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Now showing items 13172-13191 of 25283
  • Gabrenaite-Verkhovskaya, Rasa (Helsingin yliopisto, 2007)
    The particles of Potato virus A (PVA; genus Potyvirus) are helically constructed filaments that contain multiple copies of a single type of coat-protein (CP) subunit and a single copy of genome-linked protein (VPg), attached to one end of the virion. Examination of negatively-stained virions by electron microscopy revealed flexuous, rod-shaped particles with no obvious terminal structures. It is known that particles of several filamentous plant viruses incorporate additional minor protein components, forming stable complexes that mediate particle disassembly, movement or transmission by insect vectors. The first objective of this work was to study the interaction of PVA movement-associated proteins with virus particles and how these interactions contribute to the morphology and function of the virus particles. Purified particles of PVA were examined by atomic force microscopy (AFM) and immuno-gold electron microscopy. A protrusion was found at one end of some of the potyvirus particles, associated with the 5' end of the viral RNA. The tip contained two virus-encoded proteins, the genome-linked protein (VPg) and the helper-component proteinase (HC-Pro). Both are required for cell-to-cell movement of the virus. Biochemical and electron microscopy studies of purified PVA samples also revealed the presence of another protein required for cell-to-cell movement the cylindrical inclusion protein (CI), which is also an RNA helicase/ATPase. Centrifugation through a 5-40% sucrose gradient separated virus particles with no detectable CI to a fraction that remained in the gradient, from the CI-associated particles that went to the pellet. Both types of particles were infectious. AFM and translation experiments demonstrated that when the viral CI was not present in the sample, PVA virions had a beads-on-a-string phenotype, and RNA within the virus particles was more accessible to translation. The second objective of this work was to study phosphorylation of PVA movement-associated and structural proteins (CP and VPg) in vitro and, if possible, in vivo. PVA virion structural protein CP is necessary for virus cell-to-cell movement. The tobacco protein kinase CK2 was identified as a kinase phosphorylating PVA CP. A major site of CK2 phosphorylation in PVA CP was identified as a single threonine within a CK2 consensus sequence. Amino acid substitutions affecting the CK2 consensus sequence in CP resulted in viruses that were defective in cell-to-cell and long-distance movement. The CK2 regulation of virion assembly and cell-to-cell movement by phosphorylation of CP was possibly due to the inhibition of CP binding to viral RNA. Four putative phosphorylation sites were identified from an in vitro phosphorylated recombinant VPg. All four were mutated and the spread of mutant viruses in two different host plants was studied. Two putative phosphorylation site mutants (Thr45 and Thr49) had phenotypes identical to that of a wild type (WT) virus infection in both Nicotiana benthamiana and N. tabacum plants. The other two mutant viruses (Thr132/Ser133 and Thr168) showed different phenotypes with increased or decreased accumulation rates, respectively, in inoculated and the first two systemically infected leaves of N. benthamiana. The same mutants were occasionally restricted to single cells in N. tabacum plants, suggesting the importance of these amino acids in the PVA infection cycle in N. tabacum.
  • Xiang, Junlong (2015)
    Today, we are living in a data-exploding era, in which the volume of data is expanding in an unbelievable fast way and the speed is faster than any period in the history. Using machine learning algorithms for processing massive data has become a hot research area now and lots of computer scientists and developers use them to extract hidden information from massive data. However, as the volume of data has increased too much for recent years and the trend is still increasing, just by using a standalone machine to deal with these massive data is becoming unrealistic as the volume of data and the computing complexity for processing massive data has exceeded the capacity of a single machine. In order to solve this problem, in this paper, we combined Extreme Learning Machine(ELM), which is a machine learning algorithm that has the ability of extreme fast training, and mapreduce parallel framework to proposed a mapreduce-based ELM called MR_ELM. And according to some experiments by using KDDCUP99 dataset, we have proven that MR_ELM can process massive data in a parallel way without losing accuracy performance compared with local ELM.
