Substrate Selectivity and Molecular Adaptation in the Outer Membrane Proteases of Yersinia pestis and Salmonella enterica

Proteolysis is important in bacterial pathogenesis and colonization of animal and plant hosts. In this work I have investigated the functions of the bacterial outer membrane proteases, omptins, of Yersinia pestis and Salmonella enterica. Y. pestis is a zoonotic pathogen that causes plague and has evolved from gastroenteritis-causing Yersinia pseudotuberculosis about 13 000 years ago. S. enterica causes gastroenteritis and typhoid fever in humans. Omptins are transmembrane β-barrels with ten antiparallel β-strands and five surface-exposed loops. The loops are important in substrate recognition, and variation in the loop sequences leads to different substrate selectivities between omptins, which makes omptins an ideal platform to investigate functional adaptation and to alter their polypeptide substrate preferences. The omptins Pla of Y. pestis and PgtE of S. enterica are 75% identical in their amino acid sequences. Pla is a multifunctional protein with proteolytic and non-proteolytic functions, and it increases bacterial penetration and proliferation in the host. Functions of PgtE increase migration of S. enterica in vivo and bacterial survival in mouse macrophages, thus enhancing bacterial spread within the host. Mammalian plasminogen/fibrinolytic system maintains the balance between coagulation and fibrinolysis and participates in several cellular processes, e.g., cell migration and degradation of extracellular matrix proteins. This system consists of activation cascades, which are strictly controlled by several regulators, such as plasminogen activator inhibitor 1 (PAI-1), α2-antiplasmin (α2AP), and thrombin-activatable fibrinolysis inhibitor (TAFI). This work reveals novel interactions of the omptins of Y. pestis and S. enterica with the regulators of the plasminogen/fibrinolytic system: Pla and PgtE inactivate PAI-1 by cleavage at the reactive site peptide bond, and degrade TAFI, preventing its activation to TAFIa. Structure-function relationship studies with Pla showed that threonine 259 of Pla is crucial in plasminogen activation, as it prevents degradation of the plasmin catalytic domain by the omptin and thus maintains plasmin stability. In this work I constructed chimeric proteins between Pla and Epo of Erwinia pyrifoliae that share 78% sequence identity to find out which amino acids and regions in Pla are important for its functions. Epo is neither a plasminogen activator nor an invasin, but it degrades α2AP and PAI-1. Cumulative substitutions towards Pla sequence turned Epo into a Pla-like protein. In addition to threonine 259, loops 3 and 5 are critical in plasminogen activation by Pla. Turning Epo into an invasin required substitution of 31 residues located at the extracellular side of the Epo protein above the lipid bilayer, and also of the β1-strand in the N-terminal transmembrane region of the protein. These studies give an example of how omptins adapt to novel functions that advantage their host bacteria in different ecological niches.

Spectral Tuning and Adaptation to Different Light Environments of Mysid Visual Pigments

In the present thesis, questions of spectral tuning, the relation of spectral and thermal properties of visual pigments, and evolutionary adaptation to different light environments were addressed using a group of small crustaceans of the genus Mysis as a model. The study was based on microspectrophotometric measurements of visual pigment absorbance spectra, electrophysiological measurements of spectral sensitivities of dark-adapted eyes, and sequencing of the opsin gene retrieved through PCR. The spectral properties were related to the spectral transmission of the respective light environments, as well as to the phylogentic histories of the species. The photoactivation energy (Ea) was estimated from temperature effects on spectral sensitivity in the long-wavelength range, and calculations were made for optimal quantum catch and optimal signal-to-noise ratio in the different light environments. The opsin amino acid sequences of spectrally characterized individuals were compared to find candidate residues for spectral tuning. The general purpose was to clarify to what extent and on what time scale adaptive evolution has driven the functional properties of (mysid) visual pigments towards optimal performance in different light environments. An ultimate goal was to find the molecular mechanisms underlying the spectral tuning and to understand the balance between evolutionary adaptation and molecular constraints. The totally consistent segregation of absorption maxima (λmax) into (shorter-wavelength) marine and (longer-wavelength) freshwater populations suggests that truly adaptive evolution is involved in tuning the visual pigment for optimal performance, driven by selection for high absolute visual sensitivity. On the other hand, the similarity in λmax and opsin sequence between several populations of freshwater M. relicta in spectrally different lakes highlights the limits to adaptation set by evolutionary history and time. A strong inverse correlation between Ea and λmax was found among all visual pigments studied in these respects, including those of M. relicta and 10 species of vertebrate pigments, and this was used to infer thermal noise. The conceptual signal-to-noise ratios thus calculated for pigments with different λmax in the Baltic Sea and Lake Pääjärvi light environments supported the notion that spectral adaptation works towards maximizing the signal-to-noise ratio rather than quantum catch as such. Judged by the shape of absorbance spectra, the visual pigments of all populations of M. relicta and M. salemaai used exclusively the A2 chromophore (3, 4-dehydroretinal). A comparison of amino acid substitutions between M. relicta and M. salemaai indicated that mysid shrimps have a small number of readily available tuning sites to shift between a shorter - and a longer -wavelength opsin. However, phylogenetic history seems to have prevented marine M. relicta from converting back to the (presumably) ancestral opsin form, and thus the more recent reinvention of marine spectral sensitivity has been accomplished by some other novel mechanism, yet to be found

