Cross-layer Assisted TCP Algorithms for Vertical Handoff

The ever expanding growth of the wireless access to the Internet in recent years has led to the proliferation of wireless and mobile devices to connect to the Internet. This has created the possibility of mobile devices equipped with multiple radio interfaces to connect to the Internet using any of several wireless access network technologies such as GPRS, WLAN and WiMAX in order to get the connectivity best suited for the application. These access networks are highly heterogeneous and they vary widely in their characteristics such as bandwidth, propagation delay and geographical coverage. The mechanism by which a mobile device switches between these access networks during an ongoing connection is referred to as vertical handoff and it often results in an abrupt and significant change in the access link characteristics. The most common Internet applications such as Web browsing and e-mail make use of the Transmission Control Protocol (TCP) as their transport protocol and the behaviour of TCP depends on the end-to-end path characteristics such as bandwidth and round-trip time (RTT). As the wireless access link is most likely the bottleneck of a TCP end-to-end path, the abrupt changes in the link characteristics due to a vertical handoff may affect TCP behaviour adversely degrading the performance of the application. The focus of this thesis is to study the effect of a vertical handoff on TCP behaviour and to propose algorithms that improve the handoff behaviour of TCP using cross-layer information about the changes in the access link characteristics. We begin this study by identifying the various problems of TCP due to a vertical handoff based on extensive simulation experiments. We use this study as a basis to develop cross-layer assisted TCP algorithms in handoff scenarios involving GPRS and WLAN access networks. We then extend the scope of the study by developing cross-layer assisted TCP algorithms in a broader context applicable to a wide range of bandwidth and delay changes during a handoff. And finally, the algorithms developed here are shown to be easily extendable to the multiple-TCP flow scenario. We evaluate the proposed algorithms by comparison with standard TCP (TCP SACK) and show that the proposed algorithms are effective in improving TCP behavior in vertical handoff involving a wide range of bandwidth and delay of the access networks. Our algorithms are easy to implement in real systems and they involve modifications to the TCP sender algorithm only. The proposed algorithms are conservative in nature and they do not adversely affect the performance of TCP in the absence of cross-layer information.

Paradise Reconsidered : A Study of the Ophite Myth and Ritual and their Relationship to Sethianism

This thesis examines the mythology in and social reality behind a group of texts from the Nag Hammadi and related literature, to which certain leaders of the early church attached the label, Ophite, i.e., snake people. In the mythology, which essentially draws upon and rewrites the Genesis paradise story, the snake's advice to eat from the tree of knowledge is positive, the creator and his angels are demonic beasts and the true godhead is depicted as an androgynous heavenly projection of Adam and Eve. It will be argued that this unique mythology is attested in certain Coptic texts from the Nag Hammadi and Berlin 8502 Codices (On the Origin of the World, Hypostasis of the Archons, Apocryphon of John, Eugnostos, Sophia of Jesus Christ), as well as in reports by Irenaeus (Adversus Haereses 1.30), Origen (Contra Celsum 6.24-38) and Epiphanius (Panarion 26). It will also be argued that this so-called Ophite evidence is essential for a proper understanding of Sethian Gnosticism, often today considered one of the earliest forms of Gnosticism; there seems to have occurred a Sethianization of Ophite mythology. I propose that we replace the current Sethian Gnostic category by a new one that not only adds texts that draw upon the Ophite mythology alongside these Sethian texts, but also arranges the material in smaller typological units. I also propose we rename this remodelled and expanded Sethian corpus "Classic Gnostic." I have divided the thesis into four parts: (I) Introduction; (II) Myth and Innovation; (III) Ritual; and (IV) Conclusion. In Part I, the sources and previous research on Ophites and Sethians will be examined, and the new Classic Gnostic category will be introduced to provide a framework for the study of the Ophite evidence. Chapters in Part II explore key themes in the mythology of our texts, first by text comparison (to show that certain texts represent the Ophite mythology and that this mythology is different from Sethianism), and then by attempting to unveil social circumstances that may have given rise to such myths. Part III assesses heresiological claims of Ophite rituals, and Part IV is the conclusion.

Pimeä hehku : Satanismi ja saatananpalvonta 1990-luvun suomalaisessa nuorisokulttuurissa

Satanism in the Finnish Youth Culture of the 1990s The aim of this study was to investigate Satanism among Finnish youth in the 1990s. Thematic interviews of young Finnish Satanists are the basic material of this study. The research employs a theoretical framework derived from narrative psychology and the role-theoretical thinking of Dan P. McAdams. The young Satanists in Finland have been divided into two different groups: the criminal and drug using "devil-worshipping gangs"; and the more educated and philosophically oriented "Satanists" (Heino 1993). What can we say about this division? In the 1990s around Finland, there were young people calling themselves as devil- worshippers (either singular or in groups). They were strongly committed to a mythical devilish and cosmic battle, which they believed was going on in this world. They had problems with their mental health, also in their family socialization and peer groups. In their personal attitudes they were either active fighters or passive tramps. There were also rationally oriented young Satanists, that were ritually active and mainly atheistic. They strongly expressed their personal experiences of being individual and of being different than others. In their personal attitudes they were critical fighters and active survivors. They saw their lives through the satanistic 'finding-oneself experience'. They understood themselves as a "postmodern tribe" (Michel Maffesoli's sosiocultural concept): their sense of themselves was that of a dynamic collectivity which is social, dynamic, nonlocal and mythically historical. Death and black metal culture in the 1990s formed a common space for youth culture, where young individuals could work out their feelings and express their attitudes to life using dark satanic themes and symbols. The sense of "otherness" (also other than satanic) and collective demands for authenticity were essential tools that were used for identity work here. Personal disengagement from satanic/satanistic groups were observed to be gradual or quite rapid. Religious conversions back-and-forth also accured. At the end of the 1990s all off satanism in Finland bore a negative devil-worshipping stigma. Ritual homicide in South-Finland (Kerava/Hyvinkää) was connected to Satanism, which then became unpopular both in the personal life stories and alternative youth cultural circles at the beginning of the 2000s.

