Experimental and computational studies on lipoprotein lipolysis at acidic pH

Atherosclerosis is a disease of the arteries; its characteristic features include chronic inflammation, extra- and intracellular lipid accumulation, extracellular matrix remodeling, and an increase in extracellular matrix volume. The underlying mechanisms in the pathogenesis of advanced atherosclerotic plaques, that involve local acidity of the extracellular fluid, are still incompletely understood. In this thesis project, my co-workers and I studied the different mechanisms by which local extracellular acidity could promote accumulation of the atherogenic apolipoprotein B-100 (apoB-100)-containing plasma lipoprotein particles in the inner layer of the arterial wall, the intima. We found that lipolysis of atherogenic apoB-100-containing plasma lipoprotein particles (LDL, IDL, and sVLDL) by the secretory phospholipase A2 group V (sPLA2-V) enzyme, was increased at acidic pH. Also, the binding of apoB-100-containing plasma lipoprotein particles to human aortic proteoglycans was dramatically enhanced at acidic pH. Additionally, lipolysis by sPLA2-V enzyme further increased this binding. Using proteoglycan-affinity chromatography, we found that sVLDL lipoprotein particles consist of populations, differing in their affinities toward proteoglycans. These populations also contained different amounts of apolipoprotein E (apoE) and apolipoprotein C-III (apoC-III); the amounts of apoC-III and apoE per particle were highest in the population with the lowest affinity toward proteoglycans. Since PLA2-modification of LDL particles has been shown to change their aggregation behavior, we also studied the effect of acidic pH on the monolayer structure covering lipoprotein particles after PLA2-induced hydrolysis. Using molecular dynamics simulations, we found that, in acidity, the monolayer is more tightly packed laterally; moreover, its spontaneous curvature is negative, suggesting that acidity may promote lipoprotein particles fusion. In addition to extracellular lipid accumulation, the apoB-100-containing plasma lipoprotein particles can be taken up by inflammatory cells, namely macrophages. Using radiolabeled lipoprotein particles and cell cultures, we showed that sPLA2-V-modification of LDL, IDL, and sVLDL lipoproteins particles, at neutral or acidic pH, increased their uptake by human monocyte-derived macrophages.

Campylobacter Infections of Domestic Origin in Finland

Campylobacter jejuni and C. coli are the leading causes of human bacterial gastroenteritis in developed countries. Most human Campylobacter infections are sporadic and a seasonal peak in the distribution of infections can be seen in the summer months in several countries, including Finland. A variety of risk factors for Campylobacter infections have been identified; handling and eating poultry, drinking unpasteurized milk, contact with domestic animals, and travelling abroad. However, the relative importance of the different risk factors in sporadic cases of Campylobacter infection remains unknown. In most cases, the infection is self-limiting and no specific treatment is required. Campylobacter enteritis can cause a wide range of complications, including reactive arthritis (ReA) that is reported in 1-5% of the cases. Seven clinical microbiology laboratories serving different geographical areas of Finland, participated in this multi-centre study, conducted during a seasonal peak in 2002. In a matched case-control study, domestically-acquired sporadic Campylobacter infections from three geographical areas were collected. The final study comprised 100 cases and 137 controls. Risk factors for sporadic domestically-acquired Campylobacter infections were identified on the basis of a questionnaire; swimming in natural waters was found to be a novel risk factor for Campylobacter infection. Other independent risk factors were tasting or eating raw or undercooked meat and drinking untreated water from a dug well. The role of bacterial strain and host characteristics are not fully understood in Campylobacter infections. Exposure factors, demographical characteristics, and the serotype of the Campylobacter isolate may affect the severity of the enteritis. This cross-sectional study comprised 114 patients with C. jejuni enteritis, diagnosed in three clinical microbiology laboratories; most of the patients had participated in the previous case-control study. Swimming was associated with age ≤ 5 years and serotype Pen 6,7 was found significantly more often among patients reporting swimming. The geographical distribution among serotypes varied; serotype Pen 4-complex appeared more often in patients from urban areas and serotype Pen 21 among patients from more rural areas. Thus, risk factors and sources of infection for C. jejuni infection may vary among individuals depending on age and geographical location. The in vitro susceptibilities of C. jejuni and C. coli strains isolated from patients infected abroad (85 strains) or domestically (393 strains) revealed that susceptibility to erythromycin is still high, even among isolates of foreign origin. However, the novel antimicrobial agent telithromycin did not offer any advantage over erythromycin; isolates with high minimal inhibitory concentrations (MICs) for erythromycin also showed reduced susceptibility to telithromycin. Reduced susceptibility to fluoroquinolones was detected almost exclusively among isolates of foreign origin and half of these isolates with high MICs for fluoroquinolones also showed elevated MICs for doxycycline. Questionnaires concerning complications associated with C. jejuni enteritis were sent to patients two months after becoming ill; 201 patients from seven different geographical areas were included in the study. Musculoskeletal complications after C. jejuni infection were commonly reported by patients (39%). The incidence of classical ReA was 4% and that of Achilles enthesopathy and/or heel pain 9%. Other C. jejuni-associated reactive joint symptoms were commonly reported, however, due to their milder nature seldom seen and diagnosed by a physician. The severity of the enteritis may predict further complications; stomach ache during enteritis was connected to the development of later joint pain. Early antimicrobial treatment, within two days from the start of symptoms, shortened the duration of diarrhoea by two days but did not prevent later musculoskeletal complications. Campylobacter is an important human enteropathogen and causes a significant burden of illness. As the incidence of Campylobacter infections is high, the importance of the infection and the occurrence of complications will increase. This stresses the importance of understanding the risk factors for acquiring Campylobacter infection and how bacterial strain and host characteristics may affect the risk for infection. The role of antimicrobial treatment for acute Campylobacter enteritis seems to be marginal and should be used restrictively.

