Two component systems: physiological effect of a third component

Signal transduction systems mediate the response and adaptation of organisms to environmental changes. In prokaryotes, this signal transduction is often done through Two Component Systems (TCS). These TCS are phosphotransfer protein cascades, and in their prototypical form they are composed by a kinase that senses the environmental signals (SK) and by a response regulator (RR) that regulates the cellular response. This basic motif can be modified by the addition of a third protein that interacts either with the SK or the RR in a way that could change the dynamic response of the TCS module. In this work we aim at understanding the effect of such an additional protein (which we call ‘‘third component’’) on the functional properties of a prototypical TCS. To do so we build mathematical models of TCS with alternative designs for their interaction with that third component. These mathematical models are analyzed in order to identify the differences in dynamic behavior inherent to each design, with respect to functionally relevant properties such as sensitivity to changes in either the parameter values or the molecular concentrations, temporal responsiveness, possibility of multiple steady states, or stochastic fluctuations in the system. The differences are then correlated to the physiological requirements that impinge on the functioning of the TCS. This analysis sheds light on both, the dynamic behavior of synthetically designed TCS, and the conditions under which natural selection might favor each of the designs. We find that a third component that modulates SK activity increases the parameter space where a bistable response of the TCS module to signals is possible, if SK is monofunctional, but decreases it when the SK is bifunctional. The presence of a third component that modulates RR activity decreases the parameter space where a bistable response of the TCS module to signals is possible.

Microbial diagnosis of bloodstream infection: towards molecular diagnosis directly from blood.

When a bloodstream infection (BSI) is suspected, most of the laboratory results-biochemical and haematologic-are available within the first hours after hospital admission of the patient. This is not the case for diagnostic microbiology, which generally takes a longer time because blood culture, which is to date the reference standard for the documentation of the BSI microbial agents, relies on bacterial or fungal growth. The microbial diagnosis of BSI directly from blood has been proposed to speed the determination of the etiological agent but was limited by the very low number of circulating microbes during these paucibacterial infections. Thanks to recent advances in molecular biology, including the improvement of nucleic acid extraction and amplification, several PCR-based methods for the diagnosis of BSI directly from whole blood have emerged. In the present review, we discuss the advantages and limitations of these new molecular approaches, which at best complement the culture-based diagnosis of BSI.

Selection on a genetic polymorphism counteracts ecological speciation in a stick insect.

The interplay between selection and aspects of the genetic architecture of traits (such as linkage, dominance, and epistasis) can either drive or constrain speciation [1-3]. Despite accumulating evidence that speciation can progress to "intermediate" stages-with populations evolving only partial reproductive isolation-studies describing selective mechanisms that impose constraints on speciation are more rare than those describing drivers. The stick insect Timema cristinae provides an example of a system in which partial reproductive isolation has evolved between populations adapted to different host plant environments, in part due to divergent selection acting on a pattern polymorphism [4, 5]. Here, we demonstrate how selection on a green/melanistic color polymorphism counteracts speciation in this system. Specifically, divergent selection between hosts does not occur on color phenotypes because melanistic T. cristinae are cryptic on the stems of both host species, are resistant to a fungal pathogen, and have a mating advantage. Using genetic crosses and genome-wide association mapping, we quantify the genetic architecture of both the pattern and color polymorphism, illustrating their simple genetic control. We use these empirical results to develop an individual-based model that shows how the melanistic phenotype acts as a "genetic bridge" that increases gene flow between populations living on different hosts. Our results demonstrate how variation in the nature of selection acting on traits, and aspects of trait genetic architecture, can impose constraints on both local adaptation and speciation.

