Movement-associated proteins of Potato virus A: attachment to virus particles and phosphorylation

The particles of Potato virus A (PVA; genus Potyvirus) are helically constructed filaments that contain multiple copies of a single type of coat-protein (CP) subunit and a single copy of genome-linked protein (VPg), attached to one end of the virion. Examination of negatively-stained virions by electron microscopy revealed flexuous, rod-shaped particles with no obvious terminal structures. It is known that particles of several filamentous plant viruses incorporate additional minor protein components, forming stable complexes that mediate particle disassembly, movement or transmission by insect vectors. The first objective of this work was to study the interaction of PVA movement-associated proteins with virus particles and how these interactions contribute to the morphology and function of the virus particles. Purified particles of PVA were examined by atomic force microscopy (AFM) and immuno-gold electron microscopy. A protrusion was found at one end of some of the potyvirus particles, associated with the 5' end of the viral RNA. The tip contained two virus-encoded proteins, the genome-linked protein (VPg) and the helper-component proteinase (HC-Pro). Both are required for cell-to-cell movement of the virus. Biochemical and electron microscopy studies of purified PVA samples also revealed the presence of another protein required for cell-to-cell movement the cylindrical inclusion protein (CI), which is also an RNA helicase/ATPase. Centrifugation through a 5-40% sucrose gradient separated virus particles with no detectable CI to a fraction that remained in the gradient, from the CI-associated particles that went to the pellet. Both types of particles were infectious. AFM and translation experiments demonstrated that when the viral CI was not present in the sample, PVA virions had a beads-on-a-string phenotype, and RNA within the virus particles was more accessible to translation. The second objective of this work was to study phosphorylation of PVA movement-associated and structural proteins (CP and VPg) in vitro and, if possible, in vivo. PVA virion structural protein CP is necessary for virus cell-to-cell movement. The tobacco protein kinase CK2 was identified as a kinase phosphorylating PVA CP. A major site of CK2 phosphorylation in PVA CP was identified as a single threonine within a CK2 consensus sequence. Amino acid substitutions affecting the CK2 consensus sequence in CP resulted in viruses that were defective in cell-to-cell and long-distance movement. The CK2 regulation of virion assembly and cell-to-cell movement by phosphorylation of CP was possibly due to the inhibition of CP binding to viral RNA. Four putative phosphorylation sites were identified from an in vitro phosphorylated recombinant VPg. All four were mutated and the spread of mutant viruses in two different host plants was studied. Two putative phosphorylation site mutants (Thr45 and Thr49) had phenotypes identical to that of a wild type (WT) virus infection in both Nicotiana benthamiana and N. tabacum plants. The other two mutant viruses (Thr132/Ser133 and Thr168) showed different phenotypes with increased or decreased accumulation rates, respectively, in inoculated and the first two systemically infected leaves of N. benthamiana. The same mutants were occasionally restricted to single cells in N. tabacum plants, suggesting the importance of these amino acids in the PVA infection cycle in N. tabacum.

Spatial and temporal variability in midge (Nematocera) assemblages in shallow Finnish lakes (60−70 °N) : community-based modelling of past environmental change

