Chemical and source characterisation of size-segregated urban air particulate matter

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.

Rhizoctonia -Scots pine interactions: detection, impact on seedling performance and host defence gene response

Rhizoctonia spp. are ubiquitous soil inhabiting fungi that enter into pathogenic or symbiotic associations with plants. In general Rhizoctonia spp. are regarded as plant pathogenic fungi and many cause root rot and other plant diseases which results in considerable economic losses both in agriculture and forestry. Many Rhizoctonia strains enter into symbiotic mycorrhizal associations with orchids and some hypovirulent strains are promising biocontrol candidates in preventing host plant infection by pathogenic Rhizoctonia strains. This work focuses on uni- and binucleate Rhizoctonia (respectively UNR and BNR) strains belonging to the teleomorphic genus Ceratobasidium, but multinucleate Rhizoctonia (MNR) belonging to teleomorphic genus Thanatephorus and ectomycorrhizal fungal species, such as Suillus bovinus, were also included in DNA probe development work. Strain specific probes were developed to target rDNA ITS (internal transcribed spacer) sequences (ITS1, 5.8S and ITS2) and applied in Southern dot blot and liquid hybridization assays. Liquid hybridization was more sensitive and the size of the hybridized PCR products could be detected simultaneously, but the advantage in Southern hybridization was that sample DNA could be used without additional PCR amplification. The impacts of four Finnish BNR Ceratorhiza sp. strains 251, 266, 268 and 269 were investigated on Scot pine (Pinus sylvestris) seedling growth, and the infection biology and infection levels were microscopically examined following tryphan blue staining of infected roots. All BNR strains enhanced early seedling growth and affected the root architecture, while the infection levels remained low. The fungal infection was restricted to the outer cortical regions of long roots and typical monilioid cells detected with strain 268. The interactions of pathogenic UNR Ceratobasidium bicorne strain 1983-111/1N, and endophytic BNR Ceratorhiza sp. strain 268 were studied in single or dual inoculated Scots pine roots. The fungal infection levels and host defence-gene activity of nine transcripts [phenylalanine ammonia lyase (pal1), silbene synthase (STS), chalcone synthase (CHS), short-root specific peroxidase (Psyp1), antimicrobial peptide gene (Sp-AMP), rapidly elicited defence-related gene (PsACRE), germin-like protein (PsGER1), CuZn- superoxide dismutase (SOD), and dehydrin-like protein (dhy-like)] were measured from differentially treated and un-treated control roots by quantitative real time PCR (qRT-PCR). The infection level of pathogenic UNR was restricted in BNR- pre-inoculated Scots pine roots, while UNR was more competitive in simultaneous dual infection. The STS transcript was highly up-regulated in all treated roots, while CHS, pal1, and Psyp1 transcripts were more moderately activated. No significant activity of Sp-AMP, PsACRE, PsGER1, SOD, or dhy-like transcripts were detected compared to control roots. The integrated experiments presented, provide tools to assist in the future detection of these fungi in the environment and to understand the host infection biology and defence, and relationships between these interacting fungi in roots and soils. This study further confirms the complexity of the Rhizoctonia group both phylogenetically and in their infection biology and plant host specificity. The knowledge obtained could be applied in integrated forestry nursery management programmes.

