Structure and dynamics of the membrane attaching nitric oxide transporter nitrophorin 7

Nitrophorins represent a unique class of heme proteins that are able to perform the delicate transportation and release of the free-radical gaseous messenger nitric oxide (NO) in a pH-triggered manner. Besides its ability to bind to phospholipid membranes, the N-terminus contains an additional Leu-Pro-Gly stretch, which is a unique sequence trait, and the heme cavity is significantly altered with respect to other nitrophorins. These distinctive features encouraged us to solve the X-ray crystallographic structures of NP7 at low and high pH and bound with different heme ligands (nitric oxide, histamine, imidazole). The overall fold of the lipocalin motif is well preserved in the different X-ray structures and resembles the fold of other nitrophorins. However, a chain-like arrangement in the crystal lattice due to a number of head-to-tail electrostatic stabilizing interactions is found in NP7. Furthermore, the X-ray structures also reveal ligand-dependent changes in the orientation of the heme, as well as in specific interactions between the A-B and G-H loops, which are considered to be relevant for the biological function of nitrophorins. Fast and ultrafast laser triggered ligand rebinding experiments demonstrate the pH-dependent ligand migration within the cavities and the exit route. Finally, the topological distribution of pockets located around the heme as well as from inner cavities present at the rear of the protein provides a distinctive feature in NP7, so that while a loop gated exit mechanism to the solvent has been proposed for most nitrophorins, a more complex mechanism that involves several interconnected gas hosting cavities is proposed for NP7.

Homogenization Dynamics and Introduction Routes of Invasive Freshwater Fish in the Iberian Peninsula

Nonnative invasive species are one of the main global threats to biodiversity. The understanding of the traits characterizing successful invaders and invasion-prone ecosystems is increasing, but our predictive ability is still limited. Quantitative information on biotic homogenization and particularly its temporal dynamics is even scarcer. We used freshwater fish distribution data in the Iberian Peninsula in four periods (before human intervention, 1991, 1995, and 2001) to assess the temporal dynamics of biotic homogenization among river basins. The percentage of introduced species among fish faunas has increased in recent times (from 41.8% in 1991 to 52.5% in 2001), leading to a clear increase in the similarity of community composition among basins. The mean Jaccard's index increase (a measure of biotic homogenization) from the pristine situation to the present (17.1%) was similar to that for Californian fish but higher than for other studies. However, biotic homogenization was found to be a temporally dynamic process, with finer temporal grain analyses detecting transient stages of biotic differentiation. Introduced species assemblages were spatially structured along a latitudinal gradient in the Iberian Peninsula, with species related to sport fishing being characteristic of northern basins. Although the comparison of fish distributions in the Iberian Peninsula and France showed significant and generalized biotic homogenization, nonnative assemblages of northeastern Iberian basins were more similar to those of France than to those of the rest of the Iberian Peninsula, indicating a main introduction route. Species introduced to the Iberian Peninsula tended to be mainly piscivores or widely introduced species that previously had been introduced to France. Our results indicate that the simultaneous analysis of the spatial distribution of introduced assemblages (excluding native species that reflect other biogeographical patterns) and their specific traits can be an effective tool to detect introduction and invasion routes and to predict future invaders from donor regions

Effect of Seasonal Dynamics on Queen Densities of the Argentine Ant (Linepithema Humile) in an Invaded Natural Area of the NE Iberian Peninsula

The annual elimination of large numbers of Argentine ant queens near the advance front of an invasion could be a useful tool for weakening the species’ dispersion and, therefore, limiting its establishment in non-invaded areas. However, before carrying out trials to test the effectiveness of this method it would be essential to have sufficient knowledge of the effect of seasonal dynamics acting on the queens’ densities of the species in order to determine the most favourable period of the year to act. We analyzed the seasonal densities and nest dynamics of Argentine ant queens in an invaded Mediterranean natural ecosystem. We observed that the queens’ density varied depending on the season of the year and that this variation was mainly due to the seasonal dynamics of nest aggregations in winter and ant dispersions in summer. The greatest densities per litre of nest soil were observed in winter (December to March, approximately) and the lowest densities were observed in summer ( June to July). This information is essential for improving current knowledge of the Argentine ant’s biology and developing control methods based on the elimination of queens in invaded natural areas

The dynamics of biofilm bacterial communities is driven by flow wax and wane in a temporary stream