Regulation of tumor suppressor protein p53 in cellular stress and tumorigenesis

Functional loss of tumor suppressor protein p53 is a common feature in diverse human cancers. The ability of this protein to sense cellular damage and halt the progression of the cell cycle or direct the cells to apoptosis is essential in preventing tumorigenesis. Tumors having wild-type p53 also respond better to current chemotherapies. The loss of p53 function may arise from TP53 mutations or dysregulation of factors controlling its levels and activity. Probably the most significant inhibitor of p53 function is Mdm2, a protein mediating its degradation and inactivation. Clearly, the maintenance of a strictly controlled p53-Mdm2 route is of great importance in preventing neoplastic transformation. Moreover, impairing Mdm2 function could be a nongenotoxic way to increase p53 levels and activity. Understanding the precise molecular mechanisms behind p53-Mdm2 relationship is thus essential from a therapeutic point of view. The aim of this thesis study was to discover factors affecting the negative regulation of p53 by Mdm2, causing activation of p53 in stressed cells. As a model of cellular damage, we used UVC radiation, inducing a complex cellular stress pathway. Exposure to UVC, as well as to several chemotherapeutic drugs, causes robust transcriptional stress in the cells and leads to activation of p53. By using this model of cellular stress, our goal was to understand how and by which proteins p53 is regulated. Furthermore, we wanted to address whether these pathways affecting p53 function could be altered in human cancers. In the study, two different p53 pathway proteins, nucleophosmin (NPM) and promyelocytic leukemia protein (PML), were found to participate in the p53 stress response following UV stress. Subcellular translocations of these proteins were discovered rapidly after exposure to UV. The alterations in the cellular localizations were connected to transient interactions with p53 and Mdm2, implicating their significance in the regulation of p53 stress response. NPM was shown to control Mdm2-p53 interface and mediate p53 stabilization by blocking the ability of Mdm2 to promote p53 degradation. Furthermore, NPM mediated p53 stabilization upon viral insult. We further detected a connection between cellular pathways of NPM and PML, as PML was found to associate with NPM in UV-radiated cells. The observed temporal UV-induced interactions strongly imply existence of a multiprotein complex participating in the p53 response. In addition, PML controlled the UV response of NPM, its localization and complex formation with chromatin associated factors. The relevance of the UV-promoted interactions was demonstrated in studies in a human leukemia cell line, being under abnormal transcriptional repression due to expression of oncogenic PML-RARa fusion protein. Reversing the leukemic phenotype with a therapeutically significant drug was associated with similar complex formation between p53 and its partners as following UV. In conclusion, this thesis study identifies novel p53 pathway interactions associated with the recovery from UV-promoted as well as oncogenic transcriptional repression.

The efficacy and potential risks of controlling sprouting in Finnish birches (Betula spp.) with the fungal decomposer Chondrostereum purpureum

Sprouting of fast-growing broad-leaved trees causes problems in young coniferous stands, under power transmission lines and along roads and railways. Public opinion and the Finnish Forest Certification System oppose the use of chemical herbicides to control sprouting, which means that most areas with problems rely on mechanical cutting. However, cutting is a poor control method for many broad-leaved species because the removal of leaders can stimulate the sprouting of side branches and cut stumps quickly re-sprout. In order to be effective, cutting must be carried out frequently but each cut increases the costs, making this control method increasingly difficult and expensive once begun. As such, alternative methods for sprout control that are both effective and environmentally sound represent a continuing challenge to managers and research biologists. Using biological control agents to prevent sprouting has been given serious consideration recently. Dutch and Canadian researchers have demonstrated the potential of the white-rot fungus Chondrostereum purpureum (Pers. ex Fr.) Pouzar as a control agent of stump sprouting in many hardwoods. These findings have focused the attention of the Finnish forestry community on the utilization of C. purpureum for biocontrol purposes. Primarily, this study sought determines the efficacy of native C. purpureum as an inhibitor of birch stump sprouting in Finland and to clarify its mode of action. Additionally, genotypic variation in Finnish C. purpureum was examined and the environmental risks posed by a biocontrol program using this fungus were assessed. Experimental results of the study demonstrated that C. purpureum clearly affects the sprouting of birch: both the frequency of living stumps and the number of living sprouts per stump were effectively reduced by the treatment. However, the treatment had no effect on the maximum height of new sprouts. There were clear differences among fungal isolates in preventing sprouting and those that possessed high oxidative activities as measured in the laboratory inhibited sprouting most efficiently in the field. The most effective treatment time during the growing season was in early and mid summer (May July). Genetic diversity in Nordic and Baltic populations of C. purpureum was found to be high at the regional scale but locally homogeneous. This natural distribution of diversity means that using local genotypes in biocontrol programs would effectively prevent the introduction of novel genes or genotypes. While a biocontrol program using local strains of C. purpureum would be environmentally neutral, pruned birches that are close to the treatment site would have a high susceptibility to infect by the fungus during the early spring.

