DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Myanmar's two decades of partial transition to a market economy : a negative legacy for the new government

Despite more than two decades of transition from a centrally planned to a market-oriented economy, Myanmar’s economic transition is still only partly complete. The government’s initial strategy for dealing with the swelling deficits of the state economic enterprises (SEEs) was to put them under direct control in order to scrutinize their expenditures. This policy change postponed restructuring and exacerbated the soft budget constraint problem of the SEEs. While the installation of a new government in March 2011 has increased prospects for economic development, sustainable growth still requires full-scale structural reform of the SEEs and institutional infrastructure building. Myanmar can learn from the gradual approaches to economic transition in China and Vietnam, where partial reforms weakened further impetus for reforms.

Mathematical model for manoeuvrability of a riverine support patrol vessel with a pump-jet propulsion system

A study on the manoeuvrability of a riverine support patrol vessel is made to derive a mathematical model and simulate maneuvers with this ship. The vessel is mainly characterized by both its wide-beam and the unconventional propulsion system, that is, a pump-jet type azimuthal propulsion. By processing experimental data and the ship characteristics with diverse formulae to find the proper hydrodynamic coefficients and propulsion forces, a system of three differential equations is completed and tuned to carry out simulations of the turning test. The simulation is able to accept variable speed, jet angle and water depth as input parameters and its output consists of time series of the state variables and a plot of the simulated path and heading of the ship during the maneuver. Thanks to the data of full-scale trials previously performed with the studied vessel, a process of validation was made, which shows a good fit between simulated and full-scale experimental results, especially on the turning diameter

Diversity and health traits of local landraces of runner bean (Phaseolus coccineus L.) from Spain

Diversity and health traits of local landraces of runner bean (Phaseolus coccineus L.) from Spain

Leftovers in seed dispersal: ecological implications of partial seed consumption for oak regeneration

1. Successful seed dispersal by animals is assumed to occur when undamaged seeds arrive at a favourable microsite. Most seed removal and dispersal studies consider only two possible seed fates, predation or escape intact. Whether partial consumption of seeds has ecological implications for natural regeneration is unclear. We studied partial consumption of seeds in a rodent-dispersed oak species. 2. Fifteen percent of dispersed acorns were found partially eaten in a field experiment. Most damage affected only the basal portion of the seeds, resulting in no embryo damage. Partially eaten acorns had no differences in dispersal distance compared to intact acorns but were recovered at farther distances than completely consumed acorns. 3. Partially eaten acorns were found under shrub cover unlike intact acorns that were mostly dispersed to open microhabitats. 4. Partially eaten acorns were not found buried proportionally more often than intact acorns, leading to desiccation and exposure to biotic agents (predators, bacteria and fungi). However, partial consumption caused more rapid germination, which enables the acorns to tolerate the negative effects of exposure. 5. Re-caching and shrub cover as microhabitat of destination promote partial seed consumption. Larger acorns escaped predation more often and had higher uneaten cotyledon mass. Satiation at seed level is the most plausible explanation for partial consumption. 6. Partial consumption caused no differences in root biomass when acorns experienced only small cotyledon loss. However, root biomass was lower when acorns experienced heavy loss of tissue but, surprisingly, they produced longer roots, which allow the seeds to gain access sooner to deeper resources. 7.Synthesis. Partial consumption of acorns is an important event in the oak regeneration process, both quantitatively and qualitatively. Most acorns were damaged non-lethally, without decreasing both dispersal distances and the probability of successful establishment. Faster germination and production of longer roots allow partially eaten seeds to tolerate better the exposure disadvantages caused by the removal of the pericarp and the non-buried deposition. Consequently, partially consumed seeds can contribute significantly to natural regeneration and must be considered in future seed dispersal studies.

Local variability of serotinous cones in a Canary Island pine (Pinus canariensis) stand

The endemic Canary Island pine (Pinus canariensis) has an effective strategy to counteract fire disturbance in the short term. It has a mixed strategy that combines the presence of serotinous cones and thick barks with the ability to re-sprout from the trunk after a fire, a rare trait in pine species. High frequency of fires in the Canary Islands is related to human action, as natural fires by lightning or vulcan activity have very low frequency; hence, the how and whys of the presence of serotinous cones in the species is still a topic of debate. Previous studies showed that the frequency of serotinous cones varies from stand to stand. Here, we analyzed the presence of serotinous cones at a local scale. We selected a Canary Island pine stand in the transition zone between dry and humid forests in the south of Tenerife. Branches were pruned from 20 trees in order to evaluate the presence of serotinous vs. non-serotinous cones by direct verticile counting on the branches. The opening temperature of serotinous cones was assessed in the laboratory. Percentages of serotinous vs. non-serotinous cones varied from 0 to 93 %, showing high variability between trees. Opening temperatures were very high (above 65 ºC) as compared to other Mediterranean pine species with serotinous cones

Signal analysis and feature generation for pattern identification of partial discharges in high-voltage equipment

This paper proposes a method for the identification of different partial discharges (PDs) sources through the analysis of a collection of PD signals acquired with a PD measurement system. This method, robust and sensitive enough to cope with noisy data and external interferences, combines the characterization of each signal from the collection, with a clustering procedure, the CLARA algorithm. Several features are proposed for the characterization of the signals, being the wavelet variances, the frequency estimated with the Prony method, and the energy, the most relevant for the performance of the clustering procedure. The result of the unsupervised classification is a set of clusters each containing those signals which are more similar to each other than to those in other clusters. The analysis of the classification results permits both the identification of different PD sources and the discrimination between original PD signals, reflections, noise and external interferences. The methods and graphical tools detailed in this paper have been coded and published as a contributed package of the R environment under a GNU/GPL license.

