The main objective of this study, conducted by the request of the Swedish Environmental Research Institute’s (IVL) office in Beijing, was to analyse and draw lessons from Sweden’s financial support system regarding the implementation of wetlands in agriculture. Of special interest were the factors that motivate or does not motivate farmers to implement wetlands on their lands. The study was based mainly on a literature analysis, with elements of a more participatory kind, such as interviews and questionnaires with professionals from governmental-and guidance agencies. The study was carried out in February to March 2015. According to the result, key factors for successful wetland projects are: 1. Put more effort into developing long-term relationships with farmers, 2. Provide more information regarding the efficiency of the wetland to the landowner, 3. Create more flexible contracts for farmers, 4. Establish a nutrient “credit” system. Keywords: farmers willingness, financial support system, Rural Development Programme, support grants wetlands, agri-environmental measure

No description available.

Decomposition of organic material (litter) is an important part of the global carbon cycle. Environmental conditions, litter quality and the microbial community are the main factors affecting decomposition. The decomposition is divided into two phases, one fast initial phase and one slow second phase. The tea bag index (TBI) was used as a standardized method to measure decomposition rate along a latitudinal gradient. A common garden set up and extractions were made to determine the composition of the litter to investigate if climate or litter quality affected the decomposition rate. The result showed that the decomposition rate increased with higher latitude. The litter from higher latitude has more material that is easy to decompose. Natural litter abroad had higher decomposition rate than at home. On the contrary, standard litter at home had higher decomposition rate than abroad. This indicates that litter quality is more important than latitude. Further studies are needed with more sites along the gradient to conclude how climate and litter quality are affecting decomposition.

The spread of infectious diseases, between animals as well as between humans, is a topic often in focus. Outbreaks of diseases like for example foot-and-mouth disease, avian influenza, and swine influenza have in the last decades led to an increasing interest in modelling of infectious diseases since such models can be used to elucidate disease transmission and to evaluate the impact of different control strategies. Different kind of modelling techniques can be used, e.g. individual based disease modelling, Bayesian analysis, Markov Chain Monte Carlo simulations, and network analysis. The topic in this thesis is network analysis, since this is a useful method when studying spread of infect ious diseases. The usefulness lies in the fact that a network describes potential transmission routes, and to have knowledge about the structure of them is valuable in predicting the spread of diseases. This thesis contains both a method for generating a wide range of different theoretical networks, and also examination and discussion about the usefulness of network analysis as a tool for analysing transmission of infectious animal diseases between farms in a spatial context. In addition to the theoretical networks, Swedish animal transport networks are used as empirical examples. To be able to answer questions about the effect of the proportion of contacts in networks, the effect of missing links and about the usefulness of network measures, there was a need to manage to generate networks with a wide range of different structures. Therefore, it was necessary to develop a network generating algorithm. Papers I and II describes that network generating algorithm, SpecNet, which creates spatial networks. The aim was to develop an algorithm that managed to generate a wide range of network structures. The performance of the algorithm was evaluated by some network measures. In the first study, Paper I, the algorithm succeeded to generate a wide range of most of the investigated network measures. Paper II is an improvement of the algorithm to produce networks with low negative assortativity by adding two classes of nodes instead of one. Except to generate theoretical networks from scratch, it is also relevant that a network generating algorithm has the potential to regenerate a network with given specific structures. Therefore, we tested to regenerate two Swedish animal transport networks according to their structures. SpecNet managed to mimic the two empirical networks well in comparison with a non-spatial network generating algorithm that was not equally successful in regenerating the requested structures. Sampled empirical networks are rarely complete, since contacts are often missing during sampling, e. g. due to difficulties to sample or due to too short time window during sampling. In Paper III, the focus is on the effect on disease transmission, due to number of contacts in the network, as well as on the reliability of making predictions from networks with a small proportion of missing links. In addition, attention is also given to the spatial distribution of animal holdings in the landscape and on what effect this distribution has on the resulting disease transmission between the holdings. Our results indicate that, assuming weighted contacts, it is maybe risky to make predictions about disease transmission from one single network replicate with as low proportion of contacts as in most empirical animal transport networks. In case of a disease outbreak, it would be valuable to use network measures as predictors for the progress and the extent of the disease transmission. Then a reliable network is required, and also that the used network measures has the potential to make reasonable predictions about the epidemic. In Paper IV we investigate if network measures are useful as predictors for eventual disease transmissions. Moreover, we also analyse if there is some measure that correlates better with disease transmission than others. Disease transmission simulations are performed in networks with different structures to mimic diverse spatial conditions, thereafter are the simulation results compared to the values of the network structures.

