All-or-none (or something in between) transition of DNA

DNA compaction can be caused by multivalent ions as condensing agents. Both discontinuous (all-or-none) and continuous (pearl-necklace structure) transitions have been observed in experiments as the concentration of the condensing agent was increased. We have investigated the DNA transition by analytical calculations in the infinite-chain limit. A mechanism for pearl-necklace structures could be a combinatorial entropy term, which favours a mixture of globules and coils in a single chain. However, when a surface term is taken into account, it gives rise to a discontinuous transition. We also consider the role of surface charges on the globule.

On the radius of centrality in evolving communication networks

In this article, we investigate how the choice of the attenuation factor in an extended version of Katz centrality influences the centrality of the nodes in evolving communication networks. For given snapshots of a network, observed over a period of time, recently developed communicability indices aim to identify the best broadcasters and listeners (receivers) in the network. Here we explore the attenuation factor constraint, in relation to the spectral radius (the largest eigenvalue) of the network at any point in time and its computation in the case of large networks. We compare three different communicability measures: standard, exponential, and relaxed (where the spectral radius bound on the attenuation factor is relaxed and the adjacency matrix is normalised, in order to maintain the convergence of the measure). Furthermore, using a vitality-based measure of both standard and relaxed communicability indices, we look at the ways of establishing the most important individuals for broadcasting and receiving of messages related to community bridging roles. We compare those measures with the scores produced by an iterative version of the PageRank algorithm and illustrate our findings with two examples of real-life evolving networks: the MIT reality mining data set, consisting of daily communications between 106 individuals over the period of one year, a UK Twitter mentions network, constructed from the direct \emph{tweets} between 12.4k individuals during one week, and a subset the Enron email data set.

A bifurcated pathway to thiazoles and imidazoles using a modular flow microreactor

A scalable method for the preparation of 4,5-disubstituted thiazoles and imidazoles as distinct regioisomeric products using a modular flow microreactor has been devised. The process makes use of microfluidic reaction chips and packed immobilized-reagent columns to effect bifurcation of the reaction pathway.

Regulation of actin assembly by SCAR/WAVE proteins.

Actin reorganization is a tightly regulated process that co-ordinates complex cellular events, such as cell migration, chemotaxis, phagocytosis and adhesion, but the molecular mechanisms that underlie these processes are not well understood. SCAR (suppressor of cAMP receptor)/WAVE [WASP (Wiskott-Aldrich syndrome protein)-family verprolin homology protein] proteins are members of the conserved WASP family of cytoskeletal regulators, which play a critical role in actin dynamics by triggering Arp2/3 (actin-related protein 2/3)-dependent actin nucleation. SCAR/WAVEs are thought to be regulated by a pentameric complex which also contains Abi (Abl-interactor), Nap (Nck-associated protein), PIR121 (p53-inducible mRNA 121) and HSPC300 (haematopoietic stem progenitor cell 300), but the structural organization of the complex and the contribution of its individual components to the regulation of SCAR/WAVE function remain unclear. Additional features of SCAR/WAVE regulation are highlighted by the discovery of other interactors and distinct complexes. It is likely that the combinatorial assembly of different components of SCAR/WAVE complexes will prove to be vital for their roles at the centre of dynamic actin reorganization.

Dynamical properties of S-gap shifts and other shift spaces

We study the dynamical properties of certain shift spaces. To help study these properties we introduce two new classes of shifts, namely boundedly supermultiplicative (BSM) shifts and balanced shifts. It turns out that any almost specified shift is both BSM and balanced, and any balanced shift is BSM. However, as we will demonstrate, there are examples of shifts which are BSM but not balanced. We also study the measure theoretic properties of balanced shifts. We show that a shift space admits a Gibbs state if and only if it is balanced. Restricting ourselves to S-gap shifts, we relate certain dynamical properties of an S-gap shift to combinatorial properties from expansions in non-integer bases. This identification allows us to use the machinery from expansions in non-integer bases to give straightforward constructions of S -gap shifts with certain desirable properties. We show that for any q∈(0,1) there is an S-gap shift which has the specification property and entropy q . We also use this identification to address the question, for a given q∈(0,1), how many S-gap shifts exist with entropy q? For certain exceptional values of q there is a unique S-gap shift with this entropy.