Maiseman- ja luonnonhoidon taloudelliset vaikutukset Pihlajaveden metsänomistajille

Tutkimuksen tavoitteet Tutkimuksen teoreettinen osa esittelee yhteiskunnallisten hankkeiden arvottamiseen liittyvää koti- ja ulkomaista kirjallisuutta. Empiirinen osa tutkii Savonlinnasta poimitun metsätilaotoksen avulla maiseman- ja luonnonhoidon aiheuttamia taloudellisia vaikutuksia tilojen metsänomistajille sekä vertaa näitä tuloksia haastattelututkimuksesta saatuihin vastauksiin maksuhalukkuudesta monimuotoisuuden hyväksi. Lähdeaineisto Metsämaiseman- ja luonnonhoidon aiheuttamia taloudellisia vaikutuksia tutkittaessa case-aineistona käytettiin keskeisen Saimaan Pihlajaveden saaristoalueen 24 tilaa, joiden omistajat olivat tilanneet Etelä-Savon metsäkeskukselta uudentyyppisen maiseman- ja luonnonhoidon arvot huomioivan metsäsuunnitelman. Samalla aineistolla suoritettiin myös metsänomistajien haastattelu, jonka avulla selvitettiin metsänomistajien maksuhalukkuutta monimuotoisuudesta ja maisemamansuojelusta. Lisäksi kysyttiin mielipiteitä nykyisistä metsänhoitosuosituksista ja alueelle kaavailluista luonnonsuojeluhankkeista. Aineiston käsittely Taloudellisia vaikutuksia tutkittaessa maisema- ja luontoarvoja korostavaa metsäsuunnitelmalaskelmaa verrattiin maksimaaliseen puuntuotantoon tähtäävään metsäsuunnitelmaan. Näiden kahden vaihtoehtoisten laskelman välinen erotus tulkittiin monimuotoisuuden turvaamisen metsälötason puuntuotannolliseksi vaikutukseksi. Vastaavasti haastatteluosuudessa metsänomistajilta kysyttiin, kuinka paljon he olisivat valmiita luopumaan metsätuloistaan monimuotoisuuden edistämiseksi. Maksuhalukkuutta tutkittaessa käytettiin contingent valuation -menetelmää. Tulokset Siirtyminen ns. perinteisestä metsänkäsittelystä maiseman- ja luonnonhoidon huomioivaan metsänkäsittelyyn pienentää metsästä saatavia nettotuloja ensimmäisen kymmenvuotiskauden aikana 36 % eli 289 mk/ha vuosittain. Vastaavasti metsänomistajien maksuhalukkuus monimutoisuuden edistämisestä oli 5,3 % metsätuloista, joka on rahassa 18 mk/ha vuosittain. Nettotulojen merkittävä pieneneminen selittyy kohteen arvokkailla maisema-arvoilla ja ekologisten elinympäristöjen runsaalla lukumäärällä. Tulosten tilastollista luotettavuutta ei otoksen pienuuden vuoksi voitu tarkastella. Avainsanat: metsämaiseman- ja luonnonhoito, metsätulot, maksuhalukkuus, monimuotoisuus, Pihlajaveden saaristo

Selenium and its effects on growth, yield and tuber quality in potato

Selenium (Se) has been demonstrated to be an essential trace element for maintenance of animal and human health. Although it has not been confirmed to be an essential micronutrient in higher plants, there is increasing evidence that Se functions as an antioxidant in plants. Selenium has been shown to exert a beneficial effect on crop growth and promotes stress tolerance at low concentrations. However, the specific physiological mechanisms that underlie the positive effects of Se in plants have not been clearly elucidated. The aims of this study were to determine the Se concentration in potato (Solanum tuberosum L.) and the effects of Se on the accumulation of carbohydrates, growth and yield in potato plants. An additional aim was to study the impact of Se on the total glycoalkaloid concentration in immature potato tubers. The distribution of Se in different biochemical Se fractions and the effect of storage on the Se concentration were studied in Se-enriched tubers. Furthermore, the effect of Se on raw darkening and translocation of Se from seed tubers to the next tuber generation was investigated. Due to the established anti-ageing properties of Se, it was of interest to study if Se affects physiological age and growth vigour of seed tubers. The Se concentrations in the upper leaves, roots, stolons and tubers of potato increased with increasing Se supplementation. The highest Se concentration was reached in young upper leaves, roots and stolons, indicating that added selenate was efficiently utilized and taken up at an early stage. During the growing period the Se concentration declined in the aerial parts, roots and stolons of potato plants whereas an intensive accumulation took place in immature and mature tubers. Selenium increased carbohydrate accumulation in the young upper leaves and in stolons, roots and tubers at maturity. This could not be explained by increased production of photoassimilates as net photosynthesis did not differ among Se treatments. The Se treated plants produced higher tuber yields than control plants, and at the highest Se concentration (0.3 mg kg-1) lower numbers of larger tubers were harvested. Increased yield of Se treated plants suggested that Se may enhance the allocation of photoassimilates for tuber growth, acting as a strong sink for both Se and for carbohydrates. Similarly as for other plant species, the positive impact of Se on the yield of potato plants could be related to its antioxidative effect in delaying senescence. The highest Se supplementation (0.9 mg kg-1) slightly decreased the glycoalkaloid concentration of immature tubers. However, at this level the Se concentration in tubers was about 20 µg g-1 DW. A 100 g consumption of potato would provide about 500 mg of Se, which exceeds the upper safe intake level of 400 µg per day for human dietary. The low Se applications (0.0035 and 0.1 mg kg-1) diminished and retarded the degree of raw darkening in tubers stored for one and eight months, which can be attributed to the antioxidative properties of Se. The storage for 1 to 12 months did not affect the Se concentrations of tubers. In the Se enriched tubers Se was allocated to the organic Se fraction, indicating that it was incorporated into organic compounds in tubers. Elevated Se concentration in the next-generation tubers produced by the Se enriched seed tubers indicated that Se could be translocated from the seed tubers to the progeny. In the seed tubers stored for 8 months, at high levels, Se had some positive effects on the growth vigour of sprouts, but Se had no consistent effect on the growth vigour of seed tubers of optimal physiological age. These results indicate that Se is a beneficial trace element in potato plants that exerts a positive effect on yield formation and improves the processing and storage quality of table potato tubers. These positive effects of Se are, however, dependent on the Se concentration and the age of the potato plant and tuber.