Multi- and intralake datasets of fossil midge assemblages in surface sediments of small shallow lakes in Finland were studied to determine the most important environmental factors explaining trends in midge distribution and abundance. The aim was to develop palaeoenvironmental calibration models for the most important environmental variables for the purpose of reconstructing past environmental conditions. The developed models were applied to three high-resolution fossil midge stratigraphies from southern and eastern Finland to interpret environmental variability over the past 2000 years, with special focus on the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA) and recent anthropogenic changes. The midge-based results were compared with physical properties of the sediment, historical evidence and environmental reconstructions based on diatoms (Bacillariophyta), cladocerans (Crustacea: Cladocera) and tree rings. The results showed that the most important environmental factor controlling midge distribution and abundance along a latitudinal gradient in Finland was the mean July air temperature (TJul). However, when the dataset was environmentally screened to include only pristine lakes, water depth at the sampling site became more important. Furthermore, when the dataset was geographically scaled to southern Finland, hypolimnetic oxygen conditions became the dominant environmental factor. The results from an intralake dataset from eastern Finland showed that the most important environmental factors controlling midge distribution within a lake basin were river contribution, water depth and submerged vegetation patterns. In addition, the results of the intralake dataset showed that the fossil midge assemblages represent fauna that lived in close proximity to the sampling sites, thus enabling the exploration of within-lake gradients in midge assemblages. Importantly, this within-lake heterogeneity in midge assemblages may have effects on midge-based temperature estimations, because samples taken from the deepest point of a lake basin may infer considerably colder temperatures than expected, as shown by the present test results. Therefore, it is suggested here that the samples in fossil midge studies involving shallow boreal lakes should be taken from the sublittoral, where the assemblages are most representative of the whole lake fauna. Transfer functions between midge assemblages and the environmental forcing factors that were significantly related with the assemblages, including mean air TJul, water depth, hypolimnetic oxygen, stream flow and distance to littoral vegetation, were developed using weighted averaging (WA) and weighted averaging-partial least squares (WA-PLS) techniques, which outperformed all the other tested numerical approaches. Application of the models in downcore studies showed mostly consistent trends. Based on the present results, which agreed with previous studies and historical evidence, the Medieval Climate Anomaly between ca. 800 and 1300 AD in eastern Finland was characterized by warm temperature conditions and dry summers, but probably humid winters. The Little Ice Age (LIA) prevailed in southern Finland from ca. 1550 to 1850 AD, with the coldest conditions occurring at ca. 1700 AD, whereas in eastern Finland the cold conditions prevailed over a longer time period, from ca. 1300 until 1900 AD. The recent climatic warming was clearly represented in all of the temperature reconstructions. In the terms of long-term climatology, the present results provide support for the concept that the North Atlantic Oscillation (NAO) index has a positive correlation with winter precipitation and annual temperature and a negative correlation with summer precipitation in eastern Finland. In general, the results indicate a relatively warm climate with dry summers but snowy winters during the MCA and a cool climate with rainy summers and dry winters during the LIA. The results of the present reconstructions and the forthcoming applications of the models can be used in assessments of long-term environmental dynamics to refine the understanding of past environmental reference conditions and natural variability required by environmental scientists, ecologists and policy makers to make decisions concerning the presently occurring global, regional and local changes. The developed midge-based models for temperature, hypolimnetic oxygen, water depth, littoral vegetation shift and stream flow, presented in this thesis, are open for scientific use on request.

Spatial variation of climate and the impact of disturbances on local climate and forest recovery in northern Finland