Isoform specificity for oestrogen receptor and thyroid hormone receptor genes and their interactions on the NR2D gene promoter

Oestrogens are critical for the display of lordosis behaviour and, in recent years, have also been shown to be involved in synaptic plasticity. In the brain, the regulation of ionotropic glutamate receptors has consequences for excitatory neurotransmission. Oestrogen regulation of the N-methyl-d-aspartate receptor subunit 2D (NR2D) has generated considerable interest as a possible molecular mechanism by which synaptic plasticity can be modulated. Since more than one isoform of the oestrogen receptor (ER) exists in mammals, it is possible that oestrogen regulation via the ERalpha and ERbeta isoforms on the NR2D oestrogen response element (ERE) is not equivalent. In the kidney fibroblast (CV1) cell line, we show that in response to 17beta-oestradiol, only ERalpha, not ERbeta, could upregulate transcription from the ERE which is in the 3' untranslated region of the NR2D gene. When this ERE is in the 5' position, neither ERalpha nor ERbeta showed transactivation capacity. Thyroid hormone receptor (TR) modulation of ER mediated induction has been shown for other ER target genes, such as the preproenkephalin and oxytocin receptor genes. Since the various TR isoforms exhibit distinct roles, we hypothesized that TR modulation of ER induction may also be isoform specific. This is indeed the case. The TRalpha1 isoform stimulated ERalpha mediated induction from the 3'-ERE whereas the TRbeta1 isoform inhibited this induction. This study shows that isoforms of both the ER and TR have different transactivation properties. Such flexible regulation and crosstalk by nuclear receptor isoforms leads to different transcriptional outcomes and the combinatorial logic may aid neuroendocrine integration.

Characterization of proteinases from the midgut of Rhipicephalus (Boophilus) microplus involved in the generation of antimicrobial peptides

Background: Hemoglobin is a rich source of biologically active peptides, some of which are potent antimicrobials (hemocidins). A few hemocidins have been purified from the midgut contents of ticks. Nonetheless, how antimicrobials are generated in the tick midgut and their role in immunity is still poorly understood. Here we report, for the first time, the contribution of two midgut proteinases to the generation of hemocidins. Results: An aspartic proteinase, designated BmAP, was isolated from the midgut of Rhipicephalus (Boophilus) microplus using three chromatographic steps. Reverse transcription-quantitative polymerase chain reaction revealed that BmAP is restricted to the midgut. The other enzyme is a previously characterized midgut cathepsin L-like cysteine proteinase designated BmCL1. Substrate specificities of native BmAP and recombinant BmCL1 were mapped using a synthetic combinatorial peptide library and bovine hemoglobin. BmCL1 preferred substrates containing non-polar residues at P2 subsite and polar residues at P1, whereas BmAP hydrolysed substrates containing non-polar amino acids at P1 and P1`. Conclusions: BmAP and BmCL1 generate hemocidins from hemoglobin alpha and beta chains in vitro. We postulate that hemocidins may be important for the control of tick pathogens and midgut flora.

Existence of pullback attractors for pullback asymptotically compact processes

This paper is concerned with the existence of pullback attractors for evolution processes. Our aim is to provide results that extend the following results for autonomous evolution processes (semigroups) (i) An autonomous evolution process which is bounded, dissipative and asymptotically compact has a global attractor. (ii) An autonomous evolution process which is bounded, point dissipative and asymptotically compact has a global attractor. The extension of such results requires the introduction of new concepts and brings up some important differences between the asymptotic properties of autonomous and non-autonomous evolution processes. An application to damped wave problem with non-autonomous damping is considered. (C) 2009 Elsevier Ltd. All rights reserved.

Dynamics in dumbbell domains II. The limiting problem

In this work we continue the analysis of the asymptotic dynamics of reaction-diffusion problems in a dumbbell domain started in [J.M. Arrieta, AN Carvalho, G. Lozada-Cruz, Dynamics in dumbbell domains I. Continuity of the set of equilibria, J. Differential Equations 231 (2) (2006) 551-597]. Here we study the limiting problem, that is, an evolution problem in a ""domain"" which consists of an open, bounded and smooth set Omega subset of R(N) with a curve R(0) attached to it. The evolution in both parts of the domain is governed by a parabolic equation. In Omega the evolution is independent of the evolution in R(0) whereas in R(0) the evolution depends on the evolution in Omega through the continuity condition of the solution at the junction points. We analyze in detail the linear elliptic and parabolic problem, the generation of linear and nonlinear semigroups, the existence and structure of attractors. (C) 2009 Elsevier Inc. All rights reserved.