Efraim Syyrialaisen luostari: Tapausesimerkkejä munkkien luostariin vetäytymisen syistä

Tutkielma on kaksivaiheinen. Ensin esittelen apostolisen, Syyrialaisortodoksisen kirkon historiaa ja luostariperinnettä. Toisen osan tarkoitus on selvittää, liittyykö Pyhän Efraim Syyrialaisen luostarin munkkien luostariinjäämispäätökseen yhteiskunnallisia syitä ja mitä muita mahdollisia syitä voidaan löytää. Vertailen lopuksi varhaisia, 400-luvulla eläneiden kilvoittelijoiden Pyhän Efraim Syyrialaisen, Antonius Suuren ja Simeon Pylväspyhimyksen motiiveita nykykilvoittelijoiden motiiveihin, sikäli kuin se on mahdollista. Selvitän myös, onko Efraim Syyrialaisen esimerkillä ollut merkitystä nykykilvoittelijoille. Empiirinen aineisto kerättiin kahtena vuotena v. 2002 ja 2003. Tutkielmaa varten haastattelin kolmea Efraim Syyrialaisen luostarin munkkia. Pääinformanttini oli ko. luostarin seminaarin teologiopiskelija. Heidän kotitaustansa on syyrialaisortodoksinen, voimakkaasti uskonnollinen. Spiritualiteettia harjoitettiin jo lapsuudessa sekä kotona että kirkossa. Tutkielmani näkökulma on uskontohistoriallinen ja uskontososiologinen. Tutkin miten varhaiset- sekä nykypäivän kilvoittelijat ovat suhtautuneet yhteiskuntaan ja miten he ovat integroituneet luostariinsa. Kysymyksessä on nykypäivän osalta laadullinen tapaustutkimus, jonka metodeina ovat teemahaastattelu, jonka yhtenä osana olivat argumentit ja osallistruva havainnointi. Analysoin vastaukset sisällön analyysiä käyttäen. Haastatellut munkit korostivat syyrian kielen ja tradition opiskelun ja sen siirtämisen tärkeyttä seminaariin opiskelemaan hakeutumisensa, ja sen jälkeen munkiksi jäämisensä perusteluna. Pyhän Efraim Syyrialaisen esimerkin munkit kokivat olevan heille hyvin tärkeän tradition siirtäjän. Opiskelemisen ja matkustamisen mahdollisuus munkkina koettiin myös tärkeänä ja siitä syystä luostariin jäätiin, eli yhteiskunnallinen syy löytyi. Sisällön analyysissä ilmeni, että alkujaan koti edusti munkille primaarista tekijää. Sekundääristä tekijää edustivat kirkkoon kuuluva ryhmä, munkit ja luostari. Kodin ja kirkossa käynnin seurauksena tradition ja syyrian kielen oppimisen halu korostui ja niitä haluttiin lähteä opiskelemaan. Positiiviseksi viiteryhmäksi tällöin muodostuivat seminaariopiskelun aikana munkit ja muut luostarin asukkaat. Luostariin jäämisensä jälkeen primaarin tekijän voidaan huomata vaihtuneen luostariksi ja kodin asema on jäänyt sekundaariseksi. Yhteys luostarin ja ympäröivän yhteiskunnan kanssa tapahtui varhaisena aikana pääasiallisesti siten, että ihmiset tulivat kilvoittelijan luokse. Nykymunkit puolestaan käyvät niiden seurakuntalaisten kotona, jotka eivät pääse yhteisiin jumalanpalveluksiin ja auttavat heitä sielunhoidollisesti ja tarvittaessa taloudellisesti. Kirkon patriarkka Mar Ignatios Zakka I Iwasilla ja metropoliitta Eusthatios Matta Rohamilla on paljon yhteyksiä myös islaminuskoiseen väestönosaa Syyriassa. Ekumeenisia yhteyksiä on munkeillakin runsaasti. Ne mahdollistuvat erilaisissa kirkon kokouksissa ja konferensseissa sekä opiskelupaikkakunnalla Kreikassa.

