TOL Systems Research Articles

The proton-motive force is required for translocation of CDI toxins across the inner membrane of target bacteria.

Contact-dependent growth inhibition (CDI) is a mode of bacterial competition orchestrated by the CdiB/CdiA family of two-partner secretion proteins. The CdiA effector extends from the surface of CDI(+) inhibitor cells, binds to receptors on neighbouring bacteria and delivers a toxin domain derived from its C-terminal region (CdiA-CT). Here, we show that CdiA-CT toxin translocation requires the proton-motive force (pmf) within target bacteria. The pmf is also critical for the translocation of colicin toxins, which exploit the energized Ton and Tol systems to cross the outer membrane. However, CdiA-CT translocation is clearly distinct from known colicin-import pathways because ΔtolA ΔtonB target cells are fully sensitive to CDI. Moreover, we provide evidence that CdiA-CT toxins can be transferred into the periplasm of de-energized target bacteria, indicating that transport across the outer membrane is independent of the pmf. Remarkably, CDI toxins transferred under de-energized conditions remain competent to enter the target-cell cytoplasm once the pmf is restored. Collectively, these results indicate that outer- and inner-membrane translocation steps can be uncoupled, and that the pmf is required for CDI toxin transport from the periplasm to the target-cell cytoplasm.

On power of p systems using sequential and parallel rewriting

A new class of distributed computing models inspired from biology, that of P Systems, was recently introduced by Gh. Pǎun. Several variants of P Systems were already shown to be computationally universal, equal in power to Turing Machines. We investigate in this paper the power of computability of P Systems based on rewriting, with cooperation, priorities and external output. It is established that rewriting P Systems with priorities and two membranes is computationally universal, thereby making an improvement in the existing result that RE⊆RP 3(Pri). We give a new model in P Systems stressing the importance of parallelism. The power of computability of such models is investigated by comparing them with classic mechanisms in L-Systems: TOL, EOL and ETOL Systems

The Ton system can functionally replace the TolB protein in the uptake of mutated colicin U

The uptake of colicin U into sensitive cells is dependent on the Tol system. Like colicin A and the E-type colicins, colicin U contains the consensus pentapeptide DG(T/S)G(S/W) in the N-terminal 36 amino acids, which have been proposed to be involved in the interaction of colicin U with the Tol proteins. The role of the DGTGW motif in colicin U was studied by converting it into the TonB box motif DTMVV of colicin B. Uptake of the mutated colicin U (DTMVV) depended on TonB and ExbB and still remained TolA- and TolQ-dependent, but no longer required TolB. The Ton system could obviously replace the TolB function in the uptake of the mutated colicin U. The colicin U derivative is the first colicin whose uptake depends on the Ton and the Tol systems.

The Ton system can functionally replace the TolB protein in the uptake of mutated colicin U.

The uptake of colicin U into sensitive cells is dependent on the Tol system. Like colicin A and the E-type colicins, colicin U contains the consensus pentapeptide DG(T/S)G(S/W) in the N-terminal 36 amino acids, which have been proposed to be involved in the interaction of colicin U with the Tol proteins. The role of the DGTGW motif in colicin U was studied by converting it into the TonB box motif DTMVV of colicin B. Uptake of the mutated colicin U (DTMVV) depended on TonB and ExbB and still remained TolA- and TolQ-dependent, but no longer required TolB. The Ton system could obviously replace the TolB function in the uptake of the mutated colicin U. The colicin U derivative is the first colicin whose uptake depends on the Ton and the Tol systems.

A note on uniformly limited ETOL systems with unique interpretation

Abstract We briefly consider a variant of k ulETOL systems (abbreviated as k u 2 lETOL) where we require that in each derivation step, k different productions from the selected table have to be applied (if possible). We show that this subtle change leads to a new characterization of programmed grammars (without appearance checking), a result which is still unknown for the originally defined k ulETOL systems. Moreover, for k , k ′ > 1, k u 2 lE(P)TOL systems are just as powerful as k ′-u 2 lE(P)TOL systems, another result where its ul-counterpart is still open. As in the ul-case, accepting k u 2 lE(P)TOL systems are as powerful as the generating ones. Furthermore, we investigate accepting scattered context grammars.

On regularly controlled a limited tol systems

In [13], different regulation mechanisms imposed upon /c-limited TOL systems have been considered. Additionally, in this paper we investigate regularly controlled /c-limited TOL systems with or without random context and with or without appearance checking. By these kinds of control mechanisms, we further increase the generative power of the systems. Especially, we can demonstrate that for every k e IN, the family of random context regularly controlled /clTOL languages with appearance checking equals the family of recursively enumerable languages.