Visual Measurement and Modelling of Tool Wear in Rough Turning

Huolimatta korkeasta automaatioasteesta sorvausteollisuudessa, muutama keskeinen ongelma estää sorvauksen täydellisen automatisoinnin. Yksi näistä ongelmista on työkalun kuluminen. Tämä työ keskittyy toteuttamaan automaattisen järjestelmän kulumisen, erityisesti viistekulumisen, mittaukseen konenäön avulla. Kulumisen mittausjärjestelmä poistaa manuaalisen mittauksen tarpeen ja minimoi ajan, joka käytetään työkalun kulumisen mittaukseen. Mittauksen lisäksi tutkitaan kulumisen mallinnusta sekä ennustamista. Automaattinen mittausjärjestelmä sijoitettiin sorvin sisälle ja järjestelmä integroitiin onnistuneesti ulkopuolisten järjestelmien kanssa. Tehdyt kokeet osoittivat, että mittausjärjestelmä kykenee mittaamaan työkalun kulumisen järjestelmän oikeassa ympäristössä. Mittausjärjestelmä pystyy myös kestämään häiriöitä, jotka ovat konenäköjärjestelmille yleisiä. Työkalun kulumista mallinnusta tutkittiin useilla eri menetelmillä. Näihin kuuluivat muiden muassa neuroverkot ja tukivektoriregressio. Kokeet osoittivat, että tutkitut mallit pystyivät ennustamaan työkalun kulumisasteen käytetyn ajan perusteella. Parhaan tuloksen antoivat neuroverkot Bayesiläisellä regularisoinnilla.

Is Inefficiency under control in the Justice Administration?

Efficiency in the administration of justice is found to increase over time, while the variation in the efficiency of the courts tended to remain low and fall over time. This would appear to be good news, at least for the case studied here: the civil courts of first instance in Spain between 2005 and 2009. Apart from the simple passing of time, the percentage of temporary judges in the system also determines some of the differences in efficiency between courts over time. Thus, we find that the greater the percentage of temporary judges, the lower is the efficiency of the courts. Overall, the average relative efficiency level for the period 2005 to 2009 was 97.46%, suggesting the matter is under control.

Sales lead management in a global enterprise

Many companies today struggle with problems they face around sales lead management. They are suffering from inconsistent quality of leads, they miss clear sales opportunities and even cannot handle well their internal marketing lists. Meanwhile customers are better and better equipped with means to easily initiate contact via internet, via call centers etc. Investing in lead generation activities that are built on a bad process is not a good idea. Better than asking how to get more leads, companies should ask how to get better quality leads and invest in improving lead management. This study looks sales lead management as a multi step process where a company generates leads in controlled environment, qualifies them and hands over to the sales cycle. As a final step, organization needs to analyze the incomes and successes of different lead sources. Most often in sales lead management a process improvement requires setting up additional controls to enable proper tracking of all leads. A sales lead management process model for the case company is built based on the findings. Implementing the new model involves changes and improvements in some key areas of current process. Starting from the very beginning, these include redefining a bit the lead definition and revising the criteria set for qualified lead. There are some improvements to be done in the system side to enable the proposed model. Lastly a setting for responsible roles is presented.

Visualizing the spatiotemporal dynamics of DNA damage in budding yeast.

Fluorescence microscopy has enabled the analysis of both the spatial distribution of DNA damage and its dynamics during the DNA damage response (DDR). Three microscopic techniques can be used to study the spatiotemporal dynamics of DNA damage. In the first part we describe how we determine the position of DNA double-strand breaks (DSBs) relative to the nuclear envelope. The second part describes how to quantify the co-localization of DNA DSBs with nuclear pore clusters, or other nuclear subcompartments. The final protocols describe methods for the quantification of locus mobility over time.