Kohtaamisia Santiagon tiellä pyhiinvaellus matkana ja spirituaalisena kokemuksena

Pyhiinvaellustutkimuksen tavoitteena on kuvata, analysoida ja ymmärtää pyhiinvaeltajien kokemuksia ja erityisesti spirituaalisia tai sellaisiksi tulkittuja kokemuksia. Tutkimuskysymys voidaan muotoilla myös kysymällä, missä on vaeltajien mahdollisesti kokema pyhiinvaelluksen pyhä . Pyhiinvaellus suuntautuu Santiago de Compostelan kaupunkiin. Kuvattu pyhiinvaellusreitti alkaa Ranskan ja Espanjan rajalta ja kulkee Espanjan luoteiskulmassa noin 800 kilometrin päässä olevaan määränpäähän. Tutkimuksen aineistona on sähköpostikyselyn vastaukset, jotka on saatu kahdeltakymmeneltäkahdelta keväällä 2006 Santiagoon jalkaisin vaeltaneilta pyhiinvaeltajilta. Tutkimusaineistona ovat myös tutkijan omat havainnot ko. pyhiinvaellukselta. Tutkijan havainnoista on kirjoitettu kuvaus Santiagon tien pyhiinvaelluksesta ja matkan arkisista käytännöistä. Sähköpostikyselyn vastaukset, vaeltajien spirituaaliset kokemukset, on analysoitu laadullista sisällön analysointia käyttäen. Kuudesta vastauksesta on kirjoitettu myös pyhiinvaeltajan henkilökohtainen tarina. Narratiivisuus, kerronnallisuus, on tässä tutkimuksessa yksi tapa esittää, kuvata ja ymmärtää tutkimustuloksia. Tutkimus on liitetty fenomenologiseen viitekehykseen. Spirituaalisia kokemuksia on lähestytty mm. pyhiinvaellustradition, pyhän käsitteen ja uskonnollisten kokemusten näkökulmasta. Spiritualiteetin käsitettä ja spirituaalisen kokemuksen kuvaamisen mahdollisuuksia on myös pohdittu tutkimuksessa. Pyhiinvaelluksen spirituaaliset kokemukset on tutkimusraportissa jaoteltu seitsemään ryhmään: kävely, ihmiset, vapaus, luonto, rukous, kirkot ja Santiago. Lisäksi on esitetty matkaan lähdön motiiveja sekä pyhiinvaelluksen vaikutuksia elämässä. Käveleminen oli pyhiinvaelluksen ydinkokemus. Käveleminen mahdollisti meditaation tai rukoilemisen. Se aiheutti myös kärsimystä ja oli keskeinen ihmisiä yhdistävä teema. Pyhiinvaellus irrotti ihmiset erittäin hyvin arjen rutiineista ja jokapäiväisestä normaalista elämästä. Pyhiinvaelluksella vapauden tunne olikin merkittävä spirituaalinen kokemus ja ajan käsitys saattoi saa uuden ulottuvuuden. Luonto näyttäytyi merkittävänä spirituaalisen innoituksen lähteenä ja usein myös yksinolon paikkana. Kaikki pyhiinvaeltajat vierailivat kirkoissa ja katedraaleissa ja useimmat myös messuissa ja pyhiinvaeltajille järjestetyissä rukoushetkissä. Pyhiinvaelluksen uskonnollinen ulottuvuus oli kaikille läsnä myös Santiagon messussa. Kristillinen tulkintakehys kokemuksille oli koko ajan pyhiinvaeltajalle tarjolla. Kuitenkaan Santiagon vaellukseen ei välttämättä liittynyt mitään omaa spirituaalista kokemusta. Pyhiinvaelluksen merkittävät spirituaaliset kokemukset liittyivät yhteisöllisyyteen ja jaettuihin kokemuksiin. Tyypillinen moderni pyhiinvaeltaja etsi itseään pyhiinvaelluksella. Yllätyksekseen hän saattoi löytää jotain silloin kun hän antautui avoimeen vuorovaikutukseen toisten ihmisten kanssa. Lähes kaikki tutkimuksen osallistuneet pyhiinvaeltajat pitivät hyvin tärkeänä toisia pyhiinvaeltajia ja sitä, mitä he saivat toisilta ihmisiltä. Pyhiinvaellusta leimaa poikkeuksellisen avoin vuorovaikutus ja elämän jakaminen. Pyhiinvaellukseen liittyy monia individualistisia piirteitä. Spirituaalisten kokemusten näkökulmasta individualismi ei kuitenkaan saa tukea tutkimuksesta, koska yhteisöllisyys näyttää niin merkittävältä spirituaalisten kokemusten kannalta. Pyhiinvaelluksen yhteisöllisyys on avointa, vapaaehtoista ja usein myös hetkellistä. Moderni pyhiinvaeltaja näyttää uskovan enemmän omiin kokemuksiinsa ja myös toisten kokemuksiin kuin minkään kirkon opilliseen auktoriteettiin.