The structure and function of northern ecosystems are strongly influenced by climate change and variability and by human-induced disturbances. The projected global change is likely to have a pronounced effect on the distribution and productivity of different species, generating large changes in the equilibrium at the tree-line. In turn, movement of the tree-line and the redistribution of species produce feedback to both the local and the regional climate. This research was initiated with the objective of examining the influence of natural conditions on the small-scale spatial variation of climate in Finnish Lapland, and to study the interaction and feedback mechanisms in the climate-disturbances-vegetation system near the climatological border of boreal forest. The high (1 km) resolution spatial variation of climate parameters over northern Finland was determined by applying the Kriging interpolation method that takes into account the effect of external forcing variables, i.e., geographical coordinates, elevation, sea and lake coverage. Of all the natural factors shaping the climate, the geographical position, local topography and altitude proved to be the determining ones. Spatial analyses of temperature- and precipitation-derived parameters based on a 30-year dataset (1971-2000) provide a detailed description of the local climate. Maps of the mean, maximum and minimum temperatures, the frost-free period and the growing season indicate that the most favourable thermal conditions exist in the south-western part of Lapland, around large water bodies and in the Kemijoki basin, while the coldest regions are in highland and fell Lapland. The distribution of precipitation is predominantly longitudinally dependent but with the definite influence of local features. The impact of human-induced disturbances, i.e., forest fires, on local climate and its implication for forest recovery near the northern timberline was evaluated in the Tuntsa area of eastern Lapland, damaged by a widespread forest fire in 1960 and suffering repeatedly-failed vegetation recovery since that. Direct measurements of the local climate and simulated heat and water fluxes indicated the development of a more severe climate and physical conditions on the fire-disturbed site. Removal of the original, predominantly Norway spruce and downy birch vegetation and its substitution by tundra vegetation has generated increased wind velocity and reduced snow accumulation, associated with a large variation in soil temperature and moisture and deep soil frost. The changed structural parameters of the canopy have determined changes in energy fluxes by reducing the latter over the tundra vegetation. The altered surface and soil conditions, as well as the evolved severe local climate, have negatively affected seedling growth and survival, leading to more unfavourable conditions for the reproduction of boreal vegetation and thereby causing deviations in the regional position of the timberline. However it should be noted that other factors, such as an inadequate seed source or seedbed, the poor quality of the soil and the intensive logging of damaged trees could also exacerbate the poor tree regeneration. In spite of the failed forest recovery at Tunsta, the position and composition of the timberline and tree-line in Finnish Lapland may also benefit from present and future changes in climate. The already-observed and the projected increase in temperature, the prolonged growing season, as well as changes in the precipitation regime foster tree growth and new regeneration, resulting in an advance of the timberline and tree-line northward and upward. This shift in the distribution of vegetation might be decelerated or even halted by local topoclimatic conditions and by the expected increase in the frequency of disturbances.

Posted Workers and Free Movement of Services in the European Union – the Impact on National Employment and Immigration Law

This thesis examines posting of workers within the free movement of services in the European Union. The emphasis is on the case law of the European Court of Justice and in the role it has played in the liberalisation of the service sector in respect of posting of workers. The case law is examined from two different viewpoints: firstly, that of employment law and secondly, immigration law. The aim is to find out how active a role the Court has taken with regard these two fields of law and what are the implications of the Court’s judgments for the regulation on a national level. The first part of the thesis provides a general review of the Community law principles governing the freedom to provide services in the EU. The second part presents the Posted Workers’ Directive and the case law of the European Court of Justice before and after the enactment of the Directive from the viewpoint of employment law. Special attention is paid to a recent judgment in which the Court has taken a restrictive position with regard to a trade union’s right to take collective action against a service provider established in another Member State. The third part of the thesis concentrates, firstly, on the legal status of non-EU nationals lawfully resident in the EU. Secondly, it looks into the question of how the Court’s case law has affected the possibilities to use non-EU nationals as posted workers within the freedom to provide services. The final chapter includes a critical analysis of the Court’s case law on posted workers. The judgments of the European Court of Justice are the principal source of law for this thesis. In the primary legislation the focus is on Articles 49 EC and 50 EC that lay down the rules concerning the free movement of services. Within the secondary legislation, the present work principally concentrates on the Posted Workers’ Directive. It also examines proposals of the European Commission and directives that have been adopted in the field of immigration. The conclusions of the case study are twofold: while in the field of employment law, the European Court of Justice has based its judgments on a very literal interpretation of the Posted Workers’ Directive, in the field of immigration its conclusions have been much more innovative. In both fields of regulation the Court’s judgments have far-reaching implications for the rules concerning posting of workers leaving very little discretion for the Member States’ authorities.

The Politics of Pulp Investment and the Brazilian Landless Movement (MST)