Proportionality and Party Success in Europe

This thesis consists of four articles and an introductory section. The main research questions in all the articles are about proportionality and party success in Europe, at European, national or district levels. Proportionality in this thesis denotes the proximity of seat shares parties receive compared to their respective vote shares, after the electoral system’s allocation process. This proportionality can be measured through numerous indices that illustrate either the overall proportionality of an electoral system or a particular election. The correspondence of a single party’s seat shares to its vote shares can also be measured. The overall proportionality is essential in three of the articles (1, 2 and 4), where the system’s performance is studied by means of plots. In article 3, minority party success is measured by advantage-ratios that reveal single party’s winnings or losses in the votes to seat allocation process. The first article asks how proportional are the European parliamentary (EP) electoral systems, how do they compare with results gained from earlier studies and how do the EP electoral systems treat different sized parties. The reasons for different outcomes are looked for in explanations given by traditional electoral studies i.e. electoral system variables. The countries studied (EU15) apply electoral systems that vary in many important aspects, even though a certain amount of uniformity has been aspired to for decades. Since the electoral systems of the EP elections closely resemble the national elections, the same kinds of profiles emerge as in the national elections. The electoral systems indeed treat the parties differentially and six different profile types can be found. The counting method seems to somewhat determine the profile group, but the strongest variables determining the shape of a countries’ profile appears to be the average district magnitude and number of seats allocated to each country. The second article also focuses on overall proportionality performance of an electoral system, but here the focus is on the impact of electoral system changes. I have developed a new method of visualizing some previously used indices and some new indices for this purpose. The aim is to draw a comparable picture of these electoral systems’ changes and their effects. The cases, which illustrate this method, are four elections systems, where a change has occurred in one of the system variables, while the rest remained unchanged. The studied cases include the French, Greek and British European parliamentary systems and the Swedish national parliamentary system. The changed variables are electoral type (plurality changed to PR in the UK), magnitude (France splitting the nationwide district into eight smaller districts), legal threshold (Greece introducing a three percent threshold) and counting method (d’Hondt was changed to modified Sainte-Laguë in Sweden). The radar plots from elections after and before the changes are drawn for all country cases. When quantifying the change, the change in the plots area that is created has also been calculated. Using these radar plots we can observe that the change in electoral system type, magnitude, and also to some extent legal threshold had an effect on overall proportionality and accessibility for small parties, while the change between the two highest averages counting method had none. The third article studies the success minority parties have had in nine electoral systems in European heterogeneous countries. This article aims to add more motivation as to why we should care how different sized parties are treated by the electoral systems. Since many of the parties that aspire to represent minorities in European countries are small, the possibilities for small parties are highlighted. The theory of consociational (or power-sharing) democracy suggests that, in heterogeneous societies, a proportional electoral system will provide the fairest treatment of minority parties. The OSCE Lund Recommendations propose a number of electoral system features, which would improve minority representation. In this article some party variables, namely the unity of the minority parties and the geographical concentration of the minorities were included among possible explanations. The conclusions are that the central points affecting minority success were indeed these non-electoral system variables rather than the electoral system itself. Moreover, the size of the party was a major factor governing success in all the systems investigated; large parties benefited in all the studied electoral systems. In the fourth article the proportionality profiles are again applied, but this time to district level results in Finnish parliamentary elections. The level of proportionality distortion is also studied by way of indices. The average magnitudes during the studied periodrange from 7.5 to 26.2 in the Finnish electoral districts and this opens up unequal opportunities for parties in different districts and affects the shape of the profiles. The intra-country case allows the focus to be placed on the effect of district magnitude, since all other electoral systems are kept constant in an intra-country study. The time span in the study is from 1962 to 2007, i.e. the time that the districts have largely been the same geographically. The plots and indices tell the same story, district magnitude and electoral alliances matter. The district magnitude is connected to the overall proportionality of the electoral districts according to both indices, and the profiles are, as expected, also closer to perfect proportionality in large districts. Alliances have helped some small parties to gain a much higher seat share than their respective vote share and these successes affect some of the profiles. The profiles also show a consistent pattern of benefits for the small parties who ally with the larger parties.

Tracking Invasion Histories in the Sea: Facing Complex Scenarios Using Multilocus Data

In recent years, new analytical tools have allowed researchers to extract historical information contained in molecular data, which has fundamentally transformed our understanding of processes ruling biological invasions. However, the use of these new analytical tools has been largely restricted to studies of terrestrial organisms despite the growing recognition that the sea contains ecosystems that are amongst the most heavily affected by biological invasions, and that marine invasion histories are often remarkably complex. Here, we studied the routes of invasion and colonisation histories of an invasive marine invertebrate Microcosmus squamiger (Ascidiacea) using microsatellite loci, mitochondrial DNA sequence data and 11 worldwide populations. Discriminant analysis of principal components, clustering methods and approximate Bayesian computation (ABC) methods showed that the most likely source of the introduced populations was a single admixture event that involved populations from two genetically differentiated ancestral regions - the western and eastern coasts of Australia. The ABC analyses revealed that colonisation of the introduced range of M. squamiger consisted of a series of non-independent introductions along the coastlines of Africa, North America and Europe. Furthermore, we inferred that the sequence of colonisation across continents was in line with historical taxonomic records - first the Mediterranean Sea and South Africa from an unsampled ancestral population, followed by sequential introductions in California and, more recently, the NE Atlantic Ocean. We revealed the most likely invasion history for world populations of M. squamiger, which is broadly characterized by the presence of multiple ancestral sources and non-independent introductions within the introduced range. The results presented here illustrate the complexity of marine invasion routes and identify a cause-effect relationship between human-mediated transport and the success of widespread marine non-indigenous species, which benefit from stepping-stone invasions and admixture processes involving different sources for the spread and expansion of their range.

