A novel suite of cyclotides from Viola odorata: sequence variation and the implications for structure, function and stability

Cyclotides are a fascinating family of plant-derived peptides characterized by their head-to-tail cyclized backbone and knotted arrangement of three disulfide bonds. This conserved structural architecture, termed the CCK (cyclic cystine knot), is responsible for their exceptional resistance to thermal, chemical and enzymatic degradation. Cyclotides have a variety of biological activities, but their insecticidal activities suggest that their primary function is in plant defence. In the present study, we determined the cyclotide content of the sweet violet Viola odorata, a member of the Violaceae family. We identified 30 cyclotides from the aerial parts and roots of this plant, 13 of which are novel sequences. The new sequences provide information about the natural diversity of cyclotides and the role of particular residues in defining structure and function. As many of the biological activities of cyclotides appear to be associated with membrane interactions, we used haemolytic activity as a marker of bioactivity for a selection of the new cyclotides. The new cyclotides were tested for their ability to resist proteolysis by a range of enzymes and, in common with other cyclotides, were completely resistant to trypsin, pepsin and thermolysin. The results show that while biological activity varies with the sequence, the proteolytic stability of the framework does not, and appears to be an inherent feature of the cyclotide framework. The structure of one of the new cyclotides, cycloviolacin O14, was determined and shown to contain the CCK motif. This study confirms that cyclotides may be regarded as a natural combinatorial template that displays a variety of peptide epitopes most likely targeted to a range of plant pests and pathogens.

Volcanic setting of the Bajo de la Alumbrera porphyry Cu-Au deposit, Farallon Negro Volcanics, Northwest Argentina

The late Miocene Farallon Negro volcanics, comprising basaltic to rhyodacitic volcano-sedimentary rocks, host the Bajo de la Alumbrera porphyry copper-gold deposit in northwest Argentina. Early studies of the geology of the district have underpinned the general model for porphyry ore deposits where hydrothermal alteration and mineralization develop in and around porphyritic intrusions emplaced at shallow depths (2.5-3.5 km) into stratovolcanic assemblages. The Farallon Negro succession is dominated by thick sequences of volcano-sedimentary breccias, with lavas forming a minor component volumetrically. These volcaniclastic rocks conformably overlie crystalline basement-derived sedimentary rocks deposited in a developing foreland basin southeast of the Puna-Altiplano plateau. Within the Farallon Negro volcanics, volcanogenic accumulations evolved from early mafic to intermediate and silicic compositions. The younger and more silicic rocks are demonstrably coeval and comagmatic with the earliest group of mineralized porphyritic intrusions at Bajo de la Alumbrera. Our analysis of the volcanic stratigraphy and facies architecture of the Farallon Negro volcanics indicates that volcanic eruptions evolved from effusive to mixed effusive and explosive styles, as magma compositions changed to more intermediate and silicic compositions. Air early phase of mafic to intermediate voleanism was characterized by small synsedimentary intrusions with peperitic contacts, and lesser lava units scattered widely throughout the district, and interbedded with thick and extensive successions of coarse-grained sedimentary breccias. These sedimentary breccias formed from numerous debris- and hyperconcentrated flow events. A later phase of silicic volcanism included both effusive eruptions, forming several areally restricted lavas, and explosive eruptions, producing more widely dispersed (up to 5 kin) tuff units, some tip to 30-m thickness in proximal sections. Four key features of the volcanic stratigraphy suggest that the Farallon Negro volcanics need not simply record the construction of a large steep-sided polygenetic stratovolcano: (1) sheetlike, laterally continuous debris-flow and other coarse-grained sedimentary deposits are dominant, particularly in the lower sections; (2) mafic-intermediate composition lavas are volumetrically minor; (3) peperites are present throughout the sequence; and (4) fine-grained lacustrine sandstone-siltstone sequences occur in areas previously thought to be proximal to the summit region of the stratovolcano. Instead, the nature, distribution, and geometry of volcanic and volcaniclastic facies suggest that volcanism occurred as a relatively low relief, multiple-vent volcanic complex at the eastern edge of a broad, > 200-km-wide late Miocene volcanic belt and oil ail active foreland sedimentary basin to the Puna-Altiplano. Volcanism that occurred synchronously with the earliest stages of porphyry-related mineralization at Bajo de la Alumbrera apparently developed in an alluvial to ring plain setting that was distal to larger volcanic edifices.

A reference architecture for instructional educational software

Our extensive research has indicated that high-school teachers are reluctant to make use of existing instructional educational software (Pollard, 2005). Even software developed in a partnership between a teacher and a software engineer is unlikely to be adopted by teachers outside the partnership (Pollard, 2005). In this paper we address these issues directly by adopting a reusable architectural design for instructional educational software which allows easy customisation of software to meet the specific needs of individual teachers. By doing this we will facilitate more teachers regularly using instructional technology within their classrooms. Our domain-specific software architecture, Interface-Activities-Model, was designed specifically to facilitate individual customisation by redefining and restructuring what constitutes an object so that they can be readily reused or extended as required. The key to this architecture is the way in which the software is broken into small generic encapsulated components with minimal domain specific behaviour. The domain specific behaviour is decoupled from the interface and encapsulated in objects which relate to the instructional material through tasks and activities. The domain model is also broken into two distinct models - Application State Model and Domainspecific Data Model. This decoupling and distribution of control gives the software designer enormous flexibility in modifying components without affecting other sections of the design. This paper sets the context of this architecture, describes it in detail, and applies it to an actual application developed to teach high-school mathematical concepts.