Microbial quality of hemp (Cannabis sativa L.) and flax (Linum usitatissimum L.) from plants to thermal insulation

Flax and hemp have traditionally been used mainly for textiles, but recently interest has also been focused on non-textile applications. Microbial quality throughout the whole processing chain of bast fibres has not previously been studied. This study concentrates on the microbial quality and possible microbial risks in the production chain of hemp and flax fibres and fibrous thermal insulations. In order to be able to utilize hemp and flax fibres, the bast fibres must be separated from the rest of the plant. Non-cellulosic components can be removed with various pretreatment processes, which are associated with a certain risk of microbial contamination. In this study enzymatic retting and steam explosion (STEX) were examined as pretreatment processes. On the basis of the results obtained in this study, the microbial contents on stalks of both plants studied increased at the end of the growing season and during the winter. However, by processing and mechanical separation it is possible to produce fibres containing less moulds and bacteria than the whole stem. Enzymatic treatment encouraged the growth of moulds in fibres. Steam explosion reduced the amount of moulds in fibres. Dry thermal treatment used in this study did not markedly reduce the amount of microbes. In this project an emission measurement chamber was developed which was suitable for measurements of emissions from both mat type and loose fill type insulations, and capable of interdisciplinary sampling. In this study, the highest amounts of fungal emissions were in the range of 10^3 10^5 cfu/m^3 from the flax and hemp insulations at 90% RH of air. The fungal emissions from stone wool, glass wool and recycled paper insulations were below 10^2 cfu/m^3 even at 90% RH. Equally low values were obtained from bast fibrous materials in lower humidities (at 30% and 80% RH of air). After drying of moulded insulations at 30% RH, the amounts of emitted moulds were in all cases higher compared to the emissions at 90% RH before drying. The most common fungi in bast fibres were Penicillium and Rhizopus. The widest variety of different fungi was in the untreated hemp and linseed fibres and in the commercial loose-fill flax insulation. Penicillium, Rhizopus and Paecilomyces were the most tolerant to steam explosion. According to the literature, the most common fungi in building materials and indoor air are Penicillium, Aspergillus and Cladosporium, which were all found in some of the bast fibre materials in this study. As organic materials, hemp and flax fibres contain high levels of nutrients for microbial growth. The amount of microbes can be controlled and somewhat decreased by the processing methods presented.

