ALBERT

Description: The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.

Description: Different marine and coastal activities have diverse economic, environmental, and socio-cultural objectives, which can lead to conflict when these multidimensional activities coincide spatially or temporally. This is sometimes driven by a lack of understanding or other users' needs and consequentially adequate planning and the utilization of a common language is essential. By using a transparent approach based on multi-criteria analysis, we characterize and establish priorities for future development/conservation for all users in the coastal area using six representative European Case Studies with different levels of complexity. Results varied according to location, but significantly it was found that stakeholders tended to favour ecological and social over economic objectives. This paper outlines the methodology employed, the results derived, and the potential for this approach to reduce conflict in coastal and marine waters.

Description: Biological production in heterologous hosts is of interest for the production of the C4 alcohol (butanol) and other chemicals. However, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. Pseudomonas putida is a potential host for solvent production; in order to further adapt P. putida to this role, we generated mini-Tn 5 mutant libraries in strain BIRD-1 that do not consume butanol. We analyzed the insertion site of the mini-Tn 5 in a mutant that was deficient in assimilation of butanol using arbitrary PCR followed by Sanger sequencing and found that the transposon was inserted in the malate synthase B gene. Here, we show that in a second round of mutagenesis a double mutant unable to take up butanol had an insertion in a gene coding for a multisensor hybrid histidine kinase. The genetic context of the histidine kinase sensor revealed the presence of a set of genes potentially involved in butanol assimilation; qRT-PCR analysis showed induction of this set of genes in the wild type and the malate synthase mutant but not in the double mutant.

Description: The build-up of large magmatic complexes can proceed piecemeal over periods of several million years through sequences of complex processes of magma production, differentiation, assimilation, final crystallization and subsequent metasomatic modification. All these stages can produce or modify minerals used as geochronometers, such as zircon, monazite and titanite. The present study exemplifies such complex relationships, also demonstrating how a systematic approach with comprehensive sampling and careful high-resolution U–Pb analyses can yield a coherent picture of the entire magmatic process. The study was conducted on the Pavia pluton, an elongated Variscan intrusion in the Ossa–Morena Zone of Portugal. The geochronological data show that the Pavia pluton was emplaced by the amalgamation of multiple magma pulses into the crust, over a period of c . 11 Myr. An early event at ~340 Ma, revealed by xenocrystic zircon, preceded the magmatic activity at the exposed level of the pluton, but is recognized as the main magmatic event elsewhere in the Ossa–Morena Zone. A second event at 328 Ma formed tonalite, trondhjemite and granodiorite, and subordinate differentiates in the central domains of the pluton (units I and II). A third event at c . 324 Ma emplaced granodiorite in the flanking domains III–V and the contemporaneous and widespread two-mica granite in domain VI, together with late rhyodacite porphyries, microgranodiorites, aplite–pegmatite and pegmatite dikes. A fourth event at 319–317 Ma was characterized by the emplacement of some microgranites and pegmatite dikes. These two last magmatic events also had an effect on the previously emplaced rocks, causing local overgrowths and isotopic resetting of minerals. The occurrence of a fifth magmatic event at depth at 313 Ma is the inferred cause of the hydrothermal activity responsible for local zircon, monazite and titanite resorption and/or recrystallization and for some of the textures exhibited by the main rock-forming minerals. The magmatic episodes were interspersed with periods of quiescence; this cyclicity presumably reflects an external control by the transtensional tectonic regime of the Ossa–Morena Zone.