Adaptation of the Australian core food groups to enable planning of vegan and lactovegetarian diets

This work demonstrates how the Australian core food groups system can be modified to enable the planning of vegan and lactovegetarian diets as well as omnivorous diets. In the modified version the cereals, vegetables and fruits groups remain the same as in the core food groups system, while the meat group is replaced with legumes, soya products, nuts and seeds. The milk group becomes milk or fortified soya milk, to allow for both lactovegetarian and vegan diets. The core food groups standard of 70% of the recommended dietary intake was adopted as a target for determining recommendations on the minimum number of serves from each food group. As found in the development of the core food groups system, zinc was the most limiting nutrient. Vitamin B 12 and calcium were other limiting nutrients in the vegan and lactovegetarian guides. The number of serves from each group required to meet 70% of the applicable recommended dietary intake has been calculated for children from four years old, adult men and women and pregnant and lactating women. It was found that the number of serves from each food group required in the vegan and lactovegetarian planning guides was in most cases similar to the number of serves of corresponding core food groups specified for a particular population group. This suggests that the vegan and lactovegetarian planning guides could be incorporated into a modified core food groups planning guide. Such a guide would cater for the general omnivorous population as well as for those seeking to avoid meat and/or dairy products. (Aust J Nutr Diet 1999:56:22-30) Key words: vegan, vegetarian, food guide, food groups, dietary planning.

Epithelial sodium channel in airway epithelium of the newborn infant : Implications for postnatal pulmonary adaptation

The aim of the present thesis was to study the role of the epithelial sodium channel (ENaC) in clearance of fetal lung fluid in the newborn infant by measurement of airway epithelial expression of ENaC, of nasal transepithelial potential difference (N-PD), and of lung compliance (LC). In addition, the effect of postnatal dexamethasone on airway epithelial ENaC expression was measured in preterm infants with bronchopulmonary dysplasia (BPD). The patient population was formed of selected term newborn infants born in the Department of Obstetrics (Studies II-IV) and selected preterm newborn infants treated in the neonatal intensive care unit of the Hospital for Children and Adolescents (Studies I and IV) of the Helsinki University Central Hospital in Finland. A small population of preterm infants suffering from BPD was included in Study I. Studies I, III, and IV included airway epithelial measurement of ENaC and in Studies II and III, measurement of N-PD and LC. In Study I, ENaC expression analyses were performed in the Research Institute of the Hospital for Sick Children in Toronto, Ontario, Canada. In the following studies, analyses were performed in the Scientific Laboratory of the Hospital for Children and Adolescents. N-PD and LC measurements were performed at bedside in these hospitals. In term newborn infants, the percentage of amiloride-sensitive N-PD, a surrogate for ENaC activity, measured during the first 4 postnatal hours correlates positively with LC measured 1 to 2 days postnatally. Preterm infants with BPD had, after a therapeutic dose of dexamethasone, higher airway epithelial ENaC expression than before treatment. These patients were subsequently weaned from mechanical ventilation, probably as a result of the clearance of extra fluid from the alveolar spaces. In addition, we found that in preterm infants ENaC expression increases with gestational age (GA). In preterm infants, ENaC expression in the airway epithelium was lower than in term newborn infants. During the early postnatal period in those born both preterm and term airway epithelial βENaC expression decreased significantly. Term newborn infants delivered vaginally had a significantly smaller airway epithelial expression of αENaC after the first postnatal day than did those delivered by cesarean section. The functional studies showed no difference in N-PD between infants delivered vaginally and by cesarean section. We therefore conclude that the low airway epithelial expression of ENaC in the preterm infant and the correlation of N-PD with LC in the term infant indicate a role for ENaC in the pathogenesis of perinatal pulmonary adaptation and neonatal respiratory distress. Because dexamethasone raised ENaC expression in preterm infants with BPD, and infants were subsequently weaned from ventilator therapy, we suggest that studies on the treatment of respiratory distress in the preterm infant should include the induction of ENaC activity.

