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  • Kukkaro, Petra (Helsingin yliopisto, 2009)
    Viruses of Archaea are the least studied group of viruses. Fewer than 50 archaeal viruses have been reported which constitutes less than one percent of all the isolated prokaryotic viruses. Only about one third of the isolated archaeal viruses infect halophiles. The diversity of haloviruses, virus ecology in highly saline environments and the interactions of haloviruses with their hosts have been little studied. The exiguous knowledge available on halophilic systems is not only due to inadequate sampling but also reflects the extra challenge highly saline systems set on biochemical studies. In this study six new haloviruses were isolated and characterized. Viruses included four archaeal viruses and two bacteriophages. All of the other isolates exhibited head-tail morphology, except SH1 which was the first tailless icosahedral virus isolated from a high salt environment. Production and purification procedures were set up for all of these viruses and they were subjected to stability determinations. Archaeal virus SH1 was studied in more detail. Biochemical studies revealed an internal membrane underneath the protein capsid and a linear dsDNA genome. The overall structure of SH1 resembles phages PRD1, PM2 and Bam35 as well as an archaeal virus STIV. SH1 possesses about 15 structural proteins that form complexes under non-reducing conditions. Quantitative dissociation provided information about the positions of these proteins in the virion. The life cycle of SH1 was also studied. This lytic virus infects Haloarcula hispanica. Adsorption to the host cells is fairly inefficient and the life cycle rather long. Finally, virus responses in a variety of ionic conditions were studied. It was discovered that all of the studied viruses from low salt, marine and high salt environments tolerated larger range of salinities than their bacterial or archaeal hosts. The adsorption efficiency was not determined by the natural environment of a virus. Even though viruses with the slowest binding kinetics were among the haloviruses, fast binders were observed in viruses from all environments. When the salinity was altered, the virus adsorption responses were diverse. Four different behavioral patterns were observed: virus binding increased or decreased in increasing salinity, adsorption maximum was at a particular salt concentration or the salinity did not affect the binding. The way the virus binding was affected did not correlate with the environment, virus morphology or the organism the virus infects.
  • Alha, Lauri (Helsingin yliopisto, 2010)
    The first observations of solar X-rays date back to late 1940 s. In order to observe solar X-rays the instruments have to be lifted above the Earth s atmosphere, since all high energy radiation from the space is almost totally attenuated by it. This is a good thing for all living creatures, but bad for X-ray astronomers. Detectors observing X-ray emission from space must be placed on-board satellites, which makes this particular discipline of astronomy technologically and operationally demanding, as well as very expensive. In this thesis, I have focused on detectors dedicated to observing solar X-rays in the energy range 1-20 keV. The purpose of these detectors was to measure solar X-rays simultaneously with another X-ray spectrometer measuring fluorescence X-ray emission from the Moon surface. The X-ray fluorescence emission is induced by the primary solar X-rays. If the elemental abundances on the Moon were to be determined with fluorescence analysis methods, the shape and intensity of the simultaneous solar X-ray spectrum must be known. The aim of this thesis is to describe the characterization and operation of our X-ray instruments on-board two Moon missions, SMART-1 and Chandrayaan-1. Also the independent solar science performance of these two almost similar X-ray spectrometers is described. These detectors have the following two features in common. Firstly, the primary detection element is made of a single crystal silicon diode. Secondly, the field of view is circular and very large. The data obtained from these detectors are spectra with a 16 second time resolution. Before launching an instrument into space, its performance must be characterized by ground calibrations. The basic operation of these detectors and their ground calibrations are described in detail. Two C-flares are analyzed as examples for introducing the spectral fitting process. The first flare analysis shows the fit of a single spectrum of the C1-flare obtained during the peak phase. The other analysis example shows how to derive the time evolution of fluxes, emission measures (EM) and temperatures through the whole single C4 flare with the time resolution of 16 s. The preparatory data analysis procedures are also introduced in detail. These are required in spectral fittings of the data. A new solar monitor design equipped with a concentrator optics and a moderate size of field of view is also introduced.