  • Heinonen, Mira (Helsingin yliopisto, 2011)
    Breast cancer is the most common cancer among women. Although its prognosis has improved nowadays, methods to predict the progression of the disease or to treat it are not comprehensive. This thesis work was initiated to elucidate in breast carcinogenesis the role of HuR, a ubiquitously expressed mRNA-binding protein that regulates gene expression posttranscriptionally. HuR is predominantly nuclear, but it shuttles between the nucleus and the cytoplasm, and this nucleocytoplasmic translocation is important for its function as a RNA-stabilizing and translational regulator. HuR has been associated with diverse cellular processes, for example carcinogenesis. The specific aims of my thesis work were to study the prognostic value of HuR in breast cancer and to clarify the mechanisms by which HuR contributes to breast carcinogenesis. My ultimate goal is, by better understanding the role of HuR in breast carcinogenesis, to aid in the discovery of novel targets for cancer therapies. HuR expression and localization was studied in paraffin-embedded preinvasive (atypical ductal hyperplasia, ADH, and ductal carcinoma in situ, DCIS) specimens as well in sporadic and familial breast cancer specimens. Our results show that cytoplasmic HuR expression was already elevated in ADH and remained elevated in DCIS as well as in cancer specimens. Clinicopathological analysis showed that cytoplasmic HuR expression associated with the more aggressive form of the disease in DCIS, and in cancer specimens it proved an independent marker for poor prognosis. Importantly, cytoplasmic HuR expression was significantly associated with poor outcome in the subgroups of small (2 cm) and axillary lymph node-negative breast cancers. HuR proved to be the first mRNA stability protein the expression of which is associated in breast cancer with poor outcome. To explore the mechanisms of HuR in breast carcinogenesis, lentiviral constructs were developed to inhibit and to overexpress the HuR expression in a breast epithelial cell line (184B5Me). Our results suggest that HuR mediates breast carcinogenesis by participating in processes important in cell transformation, in programmed cell death, and in cell invasion. Global gene expression analysis shows that HuR regulates genes participating in diverse cellular processes, and affects several pathways important in cancer development. In addition, we identified two novel target transcripts (connective tissue growth factor, CTGF, and Ras oncogene family member 31, RAB31) for HuR. In conclusion, because cytoplasmic HuR expression in breast cancer can predict the outcome of the disease it could serve in clinics as a prognostic marker. HuR accumulates in the cytoplasm even at its non-invasive stage (ADH and DCIS) of the carcinogenic process and supports functions essential in cell alteration. These data suggest that HuR contributes to carcinogenesis of the breast epithelium.
  • Stenman, Jakob (Helsingin yliopisto, 2002)
  • Wuorinen, Olli (1927)
  • Ranki, Pia (2004)
    I den här pro gradun undersökte jag MTK:s möjliga förändring i sin intressebevakning, under åren 1975 till 2000. Jag började med att se på litteratur och tidigare forskning om korporatism, lobbying, och teorier om korporatismens ställning idag i allmänhet i stater, enligt Lewin (1992) och Munk Christiansen & Rommetvedt (1999). Jag gav också en historisk översikt över MTK som organisation. I den tidigare forskningen som jag tittade på kom fram att korporatismen i stater har gått tillbaka, för att istället ersättas av andra former av intressebevakning, lobbying. I den här pro gradun ville jag därför undersöka om detta även gäller MTK, har även MTK:s intressebevakning gått från korporatism mot lobbying? Eftersom korporatismen i allmänhet har visat på en nedgång kom jag till det hypotetiska antagandet att detta även gäller för MTK:s del, alltså ett antagande att MTK:s intressebevakning har gått från korporatism mot lobbying. MTK:s korporativa intressebevakning undersökte jag genom att se på MTK:s deltagande i riksdagens utskottsarbete, och genom att se på det statliga kommittéväsendet i Finland. Den andra formen av intressebevakning, lobbyingen, undersökte jag genom att från MTK:s årsberättelser plocka uppgifter om MTK:s representation i kommittéer, kommissioner, arbetsgrupper samt i förvaltningsorgan inom organisationer nära lantbruket. De resultat jag kom till visade på en ökning inom deltagandet i riksdagens utskottsarbete fram till det sista undersökta året då en minskning sågs. Det visade sig att kommittéväsendet i praktiken är dött idag, alltså kan inte heller MTK delta i kommittéverksamhet, men att kontakter till ministerier upprätthålls genom lobbying. En aktör bekräftade antagandet att lobbyingen ökat. Den alternativa intressebevakningen i form av representation i olika organ ökade ganska markant under den undersökta tiden, både totalt, och då jag tittade på de olika organen enligt kategorier, inom de allra flesta kategorierna. Jag kom till att mitt hypotetiska antagande visade sig stämma enligt alla andra undersökta faktorer, utom utskottsdeltagandet, som jag inte kunde uttala mig om med säkerhet.
