From genes to communities : stress tolerance in eelgrass (Zostera marina)

Shallow coastal areas are dynamic habitats that are affected by a variety of abiotic and biotic factors. In addition to the natural environmental stress, estuarine and coastal seagrass ecosystems are exposed to effects of climate change and other anthropogenic impacts. In this thesis the effect of different abiotic (shading stress, salinity and temperature) and biotic stressors (presence of co-occurring species) and different levels and combinations of stressors on the performance and survival of eelgrass (Zostera marina) was assessed. To investigate the importance of scale for stress responses, varying levels of biological organization (genotype, life stage, population and plant community) were studied in field and aquarium experiments. Light limitation, decreased salinity and increased temperature affected eelgrass performance negatively in papers I, II and III, respectively. While co-occurring plant species had no notable effect on eelgrass in paper IV, the presence of eelgrass increased the biomass of Potamogeton perfoliatus. The findings in papers II and III confirmed that more extreme levels of salinity and temperature had stronger impacts on plant performance compared to intermediate levels, but intermediate levels also had more severe effects on plants when they were exposed to several stressors, as illustrated in paper II. Thus, multiple stressors had negative synergetic effects. The results in papers I, II and III indicate that future changes in light climate, salinity and temperature can have serious impacts on eelgrass performance and survival. Stress responses were found to vary among genotypes, life stages and populations in papers I, II and III, respectively, emphasizing the importance of study scale. The results demonstrate that while stress in general affects seagrass productivity negatively, the severity of effects can vary substantially depending on the studied scale or level of biological organization. Eelgrass genotypes can differ in their stress and recovery processes, as observed in paper I. In paper II, eelgrass seedlings were less prone to abiotic stress compared to adult plants, but stress also decreased their survival considerably. This indicates that recruitment and re-colonization through seeds might be threatened in the future. Variation among population responses observed in paper III indicates that long-term local adaptation under differing selection pressures has caused divergence in salinity tolerance between Baltic eelgrass populations. This variability in stress tolerance observed in papers I and III suggests that some eelgrass genotypes and populations have a better capacity to adapt to changes and survive in a changing environment. Multiple stressors and biological level-specific responses demonstrate the uncertainty in predicting eelgrass responses in a changing environment. As eelgrass populations may differ in their stress tolerance both within and across regions, conservation strategies at both local and regional scales are urgently needed in order to ensure the survival of these important ecosystems.

Algorithmic Techniques in Gene Expression Processing. From Imputation to Visualization

The amount of biological data has grown exponentially in recent decades. Modern biotechnologies, such as microarrays and next-generation sequencing, are capable to produce massive amounts of biomedical data in a single experiment. As the amount of the data is rapidly growing there is an urgent need for reliable computational methods for analyzing and visualizing it. This thesis addresses this need by studying how to efficiently and reliably analyze and visualize high-dimensional data, especially that obtained from gene expression microarray experiments. First, we will study the ways to improve the quality of microarray data by replacing (imputing) the missing data entries with the estimated values for these entries. Missing value imputation is a method which is commonly used to make the original incomplete data complete, thus making it easier to be analyzed with statistical and computational methods. Our novel approach was to use curated external biological information as a guide for the missing value imputation. Secondly, we studied the effect of missing value imputation on the downstream data analysis methods like clustering. We compared multiple recent imputation algorithms against 8 publicly available microarray data sets. It was observed that the missing value imputation indeed is a rational way to improve the quality of biological data. The research revealed differences between the clustering results obtained with different imputation methods. On most data sets, the simple and fast k-NN imputation was good enough, but there were also needs for more advanced imputation methods, such as Bayesian Principal Component Algorithm (BPCA). Finally, we studied the visualization of biological network data. Biological interaction networks are examples of the outcome of multiple biological experiments such as using the gene microarray techniques. Such networks are typically very large and highly connected, thus there is a need for fast algorithms for producing visually pleasant layouts. A computationally efficient way to produce layouts of large biological interaction networks was developed. The algorithm uses multilevel optimization within the regular force directed graph layout algorithm.