  • Jakava-Viljanen, Miia (Helsingin yliopisto, 2007)
    Lactobacilli, common members of porcine intestinal microbiota, have been considered to be an important group of bacteria in maintaining the stability of gastrointestinal tract (GIT), preventing intestinal infections and supporting intestinal health. Because several species of lactobacilli have GRAS (generally regarded as safe) status and some of them have an ability to interact with intestinal epithelial cells, their possible applications as mucosal vaccine vector and/or probiotics have aroused interest. Selection criteria for lactobacilli to be used as vaccine vector or probiotic include the abilities to adhere to the intestinal epithelium cells and colonize the lumen of the GIT. Bacterial adhesins are often found in hair-like appendages called pili or fimbriae that extend outward from bacterial surface. Alternatively, they can be directly associated with the microbial cell surface. Surface layer proteins (Slps) of lactobacilli have been shown to confer tissue adherence. In this study, S-layer carrying lactobacilli from the intestine and faeces of pigs were isolated and their ability to adhere was studied. Besides the putative binding properties of Slps, a very large number of Slp subunits present in an S-layer make the use of the S-layer structure a very interesting alternative to surface display antigens. Therefore, the aim was to characterize the S-layer proteins. Two new surface layer proteins with potential to be tested as antigen carriers were characterized, and three slp genes were isolated, sequenced, and studied for their expression. To identify the S-layer carrying lactobacilli strains of porcine origin, a polyphasic taxonomic approach was applied. These results indicated that strains from Finland and the related L. sobrius strains, originating from elsewhere, constitute a single species, L. amylovorus, and that the name L. sobrius should be considered as a later synonym of L. amylovorus. The F18 fimbriae carrying Escherichia coli strains cause post-weaning diarrhoea and edema disease in pigs. The adhesin FedF of E. coli F18 fimbriae was characterized. The work aims at developing lactobacilli as a live mucosal vaccine vector for pigs against diseases caused by F18+ E. coli. Oral immunization of weaned piglets with adhesins is known to induce a protective mucosal immune response. Naked FedF appeared to be very unstable but we could produce it as a fusion protein with maltose binding protein (MBP). Specific adhesion to isolated porcine intestinal epithelial cells was demonstrated with MBP-FedF fusions as well as the ability of anti-MBP-FedF antibodies to prevent binding of E. coli F18 to porcine epithelial cells.
  • Seppälä, Ulla (Helsingin yliopisto, 2001)
  • Savelainen, Matti (Helsingin yliopisto, 2014)
    We constrain cosmological models where the primordial perturbations have an adiabatic and a (possi- bly correlated) cold dark matter (CDI), neutrino density (NDI) or neutrino velocity (NVI) isocurvature component. We use both a phenomenological approach, where the power spectra of primordial per- turbations are parametrized with two amplitudes at two different scales, and a slow-roll two-field inflation approach where inflation slow-roll parameters are used as primary parameters, determining the spectral indices and the ratio of tensor perturbations to scalar perturbations. We use WMAP 7- year and 9-year data combined with other CMB data and Planck 2013 CMB temperature anisotropy data. Bayesian methods indicate no preference for any of the isocurvature modes: the CMB data set tight upper bounds on any non-adiabatic contribution to the observed CMB temperature variance. We show that allowing for a primordial tensor contribution has a negligible effect on the determi- nation of the non-adiabatic contribution and vice versa, as long as the tensor spectral index obeys the first inflationary consistency relation. On large scales, the WMAP CMB data seem to constrain isocurvature tighter than the Planck data. This is due to the lack of power at low multipoles, l ∼ 2...40, in the Planck data compared to the prediction of the best-fitting adiabatic ΛCDM model. Hence the Planck data prefer a power-reducing mechanism, which the mixed adiabatic and isocurva- ture models with negative correlation or full anticorrelation can offer. With WMAP 9-year data we find that in the NDI and NVI cases larger isocurvature fractions are allowed than in the correspond- ing models with CDI. For uncorrelated perturbations, the upper limit to the primordial NDI (NVI) fraction is 24% (20%) at k = 0.002Mpc−1 and 28% (16%) at k = 0.01Mpc−1. For maximally correlated (anticorrelated) perturbations, the upper limit to the NDI fraction is 3.0% (0.9%). The non-adiabatic contribution to the CMB temperature variance can be 10% ( 13%) for the NDI (NVI) modes. For Planck data the non-adiabatic contribution to the temperature variance can be up to 7%, 9%, 5% in the CDI, NDI, NVI models. The Planck data constrain the primordial CDI fraction in specific curvaton and axion scenarios to 0.25% and 3.9%, respectively. All bounds above are at 95% CL. With the WMAP data, relaxing the pure adiabaticity assumption leads to large shifts of the preferred values of standard cosmological parameters and broadening of their posterior probability distributions. In contrast, as the Planck data determines the acoustic peak structure precisely up to the sixth acoustic peak, allowing for a mixture of the primordial adiabatic and an isocurvature mode does not significantly affect the determination of standard cosmological parameters.