Psykoottisen mielenterveyspotilaan uskonnonvapaus

Tämän tutkimuksen tarkoituksena on selvittää psykoottisen mielenterveyspotilaan uskonnonvapautta. Tutkimuskysymyksiä on kolme: Millä perusteilla psykoottisen potilaan uskonnonvapaus on turvattu ja millä perusteilla sitä rajoitetaan? Miten psykoottinen ja uskonnollinen todellisuudentulkinta eroavat toisistaan? Vaarantaako psykiatriseen todellisuudentulkintaan perustuva hoito potilaan negatiivisen uskonnonvapauden eli oikeuden elää ilman uskontoa? Tutkimusmetodina on systemaattinen analyysi. Lähteet ovat perustusoikeudet, mielenterveyslaki, potilaslaki, YK:n Principles for the protection of persons with mental illness and the improvement of mental health care, Maailman psykiatriyhdistyksen Madridin julistus ja Suomen mielenterveysseuran Mielenterveyspotilaan oikeudet. Uskonnonvapautta tarkastellaan tässä tutkimuksessa kahden eri vapauskäsityksen näkökulmasta: ulkoisena vapautena, joka edellyttää kompetenssia ja autenttisuutta, sekä ulkoisen ja sisäisen vapauden summana, johon kompetenssi ja autenttisuus sisältyvät. Psykoottisella potilaalla on ihmisyytensä ja kansalaisuutensa perusteella lähtökohtaisesti täysi uskonnonvapaus, mutta sitä voidaan rajoittaa. Jos uskonnonvapaus ymmärretään ulkoiseksi vapaudeksi, rajoittaa psykoottisen potilaan uskonnonvapautta tahdosta riippumattomassa hoidossa hänen terveytensä ja turvallisuutensa suojaaminen. Uskonnonvapauden rajoittaminen voidaan perustella sillä, ettei psykoottinen potilas täytä uskonnonvapauden edellytyksiä eli kompetenssia ja autenttisuutta, sillä, että potilaan terveyteen ja turvallisuuteen liittyvät oikeudet priorisoidaan uskonnonvapauden yläpuolelle sekä sillä, että pyritään terveyshyötyyn. Jos uskonnonvapaus ymmärretään ulkoisen ja sisäisen vapauden summaksi, on psykoosi uskonnonvapautta rajoittava tekijä, koska se tekee yksilöstä epäautenttisen ja puuttuu hänen kompetenssiinsa. Psykoosin (myös tahdosta riippumaton) hoito voidaan ymmärtää tällöin yritykseksi palauttaa uskonnonvapaus. Rajoittamalla ulkoista uskonnonvapautta pyritään maksimoimaan ulkoisen ja sisäisen uskonnonvapauden summa. Vaikka psykoottisella ja uskonnollisella todellisuudentulkinnalla on yhtäläisyyksiä, niiden toisistaan erottaminen on tärkeää, koska yksilöllä, jonka todellisuudentulkinta määritellään psykoottiseksi, on oikeus saada hoitoa, kun taas yksilön uskonnollista todellisuudentulkintaa suojaa uskonnonvapaus eikä sitä saa hoitaa sairautena. Lähteiden mukaan psykoottisen ja uskonnollisen todellisuudentulkinnan toisistaan erottaminen diagnostisten kriteerien ja lääketieteellisen tiedon avulla on lääkärin tehtävä. Tutkimuksessani esitän kaksi periaatetta, joiden avulla todellisuudentulkinnat voidaan erottaa toisistaan. Yksinäinen puu ei pala -periaatteen mukaan yksilön todellisuudentulkinta on uskonnollinen, mikäli se jaetaan jossain yhteisössä. Hedelmistään puu tunnetaan -periaatteen mukaan yksilön todellisuudentulkinta on uskonnollinen, mikäli sen terveydelliset ja sosiaaliset seuraukset ovat hyvät. Antipsykiatrinen kritiikki väittää psykiatrian olevan uskonto. Jos väite on tosi, puututaan tahdosta riippumattomassa hoidossa yksilön oikeuteen elää ilman uskontoa, sillä ko. hoidossa olevan psykoottisen potilaan on pakko suostua siihen, että häntä hoidetaan psykiatrian arvojen ja todellisuudentulkinnan mukaan. Vaikuttaa kuitenkin siltä, että jos psykiatria määritellään uskonnoksi, uskonnon käsite kärsii inflaation. Koska psykoottisen potilaan uskonnonvapaus on pohjimmiltaan eettinen kysymys, on tärkeää myöntää psykiatrian arvosidonnaisuus. Tällöin voidaan tehdä tietoisesti moraalisia päätöksiä ja kantaa moraalinen vastuu esimerkiksi diagnoosin määrittelyssä. Psykiatrian voidaan katsoa perustuvan universaaleihin arvoihin samalla tavalla kuin ihmisoikeuksienkin.

Efraim Syyrialaisen luostari: Tapausesimerkkejä munkkien luostariin vetäytymisen syistä