The Politics of Pulp Investment and the Brazilian Landless Movement (MST) The paper industry has been moving more heavily to the global South at the beginning of the 21st century. In a number of cases the rural populations of the global South have engaged in increasingly important resistance in their scuffle with the large-scale tree plantation-relying pulp investment model. The resistance had generally not yet managed to slow down Southern industrial tree plantation expansion until 2004. After all, even the MST, perhaps the strongest of the Southern movements, has limited power in comparison to the corporations pushing for plantation expansion. This thesis shows how, even against these odds, depending on the mechanisms of contention and case-specific conflict dynamics, in some cases the movements have managed to slow and even reverse plantation expansion. The thesis is based on extensive field research in the Brazilian countryside. It outlines a new theory of contentious agency promotion, emphasizing its importance in the shaping of corporate resource exploitation. The thesis includes a Qualitative Comparative Analysis of resistance influence on the economic outcomes of all (14) Brazilian large-scale pulp projects between 2004-2008. The central hypothesis of the thesis is that corporate resource exploitation can be slowed down more effectively and likely when the resistance is based on contentious agency. Contentious agency is created by the concatenation of five mutually supporting mechanisms of contention: organizing and politicizing a social movement; heterodox framing of pulp projects; protesting; networking; and embedding whilst maintaining autonomy. The findings suggest that contentious agency can slow or even reverse the expansion of industrial plantations, whereas when contentious agency promotion was inactive, fast or even unchecked plantation expansion was always the outcome. The rule applied to all the assessed 14 pulp conflict cases. The hypothesis gained strong support even in situations where corporate agency promotion was simultaneously active. In previous studies on social movements, there has been a lack of contributions that help us understand the causal mechanisms of contention influencing economic outcomes. The thesis answers to the call by merging a Polanyian analysis of the political economy with the Dynamics of Contention research program and making a case for the impact of contentious agency on capital accumulation. The research concludes that an efficient social movement can utilize mechanisms of contention to promote the potential of activism among its members and influence investment outcomes. Protesting, for example via pioneering land occupations, seemed to be particularly important. Until now, there has been no comprehensive theory on when and how contentious agency can slow down or reverse the expansion of corporate resource exploitation. The original contribution of this research is to provide such a theory, and utilize it to offer an extensive explanation on the conflicts over pulp investment in Brazil, the globalization of the paper industry, and slowing of industrial plantation expansion in the global South.

Assessment of neuroleptic-induced movement disorders in a naturalistic schizophrenia population

The prevalence and assessment of neuroleptic-induced movement disorders (NIMDs) in a naturalistic schizophrenia population that uses conventional neuroleptics were studied. We recruited 99 chronic schizophrenic institutionalized adult patients from a state nursing home in central Estonia. The total prevalence of NIMDs according to the diagnostic criteria of the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) was 61.6%, and 22.2% had more than one NIMD. We explored the reliability and validity of different instruments for measuring these disorders. First, we compared DSM-IV with the established observer rating scales of Barnes Akathisia Rating Scale (BARS), Simpson-Angus Scale (SAS) (for neuroleptic-induced parkinsonism, NIP) and Abnormal Involuntary Movement Scale (AIMS) (for tardive dyskinesia), all three of which have been used for diagnosing NIMD. We found a good overlap of cases for neuroleptic-induced akathisia (NIA) and tardive dyskinesia (TD) but somewhat poorer overlap for NIP, for which we suggest raising the commonly used threshold value of 0.3 to 0.65. Second, we compared the established observer rating scales with an objective motor measurement, namely controlled rest lower limb activity measured by actometry. Actometry supported the validity of BARS and SAS, but it could not be used alone in this naturalistic population with several co-existing NIMDs. It could not differentiate the disorders from each other. Quantitative actometry may be useful in measuring changes in NIA and NIP severity, in situations where the diagnosis has been made using another method. Third, after the relative failure of quantitative actometry to show diagnostic power in a naturalistic population, we explored descriptive ways of analysing actometric data, and demonstrated diagnostic power pooled NIA and pseudoakathisia (PsA) in our population. A subjective question concerning movement problems was able to discriminate NIA patients from all other subjects. Answers to this question were not selective for other NIMDs. Chronic schizophrenia populations are common worldwide, NIMD affected two-thirds of our study population. Prevention, diagnosis and treatment of NIMDs warrant more attention, especially in countries where typical antipsychotics are frequently used. Our study supported the validity and reliability of DSM-IV diagnostic criteria for NIMD in comparison with established rating scales and actometry. SAS can be used with minor modifications for screening purposes. Controlled rest lower limb actometry was not diagnostically specific in our naturalistic population with several co-morbid NIMDs, but it may be sensitive in measuring changes in NIMDs.