On Transmission System Design for Wireless Broadcasting

This thesis considers aspects related to the design and standardisation of transmission systems for wireless broadcasting, comprising terrestrial and mobile reception. The purpose is to identify which factors influence the technical decisions and what issues could be better considered in the design process in order to assess different use cases, service scenarios and end-user quality. Further, the necessity of cross-layer optimisation for efficient data transmission is emphasised and means to take this into consideration are suggested. The work is mainly related terrestrial and mobile digital video broadcasting systems but many of the findings can be generalised also to other transmission systems and design processes. The work has led to three main conclusions. First, it is discovered that there are no sufficiently accurate error criteria for measuring the subjective perceived audiovisual quality that could be utilised in transmission system design. Means for designing new error criteria for mobile TV (television) services are suggested and similar work related to other services is recommended. Second, it is suggested that in addition to commercial requirements there should be technical requirements setting the frame work for the design process of a new transmission system. The technical requirements should include the assessed reception conditions, technical quality of service and service functionalities. Reception conditions comprise radio channel models, receiver types and antenna types. Technical quality of service consists of bandwidth, timeliness and reliability. Of these, the thesis focuses on radio channel models and errorcriteria (reliability) as two of the most important design challenges and provides means to optimise transmission parameters based on these. Third, the thesis argues that the most favourable development for wireless broadcasting would be a single system suitable for all scenarios of wireless broadcasting. It is claimed that there are no major technical obstacles to achieve this and that the recently published second generation digital terrestrial television broadcasting system provides a good basis. The challenges and opportunities of a universal wireless broadcasting system are discussed mainly from technical but briefly also from commercial and regulatory aspect

Metodologia para obtenção de parâmetros de mecânica molecular aplicados a compostos de coordenação

A methodology is presented to obtain force field parameters to be used in molecular mechanics. The case of Ru(II) is investigated and the parameters obtained, specially its covalent radii, are employed to model Ru(II) coordination compound. The combined use of molecular mechanics with ab initio methods allowed us to predict the metal-ligand stretching force constant for Ru(II) coordination compounds.

The Role of Surfactant Properties of Extractants in Hydrometallurgical LiquidLiquid Extraction Processes

The amphiphilic nature of metal extractants causes the formation of micelles and other microscopic aggregates when in contact with water and an organic diluent. These phenomena and their effects on metal extraction were studied using carboxylic acid (Versatic 10) and organophosphorus acid (Cyanex 272) based extractants. Special emphasis was laid on the study of phase behaviour in a pre neutralisation stage when the extractant is transformed to a sodium or ammonium salt form. The pre neutralised extractants were used to extract nickel and to separate cobalt and nickel. Phase diagrams corresponding to the pre neutralisation stage in a metal extraction process were determined. The maximal solubilisation of the components in the system water(NH3)/extractant/isooctane takes place when the molar ratio between the ammonia salt form and the free form of the extractant is 0.5 for the carboxylic acid and 1 for the organophosphorus acid extractant. These values correspond to the complex stoichiometry of NH4A•HA and NIi4A, respectively. When such a solution is contacted with water a microemulsion is formed. If the aqueous phase contains also metal ions (e.g. Ni²+), complexation will take place on the microscopic interface of the micellar aggregates. Experimental evidence showing that the initial stage of nickel extraction with pre neutralised Versatic 10 is a fast pseudohomogeneous reaction was obtained. About 90% of the metal were extracted in the first 15 s after the initial contact. For nickel extraction with pre neutralised Versatic 10 it was found that the highest metal loading and the lowest residual ammonia and water contents in the organic phase are achieved when the feeds are balanced so that the stoichiometry is 2NH4+(org) = Nit2+(aq). In the case of Co/Ni separation using pre neutralised Cyanex 272 the highest separation is achieved when the Co/extractant molar ratio in the feeds is 1 : 4 and at the same time the optimal degree of neutralisation of the Cyanex 272 is about 50%. The adsorption of the extractants on solid surfaces may cause accumulation of solid fine particles at the interface between the aqueous and organic phases in metal extraction processes. Copper extraction processes are known to suffer of this problem. Experiments were carried out using model silica and mica particles. It was found that high copper loading, aromacity of the diluent, modification agents and the presence of aqueous phase decrease the adsorption of the hydroxyoxime on silica surfaces.