Planning for climate change adaptation in a neoliberal context: Influences and responses

This thesis explores how planning policy and practice is responding to the challenge of climate change, particularly in contexts where neoliberal rationales and practices frame decision making. It documents patterns of devolving government responsibilities and experiences of market based mechanisms before reporting on institutional and professional responses to these conditions. The research centred on a qualitative case study and involved thematic content analysis of policy documents and informant interviews. The contribution of the research and thesis is to establish the outlook for climate change adaptation under neoliberal conditions, and to introduce strategies for planners operating within these conditions.

Growing Up Vietnamese in Finland - Looking Back 12 Years Later : The Well-Being and Sociocultural Adaptation of Vietnamese as Children or Adolescents and as Young Adults

Varttuminen vietnamilaisena Suomessa: 12 vuoden seurantajakso – Vietnamilaisten hyvinvointi ja sosiokulttuurinen sopeutuminen lapsena/nuorena sekä nuorena aikuisena Tämä tutkimus oli määrällinen pitkittäistutkimus lapsena tai nuorena vuosina 1979-1991 Suomeen saapuneiden vietnamilaisten akkulturaatiosta (kulttuurin muutoksista), psyykkisestä hyvinvoinnista ja sosiokulttuurisesta sopeutumisesta. Tutkimukseen osallistui ensimmäisessä vaiheessa (vuonna 1992) 97 satunnaisesti valittua vietnamilaista peruskoululaista ympäri maata, joita verrattin suomalaisiin luokkatovereihin. Seurantavaiheeseen (vuonna 2004) osallistui 59 ensimmäisessä vaiheessa mukana ollutta vietnamilaista, nyt iältään 20 – 31 -vuotiaita. Tutkimuksen tavoitteena oli selvittää mitkä tekijät ennustivat akkulturaation lopputuloksia, samalla huomioiden iän ja ympäristön (kontekstin) vaikutukset psyykkiseen hyvinvointiin ja sosiokulttuuriseen sopeutumiseen. Yksittäiset akkulturaatiodimensiot (kieli, arvot ja identiteetti) osoittautuivat tärkeämmiksi psyykkiselle hyvinvoinnille ja sosiokulttuuriselle sopeutumiselle kuin etniset, kansalliset tai kaksikulttuuriset profiilit, joissa yhdistyivät ao. kieli, arvot ja identiteetti. Identiteettimuutosta tapahtui (etniseen) vietnamilaiseen suuntaan ajan kuluessa, kun taas arvomuutosta tapahtui (kansalliseen) suomalaiseen suuntaan. Sekä suomen että vietnamin kielen taito lisääntyivät ajan myötä, millä oli myönteisiä vaikutuksia sekä psyykkiseen hyvinvointiin että sosiokulttuuriseen sopeutumiseen. Lähtötilanteen psyykkinen hyvinvointi ennusti hyvinvointia (masennuksen puutetta ja itsetuntoa) aikuisena, mutta sosiokulttuurinen sopeutuminen (koulumenestys) lapsena tai nuorena ei ennustanut kouluttautumista aikuisena. Parempi suomen kielen taito ja vähemmän identifioitumista suomalaiseksi aikuisena sekä masentuneisuuden puute ja vähemmän koettua syrjintää lapsena tai nuorena erottelivat psyykkisesti paremmin voivat aikuiset (ei-masentuneet) heistä, jotka olivat masentuneita. Parempaa kouluttautumista aikuisena ennustivat toisaalta vähemmän koettua syrjintää lapsena tai nuorena ja toisaalta aikuisena parempi suomen kielen taito, suurempi kansallisten (suomalaisten) itsenäisyysarvojen kannattaminen, mutta kuitenkin vähemmän identifioitumista suomalaisiin. Koetun syrjinnän merkitys psyykkiselle hyvinvoinnille, erityisesti lapsena tai nuorena, sekä sen pitkäaikaisvaikutukset psyykkiselle hyvinvoinnille ja sosiokulttuuriselle sopeutumiselle aikuisena osoittavat tarpeen puuttua varhain psyykkisiin ongelmiin sekä parantaa etnisten ryhmien välisiä suhteita. Avainsanat: akkulturaatio, psyykkinen hyvinvointi, sosiokultuurinen sopeutuminen, kieli, arvot, identiteetti, vietnamilainen, Suomi, lapset, nuoret, nuoret aikuiset