Vadelman (Rubus idaeus) kasvunsäätö proheksadioni-kalsiumin avulla

Vadelman (Rubus idaeus L.) viljelyala on kasvanut Suomessa voimakkaasti viimeisten viiden vuoden aikana. Vuonna 2005 vadelmaa viljeltiin 473 hehtaarilla. Vadelman satoindeksi on alhainen. Sen pääverso on pitkä, mikä hankaloittaa hoitotoimenpiteitä. Kasvin satoisimmat silmut ovat pääverson kärjessä, joten latvontaa ei kannata tehdä. Suomessakin haluttaisiin kehittää vadelman kasvihuonetuotantoa satokauden pidentämiseksi. Kasvihuonetuotannossa vegetatiivisen kasvun säätäminen on vielä tärkeämpää kuin avomaan viljelyssä. Proheksadioni-kalsium (ProCa) on gibberelliinisynteesi-inhibiittori, jonka on havaittu lyhentävän nivelvälejä sekä lisäävän versojen ja lehtien hiilihydraattipitoisuutta mm. omenalla (Malus domestica Borkh.). Tämän Helsingin yliopiston soveltavan biologian laitoksella toteutetun tutkimuksen tarkoituksena oli selvittää, miten ProCa vaikuttaa kahden kesävadelmalajikkeen ensimmäisen vuoden versojen vegetatiiviseen kasvuun ja edelleen sadontuottokykyyn. Tässä pro gradu -työssä tutkittiin ProCa:n vaikutusta kahden kesävadelmalajikkeen vegetatiiviseen kasvuun, satopotentiaaliin sekä versojen ja silmujen hiilihydraattipitoisuuksiin kesällä 2005 ja talvella 2006. Koetaimina oli 120 Tulameen-lajikkeen ja 150 Glen Ample -lajikkeen tainta. Taimet käsiteltiin kesäkuussa ja käsittely uusittiin osalle taimista neljän viikon kuluttua ensimmäisestä käsittelystä. Koekäsittelyitä oli neljä: ProCa 100 ppm, ProCa 200 ppm, ProCa 100 ppm + ProCa 100 ppm ja ProCa 200 ppm + ProCa 200 ppm. Kontrollikäsittelyitä oli kaksi: vesi sekä vesi + vesi. Kesän aikana havainnoitiin pääverson pituuskasvua ja nivelien määrää. Kesän kasvatuskauden päätyttyä Glen Ample -lajikkeen silmujen ja versojen liukoiset hiilihydraatit ja tärkkelys määritettiin entsymaattisesti. Kylmävarastoinnin jälkeen (71 vrk) tammikuussa 2006 taimet siirrettiin hyötöön kasvihuoneeseen. Hyödön aikana havainnoitiin silmujen puhkeamista ja kukintaa. Hyödön päättyessä hanka- ja pääversojen kuivapaino sekä hankaversojen pituus mitattiin. Kesän 2005 aikana ProCa lyhensi uusien nivelvälien pituuksia väliaikaisesti 1 4 viikon kuluttua käsittelystä. Nivelien lukumäärässä ei tapahtunut suuria muutoksia. Tulameen-lajikkeella kasvu kiihtyi käsittelyn vaikutuksen loputtua. Nivelvälien lyhentymisen takia pääverson kokonaispituus jäi kontrolliin verrattuna 35 % lyhyemmäksi Glen Ample -lajikkeella (ProCa 200 + ProCa 200) ja 14 % lyhyemmäksi Tulameen-lajikkeella samalla käsittelyllä. Myös käsittely ProCa 200 vähensi pääverson pituutta 6 % kontrolliin verrattuna Tulameen-lajikkeella. ProCa-käsittely lisäsi versojen ja silmujen hiilihydraattipitoisuuksia, mutta tuloksissa oli paljon hajontaa. Glen Ample -lajikkeella kaksinkertaiset käsittelyt vähensivät puhjenneiden silmujen osuutta 8 15 päivän kuluttua hyödön aloittamisesta 24 29 %, mutta käsittelyiden väliset erot tasoittuivat hyödön loppuun mennessä. Lisäksi kaksinkertaiset ProCa-käsittelyt vähensivät kukkien määrää 29 44 % 33 65 päivää hyödön alusta, mutta erot tasoittuivat hyödön loppuun mennessä. Käsittelyt eivät vaikuttaneet Tulameen-lajikkeen silmujen puhkeamiseen ja kukintaan. Satopotentiaalissa ei ollut eroa ProCa-käsittelyiden välillä kummallakaan lajikkeella. Glen Ample -lajikkeella hankaversojen kokonaismäärä väheni 27 32 % kasveilla, joita oli käsitelty kaksi kertaa ProCa:lla. Hankaversot olivat kuitenkin vastaavasti 29 43 % pidempiä. Tulameen-lajikkeella ProCa 100 -käsittely vähensi hankaversojen määrää 15 %, mutta hankaversojen pituuteen käsittelyillä ei ollut vaikutusta. Käsittelyillä ei ollut vaikutusta hankaversojen nivelvälien pituuteen kummallakaan lajikkeella. Tutkimuksen perusteella kesällä annetulla ProCa-käsittelyllä voidaan lyhentää pääverson pituutta, mutta satopotentiaaliin käsittelyllä ei ole vaikutusta. Käsittelyajankohta on kriittinen, koska kukkasilmujen kehitys näyttäisi häiriintyvän, jos ruiskutus tehdään loppukesällä.

Developments and Microbiological applications in African foods: Emphasis on Nigerian Wara cheese

African indigenous foods have received limited research. Most of these indigenous foods are fermented and they form part of the rich nutritional culture of many groups in African countries. The industrialization and commercialisation of these indigenous African fermented foods should be preceded by a thorough scientific knowledge of their processing which can be vital in the elimination of hunger and poverty. This study highlighted emerging developments and the microbiology of cereal-based and cassava-based food products that constitute a major part of the human diet in most African countries. In addition, investigations were also carried out on the coagulant of the Calotropis procera plant used in traditional production of Nigerian Wara cheese and on the effects of adding a nisin producing Lactococcus lactis strain originating from human milk to Nigerian Wara cheese. Fermented cereal-based food such as ogi utilize popular African and readily available grains maize, millet or sorghum as substrates and is popular as a weaning diet in infants. In this study, the bulkiness caused by starch gelatinization was solved by amylase treatments in the investigation on cooked and fermented oat bran porridge. A similar treatment could reduce the viscosity of any cereal porridge. The properties of the Sodom apple leaves (Calotropis procera) extract in cheesemaking were studied. C. procera was affected by monovalent (K+ and Na+) and divalent (Mg2+ and Ca2+) cations during coagulation. The rennet strength of this coagulant was found to be 7 % compared to animal rennet at 35 °C. Increasing the incubation temperature to 70 °C increased the rennet strength 28-fold. The molecular weight of the partially purified protease was determined by SDS-PAGE and was confirmed by Zymography to be approximately 60 kilodaltons. The high proteolytic activity at 70 °C supported the suitability of the protease enzyme as a coagulant in future commercial production of Nigerian Wara cheese. It was also possible to extend the shelf life of Wara cheese by a nisin producing lactic acid bacteria Lactococcus lactis LAC309. The levels of nisin in both whey and curd fractions of Wara were investigated, results showed a 3 log reduction of toxicogenic Bacillus licheniformis spiked on Wara after 3 days. These studies are the first in Finland to promote the advancement of scientific knowledge in African foods. Recognizing these indigenous food products and an efficient transfer of technology from the developed countries to industrialize them are necessary towards a successful realization of the United Nations Millenium Development Program.