Prognostic markers in head and neck carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Well-known risk factors include tobacco smoking and alcohol consumption. Overall survival has improved, but is still low especially in developing countries. One reason for this is the often advanced stage of the disease at the time of diagnosis, but also lack of reliable prognostic tools to enable individualized patient treatment to improve outcome. To date, the TNM classification still serves as the best disease evaluation criterion, although it does not take into account the molecular basis of the tumor. The need for surrogate molecular markers for more accurate disease prediction has increased research interests in this field. We investigated the prevalence, physical status, and viral load of human papillomavirus (HPV) in HNSCC to determine the impact of HPV on head and neck carcinogenesis. The prevalence and genotyping of HPV were assessed with an SPF10 PCR microtiter plate-based hybridization assay (DEIA), followed by a line probe-based genotyping assay. More than half of the patients had HPV DNA in their tumor specimens. Oncogenic HPV-16 was the most common type, and coinfections with other oncogenic and benign associated types also existed. HPV-16 viral load was unevenly distributed among different tumor sites; the tonsils harbored significantly greater amounts of virus than other sites. Episomal location of HPV-16 was associated with large tumors, and both integrated and mixed forms of viral DNA were detected. In this series, we could not show that the presence of HPV DNA correlated with survival. In addition, we investigated the prevalence and genotype of HPV in laryngeal carcinoma patients in a prospective Nordic multicenter study based on fresh-frozen laryngeal tumor samples to determine whether the tumors were HPV-associated. These patients were also examined and interviewed at diagnosis for known risk factors, such as tobacco smoking and alcohol consumption, and for several other habituations to elucidate their effects on patient survival. HPV analysis was performed with the same protocols as in the first study. Only 4% of the specimens harbored HPV DNA. Heavy drinking was associated with poor survival. Heavy drinking patients were also younger than nonheavy drinkers and had a more advanced stage of disease at diagnosis. Heavy drinkers had worse oral hygiene than nonheavy drinkers; however, poor oral hygiene did not have prognostic significance. History of chronic laryngitis, gastroesophageal reflux disease, and orogenital sex contacts were rare in this series. To clarify why vocal cord carcinomas seldom metastasize, we determined tumor lymph vessel (LVD) and blood vessel (BVD) densities in HNSCC patients. We used a novel lymphatic vessel endothelial marker (LYVE-1 antibody) to locate the lymphatic vessels in HNSCC samples and CD31 to detect the blood microvessels. We found carcinomas of the vocal cords to harbor less lymphatic and blood microvessels than carcinomas arising from sites other than vocal cords. The lymphatic and blood microvessel densities did not correlate with tumor size. High BVD was strongly correlated with high LVD. Neither BVD nor LVD showed any association with survival in our series. The immune system plays an important role in tumorigenesis, as neoplastic cells have to escape the cytotoxic lymphocytes in order to survive. Several candidate HLA class II alleles have been reported to be prognostic in cervical carcinomas, an epithelial malignancy resembling HNSCC. These alleles may have an impact on head and neck carcinomas as well. We determined HLA-DRB1* and -DQB1* alleles in HNSCC patients. Healthy organ donors served as controls. The Inno-LiPA reverse dot-blot kit was used to identify alleles in patient samples. No single haplotype was found to be predictive of either the risk for head and neck cancer, or the clinical course of the disease. However, alleles observed to be prognostic in cervical carcinomas showed a similar tendency in our series. DRB1*03 was associated with node-negative disease at diagnosis. DRB1*08 and DRB1*13 were associated with early-stage disease; DRB1*04 had a lower risk for tumor relapse; and DQB1*03 and DQB1*0502 were more frequent in controls than in patients. However, these associations reached only borderline significance in our HNSCC patients.

Aerosol size distribution and its connection to cloud droplet number concentration

In order to predict the current state and future development of Earth s climate, detailed information on atmospheric aerosols and aerosol-cloud-interactions is required. Furthermore, these interactions need to be expressed in such a way that they can be represented in large-scale climate models. The largest uncertainties in the estimate of radiative forcing on the present day climate are related to the direct and indirect effects of aerosol. In this work aerosol properties were studied at Pallas and Utö in Finland, and at Mount Waliguan in Western China. Approximately two years of data from each site were analyzed. In addition to this, data from two intensive measurement campaigns at Pallas were used. The measurements at Mount Waliguan were the first long term aerosol particle number concentration and size distribution measurements conducted in this region. They revealed that the number concentration of aerosol particles at Mount Waliguan were much higher than those measured at similar altitudes in other parts of the world. The particles were concentrated in the Aitken size range indicating that they were produced within a couple of days prior to reaching the site, rather than being transported over thousands of kilometers. Aerosol partitioning between cloud droplets and cloud interstitial particles was studied at Pallas during the two measurement campaigns, First Pallas Cloud Experiment (First PaCE) and Second Pallas Cloud Experiment (Second PaCE). The method of using two differential mobility particle sizers (DMPS) to calculate the number concentration of activated particles was found to agree well with direct measurements of cloud droplet. Several parameters important in cloud droplet activation were found to depend strongly on the air mass history. The effects of these parameters partially cancelled out each other. Aerosol number-to-volume concentration ratio was studied at all three sites using data sets with long time-series. The ratio was found to vary more than in earlier studies, but less than either aerosol particle number concentration or volume concentration alone. Both air mass dependency and seasonal pattern were found at Pallas and Utö, but only seasonal pattern at Mount Waliguan. The number-to-volume concentration ratio was found to follow the seasonal temperature pattern well at all three sites. A new parameterization for partitioning between cloud droplets and cloud interstitial particles was developed. The parameterization uses aerosol particle number-to-volume concentration ratio and aerosol particle volume concentration as the only information on the aerosol number and size distribution. The new parameterization is computationally more efficient than the more detailed parameterizations currently in use, but the accuracy of the new parameterization was slightly lower. The new parameterization was also compared to directly observed cloud droplet number concentration data, and a good agreement was found.