Biofilm communities are exposed to long periods of desiccation in temporary streams. We investigated how water flow intermittency affected the bacterial community structure colonizing three different streambed compartments in a Mediterranean stream. Massive parallel sequencing revealed different bacterial communities in biofilms from sand sediments and cobbles. Bacterial communities were similar (62% of shared operational taxonomic units) in the epipsammic and hyporheic biofilms, and more diverse than those in the epilithic biofilms. The non-flow phase caused a decrease of bacterial diversity in the biofilms, when communities included only bacterial taxa assumed to be adapted to water stress. The most sensitive bacterial communities to flow intermittency were in the epilithic, where the exposure to physical stress was the highest. In sand sediments a wide group of bacterial taxa was tolerant to desiccation. During non-flow the proliferation of opportunistic taxa in the superficial compartments evidenced the biological link with the terrestrial environment. Bacterial communities better tolerate rewetting than desiccation, since a major number of taxa tolerant to rewetting occurred in all biofilms. Overall, bacterial communities in sandy compartments showed higher resistance to flow intermittency than those in epilithic biofilms

Minimum-uncertaity states and pseudoclassical dynamics. II

The set of initial conditions for which the pseudoclassical evolution algorithm (and minimality conservation) is verified for Hamiltonians of degrees N (N>2) is explicitly determined through a class of restrictions for the corresponding classical trajectories, and it is proved to be at most denumerable. Thus these algorithms are verified if and only if the system is quadratic except for a set of measure zero. The possibility of time-dependent a-equivalence classes is studied and its physical interpretation is presented. The implied equivalence of the pseudoclassical and Ehrenfest algorithms and their relationship with minimality conservation is discussed in detail. Also, the explicit derivation of the general unitary operator which linearly transforms minimum-uncertainty states leads to the derivation, among others, of operators with a general geometrical interpretation in phase space, such as rotations (parity, Fourier).

Effects of the sewage pollution in the structure and dynamics of the community of Cystoseira mediterranea (Fucales, Phaeophyceae)

We performed a study on the specific composition, structure, and dynamics of two Cystoseira mediterranea communities from the north-western Mediterranean submitted to different degrees of pollution. The structural complexity (species richness, specific distribution, and species and pattern diversity) and biomass production were lower in the polluted site. In this station, opportunistic algae (mainly Ulva rigida) loomed, and Mesophyllum lichenoides and some encrusting brown algae increased their cover. Other species (Jania rubens, and some Ceramiales) decreased their abundance when compared with the polluted site

Quantum dynamics of the parabolic model

Kvanttimekaniikan teoriassa suljettuja, ympäristöstään eristettyjä systeemejä koskevat tulokset ovat hyvin tunnettuja. Eräs tärkeä erityispiirre tällaisille systeemeille on, että niiden aikakehitys on unitaarista. Oletus siitä, että systeemi on suljettu, on osaltaan tietysti vain yksinkertaistus. Käytännössä kaikki kvanttimekaaniset systeemit vuorovaikuttavat ympäristönsä kanssa ja tästä johtuen niiden dynamiikka monimutkaistuu oleellisesti. Kuitenkin tietyissä tapauksissa systeemin aikakehitys voidaan ratkaista, ainakin approksimatiivisesti. Tärkeimpinä esimerkkeinä on ympäristön joko nopea tai erittäin hidas muutos kvanttisysteemin ominaiseen aikaskaalaan verrattuna. Näistä erityisesti jälkimmäinen on käyttökelpoinen oletus monissa fysikaalisissa tilanteissa. Tällöin voidaan suorittaa niin sanottu adiabaattinen approksimaatio. Sen mukaan systeemi, joka on aikakehityksen generoivan Hamiltonin operaattorin ominaistilassa, pysyy vastaavassa ominaistilassa ympäristön muuttuessa äärettömän hitaasti, mikäli systeemin eri energiatasot eivät leikkaa toisiaan. Todellisissa tilanteissa muutos ei tietenkään voi olla äärettömän hidasta ja myös energiatasojen leikkaukset ovat mahdollisia, jolloin tapahtuu transitio eri ominaistilojen välillä. Energiatasojen leikkauksilla on oleellisia vaikutuksia erittäin monissa fysikaalisissa prosesseissa ja niitä kuvaamaan on luotu monia malleja kvanttimekaniikan alkuajoista lähtien aina tähän päivään saakka. Nykyinen teknologinen kehitys on avannut uudenlaisen mahdollisuuden ilmiön kokeelliseen varmentamiseen ja hyödyntämiseen. Tämän vuoksi kyseisten mallien dynamiikan ja erityisesti energiatasojen useiden peräkkäisten leikkausten aiheuttamien koherenssi-ilmiöiden selvittäminen on tärkeää. Tässä työssä käsitellään kvanttimekaanisia kaksitasosysteemejä, joissa esiintyy energiatasojen leikkauksia sekä niiden pitkän aikavälin dynamiikkaa. Tutkielmassa perehdytään tarkemmin kahteen tiettyyn malliin. Näistä ensimmäinen, Landau-Zener -malli, on tunnetuin ja sovelluksissa käytetyin malli. Kuitenkin erityisen mielenkiinnon kohteena on niin kutsuttu parabolinen malli, jolle johdetaan eri approksimaatioita käyttäen asymptoottiset transitiotodennäköisyydet eri tilojen välille. Näitä verrataan numeerisiin tuloksiin.