The quality control of glycoprotein folding in the endoplasmic reticulum, a trip from trypanosomes to mammals

The present review deals with the stages of synthesis and processing of asparagine-linked oligosaccharides occurring in the lumen of the endoplasmic reticulum and their relationship to the acquisition by glycoproteins of their proper tertiary structures. Special emphasis is placed on reactions taking place in trypanosomatid protozoa since their study has allowed the detection of the transient glucosylation of glycoproteins catalyzed by UDP-Glc:glycoprotein glucosyltransferase and glucosidase II. The former enzyme has the unique property of covalently tagging improperly folded conformations by catalyzing the formation of protein-linked Glc1Man7GlcNAc2, Glc1Man8GlcNac2 and Glc1Man9GlcNAc2 from the unglucosylated proteins. Glucosyltransferase is a soluble protein of the endoplasmic reticulum that recognizes protein domains exposed in denatured but not in native conformations (probably hydrophobic amino acids) and the innermost N-acetylglucosamine unit that is hidden from macromolecular probes in most native glycoproteins. In vivo, the glucose units are removed by glucosidase II. The influence of oligosaccharides in glycoprotein folding is reviewed as well as the participation of endoplasmic reticulum chaperones (calnexin and calreticulin) that recognize monoglucosylated species in the same process. A model for the quality control of glycoprotein folding in the endoplasmic reticulum, i.e., the mechanism by which cells recognize the tertiary structure of glycoproteins and only allow transit to the Golgi apparatus of properly folded species, is discussed. The main elements of this control are calnexin and calreticulin as retaining components, the UDP-Glc:glycoprotein glucosyltransferase as a sensor of tertiary structures and glucosidase II as the releasing agent.

Molecular biology of the kallikrein-kinin system: from structure to function

The participation of the kallikrein-kinin system, comprising the serine proteases kallikreins, the protein substrates kininogens and the effective peptides kinins, in some pathological processes like hypertension and cardiovascular diseases is still a matter of controversy. The use of different experimental set-ups in concert with the development of potent and specific inhibitors and antagonists for the system has highlighted its importance but the results still lack conclusivity. Over the last few years, transgenic and gene-targeting technologies associated with molecular biology tools have provided specific information about the elusive role of the kallikrein-kinin system in the control of blood pressure and electrolyte homeostasis. cDNA and genomic sequences for kinin receptors B2 and B1 from different species were isolated and shown to encode G-protein-coupled receptors and the structure and pharmacology of the receptors were characterized. Transgenic animals expressing an overactive kallikrein-kinin system were established to study the cardiovascular effects of these alterations and the results of these investigations further corroborate the importance of this system in the maintenance of normal blood pressure. Knockout animals for B2 and B1 receptors are available and their analysis also points to the role of these receptors in cardiovascular regulation and inflammatory processes. In this paper the most recent and relevant genetic animal models developed for the study of the kallikrein-kinin system are reviewed, and the advances they brought to the understanding of the biological role of this system are discussed.

Controlling and Assessment Indirect Spend – Case Study from Beverage Industry

Over the past decades, companies’ interest in controlling indirect sourcing process has increased. New indirect procurement strategies developed for the companies are needed in order to manage their indirect costs. New cost management strategies allow companies to improve their core competences. The research methodology and used in this thesis is qualitative. The theory is based on scientific publications. Empirical data given by the case organization, and was collected in the company’s own systems and in project steering meetings. The purpose of the study was to select a new electronic system for the company and give options for the company to reduce case organization’s indirect costs. The result showed that the most effective indirect cost management strategy was adopting a new electronic procurement system.