The Art of Adaptation : A study on the Europeanization of Finland's foreign and security policy

This study examines how Finnish foreign and security policy has been influenced by the European Union and its Common Foreign and Security Policy. It points to a growing interplay and misfit between the external expectations originating from the European level and the domestic expectations and traditional ways-of-doing-things. It is concluded that the deepening European integration in the sphere of foreign, security and defence policy has played a significant role in a number of transformations in the Finnish policies since 1995. New, more European, meanings have been attached to the key concepts of Finnish foreign and security policy. Neutrality and traditional peacekeeping have been replaced by a minimalist reading of military non-alignment and participation in crisis management operations and EU battle groups. Traditional small state identity has been recast more and more as small member stateness . At the same time Finland has entered an era of post-consensus in national foreign and security policy. A key theoretical argument in the background of the study is that collective understandings attached to European policies, when not resonating well with domestic understandings, cause adaptation pressures on domestic-level processes and may lead to changes in the way interests and identities are constructed. This means that Europeanization is principally seen as identity reconstruction. Consequently, the theoretical framework of the study builds on the Europeanization research literature and constructivist IR theory on state identity. Foreign and security policy is defined as the practice in which state identity is reproduced, and the key foreign and security policy concepts are seen as the vehicles of identity production. It is concluded that for Finland, participation in the EU s foreign, security and defence policies represents not only a tool for responding to the changes in the international security environment but also a new means of self-identification. Concerning the Finnish attempts of projecting national interests on the European security policy agenda, it is concluded that they mainly relate to the compatibility of the potential development of EU s defence dimension with the Finnish military non-alignment. Although neutrality was cast aside in the official security policy when Finland joined the EU, the analysis shows that its impact has continued in the domestic political debate and in the mind-set of the decision-makers. The primary research material includes official Finnish foreign and security policy documentation and the related parliamentary debates from 1994 to 2007. This study serves also as a comprehensive empirical overview on Finland s reactions and contributions to the EU Common Foreign and Security Policy.

Adaptation in a Business Network Cooperation Context (summary section only)

In today’s business one can say that competition does not take place inside the network, but between networks. Change and dynamics are central issues in network studies, and a company, due its changing environment, can identify opportunities and threats and respond to them accordingly. These opportunities are vital, but also complex and demanding for the management. Earlier research has identified a shortcoming in explanations of how the micro-level interactions to macro-level patterns are connected. The IMP-group has been trying to fill this research gap with research on interactions within business networks. In this area of research lies the focus of research on relationships between organizations. Adaptation in cooperation is a central concept within business network research. Adaptation has been dealt with in previous literature, but the focus of the studies has mainly been outside this phenomenon, and it has mostly had a supporting role. Most literature has also described the buyers' point of view in studied supply networks, whereas much less attention has been paid to the suppliers' view on them. This study focuses on this research gap. The results of the study stress that adaptation should be included to a greater extent in the strategy work of companies. The adaptations should be carefully planned and, as far as possible, made consciously. Conscious, well-planned adaptations can be seen as investments into present and future relationships, and resources should be invested into something that does not increase the company’s dependence, but divides the power in the relationship between the companies. Adaptations should be planned so that they result in a more offensive way of responding to the demands that are placed upon the companies. In this way, the actions can be viewed and analyzed in accordance with whether the actions make the company weaker or stronger.