  • Hanif, Mubashir (Helsingin yliopisto, 2004)
    Ectomycorrhizal formation between the host tree, Pinus sylvestris and fungal symbiont, Suillus bovinus was investigated at the molecular level by isolating genes regulating the organization of the actin cytoskeleton in the fungal partner S. bovinus. An Agrobacterium tumefaciens mediated transformation (ATMT) system was developed for the ectomycorrhizal fungi in order to assign specific functions to the cloned molecules. The developed ATMT system was also used to transform a plant pathogenic fungus, Helminthosporium turcicum, to hygromycin B resistance. Small GTPases Cdc42 and Rac1, the regulators of actin cytoskeleton in eukaryotes were isolated from S. bovinus. Sbcdc42 and Sbrac1, are both expressed in vegetative and in the symbiotic hyphae of S. bovinus . Using IIF microscopy, Cdc42 and actin were co-localized at the tips of vegetative hyphae and were visualized in association with the plasma membrane in swollen cells typical to the symbiotic hyphae. These results suggest that the small GTPases Cdc42 may play a significant role in the polarized growth of S. bovinus hyphae and regulate fungal morphogenesis during ectomycorrhiza formation through reorganization of the actin cytoskeleton. The functional equality of Cdc42 was tested in yeast complementation experiments using a Saccharomyces cerevisiae temperature sensitive mutant, cdc42-1ts. The genomic clone of CDC42 was isolated from S. bovinus genomic DNA via specific primers for Cdc42. The analogous S. cerevisiae cdc42 mutations, dominant active G12V and dominant negative D118A, were generated in the Sbcdc42 gene by in-vitro mutagenesis. The ectomycorrhizal fungi, S. bovinus, P. involutus and H. cylindroporum were transformed using ATMT and phleomycin as a selectable marker. PCR screeing suggested that the T-DNA was inserted in all the three fungal genomes but the fate of integration could not be proved by Southern blot analysis. An alternative Agrobacterium strain, AGL-1 and selection marker, hygromycin was used to transform our model fungus S. bovinus. PCR and Southern analysis suggested an improved efficiency of transformation. All the transformed fungal colonies selected for hygromycin gave positives in PCR and the Southerns showed multiple or single copy T-DNA integrations into the S. bovinus genome. Using the same Agrobacterium strain and the selectable marker, a maize pathogen, H. turcicum was also subjected to ATMT. The H. turcicum transformation data suggested the single copy T-DNA integrations into the genome of the screened transformants that further confirms wider applicability of the ATMT. The plasmids carrying the wild-type (pHGCDC42) and the mutated Sbcdc42 alleles (pHGGV; pHGDA) under Agaricus bisporus gpd promoter were constructed in an A. tumefaciens vector. ATMT was used to transform S. bovinus with the plasmids carrying the wild-type and mutated Sbcdc42 alleles. The isolation of Sbcdc42 and Sbrac1 genes and some other functionally related genes from ectomycorrhizal fungus, S. bovinus will form the basis of future work to resolve the signalling pathway leading to ectomycorrhizal symbiosis. The development of ATMT system will be a valuable tool in analysing the exact function of signalling pathway components in ectomycorrhizal symbiosis or in plant pathogenic interactions. The transformation frequency and broad applicability along with the simplicity of T-DNA integration make Agrobacterium a valuable, new and a powerfull tool for targeted and insertional mutagenesis in these plant associated fungi. The developed ATMT systems should therefore make it possible to generate large number of transformants with tagged genes which could then be screened for their specific roles in symbiosis and pathogenecity, respectively.
  • Strengell, Satu (Helsingin yliopisto, 2014)
    Functional lung CT using synchrotron radiation was applied for studying regional ventilation distribution in vivo in animal lungs. This quantitative method employs the K-edge subtraction (KES) technique, which takes advantage of the sharp rise of the absorption coefficient at the binding energy of K-shell electron of a contrast agent. In KES technique two images are taken simultaneously at energies bracketing the K-edge energy of stable xenon (Xe) gas. This technique produces absorption CT images for structural evaluation and Xe density images and at the same time it allows the study of the regional ventilation heterogeneity, calculated based on wash-in series of Xe inhalation images. In this work the analysis of KES CT images was developed to show the regional differences in the airway reactions produced by the direct constrictor agonist, methacholine (MCh), and the indirect constrictor agonist, ovalbumin (OVA), in healthy and asthmatic rabbits. Moreover these constrictors were tested under the influence of cigarette smoke. The effect in airways of different administration routes of MCh, inhaled or intravenous (i.v.), was studied using low radiation dose Xe density CT images. The radiation dose in synchrotron radiation imaging of rabbit lungs in vivo, with and without Xe, was calculated and measured using several methods and compared to the image quality. Results showed that i.v. MCh caused bronchoconstriction primarily in central airways in healthy and asthmatic animals, whereas i.v. OVA only in asthmatic animals. Inhaled MCh, in both groups, affected more the periphery. On the other hand cigarette smoke inhibited the bronchoconstriction in both healthy and asthmatic animals. Theoretical and measured values of synchrotron radiation dose were consistent in this setup. Dose dependency of the image quality, defined by signal to noise ratio, was evaluated, and a threshold for detectable signal contrast was found. The optimal imaging setup was estimated using these results. These findings show the feasibility of the KES CT method for functional lung imaging of airway reactions by providing information on the regional ventilation distributions. By optimizing the image acquisition and reconstruction algorithms with existing methods, KES CT lung imaging could be adaptable for human studies in the near future.