Use of molecular epidemiology to monitor the nosocomial dissemination of methicillin-resistant Staphylococcus aureus in a University Hospital from 1991 to 2001

Methicillin-resistant Staphylococcus aureus (MRSA) has been the cause of major outbreaks and epidemics among hospitalized patients, with high mortality and morbidity rates. We studied the genomic diversity of MRSA strains isolated from patients with nosocomial infection in a University Hospital from 1991 to 2001. The study consisted of two periods: period I, from 1991 to 1993 and period II from 1995 to 2001. DNA was typed by pulsed-field gel electrophoresis and the similarity among the MRSA strains was determined by cluster analysis. During period I, 73 strains presented five distinctive DNA profiles: A, B, C, D, and E. Profile A was the most frequent DNA pattern and was identified in 55 (75.3%) strains; three closely related and four possibly related profiles were also identified. During period II, 80 (68.8%) of 117 strains showed the same endemic profile A identified during period I, 18 (13.7%) closely related profiles and 18 (13.7%) possibly related profiles and, only one strain presented an unrelated profile. Cluster analysis showed a 96% coefficient of similarity between profile A from period I and profile A from period II, which were considered to be from the same clone. The molecular monitoring of MRSA strains permitted the determination of the clonal dissemination and the maintenance of a dominant endemic strain during a 10-year period and the presence of closely and possibly related patterns for endemic profile A. However, further studies are necessary to improve the understanding of the dissemination of the endemic profile in this hospital.

Molecular epidemiology of type 1 and 2 dengue viruses in Brazil from 1988 to 2001

Dengue is a mosquito-borne viral infection that in recent decades has become a major international public health concern. Epidemic dengue fever reemerged in Brazil in 1981. Since 1990 more than one dengue virus serotype has been circulating in this tropical country and increasing rates of dengue hemorrhagic fever and dengue shock syndrome have been detected every year. Some evidence supports the association between the introduction of a new serotype and/or genotype in a region and the appearance of dengue hemorrhagic fever. In order to study the evolutionary relationships and possible detection of the introduction of new dengue virus genotypes in Brazil in the last years, we analyzed partial nucleotide sequences of 52 Brazilian samples of both dengue type 1 and dengue type 2 isolated from 1988 to 2001 from highly endemic regions. A 240-nucleotide-long sequence from the envelope/nonstructural protein 1 gene junction was used for phylogenetic analysis. After comparing the nucleotide sequences originally obtained in this study to those previously studied by others, and analyzing the phylogenetic trees, we conclude that, after the initial introduction of the currently circulating dengue-1 and dengue-2 genotypes in Brazil, there has been no evidence of introduction of new genotypes since 1988. The increasing number of dengue hemorrhagic fever cases seen in Brazil in the last years is probably associated with secondary infections or with the introduction of new serotypes but not with the introduction of new genotypes.

Changes in clinical and laboratory findings at the time of diagnosis of primary hyperparathyroidism in a University Hospital in São Paulo from 1985 to 2002

In contrast to most developed countries, most patients with primary hyperparathyroidism in Brazil are still symptomatic at diagnosis. However, we have been observing a change in this pattern, especially in the last few years. We evaluated 104 patients, 77 females and 27 males aged 11-79 years (mean: 54.4 years), diagnosed between 1985 and 2002 at a University Hospital. Diagnosis was made on the basis of clinical findings and of high total and/or ionized calcium levels, high or inappropriate levels of intact parathyroid hormone and of surgical findings in 80 patients. Patients were divided into three groups, i.e., patients diagnosed from 1985 to 1989, patients diagnosed from 1990 to 1994, and patients diagnosed from 1995 to 2002. The number of new cases diagnosed/year increased from 1.8/year in the first group to 6.0/year in the second group and 8.1/year in the third group. The first group comprised 9 patients (mean serum calcium ± SD, 13.6 ± 1.6 mg/dl), 8 of them (88.8%) defined as symptomatic. The second group comprised 30 patients (mean calcium ± SD, 12.2 ± 1.63 mg/dl), 22 of them defined as symptomatic (73.3%). The third group contained 65 patients (mean calcium 11.7 ± 1.1 mg/dl), 34 of them symptomatic (52.3%). Patients from the first group tended to be younger (mean ± SD, 43.0 ± 15 vs 55.1 ± 14.4 and 55.7 ± 17.3 years, respectively) and their mean serum calcium was significantly higher (P < 0.05). All of symptomatic patients independent of group had higher serum calcium levels (12.4 ± 1.53 mg/dl, N = 64) than asymptomatic patients (11.4 ± 1.0 mg/dl, N = 40). Our data showed an increase in the percentage of asymptomatic patients over the years in the number of primary hyperparathyroidism cases diagnosed. This finding may be due to an increased availability of diagnostic methods and/or to an increased awareness about the disease.