  • Immonen, Seena-Tuulia (2008)
    Pro gradu-tutkielmani tarkastelee suomalaista erityiskasvatusta ja erityisopetusta sekä liittää tämän keskustelu syrjäytymiseen ja nuorten koulupudokkuuteen. Tutkielmani esittää kuvauksen erityisopetuksen kehityksestä Suomessa ja herättää samalla kysymyksen, mitä erityiskasvatuksen keinoin on pyritty ratkaisemaan. Toisaalta tutkielmani etsii selvennystä pohdintaan, mitä kehityskaari kertoo suomalaisesta yhteiskunnasta. Erityisopetuksen ja erityiskasvatuksen tar-kasteluni teoreettisena viitekehyksenä toimii olemassa oleva suomalainen erityispedagoginen tutkimus. Antropologinen aineistoni sisältää antropologien huomioita koulumaailmasta ja koulupudokkuudesta sekä analyysiä sosialisaatiosta. Tutkielmassani esiintyvä pohdinta ja keskustelu keskittyy tarkastelemaan peruskoulua nuorten siirtymäriitin tapahtumapaikkana. Antropologien tutkimusten mukaan nuorten aikuistuminen kouluissa on lineaarinen siirtymäriitti. Aikuistuminen siirtymäriittinä koettelee nykypäivän koulujärjetelmää ja asettaa koulut uudenlaisen haasteen eteen. Esitän tutkielmassani miten etnografinen näkeminen avaisi kouluissa uusia mahdollisuuksia ja laajentaisi normaaliuden kapeaa käsitettä. Tutkielmani innoittajana toimi sopeutumattomaksi ja koulupudokkaiksi määritellyt erityisoppilaat, joiden kanssa vuosia tekemäni työ on antanut minulle mahdollisuuden havainnoida nuorten todellisuutta ja seurata koulua instituutiona. Spindlerin toimittama teos "Doing the Ethnography of Schooling" ja Viktor Turnerin "The Ritual Process" ovat antropologisten julkaisujen, American Anthropologist ja Anthropology and Education, ohella liittäneet oman etnografisen aineistoni tämän hetkiseen antropologiseen kasvatuskeskusteluun ja arvioihin koulumaailmasta. Oman tutkielmani kenttä on suomalainen yläkoulu ja sopeutumattomiksi määriteltyjen oppilaiden muodostama erityisopetuksen ryhmä. Aineiston keruu on tapahtunut usean vuoden ajan erityisoppilaiden kanssa tekemäni työn ohessa. Aineistoa ei ole kerätty ainoastaan osallistuvan havainnoinnin menetelmin vaikka kenttä on mahdollistanut myös oppilaiden tarkkailun. Työ erityisoppilaiden kanssa on mahdollistanut konkreettisen näköalapaikan oppilaiden todellisuuteen. Suomalaista koulujärjeselmää ja erityisopetusta tarkastellessani esitän kysymyksen, miksi tietyt oppilaat muodostavat ongelman järjestelmälle? Tutkielmani havaintojen perusteella joidenkin oppilaiden kohdalla koulut sallivat vähittäisen koulupudokkuuskehityksen. Keskityn pohtimaan, miksi koulu ei tänä päivänä kykene vastaamaan sopeutumattomiksi leimattujen oppilaiden asettamaan haasteeseen ja mikä merkitys sopeutumattomuuden leimalla nuorten elämässä on. Esitän tutkielmassani erään koulun oppilasryhmän käyttäytymisen muotoja ja arvoja, erityisesti ryhmän sisällä esiintyvää ja sen jäsenten tuntemaa uhmaa ja aggressiota. Tutkielmani tarkastelun kohteena ei ole kukaan yksittäinen henkilö vaikka esitänkin oppilaiden kanssa käymiäni sanatarkkoja keskusteluita ja kuvailen yksittäisiä tapahtumia luokkahuo-neessa tai muussa koulutoimintaan kuuluvassa ympäristössä. Tarkasteluni kohteena ovat erityisesti ryhmän keskinäinen kommunikaatio ja syrjäytymisvaarassa olevien nuorten puhetavat, käyttäytyminen ja asenne omaan tulevaisuuteen. Esittämieni keskusteluiden ja tapahtumien kuvailun avulla haluan tuoda esille kohderyhmäni nuorten kokemuksen omasta osallisuudestaan yhteiskunnan jäseninä.