  • Polianskyte, Zydrune (Helsingin yliopisto, 2009)
    Mitochondria have evolved from endosymbiotic alpha-proteobacteria. During the endosymbiotic process early eukaryotes dumped the major component of the bacterial cell wall, the peptidoglycan layer. Peptidoglycan is synthesized and maintained by active-site serine enzymes belonging to the penicillin-binding protein and the β-lactamase superfamily. Mammals harbor a protein named LACTB that shares sequence similarity with bacterial penicillin-binding proteins and β-lactamases. Since eukaryotes lack the synthesis machinery for peptidoglycan, the physiological role of LACTB is intriguing. Recently, LACTB has been validated in vivo to be causative for obesity, suggesting that LACTB is implicated in metabolic processes. The aim of this study was to investigate the phylogeny, structure, biochemistry and cell biology of LACTB in order to elucidate its physiological function. Phylogenetic analysis revealed that LACTB has evolved from penicillin binding-proteins present in the bacterial periplasmic space. A structural model of LACTB indicates that LACTB shares characteristic features common to all penicillin-binding proteins and β-lactamases. Recombinat LACTB protein expressed in E. coli was recovered in significant quantities. Biochemical and cell biology studies showed that LACTB is a soluble protein localized in the mitochondrial intermembrane space. Further analysis showed that LACTB preprotein underwent proteolytic processing disclosing an N-terminal tetrapeptide motif also found in a set of cell death-inducing proteins. Electron microscopy structural studies revealed that LACTB can polymerize to form stable filaments with lengths ranging from twenty to several hundred nanometers. These data suggest that LACTB filaments define a distinct microdomain in the intermembrane space. A possible role of LACTB filaments is proposed in the intramitochondrial membrane organization and microcompartmentation. The implications of these findings offer novel insight into the evolution of mitochondria. Further studies of the LACTB function might provide a tool to treat mitochondria-related metabolic diseases.
  • Saariaho, Anna-Helena (Helsingin yliopisto, 2006)
    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.
  • Hämäläinen, Riikka (Helsingin yliopisto, 2006)
    Mulibrey nanism is a hereditary developmental disorder, characterized by prenatal onset growth failure without postnatal catch-up growth, distinctive craniofacial features, progressive cardiopathy and failure of sexual maturation. In addition, the patients develop insulin resistance syndrome and type 2 diabetes and they have an increased risk of developing tumors. The TRIM37 gene that underlies mulibrey nanism encodes for a member of the tripartite motif (TRIM) protein family. The physiological function of TRIM37 and the pathogenetic mechanisms leading from TRIM37 dysfunction to the mulibrey nanism phenotype are unknown. However, TRIM37 localizes at least partially to peroxisomes, and possesses ubiquitin E3-ligase activity. Thus, it may mediate ubiquitin dependent protein degradation, suggesting that accumulation of yet unknown substrate proteins may underlie the disease pathogenesis. In this study, the TRIM37 gene was characterized in detail. A transcription initiation window, with several separate transcription start sites, was identified and the putative promoter region immediately upstream from the transcription initiation window was shown to possess basal promoter activity. Further, several alternative splice variants of the gene were identified, including a highly expressed testis specific variant, encoding for an identical protein product with the main transcript. Expression of TRIM37 mRNA was detected in several different tissues, with highest expression seen in testis and in brain, when the expression patterns of the two major transcripts in different human tissues were studied by quantitative real-time PCR. Several mulibrey nanism patients were studied and thirteen novel mutations in TRIM37 were found, including three mutations (p.Gly322Val, p.Cys109Ser, p.Glu271_Ser287), that are likely to express mutant TRIM37 proteins. These mutations were further shown to alter the subcellular localization of the mutant proteins. Most of the mulibrey nanism associated mutations however, lead to premature termination codons and degradation of mRNA. All the TRIM37 mutations identified to date predict loss-of-function alleles, and thus no phenotype-genotype correlation is seen among the patients. In order to understand the pathogenetic mechanisms underlying mulibrey nanism, an animal model for the disorder is needed. For the development of a Trim37 knock-out mouse, the mouse Trim37 gene was characterized. Alternative splice variants, were identified, including a testis specific variant predicting a longer protein product. Further, a strictly tissue and cell-specific pattern of Trim37 expression was observed in developing and adult mouse tissues, when studied by immunohistochemical methods. This distribution of Trim37 expression in mouse tissues is in agreement with the clinical findings in human mulibrey nanism patients. This thesis work gives new tools for the diagnostics of mulibrey nanism as well as for studying the molecular pathogenesis behind this interesting disorder.
  • Karppinen, Timo (Helsingin yliopisto, 2008)
    This thesis reports investigations into the paper wetting process and its effects on the surface roughness and the out-of-plane (ZD) stiffness of machine-made paper. The aim of this work was to test the feasibility of employing air-borne ultrasound methods to determine surface roughness (by reflection) and ZD stiffness (by through transmission) of paper during penetration of distilled water, isopropanol and their mixtures. Air-borne ultrasound provides a non-contacting way to evaluate sample structure and mechanics during the liquid penetration event. Contrary to liquid immersion techniques, an air-borne measurement allows studying partial wetting of paper. In addition, two optical methods were developed to reveal the liquid location in paper during wetting. The laser light through transmission method was developed to monitor the liquid location in partially wetted paper. The white light reflection method was primarily used to monitor the penetration of the liquid front in the thickness direction. In the latter experiment the paper was fully wetted. The main results of the thesis were: 1) Liquid penetration induced surface roughening was quantified by monitoring the ultrasound reflection from the paper surface. 2) Liquid penetration induced stiffness alteration in the ZD of paper could be followed by measuring the change in the ultrasound ZD resonance in paper. 3) Through transmitted light revealed the liquid location in the partially wetted paper. 4) Liquid movement in the ZD of the paper could be observed by light reflection. The results imply that the presented ultrasonic means can without contact measure the alteration of paper roughness and stiffness during liquid transport. These methods can help avoiding over engineering the paper which reduces raw material and energy consumption in paper manufacturing. The presented optical means can estimate paper specific wetting properties, such as liquid penetration speed, transport mechanisms and liquid location within the paper structure. In process monitoring, these methods allow process tuning and manufacturing of paper with engineered liquid transport characteristics. With such knowledge the paper behaviour during printing can be predicted. These findings provide new methods for paper printing, surface sizing, and paper coating research.