From genotype to phenotype : diversity and population structure of Flavobacterium psychrophilum

Flavobacterium psychrophilum is the etiological agent of bacterial cold-water disease (BCWD) causing high fish mortalities and significant economic losses to the freshwater salmonid aquaculture industry around the world. Today BCWD outbreaks are mainly treated with environmentally hazardous antimicrobial agents and alternative preventative measures are urgently needed in order to ensure the well-being of animals and the sustainability of aquaculture. The diversity of pathogenic bacteria challenges the development of universal control strategies and in many cases the pathogen population structure, i.e. the total genetic diversity of the species must be taken into account. This work integrates the tools of modern molecular biology and conventional phenotypic microbiology to gain knowledge about the diversity and population structure of F. psychrophilum. The present work includes genetic characterization of a large collection of isolates collected from diverse origins and years, from aquaculture in a whole region including different countries, and provides the first international validation of a universal multilocus sequence typing (MLST) approach for unambiguous genetic typing of F. psychrophilum. Population structure analyses showed that the global F. psychrophilum population is subdivided into pathogenic species-specific clones, of which one particular genetic lineage, clonal complex CC-ST2, has been responsible for the majority of BCWD outbreaks in rainbow trout (Oncorhynchus mykiss) in European aquaculture facilities over several decades. Genotypic and phenotypic population heterogeneity affecting antimicrobial resistance in F. psychrophilum within BCWD outbreaks was discovered. Specific genotypes were associated with severe infections in farmed rainbow trout and Atlantic salmon (Salmo salar), and in addition to high adherence, antimicrobial resistance was strongly associated with outbreak strains. The study brought additional support for the hypothesis of an epidemic F. psychrophilum population structure, where recombination is an important force for the generation and maintenance of genetic diversity, and a significant contribution towards mapping the genetic diversity of this important fish pathogen. Evidence indicating dissemination of virulent strains with commercial movement of fish and fish products was strengthened.

Gender, race and socioeconomic influence on diagnosis and treatment of thyroid disorders in the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)

Thyroid diseases are common, and use of levothyroxine is increasing worldwide. We investigated the influence of gender, race and socioeconomic status on the diagnosis and treatment of thyroid disorders using data from the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil), a multicenter cohort study of civil servants (35-74 years of age) from six Brazilian cities. Diagnosis of thyroid dysfunction was by thyrotropin (TSH), and free thyroxine (FT4) if TSH was altered, and the use of specific medications. Multivariate logistic regression models were constructed using overt hyperthyroidism/hypothyroidism and levothyroxine use as dependent variables and sociodemographic characteristics as independent variables. The frequencies of overt hyper- and hypothyroidism were 0.7 and 7.4%, respectively. Using whites as the reference ethnicity, brown, and black race were protective for overt hypothyroidism (OR=0.76, 95%CI=0.64-0.89, and OR=0.53, 95%CI=0.43-0.67, respectively, and black race was associated with overt hyperthyroidism (OR=1.82, 95%CI=1.06-3.11). Frequency of hypothyroidism treatment was higher in women, browns, highly educated participants and those with high net family incomes. After multivariate adjustment, levothyroxine use was associated with female gender (OR=6.06, 95%CI=3.19-11.49) and high net family income (OR=3.23, 95%CI=1.02-10.23). Frequency of hyperthyroidism treatment was higher in older than in younger individuals. Sociodemographic factors strongly influenced the diagnosis and treatment of thyroid disorders, including the use of levothyroxine.