Building complexity in O2-binding copper complexes : site-selective metalation and intermolecular O2-binding at dicopper and heterometallic complexes derived from an unsymmetric ligand

A novel unsymmetric dinucleating ligand (LN3N4) combining a tridentate and a tetradentate binding sites linked through a m-xylyl spacer was synthesized as ligand scaffold for preparing homo- and dimetallic complexes, where the two metal ions are bound in two different coordination environments. Site-selective binding of different metal ions is demonstrated. LN3N4 is able to discriminate between CuI and a complementary metal (M′ = CuI, ZnII, FeII, CuII, or GaIII) so that pure heterodimetallic complexes with a general formula [CuIM′(LN3N4)]n+ are synthesized. Reaction of the dicopper(I) complex [CuI 2(LN3N4)]2+ with O2 leads to the formation of two different copper-dioxygen (Cu2O2) intermolecular species (O and TP) between two copper atoms located in the same site from different complex molecules. Taking advantage of this feature, reaction of the heterodimetallic complexes [CuM′(LN3N4)]n+ with O2 at low temperature is used as a tool to determine the final position of the CuI center in the system because only one of the two Cu2O2 species is formed

Characterization and quantification of polyradical character

The decomposition of 〈͈Ŝ²〉 into atomic and diatomic contributions (local spin analysis) is used to detect and quantify the polyradical character of molecular systems. A model triradical system is studied in detail, and the local spin analysis is used to distinguish several patterns of local spin distributions and spin-spin interactions that can be found for different electronic states. How close a real molecular system is to an ideal system of k perfectly localized spin centers is utilized to define a measure of its k-radical character. The spin properties and triradical character of the lowest-lying electronic states of a number of all σ, all π, and σ-π organic triradicals are discussed in detail. The local spin contributions exhibit good correlation with experimental triradical stabilization energies

Progress of soybean charcoal rot under tillage and no-tillage systems in Brazil

The increase in incidence of charcoal rot caused by Macrophomina phaseolina on soybeans (Glycine max) was followed four seasons in conventional and no-till cropping systems. In the 1997/98 and 2000/01 seasons, total precipitation between sowing and harvest reached 876.3 and 846.9 mm, respectively. For these seasons, disease incidence did not differ significantly between the no-till and conventional systems. In 1998/99 and 1999/00 precipitation totaled 689.9 and 478.3 mm, respectively. In 1998/99, in the no-till system, the disease incidence was 43.7% and 53.1% in the conventional system. In 1999/00 the final incidence was 68.7% and 81.2% for the no-till and conventional systems, respectively. For these two seasons, precipitation was lower than that required for soybean crops (840 mm), and the averages of disease incidence were significantly higher in the conventional system. The concentration of microsclerotia in soil samples was higher in samples collected in conventional system at 0 - 10 cm depth. However, analysis of microsclerotia in roots showed that in years with adequate rain no difference was detected. In dry years, however, roots from plants developed under the conventional system had significantly more microsclerotia. Because of the wide host range of M. phaseolina and the long survival times of the microsclerotia, crop rotation would probably have little benefit in reducing charcoal rot. Under these study conditions it may be a better alternative to suppress charcoal rot by using the no-till cropping system to conserve soil moisture and reduce disease progress.