  • Pöyhönen, Samuli (Helsingin yliopisto, 2013)
    The articles comprising this dissertation concern classification and concept formation in the social and behavioral sciences. In particular, the emphasis in the study is on the philosophical analysis of interdisciplinary settings created by the recent intellectual developments on the interfaces between the social sciences, psychology, and neuroscience. The need for a systematic examination of the problems of conceptual coordination and integration across disciplinary boundaries is illustrated by focusing on phenomena whose satisfactory explanation requires drawing together the theoretical resources from a variety of disciplines. In philosophy, questions regarding the nature of scientific concepts have often been framed in terms of theories of natural kinds. For this reason, analysis of the notion of natural kind as well as examination of how theories of natural kinds should be connected to recent philosophical accounts of scientific explanation and mechanisms form the core of the study. Building on contemporary discussions on these topics in the philosophy of biology, the philosophy of cognitive science, and the philosophy of the social sciences, the articles develop a mechanistic theory of natural kinds in the social and behavioral sciences, and scrutinize its applicability and usefulness as a theory of conceptual change in interdisciplinary settings. The study suggests that, although the mechanistic theory cannot account for the functioning of the whole range of scientific concepts, interweaving biological, cognitive, and social mechanisms in the manner suggested by the mechanistic theory offers a naturalistic and non-reductionist basis for conceptualizing epistemic coordination across disciplinary boundaries.
  • Aaltonen, Terhi (Helsingin yliopisto, 2013)
    Almost 40 years ago, a cheese-making process was described in which milk was concentrated to the final total solids content of cheese and no whey draining was made after coagulation. This full concentration (FC) process has since been used in soft cheese-making. However in semi-hard and hard cheese-making concentrated whey proteins have had negative effect on cheese flavor and texture and therefore the technique has not been used for these products. Development of filtration techniques has made it possible to fractionate milk components. Concentration of the major cheese components, fat and casein, is possible with microfiltration (MF). The aim of this study was to develop an FC cheese process using MF and evaporation steps. Cheese-making with the FC process consists of whey protein removal and standardization of lactose and calcium contents. During whey protein removal plasmin (PL) was activated and its heat stability was increased. Protein hydrolysis by PL before cheese-making may reduce cheese yield and coagulation properties and therefore the FC process must be continuous. The calcium-protein ratio affects the final structure of cheese and can be standardized with acidification and filtration steps. During FC of milk, the viscosity of retentate increases and its processability decreases. It was found that acidification reduced the viscosity of retentate and slowed the increase of viscosity during concentration. This observation may be important for FC process development. Secondary proteolysis of FC cheese was apparently at a low level, because no free amino acids (FAA) were found at the end of ripening. Added peptidase increased the FAA content in cheese and with enzyme addition it was possible to alter the ripening process. However, peptidase addition also changed lactose fermentation, and therefore the microbiological composition of LAB changed in cheese. The effects of CaCl2 addition on FC cheese ripening were studied. It was found that CaCl2 addition increased the growth of LAB, probably due to delayed lysis of LAB. It appears that standardization of calcium content is essential to control lyses caused by LAB, which affect cheese ripening.