Havaintojärjestelmäkokeet numeerisessa sään ennustamisessa

Sään ennustamisessa tärkeä työväline on numeerinen säämalli, jossa ilmakehän tilan kuvaaminen perustuu niin sanottujen perusyhtälöiden ratkaisemiseen. Niiden avulla lasketaan tuulen nopeuden, ilmanpaineen, lämpötilan ja kosteuden muutokset pienin aika-askelin eteenpäin. Numeerinen säämalli tarvitsee lähtötiedokseen laadultaan hyviä havaintoja ilmakehän todellisesta tilasta. Joka vuorokausi kymmenet in-situ- ja kaukohavaintojärjestelmät tekevät havaintoja ilmakehästä sen pintakerroksesta ylärajaan asti. Pelkät havainnot eivät kuitenkaan riitä antamaan tarpeeksi tarkkoja lähtötietoja säämallille. Ongelman ratkaisu on data-assimilaatiojärjestelmä. Se yhdistää laatukontrollin läpikäyneen havaintotiedon ja mallitiedon, jota kutsutaan ennakkokentäksi, ja luo niiden avulla analyysin ilmakehän todellisesta tilasta. Havaintojärjestelmäkokeiden (OSE) avulla testataan havaintojärjestelmien vaikutuksia data-assimilaatiojärjestelmän tuottamien analyysien ja niistä tuotettujen sääennusteiden laatuun. OSE:n avulla selvitetään, kuinka hyvin saatavilla olevia havaintoja käytetään hyväksi, tai kannattaako jokin uusi havaintojärjestelmä ottaa mukaan operatiiviseen ennustusjärjestelmään. Tämän tutkielman aluksi tutustutaan lyhyesti numeerisiin säämalleihin, havaintojärjestelmiin ja dataassimilaatiojärjestelmiin, minkä jälkeen tehdään yleinen kirjallisuuskatsaus havaintojärjestelmäkokeiden suorittamisesta. Sen jälkeen keskitytään Doppler-säätutkan tuottamien tutkasäteen suuntaisten tuulen nopeushavaintojen hyödyntämiseen rajoitetun alueen HIRLAM-säämallissa, mitä on tutkittu viime vuosina Ilmatieteen laitoksessa (IL). Kaukohavaintojärjestelmien käyttö on lisääntynyt viime vuosien aikana kehittyneiden analyysimenetelmien ansiosta. Tavanomaisten in-situ- havaintojärjestelmien raju vähentäminen dataassimilaatiossa ei näytä kuitenkaan vielä olevan mahdollista. Kaukohavainnot ovat useiden OSE-kokeiden perusteella parantaneet analyysiä ja ennusteita erityisesti alueilla, joissa tavanomainen havaintoverkosto on harva. Tutkatuulihavaintojen on ajateltu tuovan parannuksia rajoitetun alueen säämalleihin, sillä niiden avulla saadaan tärkeää lisätietoa tuulen ageostrofisista ominaisuuksista. Sen johdosta pienen mittakaavan sääilmiöiden kuten meri- ja rinnetuulien ennustettavuuden toivotaan paranevan. IL:ssa on kehitetty tutkatuulihavaintojen käsittely- ja mallintamismenetelmiä, minkä jälkeen on suoritettu OSE Suomen tutkaverkoston tuulihavainnoilla aikavälille 1.-29.2.2008 HIRLAMin operatiiviselle 3D-VAR dataassimilaatiojärjestelmälle. Kyseisen OSE:n aineisto on saatu käyttöön tähän tutkielmaan. Kontrolliassimilaatiossa CON ovat mukana kaikki operatiiviset havaintojärjestelmät ja koeassimilaatioon RAD_ALL on syötetty myös tutkatuulihavainnot. Tässä tutkielmassa OSE:n tulokset todennetaan TEMP-tuulihavaintojen avulla tutkimalla ennakkokentän ja analyysin harhaa sekä satunnaisvirhettä. Tulosten perusteella tutkatuulihavainnot parantavat ennakkokenttää ja analyysiä erityisesti keskitroposfäärissä, mutta alatroposfäärissä vaikutus analyysiin on lähes neutraali. Koska tutkatuulihavainnot ulottuvat n. 4-6 km korkeuteen, ne eivät vaikuta ylätroposfäärin analyysiin. Tulokset eivät kuitenkaan ole tilastollisen testin perusteella tilastollisesti merkitseviä. Parhaimmillaan RAD_ALLassimilaation voidaan osoittaa olevan CON-assimilaatiota parempi 20% merkitsevyystasolla. Lopuksi suoritettu tapaustutkimus osoittaa, että tutkatuulihavaintojen vaikutus näkyy tuulen nopeuden analyysi-inkrementtikentässä sekä jossain määrin myös lyhyessä 12h pintapaine-ennusteessa Suomen alueella. Tapaustutkimuksen perusteella tutkatuulihavaintojen vaikutus analyysiin ja ennusteeseen näyttäisi olevan lähes neutraali. OSE:n toistaminen kesäkuukaudelle voisi olla hyödyllistä, koska talvella ei esiinny esimerkiksi merituulia. Tämän tutkielman tulosten perusteella tutkatuulihavaintojen käyttäminen HIRLAMin 3D-VAR assimilaatiojärjestelmässä on hyödyllistä. Avainsanat – Nyckelord – Keywords Havaintojärjestelmäkoe, data-assimilaatio, Doppler-tutkatuulihavainto Säilytyspaikka – Förvaringställe – Where deposited Kumpulan tiedekirjasto

Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Learning Nonlinear Visual Processing from Natural Images