Adaptation in triadic business relationship settings: A study in corporate travel management

ANNE HOLMA ADAPTATION IN TRIADIC BUSINESS RELATIONSHIP SETTINGS – A STUDY IN CORPORATE TRAVEL MANAGEMENT Business-to-business relationships form complicated networks that function in an increasingly dynamic business environment. This study addresses the complexity of business relationships, both when it comes to the core phenomenon under investigation, adaptation, and the structural context of the research, a triadic relationship setting. In business research, adaptation is generally regarded as a dyadic phenomenon, even though it is well recognised that dyads do not exist isolated from the wider network. The triadic approach to business relationships is especially relevant in cases where an intermediary is involved, and where all three actors are directly connected with each other. However, only a few business studies apply the triadic approach. In this study, the three dyadic relationships in triadic relationship settings are investigated in the context of the other two dyads to which each is connected. The focus is on the triads as such, and on the connections between its actors. Theoretically, the study takes its stand in relationship marketing. The study integrates theories and concepts from two approaches, the industrial network approach by the Industrial marketing and purchasing group, and the Service marketing and management approach by the Nordic School. Sociological theories are used to understand the triadic relationship setting. The empirical context of the study is corporate travel management. The study is a retrospective case study, where the data is collected by in-depth interviews with key informants from an industrial enterprise and its travel agency and service supplier partners. The main theoretical contribution of the study concerns opening a new research area in relationship marketing by investigating adaptation in business relationships with a new perspective, and in a new context. This study provides a comprehensive framework to analyse adaptation in triadic business relationship settings. The analysis framework was created with the help of a systematic combining approach, which is based on abductive logic and continuous iteration between the theory and the case study results. The framework describes how adaptations initiate, and how they progress. The framework also takes into account how adaptations spread in triadic relationship settings, i.e. how adaptations attain all three actors of the triad. Furthermore, the framework helps to investigate the outcomes of the adaptations for individual firms, for dyadic relationships, and for the triads. The study also provides concepts and classification that can be used when evaluating adaptation and relationship development in both dyadic and triadic relationships.

Forest governance and climate change adaptation : Case studies of four African countries

Africa is threatened by climate change. The adaptive capacity of local communities continues to be weakened by ineffective and inefficient livelihood strategies and inappropriate development interventions. One of the greatest challenges for climate change adaptation in Africa is related to the governance of natural resources used by vulnerable poor groups as assets for adaptation. Practical and good governance activities for adaptation in Africa is urgently and much needed to support adaptation actions, interventions and planning. The adaptation role of forests has not been as prominent in the international discourse and actions as their mitigation role. This study therefore focused on the forest as one of the natural resources used for adaptation. The general objective of this research was to assess the extent to which cases of current forest governance practices in four African countries Burkina Faso, The Democratic Republic of Congo (DRC), Ghana and Sudan are supportive to the adaptation of vulnerable societies and ecosystems to impacts of climate change. Qualitative and quantitative analyses from surveys, expert consultations and group discussions were used in analysing the case studies. The entire research was guided by three conceptual sets of thinking forest governance, climate change vulnerability and ecosystem services. Data for the research were collected from selected ongoing forestry activities and programmes. The study mainly dealt with forest management policies and practices that can improve the adaptation of forest ecosystems (Study I) and the adaptive capacity through the management of forest resources by vulnerable farmers (Studies II, III, IV and V). It was found that adaptation is not part of current forest policies, but, instead, policies contain elements of risk management practices, which are also relevant to the adaptation of forest ecosystems. These practices include, among others, the management of forest fires, forest genetic resources, non-timber resources and silvicultural practices. Better livelihood opportunities emerged as the priority for the farmers. These vulnerable farmers had different forms of forest management. They have a wide range of experience and practical knowledge relevant to ensure and achieve livelihood improvement alongside sustainable management and good governance of natural resources. The contributions of traded non-timber forest products to climate change adaptation appear limited for local communities, based on their distribution among the stakeholders in the market chain. Plantation (agro)forestry, if well implemented and managed by communities, has a high potential in reducing socio-ecological vulnerability by increasing the food production and restocking degraded forest lands. Integration of legal arrangements with continuous monitoring, evaluation and improvement may drive this activity to support short, medium and long term expectations related to adaptation processes. The study concludes that effective forest governance initiatives led by vulnerable poor groups represent one practical way to improve the adaptive capacities of socio-ecological systems against the impacts of climate change in Africa.