Tutkielma on kaksivaiheinen. Ensin esittelen apostolisen, Syyrialaisortodoksisen kirkon historiaa ja luostariperinnettä. Toisen osan tarkoitus on selvittää, liittyykö Pyhän Efraim Syyrialaisen luostarin munkkien luostariinjäämispäätökseen yhteiskunnallisia syitä ja mitä muita mahdollisia syitä voidaan löytää. Vertailen lopuksi varhaisia, 400-luvulla eläneiden kilvoittelijoiden Pyhän Efraim Syyrialaisen, Antonius Suuren ja Simeon Pylväspyhimyksen motiiveita nykykilvoittelijoiden motiiveihin, sikäli kuin se on mahdollista. Selvitän myös, onko Efraim Syyrialaisen esimerkillä ollut merkitystä nykykilvoittelijoille. Empiirinen aineisto kerättiin kahtena vuotena v. 2002 ja 2003. Tutkielmaa varten haastattelin kolmea Efraim Syyrialaisen luostarin munkkia. Pääinformanttini oli ko. luostarin seminaarin teologiopiskelija. Heidän kotitaustansa on syyrialaisortodoksinen, voimakkaasti uskonnollinen. Spiritualiteettia harjoitettiin jo lapsuudessa sekä kotona että kirkossa. Tutkielmani näkökulma on uskontohistoriallinen ja uskontososiologinen. Tutkin miten varhaiset- sekä nykypäivän kilvoittelijat ovat suhtautuneet yhteiskuntaan ja miten he ovat integroituneet luostariinsa. Kysymyksessä on nykypäivän osalta laadullinen tapaustutkimus, jonka metodeina ovat teemahaastattelu, jonka yhtenä osana olivat argumentit ja osallistruva havainnointi. Analysoin vastaukset sisällön analyysiä käyttäen. Haastatellut munkit korostivat syyrian kielen ja tradition opiskelun ja sen siirtämisen tärkeyttä seminaariin opiskelemaan hakeutumisensa, ja sen jälkeen munkiksi jäämisensä perusteluna. Pyhän Efraim Syyrialaisen esimerkin munkit kokivat olevan heille hyvin tärkeän tradition siirtäjän. Opiskelemisen ja matkustamisen mahdollisuus munkkina koettiin myös tärkeänä ja siitä syystä luostariin jäätiin, eli yhteiskunnallinen syy löytyi. Sisällön analyysissä ilmeni, että alkujaan koti edusti munkille primaarista tekijää. Sekundääristä tekijää edustivat kirkkoon kuuluva ryhmä, munkit ja luostari. Kodin ja kirkossa käynnin seurauksena tradition ja syyrian kielen oppimisen halu korostui ja niitä haluttiin lähteä opiskelemaan. Positiiviseksi viiteryhmäksi tällöin muodostuivat seminaariopiskelun aikana munkit ja muut luostarin asukkaat. Luostariin jäämisensä jälkeen primaarin tekijän voidaan huomata vaihtuneen luostariksi ja kodin asema on jäänyt sekundaariseksi. Yhteys luostarin ja ympäröivän yhteiskunnan kanssa tapahtui varhaisena aikana pääasiallisesti siten, että ihmiset tulivat kilvoittelijan luokse. Nykymunkit puolestaan käyvät niiden seurakuntalaisten kotona, jotka eivät pääse yhteisiin jumalanpalveluksiin ja auttavat heitä sielunhoidollisesti ja tarvittaessa taloudellisesti. Kirkon patriarkka Mar Ignatios Zakka I Iwasilla ja metropoliitta Eusthatios Matta Rohamilla on paljon yhteyksiä myös islaminuskoiseen väestönosaa Syyriassa. Ekumeenisia yhteyksiä on munkeillakin runsaasti. Ne mahdollistuvat erilaisissa kirkon kokouksissa ja konferensseissa sekä opiskelupaikkakunnalla Kreikassa.

The Macroeconomic Effects of Fiscal Policy in a Small Open Economy under a Flexible Exchange Rate Regime

This licentiate's thesis analyzes the macroeconomic effects of fiscal policy in a small open economy under a flexible exchange rate regime, assuming that the government spends exclusively on domestically produced goods. The motivation for this research comes from the observation that the literature on the new open economy macroeconomics (NOEM) has focused almost exclusively on two-country global models and the analyses of the effects of fiscal policy on small economies are almost completely ignored. This thesis aims at filling in the gap in the NOEM literature and illustrates how the macroeconomic effects of fiscal policy in a small open economy depend on the specification of preferences. The research method is to present two theoretical model that are extensions to the model contained in the Appendix to Obstfeld and Rogoff (1995). The first model analyzes the macroeconomic effects of fiscal policy, making use of a model that exploits the idea of modelling private and government consumption as substitutes in private utility. The model offers intuitive predictions on how the effects of fiscal policy depend on the marginal rate of substitution between private and government consumption. The findings illustrate that the higher the substitutability between private and government consumption, (i) the bigger is the crowding out effect on private consumption (ii) and the smaller is the positive effect on output. The welfare analysis shows that the less fiscal policy decreases welfare the higher is the marginal rate of substitution between private and government consumption. The second model of this thesis studies how the macroeconomic effects of fiscal policy depend on the elasticity of substitution between traded and nontraded goods. This model reveals that this elasticity a key variable to explain the exchange rate, current account and output response to a permanent rise in government spending. Finally, the model demonstrates that temporary changes in government spending are an effective stabilization tool when used wisely and timely in response to undesired fluctuations in output. Undesired fluctuations in output can be perfectly offset by an opposite change in government spending without causing any side-effects.

Genetics of T cell co-stimulatory receptors -CD28, CTLA4, ICOS and PDCD1 in immunity and transplantation