Streptococcus pneumoniae is one of the major contributors to mortality and morbidity around  the  world.  It  causes  a  wide  variety  of  diseases  ranging  from  uncomplicated respiratory  infections  to  life-threatening  invasive  infections  such  as  meningitis  and septicemia. In recent years, the effectiveness of antibiotic therapy has been hampered by  the  increasing  rates  of  resistant  pneumococci.  As  antibiotic  resistance  increases, there is a growing need for interventions that minimize opportunities for development and spread  of resistant  pneumococci.  The aim  of this  thesis  was  to learn  more  about emergence  and  spread  of  antibiotic  resistant  pneumococci  using  both  theoretical  and empirical methods.  Since the increasing prevalence of resistant pneumococci is mainly due to the spread of strains belonging to few clones, interventions for controlling pneumococcal transmission  in  the  community  were  studied.  Model  predictions  suggested  that interventions for efficiently control organism transmission should include reduction of group sizes in the day-care centers. Simulations also indicated that it appears extremely difficult  to  reduce  the  rates  of  penicillin  non-susceptible  pneumococci  by  simply decreasing  the  penicillin  consumption  assumed  that  reduced  penicillin  susceptibility does not imply a fitness cost for the organism. Managing the penicillin resistance rates in pneumococci then probably requires a more restrictive use of penicillin together with other  control  measures  such  as  vaccine  programs.  Although  clonal  spread  is  the primary  mechanism  for  the  rapid  emergence  of  resistance  in  pneumococci,  natural competence  for  genetic  transformation  also  seems  to  be  involved.  Further  molecular understanding  of competence regulation  is  important  to be  able  to prevent  horizontal spread  of  resistance  genes.  Studying  the  competence  regulation  by  theoretical  means led  to  the  conclusion  that  down-regulation  of  competence  is  probably  caused  by  a repressor acting on the comCDE operon at the level of transcription.  Despite the globally emerging frequency of resistant pneumococci, we conclude in a prospective study that antimicrobial resistance in invasive pneumococci in south-west Sweden remains limited. Any correlations between resistance pattern and clinical parameters could not be revealed. However, the serotype distribution was observed to differ  between  strains  with  reduced  susceptibility  and  fully  susceptible  strains  as isolates  with  decreased  susceptibility  more  frequently  belonged  to  the  serotypes included in the 7-valent vaccine.