  • Kilpivaara, Outi (Helsingin yliopisto, 2007)
    Breast and colorectal cancers, are common types of cancer, with over two million newly diagnosed cases annually worldwide. Cancer is a genetic disease and defects in DNA integrity restoring functions make a significant contribution to cancer risk. CHEK2 is a checkpoint kinase functioning as a regulator of cell cycle checkpoints, apoptosis, and DNA repair in response to DNA double-strand breaks. The aim of this study was to evaluate the role of CHEK2 in breast cancer predisposition in Finnish breast cancer families and in breast cancer risk at the population level. We were interested in the clinical and biological characteristics of the breast tumors associated with the CHEK2 germline mutations or aberrant CHEK2 protein expression and the effect on survival of patients with these CHEK2 defects. We also assessed the role of CHEK2 mutations, namely 1100delC and I157T, in colorectal cancer susceptibility in Finland. CHEK2 I157T was found to be a low-penetrance breast cancer susceptibility allele, conferring a 1.4-fold risk for carriers. Reduced or absent CHEK2 protein expression was observed in one-fifth of breast tumors from patients unselected for family history, implying that defective CHEK2 signaling contributes to tumorigenesis. Reduction in CHEK2 expression was more common in tumors with larger diameter and ER expression, but with regard to other tumor characteristics and prognosis of a patient no association was observed. Results from comparison of CHEK2 1100delC carrier tumors with noncarrier tumors were in line with the findings from the CHEK2 expression study. Tumors from CHEK2 1100delC carriers were more often of higher grade than tumors from noncarriers, and they also tended to be ER-positive more often, although generally 1100delC status does not seem to radically affect the tumor characteristics. Our results suggest that CHEK2 1100delC may not be a susceptibility allele for CRC, although a very small effect cannot be excluded. Furthermore, CHEK2 1100delC is equally frequent in HBCC (hereditary breast and colorectal cancer) phenotype families and in breast cancer families. Over 1000 CRC cases were screened for CHEK2 I157T, and a significantly higher frequency of I157T was observed among both familial and sporadic CRC cases. The relation of CHEK2 I157T with familial CRC has not been studied previously. CHEK2 I157T seems to be a susceptibility allele for both familial and sporadic CRC, conferring a 1.5-fold risk for carriers of this variant. CHEK2 I157T has been proposed to have a role as a multiple cancer susceptibility allele, which is supported by our results since we observed a trend towards higher frequency of the variant among cases with multiple primary tumors or those with a family history of cancer. During the last five years CHEK2 has established its role as an important cancer susceptibility gene. It has become apparent that CHEK2 is a low-penetrance susceptibility gene for several cancer types, significantly contributing to familial cancer risk as well as to cancer risk at the population level.
  • Jakovleva, Natalia (Helsingin yliopisto, 2012)
    This study is a historical and semantic description of the notion of the human document (document humain), borrowed by Russian critics from the literary theory of French Naturalism. To this day the term remains current in the Russian language in fictional and scholarly texts, mostly in the humanities. Becoming something of a cliché, however, it has lost its strict, narrow sense. This book details the evolution of the notion over the relatively long period of its existence. The term itself was invented by two French writers the Goncourt brothers, whose works were less known to Russian readers than, for instance, the ideas of Hyppolite Taine, where one could find semantically similar formulas. Meanwhile the texts of Emile Zola achieved particular popularity in Russia, and the human document played a key role in Zola s aesthetics, especially in his theory of the experimental novel . For Zola the human document rejected the ideology of Romanticism with its orientation on inventive and captivating fictions. It is a noteworthy fact that Zola s works devoted to the experimental novel were first published in Russian, since the French writer was collaborating with Russian periodicals. At the same time, similar expressions were wide spread in Russian critical discourse: for example, the prominent and influential critic Nikolay Mikhaylovsky oft en used synonyms like documents about the human, and one can find other derivatives like female document or Parisian document . On the other hand, Russian reception of Zola s declared interest in psychic physiology and human degradation was also negative, and in the end of the nineteenth century the human document acquired a range of pejorative connotations. As Naturalist theories were gradually becoming obsolete and disappearing, the term s semantic associations were markedly transformed. The 1910s were a crucial period in its history. Although one can find the term in the texts of Russian Naturalists like the prolific writer Aleksandr Amfiteatrov, it was no longer strictly connected with this aesthetical and intellectual tradition. Displaced and half-forgotten, human document appears in the contexts of women s literature , memoirs, and even autobiographies about the 1905 revolution. Now it was associated with different documentary genres, such as diaries and confessions, as with the literary strategy of frank or true expression. This suggests that the term was becoming a part of the rhetoric of anti-literature . As a result, the positive ideal of frank testimony was combined with psychic physiology s negative associations, and this ambiguity allowed the application of the term to a certain set of specific subjects. For example, it was connected with the marginal hero of the age , i.e. the time of decadence and social decline (the revolutionary, the scoundrel, the cynic, and so on). The 1920s and 1930s were the heyday of the human document . The term was rarely used in early Soviet literature but flourished among Russian emigre writers. Thanks to the older generation, who actively took part in pre-revolutionary literary discussions, this cliche gradually returned to the pages of émigré periodicals. In the 1930s, as in Zola s time, it assumed the form of a literary manifesto and united different circles of young Russian writers, mostly in France. Human document became a keyword in the famous discussion between two prominent figures of the Paris emigration, Vladislav Khodasevich and Georgy Adamovich, who considered the goal of a new literature to be the return to raw, frank self-expression. This new development in the history of the term was partly supported by the interest of contemporary French writers like Louis-Ferdinand Celine in naturalistic literary devices. In this period human document became a kind of synonym for a certain sort of poetry which was called the Parisian note . It is not unusual that this cliché sometimes appeared in Soviet criticism as a means of describing and then belittling émigré literature. It arose in the mid-1960s, probably after the polemics about frankness in literature and then was borrowed by literary scholar Lydia Ginzburg, who worked on the history of documentary genres in Russian literature.