The paradigm of computational vision hypothesizes that any visual function -- such as the recognition of your grandparent -- can be replicated by computational processing of the visual input. What are these computations that the brain performs? What should or could they be? Working on the latter question, this dissertation takes the statistical approach, where the suitable computations are attempted to be learned from the natural visual data itself. In particular, we empirically study the computational processing that emerges from the statistical properties of the visual world and the constraints and objectives specified for the learning process. This thesis consists of an introduction and 7 peer-reviewed publications, where the purpose of the introduction is to illustrate the area of study to a reader who is not familiar with computational vision research. In the scope of the introduction, we will briefly overview the primary challenges to visual processing, as well as recall some of the current opinions on visual processing in the early visual systems of animals. Next, we describe the methodology we have used in our research, and discuss the presented results. We have included some additional remarks, speculations and conclusions to this discussion that were not featured in the original publications. We present the following results in the publications of this thesis. First, we empirically demonstrate that luminance and contrast are strongly dependent in natural images, contradicting previous theories suggesting that luminance and contrast were processed separately in natural systems due to their independence in the visual data. Second, we show that simple cell -like receptive fields of the primary visual cortex can be learned in the nonlinear contrast domain by maximization of independence. Further, we provide first-time reports of the emergence of conjunctive (corner-detecting) and subtractive (opponent orientation) processing due to nonlinear projection pursuit with simple objective functions related to sparseness and response energy optimization. Then, we show that attempting to extract independent components of nonlinear histogram statistics of a biologically plausible representation leads to projection directions that appear to differentiate between visual contexts. Such processing might be applicable for priming, \ie the selection and tuning of later visual processing. We continue by showing that a different kind of thresholded low-frequency priming can be learned and used to make object detection faster with little loss in accuracy. Finally, we show that in a computational object detection setting, nonlinearly gain-controlled visual features of medium complexity can be acquired sequentially as images are encountered and discarded. We present two online algorithms to perform this feature selection, and propose the idea that for artificial systems, some processing mechanisms could be selectable from the environment without optimizing the mechanisms themselves. In summary, this thesis explores learning visual processing on several levels. The learning can be understood as interplay of input data, model structures, learning objectives, and estimation algorithms. The presented work adds to the growing body of evidence showing that statistical methods can be used to acquire intuitively meaningful visual processing mechanisms. The work also presents some predictions and ideas regarding biological visual processing.

Luottamuksenhallinta web-palveluympäristössä

Tutkielmassa käsitellään luottamuksenhallintaa web-palveluympäristössä. Dynaaminen toimintaympäristö asettaa vaatimuksia luottamuksenhallintajärjestelmälle, jota käytetään paitsi paikallisten pääsynhallintapäätösten tekemiseen, myös laajemman mittakaavan päätöksenteon tukena, useiden autonomisten toimijoiden muodostamien yhteisöjen hallinnassa. Tutkielma esittelee Trust Based on Evidence -projektissa kehitetyn luottamuksenhallintajärjestelmän tiedollisen ja toiminnallisen mallin, paikallisesta ja yhteisön näkökulmasta. Mallia selkeytetään web-palveluympäristöön sijoittuvan esimerkin avulla. Luottamuksen käsitteen rakentamiseksi esitellään myös eri osa-alueille sijoittuvia luottamuksen malleja ja luottamusta käyttäviä järjestelmiä. Avoimessa verkkoympäristössä palveluntarjoaja joutuu tasapainottelemaan kahden osin vastakkaisen tavoitteen välillä: toisaalta järjestelmän tulisi olla mahdollisimman avoin, jotta se houkuttelisi käyttäjiä, toisaalta liiallinen avoimuus kasvattaa tietomurron riskiä. Kompromissin löytäminen on hankaloitunut edelleen saavutettavien käyttäjien määrän kasvaessa ja tarjottavien palvelujen monimutkaistuessa. Tehtävä vaatii toisaalta erikoistapauksien käsittelyä, toisaalta yleistettävyyttä laajan käyttäjistön suhteen. Tietoturvan ylläpidon automatisointia ovat edistäneet muun muassa politiikkapäätösten erottaminen toteutuksesta ja mahdollisten tietomurron merkkien tarkkailun delegointi siihen erikoistuneille ohjelmille (IDS). Palvelujen käyttäjistön kasvaessa ja siirtyessä nimettömämmiksi kurinpito ja tarkkailu kuitenkin vaikeutuvat entisestään, eikä ylläpitäjiä riitä sidottavaksi jatkuvaan käyttäjien vahtimiseen. Monesti valvoja voikin vain poistaa käyttöoikeuden häiriköltä, jolloin esimerkiksi hieman lievemmälle sääntöjen ``venyttämiselle'' ei juuri voi tehdä mitään. Luottamuksenhallinta helpottaa rikkomuksiin ja toisaalta hyvään käytökseen reagoimista asteittain. Sen pohjalta käyttäjien valvontaan, pääsynhallintaan ja resurssien rajoitukseen liittyvä hienosäätö voidaan tuoda ymmärrettäväksi osaksi ylläpitoa ja pitkälti myös automatisoida. Avainsanat: luottamuksenhallinta, Web Services

Hautamuistomerkki elämän ja kuoleman tulkitsijana : Heikki Häiväojan, Kain Tapperin ja Matti Peltokankaan tekemät hautamuistomerkit 1952-2002