Co-stimulatory signals are essential for the activation of naïve T cells and productive immune response. Naïve T cells receive first, antigen-specific signal through T cell receptor. Co-stimulatory receptors provide the second signal which can be either activating or inhibitory. The balance between signals determines the outcome of an immune response. CD28 is crucial for T cell activation; whereas cytotoxic T lymphocyte associated antigen 4 (CTLA4) mediates critical inhibitory signal. Inducible co-stimulator (ICOS) augments cytokine expression and plays role in immunoglobulin class switching. Programmed cell death 1 (PDCD1) acts as negative regulator of T cell proliferation and cytokine responses. The co-stimulatory receptor pathways are potentially involved in self-tolerance and thus, they provide a promising therapeutic strategy for autoimmune diseases and transplantation. The genes encoding CD28, CTLA4 and ICOS are located adjacently in the chromosome region 2q33. The PDCD1 gene maps further, to the region 2q37. CTLA4 and PDCD1 are associated with the risk of a few autoimmune diseases. There is strong linkage disequilibrium (LD) on the 2q33 region; the whole gene of CD28 exists in its own LD block but CTLA4 and the 5' part of ICOS are within a same LD block. The 3' part of ICOS and PDCD1 are in their own separate LD blocks. Extended haplotypes covering the 2q33 region can be identified. This study focuses on immune related conditions like coeliac disease (CD) which is a chronic inflammatory disease with autoimmune features. Immunoglobulin A deficiency (IgAD) belongs to the group of primary antibody deficiencies characterised by reduced levels of immunoglobulins. IgAD co-occurs often with coeliac disease. Renal transplantation is needed in the end stage kidney diseases. Transplantation causes strong immune response which is tried to suppress with drugs. All these conditions are multifactorial with complex genetic background and multiple environmental factors affecting the outcome. We have screened ICOS for polymorphisms by sequencing the exon regions. We detected 11 new variants and determined their frequencies in Finnish population. We have measured linkage disequilibrium on the 2q33 region in Finnish as well as other European populations and observed conserved haplotypes. We analysed genetic association and linkage of the co-stimulatory receptor gene region aiming to study if it is a common risk locus for immune diseases. The 2q33 region was replicated to be linked to coeliac disease in Finnish population and CTLA4-ICOS haplotypes were found to be associated with CD and IgAD being the first non-HLA risk locus common for CD and immunodeficiencies. We also showed association between ICOS and the outcome of kidney transplantation. Our results suggest new evidence for CTLA4-ICOS gene region to be involved in susceptibility of coeliac disease. The earlier published contradictory association results can be explained by involvement of both CTLA4 and ICOS in disease susceptibility. The pattern of variants acting together rather than a single polymorphism may confer the disease risk. These genes may predispose also to immunodeficiencies as well as decreased graft survival and delayed graft function. Consequently, the present study indicates that like the well established HLA locus, the co-stimulatory receptor genes predispose to variety of immune disorders.

The Pseudomonas syringae-derived HrpA pilins - molecular characterization and biotechnological application of the transcripts

Many Gram-negative bacteria pathogenic to plants and animals possess type III secretion systems that are used to cause disease. Effector proteins are injected into host cells using the type III secretion machineries. Despite vigorous studies, the nature of the secretion signal for type III secreted proteins still remains elusive. Both mRNA and proteinaceous signals have been proposed. Findings on coupling of translation to secretion by the type III secretion systems are also still contradictory. This study dealt with the secretion signal of HrpA from Pseudomonas syringae pathovar tomato. HrpA is the major component of the type III secretion system-associated Hrp pilus and a substrate for the type III secretion systems. The secretion signal was shown to reside in the first 15 codons or amino acids, a location typical for type III secretion signals. Translation of HrpA in the absence of a functional type III secretion system was established, but it does not exclude the possibility of coupling of translation to secretion when the secretion apparatus is present. The hrpA transcripts from various unrelated plant pathogenic bacteria were shown to be extremely stable. The biological relevance of this observation is unknown, but possible explanations include the high prevalence of HrpA protein, an mRNA secretion signal or timing of secretion. The hrpA mRNAs are stable over a wide range of temperatures, in the absence of translating ribosomes and even in the heterologous host Escherichia coli. The untranslated regions (UTRs) of hrpA transcripts from at least 20 pathovars of Pseudomonas syringae are highly homologous, whilst their coding regions exhibit low similarity. The stable nature of hrpA messenger RNAs is likely to be due to the folding of their 5 and 3 UTRs. In silico the UTRs seem to form stem-loop structures, the hairpin structures in the 3 UTRs being rich in guanidine and cytosine residues. The stable nature of the hrpA transcript redirected the studies to the stabilization of heterologous transcripts and to the use of stable messenger RNAs in recombinant protein production. Fragments of the hrpA transcript can be used to confer stability on heterologous transcripts from several sources of bacterial and eukaryotic origin, and to elevate the levels of production of the corresponding recombinant proteins several folds. hrpA transcript stabilizing elements can be used for improving the yields of recombinant proteins even in Escherichia coli, one of the most commonly used industrial protein production hosts.

Characterization of the molecular components and function of BARE-1, Hin-Mu and Mu transposition machineries