  • Edelman, Sanna (Helsingin yliopisto, 2005)
  • Simell, Birgit (Helsingin yliopisto, 2003)
  • Hölttä, Veera (Juvenes Print, 2012)
    T cells are CD4 lymphocytes participating in cell-mediated immunity, and play a critical role in immune-mediated diseases. T cells divide further into subclasses such as Th1, Th2, and Th17 that participate in mucosal immunity responses caused by extracellular pathogens and also play a role in autoimmune diseases. Th17 cells produce cytokines called the interleukin-17 family (IL-17). Regulatory CD4+ T cells marked by CD4, CD25, and forkhead box P3 (FOXP3), contribute to maintaining tolerance and regulating immune responses to antigens. This doctoral thesis studies the role of IL-17 type of immunity in intestinal inflammation in Crohn s disease, ulcerative colitis, celiac disease, and type I diabetes (T1D). In particular, the study explores the balance between effector and regulatory T cells in active and inactive Crohn s disease in adults, as well as in pediatric patients with Crohn s disease and ulcerative colitis. Furthermore, the investigation focuses on the effect of anti-TNF-α treatment on the effector and regulatory T cells in Crohn s disease in adults. Adult patients with Crohn s disease had higher numbers of intestinal IL-17+ and FOXP3+ cells than did control subjects, both before and after the anti-TNF-α treat-ment. Intestinal interferon-γ and IL-17 mRNA expression was higher in Crohn s disease and remained elevated after anti-TNF-α treatment, although the treatment improved intestinal balance between IL-17+ effector and regulatory T cells. In Crohn s disease, mRNA expression of IL-17A, IL-6, and FOXP3 was increased. Fecal IL-17 concentration showed increase in patients with active disease. IL-17 enhanced the IL-8 and TNF-α response of the epithelial cell line to lipopolysaccha-ride in vitro. The findings suggest that activation of the IL-17 axis is fundamentally connected to the etiology of Crohn s disease and may represent the basis for the relapsing nature of the disease. In pediatric patients, IL-17, IL-22, IL-6, and FOXP3+ mRNA up-regulation and increase in the number of IL-17+ and FOXP3+ cells existed in inflammatory bowel disease. Activation of the IL-17/IL-22 axis and up-regulation of FOXP3 occurred both in pediatric Crohn s disease and ulcerative colitis, indicating shared immuno-logical aberrancy. In pediatric patients with untreated celiac disease, the mucosal expression of IL-17 and FOXP3 transcripts were elevated as compared with TGA-negative reference children, children with potential celiac disease, gluten-free diet-treated children with celiac disease, or children with T1D. Enhanced spontaneous secretion of IL-1β, IL-6, and IL-17 occurred in biopsy specimens from patients with untreated celiac disease. Activation of anti-apoptotic bcl-2 in IL-17-treated CaCo-2 epithelial cells suggests that IL-17 might be involved in mucosal protection. Up-regulation of IL-17, howev-er, could serve as a biomarker for the development of villous atrophy and active celiac disease.