Grave sculpture as interpreter of life and death. Grave sculptures done by Heikki Häiväoja, Kain Tapper and Matti Peltokangas 1952-2002. The thoughts of Philippe Ariès and Erwin Panofsky on western funeral art constitute the starting point of this study. These scholars speak about the 20th century as a period of decline regarding western funeral art. The reason for this situation lies, according to them, in the fact that death has been rejected and become a private affair in modern society. Especially Panofsky sees an important reason for the decay of funeral art also in the separation of death from religion. In this study, I approach the view of Ariès and Panofsky from the angle of Finnish funeral art. The subject of the study is grave sculptures of three Finnish sculptors: Heikki Häiväoja, Kain Tapper and Matti Peltokangas, from 1952 to 2002. (The analysis of the grave sculptures has been performed with the Iconology of Erwin Panofsky. The analysis has been deepened by the ideas of a graveyard as a semiotic text according to Werner Enninger and Christa Schwens. In order to confirm their argumentation, they analyse the graveyard text with the model of communicative functions of Roman Jakobson and verify that the graveyard is a cultural text according to Juri Lotman.) Results of the study In the grave sculptures of the sculptors, different worldviews appear alongside Christian thoughts indicating a new stage in the tradition of funeral art. In the grave sculptures characterised as Christian, the view of life after death is included. In these memorials the direction of life is prospective, pointing to the life beyond. Death is a border, beyond which one is unable to see. Nevertheless the border is open or marked by the cross. On this open border, death is absence of pain, glory and new unity. In memorials with different worldviews, the life beyond is a possibility which is not excluded. Memorials interpret life retrospectively; life is a precious memory which wakens grief and longing. Many memorials have metaphysical and mystic features. In spite of democratization the order and valuation of social classes appear in some memorials. The old order also materializes in the war memorials relating the same destiny of the deceased. Different burial places, nevertheless, do not indicate social inequality but are rather signs of diversity. The sculptors' abstract means of modern funeral art deepen the handling of the subject matter of death and reveal the mystery of it. Grave sculptures are a part of Finnish and sacral modern art, and there is an interaction between funeral art and modern art. Modern art acquires a new dimension, when grave sculptures become a part of its field. Grave sculptures offer an alternative to anonymous burying. The memorial is a sign of the end of life; it gives death significance and publicity and creates a relation to the past of the society. In this way, grave sculptures are a part of the chain of memory of the western funeral art, which extends throughout Antiquity until ancient Egypt. (In this study I have spoken of funeral art as a chain of memory using the thoughts of Danièle Hervieu-Léger.) There are no signs of decay in the grave sculptures, on the contrary the tradition of funeral art continues in them as a search for the meaning of life and death and as an intuitive interpretation of death. As such, grave sculptures are part of the Finnish discussion of death.

Kirkon vai valtion kirjat? : Uskontokuntasidonnaisuuden ongelma Suomen väestökirjanpidossa 1839-1904

The Population Register – run by the Church or the state? The problem posed by the obligation to belong to a religious community in the registration of births and deaths in Finland between 1839 and 1904 The Lutheran Church of Finland is the nation’s largest church; approximately 82 per cent of Finns were members in 2007. The Church ran an official register of its members until 1999, when the state then undertook this task. The registration of births and deaths by the Church has a long history dating back to the 17th century, when Bishop Johannes Gezelius Sr. decreed that all parish members would have to be recorded in parish registers. These registers were used to control how well parish members knew the Christian doctrine and, gradually, also if they were literate. Additionally, the Church attempted to ensure by means of the parish registers that parish members went to Holy Communion annually. Since everyone was a member of the Lutheran Church, the state also took advantage of the parish registers and used them for the purposes of tax collection and conscription. The main research theme of “The Population Register – run by the Church or the state?” goes back to these times. The actual research period covers the years of 1839–1904. At that time Finland was under Russian rule, although autonomous. In the late 19th century the press and different associations in Finland began to engage in public debate, and the country started moving from a submissive society to a civic one. The identity of the Lutheran Church also became more prominent when the Church Act and the General Synod were realised in 1869. A few years earlier, municipal and parish administrations had been separated, but the general registration of births and deaths was left to the Church to see to. In compliance with the constitution of the country, all the inhabitants in principle still had to be Lutheran. In practice, the situation was different. The religious and ideological realms diversified, and the Lutheran concept of religion was no longer acceptable to everyone. The conflict was reflected in the registration of births and deaths, which was linked to the Lutheran Church and its parish registers. Nobody was allowed to leave the Church, there was no civil register, and the Lutheran Church did not consent to record unbaptized children in the parish registers. Therefore such children were left without civil rights. Thus the obligation to belong to a religious community had become a problem in the registration of births and deaths. The Lutheran clergy also appealed to the 1723 privileges, according to which they had been exempted from the drawing up of additional population registers. In 1889 Finland passed the Dissenters Act. By virtue of this act the Baptists and the Methodists left the state Church, but this was not the case with the members of the free churches. The freethinkers had to retain their church membership, as the law did not apply to them. This meant that the unbaptized children of the members of the free churches or those of freethinkers were still not entered in any registers. The children were not able to go to school, work for the state or legally marry. Neither were they able to inherit property, as they did not legally exist. The system of parish registers was created when everyone was required to be a member of the Lutheran Church, but it did not work when liberal attitudes eventually penetrated the sphere of religion, too. The government´s measures to solve the problem were slow and cautious, partly because Finland was part of Russia, partly because there were only about 100 unbaptized children. As the problem group was small and the state´s resources were limited, no general civil register was established. The state accepted the fact that in spite of the problems, the Evangelical Lutheran Church and the congregations of dissenters were the only official establishments to run populations registers in the country, and for social purposes, too. In 1900 the Diet of Finland finally approved a limited civil register, which unbaptized children and unregistered foreigners would be recorded in. Due to political reasons the civil register did not come into existence until 1917, after the actual research period.