Studies on the assessment of the adequacy of anesthesia

Several hypnosis monitoring systems based on the processed electroencephalogram (EEG) have been developed for use during general anesthesia. The assessment of the analgesic component (antinociception) of general anesthesia is an emerging field of research. This study investigated the interaction of hypnosis and antinociception, the association of several physiological variables with the degree of intraoperative nociception, and aspects of EEG Bispectral Index Scale (BIS) monitoring during general anesthesia. In addition, EEG features and heart rate (HR) responses during desflurane and sevoflurane anesthesia were compared. A propofol bolus of 0.7 mg/kg was more effective than an alfentanil bolus of 0.5 mg in preventing the recurrence of movement responses during uterine dilatation and curettage (D C) after a propofol-alfentanil induction, combined with nitrous oxide (N2O). HR and several HR variability-, frontal electromyography (fEMG)-, pulse plethysmography (PPG)-, and EEG-derived variables were associated with surgery-induced movement responses. Movers were discriminated from non-movers mostly by the post-stimulus values per se or normalized with respect to the pre-stimulus values. In logistic regression analysis, the best classification performance was achieved with the combination of normalized fEMG power and HR during D C (overall accuracy 81%, sensitivity 53%, specificity 95%), and with the combination of normalized fEMG-related response entropy, electrocardiography (ECG) R-to-R interval (RRI), and PPG dicrotic notch amplitude during sevoflurane anesthesia (overall accuracy 96%, sensitivity 90%, specificity 100%). ECG electrode impedances after alcohol swab skin pretreatment alone were higher than impedances of designated EEG electrodes. The BIS values registered with ECG electrodes were higher than those registered simultaneously with EEG electrodes. No significant difference in the time to home-readiness after isoflurane-N2O or sevoflurane-N2O anesthesia was found, when the administration of the volatile agent was guided by BIS monitoring. All other early and intermediate recovery parameters were also similar. Transient epileptiform EEG activity was detected in eight of 15 sevoflurane patients during a rapid increase in the inspired volatile concentration, and in none of the 16 desflurane patients. The observed transient EEG changes did not adversely affect the recovery of the patients. Following the rapid increase in the inhaled desflurane concentration, HR increased transiently, reaching its maximum in two minutes. In the sevoflurane group, the increase was slower and more subtle. In conclusion, desflurane may be a safer volatile agent than sevoflurane in patients with a lowered seizure threshold. The tachycardia induced by a rapid increase in the inspired desflurane concentration may present a risk for patients with heart disease. Designated EEG electrodes may be superior to ECG electrodes in EEG BIS monitoring. When the administration of isoflurane or sevoflurane is adjusted to maintain BIS values at 50-60 in healthy ambulatory surgery patients, the speed and quality of recovery are similar after both isoflurane-N2O and sevoflurane-N2O anesthesia. When anesthesia is maintained by the inhalation of N2O and bolus doses of propofol and alfentanil in healthy unparalyzed patients, movement responses may be best avoided by ensuring a relatively deep hypnotic level with propofol. HR/RRI, fEMG, and PPG dicrotic notch amplitude are potential indicators of nociception during anesthesia, but their performance needs to be validated in future studies. Combining information from different sources may improve the discrimination of the level of nociception.

Exhaled nitric oxide : Variability and association with bronchial hyperresponsiveness and atopy