  • Mikkola, Jaakko (Helsingin yliopisto, 2011)
    Tämä työ käsittelee hämäläistä Lammin pitäjää ja seurakuntaa vuoden 1918 sisällissodassa. Se kuvaa arkistolähteiden avulla sisällissodan tapahtumia ja niiden tulkintaa Lammilla. Tutkimus katsoo punaiselle puolelle jääneen maalaispitäjän ja -seurakunnan näkökulmasta, miksi sisällissota syttyi, mitä sen aikana tapahtui, miten se vaikutti ja miten sisällissotaa kuvataan muisteluissa. Tämä tieto linkitetään yleiseen historialliseen ja osin myös folkloristiseen tietoon sisällissodasta. Keskeiseksi teemaksi nousee paikallisyhteisön jatkuvuus ja lammilaisten tulkinta muiden aiheuttamasta sodasta. Sisällissodan sytyttyä Lammi jäi rintaman punaiselle puolelle, kun punaiset joukot etenivät Lammin läpi kohti pohjoista. Lammin suojeluskunnan onnistui riisua paikalliset punaiset aseista sodan aluksi, ja näin Lammi jäi valkoisten haltuun. Kuitenkin pian muualta tulleet punaiset marssivat pitäjään. Punaisen vallan aika Lammilla oli varsin maltillinen ja välikohtauksia oli vähän. Lammin tilanne eli pitkälti rintamatapahtumien mukaan. Huhtikuussa saksalaiset valloittivat pitäjän taistelun jälkeen. Punaisten vetäytymisvaiheessa Lammilla tapahtui joitakin murhia ja väkivaltaisuuksia. Saksalaiset polttivat Lammin kirkon tuhotessaan punaisten asevarastoja. Valkoisten tultua alkoivat teloitukset, joissa surmattiin toistakymmentä punaista. Moni lammilainen punainen teloitettiin muualla. Sota näyttäytyi lammilaisille ulkopuolisten aiheuttamana sotana, koska oman paikkakunnan sisäiset tapahtumat eivät yksinään johtaneet vallankumoukseen, vaan siihen tarvittiin ulkopuolisten apua. Keskeisiin sotatapahtumiin liittyivät aina ulkopuoliset. Ulkopuolisuuden korostaminen näkyy myös sodan tulkinnoissa. Esimerkiksi teloittajat tulkittiin usein jälkikäteen ulkopuolisiksi, ja näin paha ulkoistettiin oman pitäjän yhtenäisyyden nimissä. Myös saksalaisten toimet loivat vaikutelman, että paha tuli pitäjän ulkopuolelta. Lammi säilytti yhteisöllisen jatkuvuutensa sisällissodan aikana, sillä koulut ja rippikoulu pysyivät toiminnassa sekä kirkollisia toimituksia järjestettiin normaalisti. Jumalanpalveluksia ei voitu järjestää kirkon ollessa punaisten asevarastona. Seurakunnan pappi sai muutamaa häirintätapausta lukuun ottamatta työskennellä rauhassa. Myös kunnallishallinnossa jatkoivat vanhat valkoiset kunnallismiehet. Tutkimus osoittaa, ettei sisällissota aiheuttanut Lammille syvää murrosta, vaan pitäjä palasi jatkuvuuteen sodan jälkeen varsin nopeasti. Sota oli vain murtuma jatkuvuudessa, ja sen konkreettiset jäljet, kuten kirkko, korjattiin pian. Silti vielä tänäkin päivänä sisällissota näkyy lammilaisessa maisemassa muistomerkkeinä ja joukkohautoina.