Liquidity levels of Finnish SME’s from 2007 to 2013 and a closer analysis of the IC sector

TAVOITTEET: Tämän tutkielman tarkoitus on tarkastella eri toimialojen likviditeettitasoja vuosien 2007 ja 2013 välillä. Se tarkastelee myös kassanhallinnan ja likviditeetin kirjallisuutta, erilaisia likviditeettiä kuvaavia tunnuslukuja sekä asioita, joilla on vaikutusta likviditeettiin. Tämän lisäksi se tutkii informaatio ja kommunikaatio sektoria tarkemmin. DATA: Data on kerätty Orbis tietokannasta. Toimialakohtaiset keskiarvot on laskettu joko kappaleen 2 esittämillä kaavoilla tai noudettu suoraan tietokannasta. Hajonta kuvaajat on tehty Excelillä ja korrelaatio matriisi ja regressioanalyysit SAS EG:llä. TULOKSET: Tämä tutkimus esittää toimialakohtaiset keskiarvot liquidity ratiosta, solvency ratiosta sekä gearingista, kuten monista muista likviditeettiä kuvaavista tai siihen vaikuttavista tunnusluvuista. Tutkimus osoittaa, että keskimäärin likviditeetti ja maksuvalmius ovat säilyneet melko samana, mutta toimialakohtaiset muutokset ovat voimakkaita. IC sektorilla likviditeettiin vaikuttaa katetuotto, työntekijöiden määrä, liikevaihto, taseen määrä sekä maksuaika.

From protest to powerlessness : a Marxist analysis of the Ontario NDP /

Using Marxist state theory as an analytical framework, this thesis explains the problems faced by the Ontario New Democratic Party government (1990-1995) in implementing a social democratic agenda. Not only was the government constrained in its ability to implement progressive policy, but it was also pushed to implement a Social Contract (involving legislated wage cuts to public sector employees) that alienated the party's base of support, making it more difficult for the party to organize in the future. Although this study relies predominantly on a reinterpretation of existing research on the topic, some primary research is used in the analysis, including interviews with members of the labour movement and former MPPs and analysis of the news media's treatment of the party/ government. Historical and class analytical perspectives are used to explain the evolution of the ONDP's structure and policies, as well as to assess the relative strength of the working class and its ability to support a social democratic political agenda. It was found that the ONDP' s unwillingness to develop a long term plan for social democracy, and its inability to act as a mass party or to build a strong working class movement, made it more difficult for the party to succeed when it formed the government. Moreover, the class nature of the capitalist state, along with pressure exerted by a well mobilized capitalist class, worked to limit the government' s options.

Preparing students for the transition from college to work /

The purpose of this study was to examine the perceived preparedness of college students for the transition from college to full-time employment. The study was concerned with the interest and rationale behind developing a required Exit Course for college students in order to improve the college to work transition. As well, possible content of an Exit Course was evaluated. The importance of addressing college to work transitions is highlighted by two phenomena. First, there are specific employability skills that employers in Canada are seeking in newly hired employees. Second, the provincial government in Ontario is determining college funding based on graduate employment statistics which are measured by graduate satisfaction, graduate employment, and employer satisfaction. The research concentrated on the following stakeholders involved in the transition from college to work: (a) current students, (b) recent graduates, (c) support staff who assist students in college to work transition (Career Educators), and (d) employers. Through qualitative research, including focus groups and interviews, these stakeholder groups participated in the research to determine if the Exit Course was a viable solution to facilitate the transition from college to work. Focus groups were conducted with current students, while one-on-one, semi-structured interviews were conducted with recent graduates, Career Educators, and employers. Common themes elicited from the participants included the following: (a) although students were perceived by the participants of this study to be technically prepared for employment, they were perceived to have weak job search skills and unrealistic expectations of the world of work unless they had received the benefits of a Co-operative Education experience; (b) an Exit Course was seen as a viable solution to the issues involved in college to work transition; (c) an Exit Course should be comprised of skills necessary to obtain and succeed in a job and the course should be taught by individuals with extensive qualifications in this area; and (d) there is a need to develop college and business partnerships to ensure that students are connected to employers. Educators within post secondary institutions, specifically colleges, can benefit from the information provided within this study to gain a better understanding of the perceived level of preparedness of students for the transition from college to work. Suggestions with regard to how to improve this transition were made, with specific reference to the addition of an Exit Course as one possible solution.

