Browsing by Subject "genotyyppi"

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  • Virtanen, Elina (Helsingfors universitet, 2014)
    Hepatitis C virus (HCV) is a globally significant blood-borne agent causing liver diseases. HCV has infected over 170 million people worldwide and it has become a significant causative agent of chronic liver inflammation also in Finland. HCV is a very diverse group of viruses that is divided into genotypes 1–7 as well as subtypes. HCV infection can be treated with antiviral drugs, and the drug of choice as well as treatment success are determined by the HCV genotype that the patient is carrying. The aim of this study was to develop a new, sequencing based HCV genotyping method for the Laboratory of the Hospital District of Helsinki and Uusimaa (HUSLAB), at the Department of Virology and Immunology. The focus of the study was to establish a steady and robust genotyping method that would be suitable for the workflow in clinical diagnostics. The samples used in this study had been previously analysed in regular HCV genotyping diagnostics at HUSLAB. The genomic regions chosen for amplification with several different primer options were 5’UTR, core/E1 and NS5B. 5’UTR turned out to be the only suitable option for the diagnostic workflow. The amplification products were sequenced using Sanger method. Amplification of the whole HCV genome in several different reaction conditions for 454 deep sequencing was also attempted to obtain information about possible mixed infections and drug resistance changes in the genome. In this study, a new HCV genotyping method based on Sanger sequencing of the 5’UTR region was successfully established. The method is robust, stable and suitable for the use in clinical diagnostics. The established HCV genotyping method is the first entirely sequencing-based method in clinical viral diagnostics in Finland. The secondary aim, amplification of the whole HCV genome using a method suitable for the workflow of clinical diagnostics was not achieved. Given the demands and restrictions of the workflow of clinical diagnostics we can conclude that routine HCV genotyping with deep sequencing methods is for the present not yet possible.
  • Huiko, Marjo (Helsingin yliopisto, 2021)
    This thesis was undertaken to determine effects of genotype, vernalization and harvesting on the root growth of grass plants. Greenhouse experiments were carried out at Viikki experimental farm of University of Helsinki. The thesis was a part of a larger research of grasses. Grass species were two timothy (Phleum pratense L.) parental lines, northern (021/1) and southern (B112) genotype (Boreal Plant Breeding Ltd). The trial material was propagated using the plant material conserve of Viikki. A half of the trial material got a vernalization treatment (10 weeks) after pre-breeding (2 weeks, DL 12 h) and the other half of plants got only pre-breeding (3 weeks, DL 12h) before establishment of two separate trials in rhitsotubes and rhitsotrones. High, growth stage, dry matter of shoots and roots, depth of the root system and shoot to root ratios were measured from rhitsotubes seven times during the study. The growth samples from rhitzotrones were collected twice. The harvesting was done in the middle of the study from both separate trials. Genotype had an influence on all measured growth features in both separate trials. Treatments of southern genotypes were mainly higher, development was faster and dry matter of shoots was greater at harvest time compared to the same treatments of the northern genotype. There were no differences on growth features between genotypes in the end. The dry matter of roots was also greater at the harvest time with treatments of the southern genotype. In the end of the trial there were no differences between genotypes or treatments, but the genotype influenced on root growth in repeated measurements between weeks 6-8. The root system of the southern genotype spread out in deeper soil layers with both treatments and survived better after harvesting compared to treatments of the northern genotype. The vernalization had influence on growth features and the root system with most of the occasions of measurements with both the genotypes. The vernalization reduced biomass of roots in the both separate trials. This was partly due to low weight of shoots especially in the beginning of the study. In the other hand the vernalization improved on development before the harvesting and the carbohydrates allocated on shoots instead of roots. This was visible especially in the rhitsotubes. Differences between vernalized and non-vernalized treatments were levelled towards the end of the study. The vernalization increased growth of roots to deeper soil layers comparing to the non-vernalized treatment with the northern genotype. In weekly monitoring the growth of roots of both the vernalized genotypes were strong before ending the study. This might cite better overwintering but in the other hand shoot to root ratios were almost the same in all treatments. This study showed out that a plant tries to keep the growth of shoots and roots in balance but also that the biomass allocates in shoots in the beginning of the growing season and more in roots after harvesting. According to this study adding the southern genetic heritage to the timothy refinement programs brings higher yield level and moreover more abundant and deeper root system.