Transposable elements, transposons, are discrete DNA segments that are able to move or copy themselves from one locus to another within or between their host genome(s) without a requirement for DNA homology. They are abundant residents in virtually all the genomes studied, for instance, the genomic portion of TEs is approximately 3% in Saccharomyces cerevisiae, 45% in humans, and apparently more than 70% in some plant genomes such as maize and barley. Transposons plays essential role in genome evolution, in lateral transfer of antibiotic resistance genes among bacteria and in life cycle of certain viruses such as HIV-1 and bacteriophage Mu. Despite the diversity of transposable elements they all use a fundamentally similar mechanism called transpositional DNA recombination (transposition) for the movement within and between the genomes of their host organisms. The DNA breakage and joining reactions that underlie their transposition are chemically similar in virtually all known transposition systems. The similarity of the reactions is also reflected in the structure and function of the catalyzing enzymes, transposases and integrases. The transposition reactions take place within the context of a transposition machinery, which can be particularly complex, as in the case of the VLP (virus like particle) machinery of retroelements, which in vivo contains RNA or cDNA and a number of element encoded structural and catalytic proteins. Yet, the minimal core machinery required for transposition comprises a multimer of transposase or integrase proteins and their binding sites at the element DNA ends only. Although the chemistry of DNA transposition is fairly well characterized, the components and function of the transposition machinery have been investigated in detail for only a small group of elements. This work focuses on the identification, characterization, and functional studies of the molecular components of the transposition machineries of BARE-1, Hin-Mu and Mu. For BARE-1 and Hin-Mu transpositional activity has not been shown previously, whereas bacteriophage Mu is a general model of transposition. For BARE-1, which is a retroelement of barley (Hordeum vulgare), the protein and DNA components of the functional VLP machinery were identified from cell extracts. In the case of Hin-Mu, which is a Mu-like prophage in Haemophilus influenzae Rd genome, the components of the core machinery (transposase and its binding sites) were characterized and their functionality was studied by using an in vitro methodology developed for Mu. The function of Mu core machinery was studied for its ability to use various DNA substrates: Hin-Mu end specific DNA substrates and Mu end specific hairpin substrates. The hairpin processing reaction by MuA was characterized in detail. New information was gained of all three machineries. The components or their activity required for functional BARE-1 VLP machinery and retrotransposon life cycle were present in vivo and VLP-like structures could be detected. The Hin-Mu core machinery components were identified and shown to be functional. The components of the Mu and Hin-Mu core machineries were partially interchangeable, reflecting both evolutionary conservation and flexibility within the core machineries. The Mu core machinery displayed surprising flexibility in substrate usage, as it was able to utilize Hin-Mu end specific DNA substrates and to process Mu end DNA hairpin substrates. This flexibility may be evolutionarily and mechanistically important.

GDNF family receptors in peripheral target innervation and hormone production

Glial cell line-derived neurotrophic factor (GDNF) family ligands: GDNF, neurturin, persephin and artemin, signal through a receptor tyrosine kinase Ret by binding first to a co-receptor (GFRα1-4) that is attached to the plasma membrane. The GDNF family factors can support the survival of various peripheral and central neuronal populations and have important functions also outside the nervous system, especially in kidney development. Activating mutations in the RET gene cause tumours in neuroendocrine cells, whereas inactivating mutations in RET are found in patients with Hirschsprung s disease (HSCR) characterized by loss of ganglionic cells along the intestine. The aim of this study was to examine the in vivo functions of neurturin receptor GFRα2 and persephin receptor GFRα4 using knockout (KO) mice. Mice lacking GFRα2 grow poorly after weaning and have deficits in parasympathetic and enteric innervation. This study shows that impaired secretion of the salivary glands and exocrine pancreas contribute to growth retardation in GFRα2-KO mice. These mice have a reduced number of intrapancreatic neurons and decreased cholinergic innervation of the exocrine pancreas as well as reduced excitatory fibres in the myenteric plexus of the small intestine. This study also demonstrates that GFRα2-mediated Ret signalling is required for target innervation and maintenance of soma size of sympathetic cholinergic neurons and sensory nociceptive IB4-binding neurons. Furthermore, lack of GFRα2 in mice results in deficient perception of temperatures above and below thermoneutrality and in attenuated inflammatory pain response. GFRα4 is co-expressed with Ret predominantly in calcitonin-producing thyroid C-cells in the mouse. In this study GFRα4-deficient mice were generated. The mice show no gross developmental deficits and have a normal number of C-cells. However, young but not adult mice lacking GFRα4 have a lower production of calcitonin in thyroid tissue and consequently, an increased bone formation rate. Thus, GFRα4/Ret signalling may regulate calcitonin production. In conclusion, this study reveals that GFRα2/Ret signalling is crucial for the development and function of specific components of the peripheral nervous system and that GFRα4-mediated Ret signalling is required for controlling transmitter synthesis in thyroid C-cells.

A systematic-ecological approach to Baltic Sea ice studies of algae and protists

The seasonal occurrence of sea ice that annually covers almost half the Baltic Sea area provides a unique habitat for halo- and cold temperature-tolerant extremophiles. Baltic Sea ice biology has more than 100 years of tradition that began with the floristic observation of species by the early pioneers using light microscopic techniques that were the only thing available at the time. Since the discovery of life within sea ice, more technologies have become available for taxonomy. Electron microscopy and genetic evidence have been used to identify sea ice biota revealing increased numbers of taxa. Meanwhile ecologists have used light microscopic cell enumeration in addition to the chemical and physical properties of sea ice in attempts to explain the food web structure of sea ice and its functions. Thus, during the Baltic winter, the sea ice hosts more abundant and diverse microbial communities than the water column beneath it. These communities are typically dominated by autotrophic diatoms together with a diverse assortment of dinoflagellates, auto- and heterotrophic flagellates, ciliates, metazoan rotifers and bacteria, which are mostly responsible for the recycling of nutrients. This thesis comprises ecological and systematic studies. In addition to the results of the previous studies carried out on landfast ice, the data presented here provide new insight into the spatial distribution of pelagial sea ice, which has remained largely unexplored. The studies reveal spatial heterogeneity in the pelagial sea ice of the Gulf of Bothnia. There were mismatches in chlorophyll-a concentrations and in photosynthetic efficiencies of the communities studied. The temporal succession was followed and experimental studies performed investigating the community responses towards increased or decreased light in landfast ice in the Gulf of Finland. The systematic studies carried out with established dinoflagellate cultures revealed a new resting cyst belonging to common sea ice dinoflagellate, Scrippsiella hangoei (Schiller) Larsen 1995. The cyst can be used to explain the overwintering of this species during prolonged periods of darkness. The dissimilarities and similarities in the material isolated from the sea ice called for description of a new subspecies Heterocapsa arctica ssp. frigida. The cells obtained in the cultured material were unlike those of the previously described species, necessitating description of ssp. frigida. As a result of its own unique habitus, the subspecies had been noted by Finnish taxonomists during the past three decades and thus its annual occurrence and geographical distribution in the Baltic Sea. This illustrates how combining ecology and systematics increases our understanding of organisms.

