

Characterizing PSPACE with Shallow Non-Confluent P Systems

In P systems with active membranes, the question of understanding the power of non-confluence within a polynomial time bound is still an open problem. It is known that, for shallow P systems, that is, with only one level of nesting, non-con uence allows them to solve conjecturally harder problems than con uent P systems, thus reaching PSPACE. Here we show that PSPACE is not only a bound, but actually an exact characterization. Therefore, the power endowed by non-con uence to shallow P systems is equal to the power gained by con uent P systems when non-elementary membrane division and polynomial depth are allowed, thus suggesting a connection between the roles of non-confluence and nesting depth

The Effects of Serotonin on Functionally Diverse Isolated Lamprey Spinal Cord Neurons

The experiments reported here showed that application of serotonin (5-hydroxytryptamine, 5-HT) (100 µ M) did not induce any significant current through the membranes of any of the spinal neurons studied (n = 62). At the same time, the membranes of most motoneurons and interneurons (15 of 18) underwent slight depolarization (2–6 mV) in the presence of 5-HT, which was not accompanied by any change in the input resistance of the cells. Depolarization to 10–20 mV occurred in some cells (3 of 18) of these functional groups, this being accompanied by 20–60% decreases in input resistance. The same concentration of 5-HT induced transient low-amplitude depolarization of most sensory spinal neurons (dorsal sensory cells), this changing smoothly to long-term hyperpolarization by 2–7 mV. The input resistance of the cell membranes in these cases showed no significant change (n = 8). Data were obtained which provided a better understanding of the mechanism by which 5-HT modulates the activity of spinal neurons. Thus, 5-HT facilitates chemoreceptive currents induced by application of NMDA to motoneurons and interneurons, while the NMDA responses of dorsal sensory cells were decreased by 5-HT. 5-HT affected the post-spike afterresponses of neurons. 5-HT significantly decreased the amplitude of afterhyperpolarization arising at the end of the descending phase of action potentials in motoneurons and interneurons and increased the amplitude of afterdepolarization in these types of cells. In sensory spinal neurons, 5-HT had no great effect on post-spike afterresponses. The results obtained here support the suggestion that 5-HT significantly modulates the activity of spinal neurons of different functional types. 5-HT facilitates excitation induced by subthreshold depolarization in motoneurons and some interneurons, facilitating the generation of rhythmic discharges by decreasing afterhyperpolarization. In sensory cells, 5-HT enhances inhibition due to hyperpolarization, suppressing NMDA currents. The differences in the effects of 5-HT on functionally diverse neurons are presumed to be associated with the combination of different types of 5-HT receptors on the membranes of these types of spinal neurons

The DBSCAN Clustering Algorithm on P Systems

We show how to implement the DBSCAN clustering algorithm (Density Based Spatial Clustering of Applications with Noise) on membrane systems using evolution rules with promoters and priorities

Characterizing PSPACE with Shallow Non-Confluent P Systems

In P systems with active membranes, the question of understanding the power of non-confluence within a polynomial time bound is still an open problem. It is known that, for shallow P systems, that is, with only one level of nesting, non-con uence allows them to solve conjecturally harder problems than con uent P systems, thus reaching PSPACE. Here we show that PSPACE is not only a bound, but actually an exact characterization. Therefore, the power endowed by non-con uence to shallow P systems is equal to the power gained by con uent P systems when non-elementary membrane division and polynomial depth are allowed, thus suggesting a connection between the roles of non-confluence and nesting depth