Description: The modern view of logical reasoning as modeled by a consequence operator (instead of simply by a set of theorems) has allowed for huge developments in the study of logic as an abstract discipline. Still, it is unable to explain why it is often the case that the same designation is used, in an ambiguous way, to describe several distinct modes of reasoning over the same logical language. A paradigmatic example of such a situation is ‘modal logic’, a terminology which can encompass reasoning over Kripke frames, but also over Kripke models, and in any case either locally (at a fixed world) or globally (at all worlds). Herein, we adopt a novel abstract notion of logic presented as a lattice-structured hierarchy of consequence operators, and explore some common proof-theoretic and model-theoretic ways of presenting such hierarchies through a collection of meaningful examples. In order to illustrate the usefulness of the notion of hierarchical consequence operators we address a few questions in the theory of combined logics, where a suitable abstract presentation of the logics being combined is absolutely essential. We show how to define the operation, in general, and we achieve a number of interesting preservation results for fibring within the context of 2 -hierarchies.

Description: The PtxS and PtxR regulators control the expression of the glucose dehydrogenase genes from the P gad promoter in Pseudomonas aeruginosa . These regulators bind to their cognate operators, that are separated by ~50 nt, within the promoter region and interact with each other creating a DNA-loop that prevents RNA polymerase promoter access. Binding of the 2-ketogluconate effector to PtxS caused PtxS/PtxR complex dissociation and led to the dissolution of the repression loop facilitating the entry of the RNA polymerase and enabling the transcription of the gad gene. We have identified a hydrophobic surface patch on the PtxR putative surface that was hypothesized to correspond to the binding site for PtxS. Two surface-exposed residues in this patch, V173 and W269, were replaced by alanine. Isothermal titration calorimetry assays showed that PtxS does not interact with the mutant variants of PtxR. Electrophoretic mobility shift assay and DNAase I footprinting assays proved that both regulators bind to their target operators and that failure to interact with each other prevented the formation of the DNA-loop. In vitro transcription showed that PtxS per se is sufficient to inhibit transcription from the P gad promoter, but that affinity of PtxS for its effector is modulated by PtxR.

Description: Marine spatial management is challenged by complex situations in European countries where multiple stakeholder interests and many management options have to be balanced. EU policy initiatives such as the proposed Marine Spatial Planning Directive, are in different ways targeting area allocation in European waters. In this circumstance, EU marine management needs assessments based on a satisfactory evaluation framework design that can ensure a transparent treatment of different types of information including interests, values, and facts. The main goal of this article is to introduce an evaluation framework applicable to marine management in European countries. This so-called CoExist framework maps out different types of relevant knowledge to assess future possibilities for use or no-use of marine areas and links this with appropriate management measures. The CoExist framework is based on the principles of ensuring transparent treatment of different types of information as well as appropriate stakeholder representation which can ensure legitimacy. Empirical findings in six European case studies have been obtained while conducting the CoExist framework. Applying the basic principles of the CoExist framework when planning future management directions of the coexistence of multiple activities in the long-run will expectedly affect the ecological and social-cultural goals by counterbalancing the economic ones.

Description: In the human pathogen Pseudomonas aeruginosa , the GltR regulator is required for glucose transport, whereas GtrS is a sensor kinase that plays a key role in mediating bacteria–host interaction and pathogen dissemination in the host. We show that GtrS and GltR form a two-component system that regulates the expression from the promoters P edd/gap-1 , P oprB and P glk , which control the expression of genes involved in glucose metabolism and transport. In addition, the GtrS/GltR pair regulates the expression of toxA that encodes exotoxin A, the primary virulence factor. Microcalorimetry-based ligand screening of the recombinant GtrS ligand-binding domain revealed specific binding of 2-ketogluconate (2-KG) ( K D = 5 μM) and 6-phosphogluconate ( K D = 98 μM). These effectors accelerate GtrS autophosphorylation, with concomitant transphosphorylation of GltR leading to a three-fold increase in transcription. Surprisingly, in vivo a similar increase in expression from the above promoters was observed for the mutant deficient in GltR regardless of the presence of effectors. The GltR operator site was found to contain the consensus sequence 5'-tgGTTTTTc-3'. We propose that 2-KG is a key metabolite in the stringent transcriptional control of genes involved in virulence and glucose metabolism. We show that GltR is a transcriptional repressor that is released from DNA upon phosphorylation.