The ecosystems of the world are currently facing a variety of anthropogenic perturbations, such as climate change, fragmentation and destruction of habitat, overexploitation of natural resources and invasions of alien species. How the ecosystems will be affected is not only dependent on the direct effects of the perturbations on individual species but also on the trophic structure and interaction patterns of the ecological community. Of particular current concern is the response of ecological communities to climate change. Increased global temperature is expected to cause an increased intensity and frequency of weather extremes. A more unpredictable and more variable environment will have important consequences not only for individual species but also for the dynamics of the entire community. If we are to fully understand the joint effects of a changing climate and habitat fragmentation, there is also a need to understand the spatial aspects of community dynamics. In the present work we use dynamic models to theoretically explore the importance of local (Paper I and II) and spatial processes (Paper III-V) for the response of multi-trophic communities to different kinds of perturbations. In paper I we investigate how species richness and correlation in species responses to a highly variable environment affect the risk of extinction cascades. We find that the risk of extinction cascades increases with increasing species richness especially when the correlation among species is low. Initial stochastic extinctions of primary producer species unleash bottomup extinction cascades, where specialist consumers are especially vulnerable. Although the risks of extinction cascades were higher in the species-rich systems, we found that the temporal stability of aggregate abundance of primary producers increased with increasing richness. Thus, species richness had a two-sided effect on community stability. Also during the extinction cascades it is possible that more robust species and interaction patterns will be selected which would further act to stabilize the post-extinction communities. In paper II we explore how the process of disassembly affects the structure of the interaction network and the robustness of the community to additional disturbances. We find that the disassembled communities are structurally different and more resistant to disturbances than equally sized communities that have not gone through a phase of disassembly. The disassembled communities are topologically as well as dynamically more stable than non-disassembled communities. In paper III, IV and V we expand the analysis to incorporate the spatial dimension. In paper III we analyze how metacommunities (a set of local communities coupled by species dispersal) in spatially explicit landscapes respond to environmental variation. We examine how this response is affected by varying 1) species richness in the local communities, 2) the degree of correlation in species response to the environmental variation, between species within patches (species correlation) and among patches (spatial correlation) and 3) dispersal pattern of species. First we can confirm that our previous findings from paper I regarding local species richness and correlation among species within a patch are robust to the inclusion of a spatial dimension. However our results also show that the spatial dynamics are of great importance: first we find that the risk of global extinctions increases with increasing spatial correlation. Second we find that the pattern and rate of dispersal are important; a high migration rate in combination with localized dispersal decrease the risk of global extinctions whereas a global dispersal pattern increases the risk of global extinctions. When dispersal is global the subpopulations of a species become more synchronized which reduces the potential for a patch to become recolonized following extinctions. We also demonstrate the importance of both local and spatial processes when examining the temporal stability of primary production at the scale of metapopulations, local communities and metacommunities. In paper IV we investigate how the spatial structure of the landscape (number of patches) and dispersal pattern of species affect a metacommunities response to increased mortality during dispersal and local loss of species. We find a two-sided effect of dispersal on metacommunity persistence; on the one hand, high migration rate significantly reduces the risk of bottom-up extinction cascades following the removal of a species when dispersal involves no risk. On the other hand, high migration rate increases extinction risks when dispersal imposes a risk to the dispersing individuals, especially when dispersal is global. Species with long generation times at the highest trophic level are particularly vulnerable to extinction when dispersal involves a risk. These results suggest that decreasing the mortality risk of dispersing individuals by constructing habitat corridors or by improving the quality of the habitat matrix might greatly increase the robustness of metacommunities to local loss of species by enhancing recolonisations and rescue effects. In paper V we use network theory to identify keystone patches in the landscape, patches that are of critical importance for the local and global persistence of species in the metacommunity. By deleting patches one at a time and investigating the risk of local and global extinctions we quantified the importance of a patch’s position in the landscape for the persistence of species within the metacommunity. A selection of indices were used including some local indices that measure the connectedness of a patch in the intact network and some indices which measure the decrease in a global index after the deletion of the patch from the network. Global indices are those that give an impression of the connectivity of the entire patch network. We find that deletion of patches contributing strongly to the connectivity of the entire patch network had the most negative effect on species persistence.

In this Thesis I have investigated the use of nanostructured films as sensing and contact layers for field effect gas sensors in order to achieve high sensitivity, selectivity, and long term stability of the devices in corrosive environments at elevated temperatures. Electrochemically synthesized Pd and Au nanoparticles deposited as sensing layers on capacitive field effect devices were found to give a significant response to NOx with small, or no responses to H2, NH3, and C3H6. Pt nanoparticles incorporated in a TiC matrix are catalytically active, but the agglomeration and migration of the Pt particles towards the substrate surface reduces the activity of the sensing layer. Magnetron sputtered epitaxial films from the Ti-Si-C and the Ti-Ge-C systems were grown on 4H-SiC substrates in order to explore their potential as high temperature stable ohmic contact materials to SiC based field effect gas sensors. Ti3SiC2 thin films deposited on 4H-SiC substrates were found to yield ohmic contacts to n-type SiC after a high temperature rapid thermal anneal at 950 ºC. Investigations on the growth mode of Ti3SiC2 thin films with varying Si content on 4H-SiC substrates showed the growth to be lateral step-flow with the propagation of steps with a height as small as half a unit cell. The amount of Si present during deposition leads to differences in surface faceting of the films and Si-supersaturation conditions gives growth of Ti3SiC2 films with the presence of TiSi2 crystallites. Current-voltage measurements of the as-deposited Ti3GeC2 films indicate that this material is also a promising candidate for achieving long term stable contact layers to 4H-SiC for operation at elevated temperatures in corrosive environments. Further investigations into the Ti-Ge-C system showed that the previously unreported solid solutions of (Ti,V)2GeC, (Ti,V)3GeC2 and (Ti,V)4GeC3 can be synthesized, and it was found that the growth of these films is affected by the nature of the substrate.