Geostical analysis of spatial dynamics of Citrus Variegated Chlorossis

The spatial dynamics of Citrus Variegated Chlorosis (CVC) was studied in a five-year old commercial orchard of 'Valencia' sweet orange (Citrus sp.) trees, located in the northern region of the state of São Paulo, Brazil. One thousand trees were assessed in 25 rows of 40 trees, planted at 8 x 5 m spacing. Disease incidence data were taken beginning in March 1994 and ending in January 1996, at intervals of four to five months. Disease aggregation was observed through the dispersion index analysis (Ib), which was calculated by dividing the area into quadrants. CVC spatial dynamics was examined using semivariogram analysis, which revealed that the disease was aggregated in the field forming foci of 10 to 14 m. For each well-fitted model, a kriging map was created to better visualize the distribution of the disease. The spherical model was the best fit for the data in this study. Kriging maps also revealed that the incidence of CVC increased in periods during which the trees underwent vegetative growth, coinciding with greater expected occurrence of insect vectors of the bacterium in the field.

Small and Large Scale Dynamics in the Milky Way

This thesis contains dynamical analysis on four different scales: the Solar system, the Sun itself, the Solar neighbourhood, and the central region of the Milky Way galaxy. All of these topics have been handled through methods of potential theory and statistics. The central topic of the thesis is the orbits of stars in the Milky Way. An introduction into the general structure of the Milky Way is presented, with an emphasis on the evolution of the observed value for the scale-length of the Milky Way disc and the observations of two separate bars in the Milky Way. The basics of potential theory are also presented, as well as a developed potential model for the Milky Way. An implementation of the backwards restricted integration method is shown, rounding off the basic principles used in the dynamical studies of this thesis. The thesis looks at the orbit of the Sun, and its impact on the Oort cloud comets (Paper IV), showing that there is a clear link between these two dynamical systems. The statistical atypicalness of the orbit of the Sun is questioned (Paper I), concluding that there is some statistical typicalness to the orbit of the Sun, although it is not very significant. This does depend slightly on whether one includes a bar, or not, as a bar has a clear effect on the dynamical features seen in the Solar neighbourhood (Paper III). This method can be used to find the possible properties of a bar. Finally, we look at the effect of a bar on a statistical system in the Milky Way, seeing that there are not only interesting effects depending on the mass and size of the bar, but also how bars can capture disc stars (Paper II).

Innovations of ageing and societal transition : Dynamics of change of the socio-technical regime of ageing