Evil Gods and Reckless Saviours : Adaptation and Appropriation in Late Twentieth Century Jesus-Novels

Late twentieth century Jesus-novels search after a completely new picture of Jesus. Novels written for instance by Norman Mailer, José Saramago, Michèle Roberts, Marianne Fredriksson, and Ki Longfellow provide an inversive revision of the canonic Gospels. They read the New Testament in terms of the present age. In their adaptation the story turns often into a critique of the whole Christian history. The investigated contrast-novels end up with an appropriation that is based on prototypical rewriting. They aim at the rehabilitation of Judas, and some of them make Mary Magdalane the key figure of Christianity. Saramago describes God as a blood thirsty tyrant, and Mailer makes God combat with the Devil in a manichean sense as with an equal. Such ideas are familiar both from poststructuralist philosophy and post-metaphysical death-of-God theology. The main result of the intertextual analysis is that these scholars have adopted Nietzschean ideas in their writing. Quite unlike earlier Jesus-novels, these more recent novels present a revision that produces discontinuity with the original source text, the New Testament. The intertextual strategy is based on contradiction. The reader wittnesses contesting and challenging, the authors attack Biblical beliefs and attempt to dissolve Christian doctrines. An attack on Biblical slave morality and violent concept of God deprives Jesus of his Jewish Messianic identity, makes Old Testament law a contradiction of life, calls sacrificial soteriology a violent pattern supporting oppression, and presents God as a cruel monster who enslaves people under his commandments and wishes their death. The new Jesus-figure contests Mosaic Law, despises orthodox Judaism, abandons Jewish customs and even questions Old Testament monotheism. In result, the novels intentionally transfer Jesus out of Judaism. Furthermore, Jewish faith appears in a negative light. Such an intertextual move is not open anti-Semitism but it cannot avoid attacking Jewish worship. Why? One reason that explains these attitudes is that Western culture still carries anti-Judaic attitudes beneath the surface covered with sentiments of equality and tolerance. Despite the evident post-holocaust consciousness present in the novels, they actually adopt an arrogant and ironical refutation of Jewish beliefs and Old Testament faith. In these novels, Jesus is made a complete opposite and antithesis to Judaism. Key words: Jesus-novel, intertextuality, adaptation, slave morality, Nietzsche, theodicy, patriarchy.

Climatic adaptation of Norway spruce (Picea abies (L.) Karsten) in Finland based on male flowering phenology.

Anthesis was studied at the canopy level in 10 Norway spruce stands from 9 localities in Finland from 1963 to 1974. Distributions of pollen catches were compared to the normal Gaussian distribution. The basis for the timing studies was the 50 per cent point of the anthesis-fitted normal distribution. Development up to this point was given in calendar days, in degree days (>5 °C) and in period units. The count of each parameter began on March 19 (included). Male flowering in Norway spruce stands was found to have more annual variation in quantity than in Scots pine stands studied earlier. Anthesis in spruce in northern Finland occurred at a later date than in the south. The heat sums needed for anthesis varied latitudinally less in spruce than in pine. The variation of pollen catches in spruce increased towards north-west as in the case of Scots pine. In the unprocessed data, calendar days were found to be the most accurate forecast of anthesis in Norway spruce both for a single year and for the majority of cases of stand averages over several years. Locally, the period unit could be a more accurate parameter for the stand average. However, on a calendar day basis, when annual deviations between expected and measured heat sums were converted to days, period units were narrowly superior to days. The geographical correlations respect to timing of flowering, calculated against distances measured along simulated post-glacial migration routes, were stronger than purely latitudinal correlations. Effects of the reinvasion of Norway spruce into Finland are thus still visible in spruce populations just as they were in Scots pine populations. The proportion of the average annual heat sum needed for spruce anthesis grew rapidly north of a latitude of ca. 63° and the heat sum needed for anthesis decreased only slighty towards the timberline. In light of flowering phenology, it seems probable that the northwesterly third of Finnish Norway spruce populations are incompletely adapted to the prevailing cold climate. A moderate warming of the climate would therefore be beneficial for Norway spruce. This accords roughly with the adaptive situation in Scots pine.