Research, knowledge and design

The discussion about relations between research and design has a number of strands, and presumably motivations. Putting aside the question whether or not design or “creative endeavour” should be counted as research, for reasons to do with institutional recognition or reward, the question remains how, if at all, is design research? This question is unlikely to have attracted much interest but for matters external to Architecture within the modern university. But Architecture as a discipline now needs to understand research much better than in the past when ‘research’ was whatever went on in building science, history or people/environment studies. In this paper, I begin with some common assumptions about design, considered in relation to research, and suggest how the former can constitute or be a mode of the latter. Central to this consideration is an understanding of research as the production of publicly available knowledge. The method is that of conceptual analysis which is much more fruitful than is usually appreciated. This work is part of a larger project in philosophy of design, in roughly the analytical tradition.

When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface

The Indo-West Pacific is characterized by extraordinary marine species diversity. The evolutionary mechanisms responsible for generating this diversity remain puzzling, but are often linked to Pleistocene sea level fluctuations. The impact of these sea level changes on the population genetic architecture of the estuarine fish Lates calcarifer are investigated via a natural experiment in a region of the Indo-West Pacific known to have undergone considerable change during the Pleistocene. L. calcarifer, a coastline-restricted catadromous teleost, provides an excellent model for studying the effects of sea level change as its habitat requirements potentially make it sensitive to the region's physical history. Evidence was found for a large phylogenetic break (4% mtDNA control region; 0.47% ATPase 6 and 8) either side of the Torres Strait, which separates the Western Pacific and Indian Oceans, although some mixing of the clades was evident. This suggests clinal secondary introgression of the clades via contemporary gene flow. Further, populations on Australia's east coast appear to have passed through a bottleneck. This was linked to the historical drying of the Great Barrier Reef coastal lagoon, which resulted in a significant loss of habitat and forced retreat into isolated refugia. These results suggest that historical eustatic changes have left a significant imprint on the molecular diversity within marine species as well as among them in the Indo-West Pacific.

Three-dimensional quantum solitons with parametric coupling

We consider the quantum field theory of two bosonic fields interacting via both parametric (cubic) and quartic couplings. In the case of photonic fields in a nonlinear optical medium, this corresponds to the process of second-harmonic generation (via chi((2)) nonlinearity) modified by the chi((3)) nonlinearity. The quantum solitons or energy eigenstates (bound-state solutions) are obtained exactly in the simplest case of two-particle binding, in one, two, and three space dimensions. We also investigate three-particle binding in one space dimension. The results indicate that the exact quantum solitons of this field theory have a singular, pointlike structure in two and three dimensions-even though the corresponding classical theory is nonsingular. To estimate the physically accessible radii and binding energies of the bound states, we impose a momentum cutoff on the nonlinear couplings. In the case of nonlinear optical interactions, the resulting radii and binding energies of these photonic particlelike excitations in highly nonlinear parametric media appear to be close to physically observable values.

Computational chemistry on Fujitsu vector-parallel processors: Development and performance of applications software

In this and a preceding paper, we provide an introduction to the Fujitsu VPP range of vector-parallel supercomputers and to some of the computational chemistry software available for the VPP. Here, we consider the implementation and performance of seven popular chemistry application packages. The codes discussed range from classical molecular dynamics to semiempirical and ab initio quantum chemistry. All have evolved from sequential codes, and have typically been parallelised using a replicated data approach. As such they are well suited to the large-memory/fast-processor architecture of the VPP. For one code, CASTEP, a distributed-memory data-driven parallelisation scheme is presented. (C) 2000 Published by Elsevier Science B.V. All rights reserved.

An equivalent algorithm for simulating thermal effects of magma intrusion problems in porous rocks

An equivalent algorithm is proposed to simulate thermal effects of the magma intrusion in geological systems, which are composed of porous rocks. Based on the physical and mathematical equivalence, the original magma solidification problem with a moving boundary between the rock and intruded magma is transformed into a new problem without the moving boundary but with a physically equivalent heat source. From the analysis of an ideal solidification model, the physically equivalent heat source has been determined in this paper. The major advantage in using the proposed equivalent algorithm is that the fixed finite element mesh with a variable integration time step can be employed to simulate the thermal effect of the intruded magma solidification using the conventional finite element method. The related numerical results have demonstrated the correctness and usefulness of the proposed equivalent algorithm for simulating the thermal effect of the intruded magma solidification in geological systems. (C) 2003 Elsevier B.V. All rights reserved.