The oncogene c-­‐Myc is overexpressed in many types of human cancers and regulation of c-­‐Myc expression is crucial in a normal cell. The intrinsically disordered N-­‐terminal transactivation domain interacts with a wide range of proteins regulating c-­‐Myc activity. The highly conserved Myc box I region includes residues Thr58 and Ser62, which are involved in the phosphorylation events that control c-­‐Myc degradation by ubiquitination. Aggressive cell growth, leading to tumor formation, occurs if activated c-­‐ Myc is not degraded by ubiquitination. Such events may be triggered by defects in the regulated network of interactions involving Pin1 and phospho-­‐dependent kinases. In this thesis, the properties of the intrinsically disordered unphosphorylated c-­‐Myc1-­‐88 and its interaction with Bin1 are studied by nuclear magnetic resonance (NMR) spectroscopy and surface plasmon resonance (SPR). Furthermore, the interaction of Myc1-­‐88 with Pin1 is analyzed in molecular detail, both for unphosphorylated and Ser62 phosphorylated c-­‐Myc1-­‐88, providing a first molecular description of a disordered but specific c-­‐Myc complex. A detailed analysis of the dynamics and structural properties of the transcriptional activator TAF in complex with TBP, both by NMR spectroscopy and crystallography, provides insight into transcriptional regulation and how c-­‐Myc could interact with TBP. Finally, the structure of a novel N-­‐terminal domain motif in FKBP25, which we name the Basic Tilted Helix Bundle (BTHB) domain, and its binding to YY1, which also binds c-­‐Myc, is described. By investigating the structural and dynamic properties of c-­‐Myc and c-­‐Myc-­‐interacting proteins, this thesis thus provides further insight to the molecular basis for c-­‐Myc functionality in transcriptional regulation.

Biological and chemical reactions involved in physiological processes are often complex and very sophisticated. Such processes can be mimicked in the laboratory to obtain important knowledge, valuable for the  development of new diagnostic methods, drugs and biosensors. This  thesis includes investigations of bio-functionalized surfaces that can be used as model systems to mimic naturally existing biomolecular recognition processes. In this thesis, three different peptides, of our own design, that mimic parts of the second and third intracellular loops of the α2A-adrenergic receptor, are studied. The peptides were immobilized onto gold substrates, through thiol chemistry. The interaction between the peptides and the G-protein was investigated using surface plasmon resonance (SPR). The G-protein showed the highest binding capability for surfaces functionalized with a peptide mimicking the n-terminal of the third intracellular loop (GPR-i3n). The binding was enhanced when the pure GPR-i3n peptide was mixed with a short oligopeptide (3GC). A tentative explanation for the obtained results is that the presence of the 3GC molecule enables conformational changes of the GPR-i3n monolayer which affect the interaction with the G-protein. The results from the SPR measurements also indicated that the conformation of the G-protein was kept intact during the interaction with a peptide mimicking the c-terminal of the third intracellular loop (GPR-i3c). Multilayers were formed on the surfaces functionalized with a peptide mimicking the second intracellular loop (GPR-i2c) and the GPR-i3n peptide. We suggest that conformational changes of the G-protein are induced during the interaction with the surfaces functionalized with the GPR-i3n and GPR-i2c peptides. Comprehensive surface characterizations of four biomolecular systems, based upon the functional groups: noradrenaline, phenylboronic-ester, phenylboronic-acid and benzenesulfonamide, are presented in the thesis. The aim is to develop a platform for detailed molecular recognition studies on surfaces. The molecular systems were characterized using infrared spectroscopy, X-ray photoelectron spectroscopy, near edge X-ray absorption fine structure spectroscopy, ellipsometry and contact angle goniometry. Noradrenaline was chosen as it is a neurotransmitter that interacts with the extracellular loops of adrenergic receptors. In this work, the noradrenaline analogue (Nor-Pt) of our own design, was equipped with a -SH handle to be linked to surfaces and with the free noradrenaline group available for interaction studies. The Nor-Pt molecules were organized on the surfaces with the sulfur atom close to the gold substrate and the aromatic ring available for possible interactions with other biomolecules in the ambient media. The main component of the C=O vibrational mode present in the amide moiety had a parallel orientation relative to the plane of the gold surface, based on the infrared spectroscopy results. The phenylboronic system was designed as a simple mimicry of an  adrenergic receptor as the boronic acid functional group binds to diol containing molecules such as noradrenaline. The boronic  esterterminated alkane thiol (BOR-Capped) was chemisorbed onto gold substrates. We showed that BOR-Capped was linked to the gold substrate via thiolate bond formation and formed a well-organized monolayer. The pinacolyl protection group was removed directly from the BOR-Capped monolayer on the surfaces, which resulted in an unprotected monolayer terminated with the boronic acid functional group (BOR-Uncapped). The strong chemical bond to the gold substrate was retained during the deprotection procedure as only thiolate sulfur species were observed for the BOR-Uncapped molecular system. The benzenesulfonamide based molecule was designed as a model system for bioselective surfaces. An amine-terminated alkane thiol was adsorbed onto a gold substrate. In a second step, a benzenesulfonamide derivative was linked to the amine-terminated monolayer by the formation of an amide bond. We showed that the resulting benzenesulfonamide-terminated alkane thiol (AUT-C6) formed a well-organized and semi-thick monolayer on the gold substrate. The polarization dependence of NEXAFS was used to determine the average tilt angle of the aromatic ring structures of Nor-Pt, BOR-Capped, BOR-Uncapped and AUT-C6. The results indicate that the aromatic ring planes of BOR-Capped and AUT-C6 have a preferential orientation toward the surface normal. The aromatic ring structures of Nor-Pt and BOR-Uncapped were determined to have a more tilted orientation relative to the gold surface normal. Finally, the interaction between carbonic anhydrase and the AUT-C6 molecule was investigated using surface plasmon resonance and ellipsometry. The surface immobilized benzenesulfonamide was shown to bind to carbonic anhydrase and the results indicated that the interaction is specific.