Strongly damped wave problems: Bootstrapping and regularity of solutions

The aim of the article is to present a unified approach to the existence, uniqueness and regularity of solutions to problems belonging to a class of second order in time semilinear partial differential equations in Banach spaces. Our results are applied next to a number of examples appearing in literature, which fall into the class of strongly damped semilinear wave equations. The present work essentially extends the results on the existence and regularity of solutions to such problems. Previously, these problems have been considered mostly within the Hilbert space setting and with the main part operators being selfadjoint. In this article we present a more general approach, involving sectorial operators in reflexive Banach spaces. (C) 2008 Elsevier Inc. All rights reserved.

Non-autonomous semilinear evolution equations with almost sectorial operators

Inspired by the theory of semigroups of growth a, we construct an evolution process of growth alpha. The abstract theory is applied to study semilinear singular non-autonomous parabolic problems. We prove that. under natural assumptions. a reasonable concept of solution can be given to Such semilinear singularly non-autonomous problems. Applications are considered to non-autonomous parabolic problems in space of Holder continuous functions and to a parabolic problem in a domain Omega subset of R(n) with a one dimensional handle.

GRASP heuristic with path-relinking for the multi-plant capacitated lot sizing problem

This paper addresses the independent multi-plant, multi-period, and multi-item capacitated lot sizing problem where transfers between the plants are allowed. This is an NP-hard combinatorial optimization problem and few solution methods have been proposed to solve it. We develop a GRASP (Greedy Randomized Adaptive Search Procedure) heuristic as well as a path-relinking intensification procedure to find cost-effective solutions for this problem. In addition, the proposed heuristics is used to solve some instances of the capacitated lot sizing problem with parallel machines. The results of the computational tests show that the proposed heuristics outperform other heuristics previously described in the literature. The results are confirmed by statistical tests. (C) 2009 Elsevier B.V. All rights reserved.

A general Trotter-Kato formula for a class of evolution operators

In this article we prove new results concerning the existence and various properties of an evolution system U(A+B)(t, s)0 <= s <= t <= T generated by the sum -(A(t) + B(t)) of two linear, time-dependent, and generally unbounded operators defined on time-dependent domains in a complex and separable Banach space B. In particular, writing L(B) for the algebra of all linear bounded operators on B, we can express U(A+B)(t, s)0 <= s <= t <= T as the strong limit in C(8) of a product of the holomorphic contraction semigroups generated by -A (t) and - B(t), respectively, thereby proving a product formula of the Trotter-Kato type under very general conditions which allow the domain D(A(t) + B(t)) to evolve with time provided there exists a fixed set D subset of boolean AND(t is an element of)[0,T] D(A(t) + B(t)) everywhere dense in B. We obtain a special case of our formula when B(t) = 0, which, in effect, allows us to reconstruct U(A)(t, s)0 <=(s)<=(t)<=(T) very simply in terms of the semigroup generated by -A(t). We then illustrate our results by considering various examples of nonautonomous parabolic initial-boundary value problems, including one related to the theory of timedependent singular perturbations of self-adjoint operators. We finally mention what we think remains an open problem for the corresponding equations of Schrodinger type in quantum mechanics.

A Trotter-Kato product formula for a class of non-autonomous evolution equations

In this article dedicated to Professor V. Lakshmikantham on the occasion of the celebration of his 84th birthday, we announce new results concerning the existence and various properties of an evolution system UA+B(t, s)(0 <= s <= t <= T) generated by the sum -(A(t)+B(t)) of two linear, time-dependent and generally unbounded operators defined on time-dependent domains in a complex and separable Banach space B. In particular, writing G(B) for the algebra of all linear bounded operators on B, we can express UA+B(t, s)(0 <= s <= t <= T) as the strong limit in L(B) of a product of the holomorphic contraction semigroups generated by -A(t) and -B(t), thereby getting a product formula of the Trotter-Kato type under very general conditions which allow the domain D(A(t)+B(t)) to evolve with time provided there exists a fixed set D subset of boolean AND D-t epsilon[0,D-T](A(t)+B(t)) everywhere dense in B. We then mention several possible applications of our product formula to various classes of non-autonomous parabolic initial-boundary value problems, as well as to evolution problems of Schrodinger type related to the theory of time-dependent singular perturbations of self-adjoint operators in quantum mechanics. We defer all the proofs and all the details of the applications to a separate publication. (C) 2008 Elsevier Ltd. All rights reserved.