  • Sillanpää, Markus (Helsingin yliopisto, 2006)
    Recent epidemiological studies have shown a consistent association of the mass concentration of urban air thoracic (PM10) and fine (PM2.5) particles with mortality and morbidity among cardiorespiratory patients. However, the chemical characteristics of different particulate size ranges and the biological mechanisms responsible for these adverse health effects are not well known. The principal aims of this thesis were to validate a high volume cascade impactor (HVCI) for the collection of particulate matter for physicochemical and toxicological studies, and to make an in-depth chemical and source characterisation of samples collected during different pollution situations. The particulate samples were collected with the HVCI, virtual impactors and a Berner low pressure impactor in six European cities: Helsinki, Duisburg, Prague, Amsterdam, Barcelona and Athens. The samples were analysed for particle mass, common ions, total and water-soluble elements as well as elemental and organic carbon. Laboratory calibration and field comparisons indicated that the HVCI can provide a unique large capacity, high efficiency sampling of size-segregated aerosol particles. The cutoff sizes of the recommended HVCI configuration were 2.4, 0.9 and 0.2 μm. The HVCI mass concentrations were in a good agreement with the reference methods, but the chemical composition of especially the fine particulate samples showed some differences. This implies that the chemical characterization of the exposure variable in toxicological studies needs to be done from the same HVCI samples as used in cell and animal studies. The data from parallel, low volume reference samplers provide valuable additional information for chemical mass closure and source assessment. The major components of PM2.5 in the virtual impactor samples were carbonaceous compounds, secondary inorganic ions and sea salt, whereas those of coarse particles (PM2.5-10) were soil-derived compounds, carbonaceous compounds, sea salt and nitrate. The major and minor components together accounted for 77-106% and 77-96% of the gravimetrically-measured masses of fine and coarse particles, respectively. Relatively large differences between sampling campaigns were observed in the organic carbon content of the PM2.5 samples as well as the mineral composition of the PM2.5-10 samples. A source assessment based on chemical tracers suggested clear differences in the dominant sources (e.g. traffic, residential heating with solid fuels, metal industry plants, regional or long-range transport) between the sampling campaigns. In summary, the field campaigns exhibited different profiles with regard to particulate sources, size distribution and chemical composition, thus, providing a highly useful setup for toxicological studies on the size-segregated HVCI samples.
  • Saarnio, Karri (Helsingin yliopisto, 2013)
    Biomass burning has lately started to attract attention because there is a need to decrease the carbon dioxide (CO2) emissions from the combustion of fossil fuels. Biomass is considered as CO2 neutral fuel. However, the burning of biomass is one of the major sources of fine particles both at the local and global scale. In addition to the use of biomass as a fuel for heat energy production, biomass burning emissions can be caused, e.g. by slash-and-burn agriculture and wild open-land fires. Indeed, the emissions from biomass burning are crucially important for the assessment of the potential impacts on global climate and local air quality and hence on human health. The chemical composition of fine particles has a notable influence on these impacts. The overall object of this thesis was to gain knowledge on the chemistry of fine particles that originate from biomass burning as well as on the contribution of biomass burning emissions to the ambient fine particle concentrations. For this purpose novel analytical methods were developed and tested in this thesis. Moreover, the thesis is based on ambient aerosol measurements that were carried out in six European countries at 12 measurement sites during 2002 2011. Additionally, wood combustion experiments were conducted in a laboratory. The measurements included a wide range of techniques: filter and impactor samplings, offline chemical analyses (chromatographic and mass spectrometric techniques, thermal-optical method), and online measurements of particles physical properties and chemical composition (incl. particle number and mass concentrations and size distributions, concentrations of carbonaceous components, water-soluble ions, and tracer compounds). This thesis presents main results of different studies aimed towards chemical characterisation of fine particle emissions from biomass burning. It was found that wood combustion had a significant influence on atmospheric fine particle concentrations in the Helsinki Metropolitan Area in the cold season. Especially in the residential areas local wood combustion emissions were occasionally substantial. A notable contribution of particles originating from wood combustion was detected both at suburban and urban areas caused by emissions that were distributed regionally or they were long-range transported. In addition to the wood combustion emissions, transported smokes from open-land fires in Russia and the Baltic countries affected the air quality in Helsinki in the warm season. Source-specific tracer compounds were used in the thesis for identifying the biomass burning source of fine particles. The most used tracer compounds were anhydrosugars (levoglucosan, mannosan, and galactosan) that originate specifically in the pyrolysis of cellulose and hemicelluloses, the main components of plant biomass. In summary, the sampling and analytical methods needed for the online chemical characterisation of fine particles from biomass burning were developed in order to provide precise and prompt high-time-resolution information on biomass burning emissions. The results and the implications of this thesis provide new information on the concentrations and sources of fine particles in the boreal region.