Environmental variation is an essential part of population dynamics, and two characteristics of such variation—variance and the temporal autocorrelation termed ‘noise colour’—are essential for determining the persistence of a population. In addition, the spatial correlation of local environmental variation between habitat patches (i.e., synchrony) is equally important in subdivided populations connected via dispersal. The research underlying this thesis explored the effects of noise colour and synchrony on population dynamics. The dynamics were studied primarily in single-species models with fast or slow population responses to environmental changes, and several-species systems (i.e., food webs) with different stability properties were also considered. Populations were spatially subdivided with local dynamics in discrete patches, and patch positions were modelled either implicitly or explicitly, with different landscape configurations in the latter case. It has previously been shown that the effect of increased environmental redness on extinction risk in nonspatial models depends on population responsiveness, seen as increased and decreased risks for fast and slow responding populations, respectively. Here, increased redness of noise decreased the extinction risk for fast-responding populations (in accordance with non-spatial studies) in a simple implicit landscape model (Papers I and II). Slow-responding populations in some cases showed a raised extinction risk for intermediate noise colour values (Paper I), which does not agree with earlier results. However, increasing the spatial complexity evened out the differences that were caused by responsiveness (Papers III and IV). Thus, in general, the explicit landscape models displayed a decrease in extinction risk with increasing environmental redness regardless of whether the populations were fast or slow in responding to environmental variation. Still, fast and slow responsiveness of populations differed in relation to the following: overall levels of extinction risk (Papers I, III, and IV), synchrony of population variations (Paper II), colour of population variations (Paper II), and response to landscape structure (Papers III and IV). For fast-responding populations, the degree of synchrony of population variations was similar to the synchrony of environmental noise (Paper II). Local populations of a model organism that responded slowly to environmental variation were more synchronized than the environmental variation itself, and the largest shift between the environment and the populations was seen for intermediate red noise colours (Paper II). This indicated that dispersal-induced population synchrony could be enhanced by reddened noise. Landscape configuration proved to be important for the general levels of extinction risk. This effect was most pronounced for fast-responding populations (Papers III and IV) and became even more distinct when distance-dependent synchrony was added between the environmental variations (Paper IV). Adding explicit landscapes led to an decrease in the differences between fast- and slow-responding populations, when considering the influence of noise colour on extinction risk. Also, landscape configuration affected the importance of degree of synchrony through its impact on distances between patches, which resulted in configurations where extinction risk depended solely on noise colour. The effects on stability exerted by populations embedded in food webs were investigated in an implicit landscape model (Paper V). Three types of food webs with different properties of inherent stability all showed a decrease in stability at increased environmental variance and increased redness of environmental variation. In conclusion, the single-species models showed that the survival conditions of populations that were near extinction were improved by all of the following: decreased synchrony, reddening of noise, and aggregation of patches. The results of the web simulations indicate that we need better understanding of how findings obtained using single-species models can be used to reveal the effects of noise colour on species communities. From a management perspective, altering landscape structure may compensate for increased extinction risks caused by changed noise colour of environmental variation, which is a predicted outcome of climate change.