  • Kymäläinen, Sonja (Helsingfors universitet, 2016)
    The woodland strawberry (Fragaria vesca) exists almost in the entire Northern Hemisphere. Short daylength and low temperature induce flowering in autumn. Flowering begins in the next growing season when daylength becomes longer and temperature increases. The aim of this study was to find out the critical daylength for flower induction in woodland strawberry genotypes from different latitudes. The aim was to find out differences in vegetative growth, flowering and FT-gene expression between different genotypes in three daylengths. In this study ten different genotypes from different latitudes were used as the plant material. There were three daylength treatments; 12h, 14h and 16h. After six weeks of treatments plants were moved to greenhouse where the daylength was long (18h). In this study the number of stolons and crowns, petiole length, flowering time and the number of inflorescences were observed. In addition RNA was isolated from five genotypes and the expression of FT-gene was determined. The beginning of flowering depended on daylength and genotype. The northern genotypes began to flower soon after all treatments and they also formed more inflorescences than the southern genotypes. The southern genotypes flowered last and only after 12h and 14h treatments. FT-gene expression was noticed only in 16h daylength and the expression was the strongest in southern genotypes which didn´t begin flowering in this treatment. The petiole lengths were shorter in northern genotypes than in southern genotypes. The number of crowns depended on daylength. In 12h daylength there were more crowns than in 16h daylength. On the other hand there weren´t differences in the number of crowns between the genotypes. The critical daylength for flower induction depends on the latitude of the origin. The critical daylength for flower induction was noticed to be over 16h in Norwegian genotypes. The critical daylength for flower induction is over 14h but under 16h in Finnish and Central Europe genotypes. In southern genotypes the critical daylength for flower induction is over 12h but under 14h. Longer daylengths enhance vegetative growth except crown branching.
  • Töttölä, Henni (Helsingin yliopisto, 2018)
    Timoteitä (Phleum pratense L.) viljellään Suomessa karjalle rehuksi. Sen kasvuston rakenne vaikuttaa satoon ja sadon ominaisuuksiin. Typpilannoituksen, vernalisaation ja genotyypin kaikkia vaikutuksia näihin ominaisuuksiin ei vielä tiedetä tarkkaan. Tietoa tarvitaan uusien lajikkeiden typpilannoitussuositusten kehittämiseen sekä avuksi timotein lajikejalostuksessa sopeuduttaessa ilmastonmuutokseen ja maataloustuotannon kestävään tehostamiseen. Tämän tutkimuksen tavoitteena oli selvittää miten typpilannoitus, vernalisaatio ja kasvin perimä vaikuttavat timotein kasvustorakenteeseen ja miten typpi vaikuttaa vernlaisaatio geeneihin ja kukintaan. Kokeessa oli mukana kaksi timotein genotyyppiä, eteläinen (BorE) ja pohjoinen (BorP), jotka eroavat toisistaan vernalisaatiovaatimukseltaan. Typpitasoja oli kolme, jotka vastasivat peltolannoituksen tasoja 11,6 kg N/ha (N1), 278,3 kg N/ha (N2) ja 545,0 kg N/ha (N3). Kasvit joko vernalisoitiin 10 viikon ajan tai niitä ei vernalisoitu ennen siirtoa kasvihuoneelle pitkään päivään. Kasveista mitattiin viikottain korren pituus, versojen lukumäärä ja lehtien lukumäärä, sekä kokeen lopussa kuiva-aineen kertyminen sekä versotyyppien lukumäärä (GEN, ELONG, VEG). Kasveista kerättiin näytteitä ennen pitkään päivään tai vernalisaatioon siirtämistä sekä 1-4 vk kasvihuoneelle siirron jälkeen RNA näytteet, joista analysoitiin PpVRN1 ja PpVRN3 geenien ilmeneminen qPCR analyysillä. Typpilannoitus vaikutti tilastollisesti merkittävästi kaikkiin mitattuihin tekijöihin kasvustorakenteessa. Typpi lisäsi erityisesti versojen lukumäärää ja se alensi tai viivästytti erityisesti PpVRN3 geenin ilmenemistä. Vernalisoimattomassa BorE kasveissa typpi lisäsi myös GEN versojen lukumäärää. Typellä oli kaiken kaikkiaan tilastollisesti merkittävä vaikutus VRN geenien ilmenemiseen. Lisäksi genotyyppi vaikutti kasvustorakenteen siten, että BorE olivat keskimäärin korkeampia. Timotein genotyyppi vaikutti typen vasteeseen ainoastaan korsijakauman kautta. Typpilannoituksella ja sen määrällä havaittiin olevan vaikutusta timotein kasvustorakenteeseen, kukkivien versojen lukumäärään sekä vernalisaatiogeenien ilmenemiseen. Typen vaikutukset eivät kuitenkaan olleet yksiselitteisiä vaan yhdysvaikutuksia esiintyi runsaasti. Typen vaikutukset kukintaan oli selkeämpi BorE kasveissa, mikä voi viitata siihen, että vernalisaatiolla ja sen vaatimuksella voi olla merkitystä genotyypin typpivasteeseen.