The purpose of this dissertation is to examine the dynamics of the socio-technical system in the field of ageing. The study stems from the notion that the ageing of the population as a powerful megatrend has wide societal effects, and is not just a matter for the social and health sector. The central topic in the study is change: not only the age structures and structures of society are changing, but also at the same time there is constant development, for instance, in technologies, infrastructures and cultural perceptions. The changing concept of innovation has widened the understanding of innovations related to ageing from medical and assistive technological innovations to service and social innovations, as well as systemic innovations at different levels, which means the intertwined and co-evolutionary change in technologies, structures, services and thinking models. By the same token, the perceptions of older people and old age are becoming more multi-faceted: old age is no longer equated to illnesses and decline, but visions of active ageing and a third age have emerged, which are framed by choices, opportunities, resources and consumption in later life. The research task in this study is to open up the processes and mechanisms of change in the field of ageing, which are studied as a complex, multi-level and interrelated socio-technical system. The question is about co-effective elements consisting of macro-level landscape changes, the existing socio-technical regime (the rule system, practices and structures) and bottom-up niche-innovations. Societal transitions do not account for the things inside the regime alone, or for the long-term changes in the landscape, nor for the radical innovations, but for the interplay between all these levels. The research problem is studied through five research articles, which offer micro-level case studies to macro-level phenomenon. Each of the articles focus on different aspects related to ageing and change, and utilise various datasets. The framework of this study leans on the studies of socio-technical systems and multi-level perspective on transitions mainly developed by Frank Geels. Essential factors in transition from one socio-technological regime to another are the co-evolutionary processes between landscape changes, regime level and experimental niches. Landscape level changes, like the ageing of the population, destabilise the regime in the forms of coming pressures. This destabilization offers windows for opportunity to niche-innovations outside or at fringe of the regime, which, through their breakthrough, accelerate the transition process. However, the change is not easy because of various kinds of lock-ins and inertia, which tend to maintain the stability of the regime. In this dissertation, a constructionist approach of society is applied leaning mainly to the ideas of Anthony Giddens’ theory of structuration, with the dual nature of structures. The change is taking place in the interplay between actors and structures: structures shape people’s practices, but at the same time these practices constitute and reproduce social systems. Technology and other material aspects, as part of socio-technical systems, and the use of them, also take part in the structuration process. The findings of the study point out that co-evolutionary and co-effective relationships between economic, cultural, technological and institutional fields, as well as relationships between landscape changes, changes in the local and regime-level practices and rule systems, are a very complex and multi-level dynamic socio-technical phenomenon. At the landscape level of ageing, which creates the pressures and triggers to the regime change, there are three remarkable megatrends: demographic change, changes in the global economy and the development of technologies. These exert pressures to the socio-technical regime, which as a rule system is experiencing changes in the form of new markets and consumer habits, new ways of perceiving ageing, new models of organising the health care and other services and as new ways of considering innovation and innovativeness. There are also inner dynamics in the relationships between these aspects within the regime. These are interrelated and coconstructed: the prevailing perceptions of ageing and innovation, for instance, reflect the ageing policies, innovation policies, societal structures, organising models, technology and scientific discussion, and vice versa. Technology is part of the inner dynamics of the sociotechnological regime. Physical properties of the artefacts set limitations and opportunities with regard to their functions and uses. The use of and discussion about technology, contributes producing and reproducing the perceptions of old age. For societal transition, micro-level changes are also needed, in form of niche-innovations, for instance new services, organisational models or new technologies, Regimes, as stabilitystriven systems, tend to generate incremental innovations, but radically new innovations are generated in experimental niches protected from ‘normal’ market selection. The windows of opportunity for radical novelties may be opened if the circumstances are favourable for instance by tensions in the socio-technical regime affected by landscape level changes. This dissertation indicates that a change is taking place, firstly, in the dynamic interactionbetween levels, as a result of purposive action and governance to some extent. Breaking the inertia and using the window of opportunity for change and innovation offered by dynamics between levels, presupposes the actors’ special capabilities and actions such as dynamic capabilities and distance management. Secondly, the change is taking place the socio-technological negotiations inside the regime: interaction between technological and social, which is embodied in the use of technology. The use of technology includes small-level contextual scripts that also participate in forming broader societal scripts (for instance defining old age at the society level), which in their turn affect the formation of policies for innovation and ageing. Thirdly, the change is taking place by the means of active formation of the multi-actor innovation networks, where the role of distance management is crucial to facilitate the communication between actors coming from different backgrounds as well as to help the niches born outside the regime to utilise the window of opportunity offered by regime destabilisation. This dissertation has both theoretical and practical contributions. This study participates in the discussion of action-oriented view on transition by opening up of the socio-technological, coevolutionary processes of the multi-faceted phenomenon of ageing, which has lacked systematic analyses. The focus of this study, however, is not on the large-scale coordination and governance, but rather on opening up the incremental elements and structuration processes, which contribute to the transition little by little, and which can be affected to. This increases the practical importance of this dissertation, by highlighting the importance of very tiny, everyday elements in the change processes in the long run.

Numerics of Spacecraft Dynamics

Whenever a spacecraft is launched it is essential that the algorithms in the on-board software systems and at ground control are efficient and reliable over extended periods of time. Geometric numerical integrators, and in particular variational integrators, have both these characteristics. In "Numerics of Spacecraft Dynamics" new numerical integrators are presented and analysed in depth. These algorithms have been designed specifically for the dynamics of spacecraft and artificial satellites in Earth orbits. Full analytical solutions to a class of integrable deformations of the two-body problem in classical mechanics are derived, and a systematic method to compute variational integrators to arbitrary order with a computer algebra system is introduced.