Effect of scission of hydrogen bonds by phenol on phase behaviour and physical properties of polydiacetylene gels: P(3BCMU) and P(4BCMU)

We report the effect of phenol on the phase behaviour and physical properties of polydiacetylene gels. Specifically, they are o-dichlorobenzene ( o-DCB) solution of poly[4,6-decadiyne-1,10-diol-bis(n-butoxycarbonylmethylurethane)], abbreviated as P(3BCMU), and toluene (Tol) solution of poly[5,7-dodecadiyne-1,12-diol-bis(n-butoxycarbonylmethylurethane)], abbreviated as P(4BCMU). The polymer concentration was 0.1 to 2 wt%, and the molar ratio z of phenol to the monomer unit of the polydiacetylenes was regulated within 20. The gel-to-sol transition temperatures T t were determined by measurements of shear modulus for the P(3 BCMU) o- DCB system and by a falling ball method for the P(4BCMU)/Tol systems. T t decreased with increasing z and the systems with polymer concentration of 1 wt% turned into a sol at room temperature in the range of z ≳ 10. The temperature dependence of alternating-current (a.c.) conductivity σ ac at 1 kHz exhibited a maximum at a temperature ca. 20 K below the transition temperature. The value of σ ac decreased steeply at the electrical transition temperature T σ , which also decreased with increasing z. Ultra-violet and visible-light spectra for the P(3 BCMU) o- DCB and P(4BCMU)/Tol systems shifted to the short-wavelength side with increasing z. The infra-red spectra indicate that the intramolecular hydrogen bonds between the NH and CO groups of the side groups are cleaved by phenol. These results indicate that the conjugated rod-like conformation is made unstable by phenol. To clarify the mechanism of crosslinks of the gel network, the crystallinity of concentrated P(3BCMU) gels was determined by wide-angle X-ray diffraction. No crystallinity was observed in the gels of C less than 30 wt%.

Regulation ofK-limited etol systems

In this paper we consider different regulation mechanisms imposed upon k-limited ETOL systems. We investigate matrix, periodically time varying, graph-controlled and programmed systems on the one side and random context and random context with appearance checking systems on the other side. We also regard mixtures of these two types. By these means, in case of k-limited TOL systems, we increase the generative power of the systems while in case of k-limited ETOL systems this is, at least partially, not true. We compare the different language families with each other as well as with other known language families.

On the relations between the degree of synchronization and the degree of nondeterminism ink-limited and uniformlyk-limited tol systems

k-limited and uniformly k-limited TOL systems provide limitations of the parallel rewriting of TOL systems. According to these systems the rewriting is carried out in a manner which lies between fully parallel and sequential rewriting. The degree ofsynchronization of such a system or of a TOL system is given by the number of its tables and the degree of nondeterminism is defined by the maximum, taken over all tables, of the maximal number of productions with the same left side in such a table. For a language L generated by such a system, taking the minimum of the corresponding degree of all such systems generating L, we get the corresponding complexity measures of the languages of the appropriate language families. As a new complexity measure we introduce the product of both degrees. The relations between these different measures are investigated.

A note on recurrent words

We introduce the notion of recurrent words in TOL systems. We prove that for an arbitrarily given TOL system G and an arbitrarily given word w it is decidable whether or not w is recurrent in G . We also solve an open and related problem for recurrent words in Markov DTOL systems.

TIL systems and languages

TIL systems are L systems accommodating both the possibility of reaction to changes in environment and the possibility of cell interactions. In this sense they constitute an extension of TOL systems and IL systems. This paper investigates mathematical properties of the class of TIL systems and of the class of languages generated by them.

TOL systems and languages

We discuss a family of systems and languages (called TOL) which have originally arisen from the study of mathematical models for the development of some biological organisms. From a formal language theory point of view, a TOL system is a rewriting system where at each step of a derivation every symbol in a string is rewritten in a context-free way, but different rewriting steps may use different sets of production rules and the language consists of all strings derivable from the single fixed string (the axiom). The family of TOL languages (as well as its different subfamilies considered here) is not closed with respect to usually considered operations; it is “incomparable” with context-free languages, but it is contained in the family of context-free programmed languages. TOL languages form an infinite hierarchy with respect to “natural” complexity measures introduced in this paper.