Gadamer's transformation of hermeneutics : from Dilthey to Heidegger

Abstract: The purpose of this paper is to show how Gadamer's hermeneutics synthesizes the insights of both Heidegger and Dilthey in order to introduce a new hermeneutics. Gadamer's hermeneutics is based not only on the priority of ontology, as Heidegger insists, and neither is it only a product of life which can be objectively understood through study and rigorous method, as Dilthey suggests. For Gadamer, hermeneutics is the bringing together of ontology in terms of history. By this synthesis Gadamer not only places himself within the context of a Lebensphilosophie, but also shows that it is within language that Being can be disclosed according to a lived context. Throughout this paper the philosophies ofDilthey and Heidegger are explicated within a historical context as to bring out how, and why, Gadamer sees the need to surpass these philosophies. Through Gadamer's philosophy of play and the game, language, the dialogical model, application, and the fusion of horizons we can see how Gadamer's critique and questioning of these two philosophy leads to his new hermeneutics. Special attention is paid to the role in which these two contrasting philosophies were used to complement each other in the product of Gadamer' s philosophical hermeneutics as it is presented in his major work Truth andMethod. For Gadamer, the task of understanding is never complete. Therefore, his hermeneutics remains a dynamic structure with which we can always question the past and our traditions. This paper seeks to show his philosophical movements within these questions

The relation of attentional, emotional, and social regulation to cognitive competence, from infancy to school entry

Recent research on the sources of cognitive competence in infancy and early childhood has highlighted the role of social and emotional factors (for example, Lewis, 1993b). Exploring the roots of competence requires a longitudinal and multivariate approach. To deal with the resulting complexity, potentially integrative theoretical constructs are required. One logical candidate is self-regulation. Three key developmental questions were the focus of this investigation. 1) Does infant self-regulation (attentional, emotional, and social) predict preschool cognitive competence? 2) Does infant self-regulation predict preschool self-regulation? 3) Does preschool self-regulation predict concurrent preschool cognitive competence? One hundred preschoolers (46 females, 54 males; mean age = 5 years, 11 months) who had participated at 9- and/ or 12-months of age in an object permanence task were recruited to participate in this longitudinal investigation. Each subject completed four scales of the WPPSI-R and two social cognitive tasks. Parents completed questionnaires about their preschoolers' regulatory behaviours (Achenbach's Child Behavior Checklist [1991] and selected items from Eisenberg et ale [1993] and Derryberry & Rothbart [1988]). Separate behavioural coding systems were developed to capture regulatory capabilities in infancy (from the object permanence task) and preschool (from the WPPSIR Block Design). Overall, correlational and multiple regression results offered strong affirmative answers to the three key questions (R's = .30 to .38), using the behavioural observations of self-regulation. Behavioural regulation at preschool substantially predicted parental reports of regulation, but the latter variables did not predict preschool competence. Infant selfregulation and preschool regulation made statistically independent contributions to competence, even though regulation at Time 1 and Time 2 ii were substantially related. The results are interpreted as supporting a developmental pathway in which well-regulated infants more readily acquire both expertise and more sophisticated regulatory skills. Future research should address the origins of these skills earlier in infancy, and the social contexts that generate them and support them during the intervening years.