Marking one-summer old whitefish with fluorescent pigment spraying method and results of whitefish stockings in the Gulf of Bothnia

Anadromous whitefish is one of the most important fish species in the Finnish coastal fisheries in the Gulf fo Bothnia. To compensate the lost reproduction due to river damming and to support the fisheries, several million one-summer old whitefish are released yearly into the Gulf of Bothnia. Since there are naturally reproducing whitefish in the Gulf as well, and the wild and stocked fish can not be separated in the catch, stocking impact can only be estimated by marking the stocked fish. Due to the small size and large number of released whitefish, the scattered fishery and large area where the whitefish migrate, most of the traditionally used fish marking methods were either unsuitable (e.g. Carlin-tags) or proved to be too expensive (e.g. coded wire tags). Fluorescent pigment spraying method offers a fast and cost-effective method to mass-mark young fish. However, the results are not always satisfactory due to low long-time retention of the marks in some species. The method has to be tested and proper marking conditions and methods determined for each species. This thesis is based on work that was accomplished while developing the fluorescent pigment spraying method for marking one-summer old whitefish fingerlings, and it draws together the results of mass-marking whitefish fingerlings that were released in the Gulf of Bothnia. Fluorescent pigment spraying method is suitable for one-summer old whitefish larger than 8 cm total length. The water temperature during the marking should not exceed 10o C. Suitable spraying pressure is 6 bars measured in the compressor outlet, and the distance of the spraying gun nozzle should be ca 20 cm from the fish. Under such conditions, the marking results in long-term retention of the mark with low or no mortality. The stress level of the fish (measured as muscle water content) rises during the marking procedure, but if the fish are allowed to recover after marking, the overall stress level remains within the limits observed in normal fish handling during the capture-loading-transport-stocking procedure. The marked whitefish fingerlings are released into the sea at larger size and later in the season than the wild whitefish. However, the stocked individuals migrate to the southern feeding grounds in a similar pattern to the wild ones. The catch produced by whitefish stocking in the Gulf of Bothnia varied between released fingerling groups, but was within the limits reported elsewhere in Finland. The releases in the southern Bothnian Bay resulted in a larger catch than those made in the northern Bothnian Bay. The size of the released fingerlings seemed to have some effect on survival of the fish during the first winter in the sea. However, when the different marking groups were compared, the mean fingerling size was not related to stocking success.

Differentiation of neural stem cells in fragile X syndrome

Multipotent stem cells can self-renew and give rise to multiple cell types. One type of mammalian multipotent stem cells are neural stem cells (NSC)s, which can generate neurons, astrocytes and oligodendrocytes. NSCs are likely involved in learning and memory, but their exact role in cognitive function in the developing and adult brain is unclear. We have studied properties of NSCs in fragile X syndrome (FXS), which is the most common form of inherited mental retardation. FXS is caused by the lack of functional fragile X mental retardation protein (FMRP). FMRP is involved in the regulation of postsynaptic protein synthesis in a group I metabotropic glutamate receptor 5 (mGluR5)-dependent manner. In the absence of functional FMRP, the formation of functional synapses is impaired in the forebrain which results in alterations in synaptic plasticity. In our studies, we found that FMRP-deficient NSCs generated more neurons and less glia than control NSCs. The newborn neurons derived from FMRP-deficient NSCs showed an abnormally immature morphology. Furthermore, FMRP-deficient NSCs exhibited aberrant oscillatory Ca2+ responses to glutamate, which were specifically abolished by an antagonist of the mGluR5 receptor. The data suggested alterations in glutamatergic differentiation of FMRP-deficient NSCs and were further supported by an accumulation of cells committed to glutamatergic lineage in the subventricular zone of the embryonic Fmr1-knockout (Fmr1-KO) neocortex. Postnatally, the aberrant cells likely contributed to abnormal formation of the neocortex. The findings suggested a defect in the differentiation of distinct glutamatergic mGluR5 responsive cells in the absence of functional FMRP. Furthermore, we found that in the early postnatal Fmr1-KO mouse brain, the expression of mRNA for regulator of G-protein signalling-4 (RGS4) was decreased which was in line with disturbed G-protein signalling in NSCs lacking FMRP. Brain derived neurotrophic factor (BDNF) promotes neuronal differentiation of NSCs as the absence of FMRP was shown to do. This led us to study the effect of impaired BDNF/TrkB receptor signaling on NSCs by overexpression of TrkB.T1 receptor isoform. We showed that changes in the relative expression levels of the full-length and truncated TrkB isoforms influenced the replication capacity of NSCs. After the differentiation, the overexpression of TrkB.T1 increased neuronal turnover. To summarize, FMRP and TrkB signaling are involved in normal differentiation of NSCs in the developing brain. Since NSCs might have potential for therapeutic interventions in a variety of neurological disorders, our findings may be useful in the design of pharmacological interventions in neurological disorders of learning and memory.