Airway inflammation is a key feature of bronchial asthma. In asthma management, according to international guidelines, the gold standard is anti-inflammatory treatment. Currently, only conventional procedures (i.e., symptoms, use of rescue medication, PEF-variability, and lung function tests) were used to both diagnose and evaluate the results of treatment with anti-inflammatory drugs. New methods for evaluation of degree of airway inflammation are required. Nitric oxide (NO) is a gas which is produced in the airways of healthy subjects and especially produced in asthmatic airways. Measurement of NO from the airways is possible, and NO can be measured from exhaled air. Fractional exhaled NO (FENO) is increased in asthma, and the highest concentrations are measured in asthmatic patients not treated with inhaled corticosteroids (ICS). Steroid-treated patients with asthma had levels of FENO similar to those of healthy controls. Atopic asthmatics had higher levels of FENO than did nonatopic asthmatics, indicating that level of atopy affected FENO level. Associations between FENO and bronchial hyperresponsiveness (BHR) occur in asthma. The present study demonstrated that measurement of FENO had good reproducibility, and the FENO variability was reasonable both short- and long-term in both healthy subjects and patients with respiratory symptoms or asthma. We demonstrated the upper normal limit for healthy subjects, which was 12 ppb calculated from two different healthy study populations. We showed that patients with respiratory symptoms who did not fulfil the diagnostic criteria of asthma had FENO values significantly higher than in healthy subjects, but significantly lower than in asthma patients. These findings suggest that BHR to histamine is a sensitive indicator of the effect of ICS and a valuable tool for adjustment of corticosteroid treatment in mild asthma. The findings further suggest that intermittent treatment periods of a few weeks’ duration are insufficient to provide long-term control of BHR in patients with mild persistent asthma. Moreover, during the treatment with ICS changes in BHR and changes in FENO were associated. FENO level was associated with BHR measured by a direct (histamine challenge) or indirect method (exercise challenge) in steroid-naïve symptomatic, non-smoking asthmatics. Although these associations could be found only in atopics, FENO level in nonatopic asthma was also increased. It can thus be concluded that assessment of airway inflammation by measuring FENO can be useful for clinical purposes. The methodology of FENO measurements is now validated. Especially in those patients with respiratory symptoms who did not fulfil the diagnostic criteria of asthma, FENO measurement can aid in treatment decisions. Serial measurement of FENO during treatment with ICS can be a complementary or an alternative method for evaluation in patients with asthma.

Evaluation and modelling of the spatial and temporal variability of particulate matter in urban areas

This thesis contains three subject areas concerning particulate matter in urban area air quality: 1) Analysis of the measured concentrations of particulate matter mass concentrations in the Helsinki Metropolitan Area (HMA) in different locations in relation to traffic sources, and at different times of year and day. 2) The evolution of traffic exhaust originated particulate matter number concentrations and sizes in local street scale are studied by a combination of a dispersion model and an aerosol process model. 3) Some situations of high particulate matter concentrations are analysed with regard to their meteorological origins, especially temperature inversion situations, in the HMA and three other European cities. The prediction of the occurrence of meteorological conditions conducive to elevated particulate matter concentrations in the studied cities is examined. The performance of current numerical weather forecasting models in the case of air pollution episode situations is considered. The study of the ambient measurements revealed clear diurnal variation of the PM10 concentrations in the HMA measurement sites, irrespective of the year and the season of the year. The diurnal variation of local vehicular traffic flows seemed to have no substantial correlation with the PM2.5 concentrations, indicating that the PM10 concentrations were originated mainly from local vehicular traffic (direct emissions and suspension), while the PM2.5 concentrations were mostly of regionally and long-range transported origin. The modelling study of traffic exhaust dispersion and transformation showed that the number concentrations of particles originating from street traffic exhaust undergo a substantial change during the first tens of seconds after being emitted from the vehicle tailpipe. The dilution process was shown to dominate total number concentrations. Minimal effect of both condensation and coagulation was seen in the Aitken mode number concentrations. The included air pollution episodes were chosen on the basis of occurrence in either winter or spring, and having at least partly local origin. In the HMA, air pollution episodes were shown to be linked to predominantly stable atmospheric conditions with high atmospheric pressure and low wind speeds in conjunction with relatively low ambient temperatures. For the other European cities studied, the best meteorological predictors for the elevated concentrations of PM10 were shown to be temporal (hourly) evolutions of temperature inversions, stable atmospheric stability and in some cases, wind speed. Concerning the weather prediction during particulate matter related air pollution episodes, the use of the studied models were found to overpredict pollutant dispersion, leading to underprediction of pollutant concentration levels.

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.