  • Poussu, Eini (Helsingin yliopisto, 2007)
    Transposons, mobile genetic elements that are ubiquitous in all living organisms have been used as tools in molecular biology for decades. They have the ability to move into discrete DNA locations with no apparent homology to the target site. The utility of transposons as molecular tools is based on their ability to integrate into various DNA sequences efficiently, producing extensive mutant clone libraries that can be used in various molecular biology applications. Bacteriophage Mu is one of the most useful transposons due to its well-characterized and simple in vitro transposition reaction. This study establishes the properties of the Mu in vitro transposition system as a versatile multipurpose tool in molecular biology. In addition, this study describes Mu-based applications for engineering proteins by random insertional transposon mutagenesis in order to study structure-function relationships in proteins. We initially characterized the properties of the minimal Mu in vitro transposition system. We showed that the Mu transposition system works efficiently and accurately and produces insertions into a wide spectrum of target sites in different DNA molecules. Then, we developed a pentapeptide insertion mutagenesis strategy for inserting random five amino acid cassettes into proteins. These protein variants can be used especially for screening important sites for protein-protein interactions. Also, the system may produce temperature-sensitive variants of the protein of interest. Furthermore, we developed an efficient screening system for high-resolution mapping of protein-protein interfaces with the pentapeptide insertion mutagenesis. This was accomplished by combining the mutagenesis with subsequent yeast two-hybrid screening and PCR-based genetic footprinting. This combination allows the analysis of the whole mutant library en masse, without the need for producing or isolating separate mutant clones, and the protein-protein interfaces can be determined at amino acid accuracy. The system was validated by analysing the interacting region of JFC1 with Rab8A, and we show that the interaction is mediated via the JFC1 Slp homology domain. In addition, we developed a procedure for the production of nested sets of N- and C-terminal deletion variants of proteins with the Mu system. These variants are useful in many functional studies of proteins, especially in mapping regions involved in protein-protein interactions. This methodology was validated by analysing the region in yeast Mso1 involved in an interaction with Sec1. The results of this study show that the Mu in vitro transposition system is versatile for various applicational purposes and can efficiently be adapted to random protein engineering applications for functional studies of proteins.
  • Vilen, Heikki (Helsingin yliopisto, 2006)
    Transposons are mobile elements of genetic material that are able to move in the genomes of their host organisms using a special form of recombination called transposition. Bacteriophage Mu was the first transposon for which a cell-free in vitro transposition reaction was developed. Subsequently, the reaction has been refined and the minimal Mu in vitro reaction is useful in the generation of comprehensive libraries of mutant DNA molecules that can be used in a variety of applications. To date, the functional genetics applications of Mu in vitro technology have been subjected to either plasmids or genomic regions and entire genomes of viruses cloned on specific vectors. This study expands the use of Mu in vitro transposition in functional genetics and genomics by describing novel methods applicable to the targeted transgenesis of mouse and the whole-genome analysis of bacteriophages. The methods described here are rapid, efficient, and easily applicable to a wide variety of organisms, demonstrating the potential of the Mu transposition technology in the functional analysis of genes and genomes. First, an easy-to-use, rapid strategy to generate construct for the targeted mutagenesis of mouse genes was developed. To test the strategy, a gene encoding a neuronal K+/Cl- cotransporter was mutagenised. After a highly efficient transpositional mutagenesis, the gene fragments mutagenised were cloned into a vector backbone and transferred into bacterial cells. These constructs were screened with PCR using an effective 3D matrix system. In addition to traditional knock-out constructs, the method developed yields hypomorphic alleles that lead into reduced expression of the target gene in transgenic mice and have since been used in a follow-up study. Moreover, a scheme is devised to rapidly produce conditional alleles from the constructs produced. Next, an efficient strategy for the whole-genome analysis of bacteriophages was developed based on the transpositional mutagenesis of uncloned, infective virus genomes and their subsequent transfer into susceptible host cells. Mutant viruses able to produce viable progeny were collected and their transposon integration sites determined to map genomic regions nonessential to the viral life cycle. This method, applied here to three very different bacteriophages, PRD1, ΦYeO3 12, and PM2, does not require the target genome to be cloned and is directly applicable to all DNA and RNA viruses that have infective genomes. The method developed yielded valuable novel information on the three bacteriophages studied and whole-genome data can be complemented with concomitant studies on individual genes. Moreover, end-modified transposons constructed for this study can be used to manipulate genomes devoid of suitable restriction sites.