  • Lukkari, Kaarina (Helsingin yliopisto, 2008)
    Chemical characteristics and behaviour of sediment phosphorus in the northeastern Baltic Sea Eutrophication is a severe environmental problem in the Baltic Sea, especially in the Gulf of Finland and the Archipelago Sea, and it is enhanced by the release of phosphorus (P) from bottom sediments. The release of P from sediment reserves largely depends on the occurrence of P in different chemical forms and on the prevailing conditions, especially on the presence of oxygen. This study examines the chemical character and the vertical distribution of sediment P in two shallow estuaries, in shallow coastal sediments overlain by oxic near-bottom water, and in poorly oxygenated open sea sediments in the northeastern Baltic Sea. The objective was to evaluate how much of the sediment P is buried and removed from the nutrient cycle, and how much of it is in forms that can be released from the sediment to the overlaying water over time. Relationships between the distribution of the different P forms and the chemical and physical properties of the sediment, sediment pore water, and near-bottom water were determined in order to examine the behaviour of P at the sediment-water interface. The results show that the chemical character of sediment P varied in the different areas. Generally, in the outer estuaries and in the organic-rich coastal areas in the eastern Gulf of Finland, the sediments were higher in P than the sediments in the poorly oxygenated open sea areas in the central and western Gulf. The estuary sediments that received erosion-transported material were characterised by P bound to hydrated oxides of iron and aluminum. Iron-bound P is sensitive to changes in redox-conditions, but part of it was buried in the estuaries, possibly because of high sedimentation rates and incomplete reduction of iron. The open sea sediments in the central and western Gulf of Finland were dominated by apatite-P, which was also abundant in the areas strongly affected by sediment transportation. The burial of sediment P was most effective in the areas rich in apatite-P, which is a relatively stable form of P in sediment. In the eastern Gulf of Finland, organic P forms predominated in the organic-rich sediments. A part of these P forms will be buried, while part will be degraded in the long term, releasing soluble P to the pore water. In the poorly oxygenated areas, iron compounds at the sediment surface are not able to retain P released during mineralisation of organic matter or reduction-induced dissolution of iron-compounds in deep sediment layers. However, in the shallow coastal areas overlain by oxic near-bottom water, the organic-rich surface sediment can also become temporarily reduced and release P from the sediment to the overlaying water. The considerable variation in the chemical composition of sediment P reserves in the northeastern Baltic Sea proved that it is an important factor and should be taken into account when evaluating the release of sediment P and the role of P reserves in bottom sediments in eutrophication.
  • Carbone, Samara (Helsingin yliopisto, 2014)
    Fine particles affect climate change in complex ways that are not fully understood and were verified to be harmful to animal and human health. For these reasons information concerning their composition is important to understand their behaviour and to elaborate strategies to mitigate air pollution in urban environments. The overall objective of this study was to investigate in more detail chemical characteristics of ambient particulate matter (PM) and its sources. Studies made in laboratory and during field were used to study composition of fresh emissions, changes during aging, and finally composition of submicron PM (PM1) observed in ambient air. For that the field studies were performed at three different sites: rural, urban, and background urban with the HR-ToF-AMS and ACSM, instruments that measured only the non-refractory PM1 (NR-PM1). For this reason the new SP-AMS was further characterized in order to evaluate its feasi-bility to detect trace metals. The use of the positive matrix factorization (PMF) has shown useful in the identification of PM sources. Thus, the PMF was applied to the mass spectrometers datasets and 11 different components of the organic aerosol (OA) were identified, 6 types of oxygenated OAs (OOAs), one containing substantial organosulfate fragments from methanesulfonic acid (MSA), long-range transported biomass burning OA (LRT-BBOA), nitrogen-containing OA (NOA), local BBOA, coffee roastery OA (CROA), and hydrocarbon-like OA (HOA). The last three most likely represented the primary organic aerosol (POA), while the others represented the secondary OA (SOA). The OM was dominated by aerosol particles of secondary origin (65%). The investigation of different properties of the PM1 revealed more information about its composition and sources. A comparison of the AMS data with those from additional instrumentation indicated that most of the PM1 was non-refractory. The water-solubility of the OM indicated that the low-volatility OOA (LV-OOA) and the LRT-BBOA were the most water-soluble components. The SV-OOA presented clear semi-volatile character when investigated as a function of the local air temperature, decreasing in concentration with the air temperature increase. Concerning the aerosol neutralization, in most sites the results indicated enough ammonium to neutralize the major inorganic anions, except for Helsinki during wintertime when the aerosol particles were acidic most of the time. The size-resolved chemical composition was investigated in detail to different episodes and revealed internally and externally mixed aerosol particles in two different modes, an accumulation (~470 nm) and a lower mode (~130nm). The different modes were composed of different compounds and suggested a rather acidic lower mode mainly dominated by nitrate most likely from local traffic emissions. The laboratory experiments accomplished with the SP-AMS successfully confirmed the feasibility of detection of trace metals. 13 different metals were identified through the determination of isotopic patterns. Furthermore, the negative mass defect, typical from metals, was observed useful in their identification in the mass spectrum. The measurement of trace metals by the SP-AMS represents a step forward in the study of sources and might be extremely useful in the next source apportionment studies.