An integration of partial evaluation in a generic abstract interpretation framework

Information generated by abstract interpreters has long been used to perform program specialization. Additionally, if the abstract interpreter generates a multivariant analysis, it is also possible to perform múltiple specialization. Information about valúes of variables is propagated by simulating program execution and performing fixpoint computations for recursive calis. In contrast, traditional partial evaluators (mainly) use unfolding for both propagating valúes of variables and transforming the program. It is known that abstract interpretation is a better technique for propagating success valúes than unfolding. However, the program transformations induced by unfolding may lead to important optimizations which are not directly achievable in the existing frameworks for múltiple specialization based on abstract interpretation. The aim of this work is to devise a specialization framework which integrates the better information propagation of abstract interpretation with the powerful program transformations performed by partial evaluation, and which can be implemented via small modifications to existing generic abstract interpreters. With this aim, we will relate top-down abstract interpretation with traditional concepts in partial evaluation and sketch how the sophisticated techniques developed for controlling partial evaluation can be adapted to the proposed specialization framework. We conclude that there can be both practical and conceptual advantages in the proposed integration of partial evaluation and abstract interpretation.

An efficient ‘a priori’ model reduction for boundary element models

The Boundary Element Method (BEM) is a discretisation technique for solving partial differential equations, which offers, for certain problems, important advantages over domain techniques. Despite the high CPU time reduction that can be achieved, some 3D problems remain today untreatable because the extremely large number of degrees of freedom—dof—involved in the boundary description. Model reduction seems to be an appealing choice for both, accurate and efficient numerical simulations. However, in the BEM the reduction in the number of degrees of freedom does not imply a significant reduction in the CPU time, because in this technique the more important part of the computing time is spent in the construction of the discrete system of equations. In this way, a reduction also in the number of weighting functions, seems to be a key point to render efficient boundary element simulations.

Identifying yeats belonging to the Brettanomyces/Dekkera genera through the use of selective-differential media

The purpose of this work was to compare and optimise different selective and differential media to aid in isolating spoilage yeasts belonging to the Brettanomyces/Dekkera genera. Growth media containing selective and differential factors were employed. These were inoculated with strains of yeast representing Spanish oenological microbiota. Lastly, some of these isolation media were successfully applied in 24 types of wine with a high ethylphenol content, all of which were from the Haro Oenological Station (La Rioja, Spain). p-coumaric acid was determined using High performance liquid chromatography-photodiode-array detection-electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS); 4-ethylphenol by using Solid phase micro extraction-gas chromatography-mass spectrometry (SPME-GC-MS); and the rest of the analysis was carried out using official OIV methodology. Actidione is the most effective selective factor for isolating Brettanomyces/Dekkera yeast genera. Other secondary selective factors (selective carbon sources, sorbic acid and ethanol as a microbicide agent) may be used successfully to eliminate potential false positivities; however, they slow growth and delay the time to obtain results.

Stabilization in a two-species chemotaxis system with logistic source

We study a system of three partial differential equations modelling the spatiotemporal behaviour of two competitive populations of biological species both of which are attracted chemotactically by the same signal substance. For a range of the parameters the system possesses a uniquely determined spatially homogeneous positive equilibrium (u?, v?) globally asymptotically stable within a certain nonempty range of the logistic growth coefficients.

Perfect imaging of three object points with only two analytic lens surfaces in two dimensions

In this work, a new two-dimensional analytic optics design method is presented that enables the coupling of three ray sets with two lens profiles. This method is particularly promising for optical systems designed for wide field of view and with clearly separated optical surfaces. However, this coupling can only be achieved if different ray sets will use different portions of the second lens profile. Based on a very basic example of a single thick lens, the Simultaneous Multiple Surfaces design method in two dimensions (SMS2D) will help to provide a better understanding of the practical implications on the design process by an increased lens thickness and a wider field of view. Fermat?s principle is used to deduce a set of functional differential equations fully describing the entire optical system. The transformation of these functional differential equations into an algebraic linear system of equations allows the successive calculation of the Taylor series coefficients up to an arbitrary order. The evaluation of the solution space reveals the wide range of possible lens configurations covered by this analytic design method. Ray tracing analysis for calculated 20th order Taylor polynomials demonstrate excellent performance and the versatility of this new analytical optics design concept.