On the mechanical behavior of compacted pack ice : A theoretical and numerical investigation

Pack ice is an aggregate of ice floes drifting on the sea surface. The forces controlling the motion and deformation of pack ice are air and water drag forces, sea surface tilt, Coriolis force and the internal force due to the interaction between ice floes. In this thesis, the mechanical behavior of compacted pack ice is investigated using theoretical and numerical methods, focusing on the three basic material properties: compressive strength, yield curve and flow rule. A high-resolution three-category sea ice model is applied to investigate the sea ice dynamics in two small basins, the whole Gulf Riga and the inside Pärnu Bay, focusing on the calibration of the compressive strength for thin ice. These two basins are on the scales of 100 km and 20 km, respectively, with typical ice thickness of 10-30 cm. The model is found capable of capturing the main characteristics of the ice dynamics. The compressive strength is calibrated to be about 30 kPa, consistent with the values from most large-scale sea ice dynamic studies. In addition, the numerical study in Pärnu Bay suggests that the shear strength drops significantly when the ice-floe size markedly decreases. A characteristic inversion method is developed to probe the yield curve of compacted pack ice. The basis of this method is the relationship between the intersection angle of linear kinematic features (LKFs) in sea ice and the slope of the yield curve. A summary of the observed LKFs shows that they can be basically divided into three groups: intersecting leads, uniaxial opening leads and uniaxial pressure ridges. Based on the available observed angles, the yield curve is determined to be a curved diamond. Comparisons of this yield curve with those from other methods show that it possesses almost all the advantages identified by the other methods. A new constitutive law is proposed, where the yield curve is a diamond and the flow rule is a combination of the normal and co-axial flow rule. The non-normal co-axial flow rule is necessary for the Coulombic yield constraint. This constitutive law not only captures the main features of forming LKFs but also takes the advantage of avoiding overestimating divergence during shear deformation. Moreover, this study provides a method for observing the flow rule for pack ice during deformation.

Atomic scale engineering of carbon nanotubes

Carbon nanotubes, seamless cylinders made from carbon atoms, have outstanding characteristics: inherent nano-size, record-high Young’s modulus, high thermal stability and chemical inertness. They also have extraordinary electronic properties: in addition to extremely high conductance, they can be both metals and semiconductors without any external doping, just due to minute changes in the arrangements of atoms. As traditional silicon-based devices are reaching the level of miniaturisation where leakage currents become a problem, these properties make nanotubes a promising material for applications in nanoelectronics. However, several obstacles must be overcome for the development of nanotube-based nanoelectronics. One of them is the ability to modify locally the electronic structure of carbon nanotubes and create reliable interconnects between nanotubes and metal contacts which likely can be used for integration of the nanotubes in macroscopic electronic devices. In this thesis, the possibility of using ion and electron irradiation as a tool to introduce defects in nanotubes in a controllable manner and to achieve these goals is explored. Defects are known to modify the electronic properties of carbon nanotubes. Some defects are always present in pristine nanotubes, and naturally are introduced during irradiation. Obviously, their density can be controlled by irradiation dose. Since different types of defects have very different effects on the conductivity, knowledge of their abundance as induced by ion irradiation is central for controlling the conductivity. In this thesis, the response of single walled carbon nanotubes to ion irradiation is studied. It is shown that, indeed, by energy selective irradiation the conductance can be controlled. Not only the conductivity, but the local electronic structure of single walled carbon nanotubes can be changed by the defects. The presented studies show a variety of changes in the electronic structures of semiconducting single walled nanotubes, varying from individual new states in the band gap to changes in the band gap width. The extensive simulation results for various types of defect make it possible to unequivocally identify defects in single walled carbon nanotubes by combining electronic structure calculations and scanning tunneling spectroscopy, offering a reference data for a wide scientific community of researchers studying nanotubes with surface probe microscopy methods. In electronics applications, carbon nanotubes have to be interconnected to the macroscopic world via metal contacts. Interactions between the nanotubes and metal particles are also essential for nanotube synthesis, as single walled nanotubes are always grown from metal catalyst particles. In this thesis, both growth and creation of nanotube-metal nanoparticle interconnects driven by electron irradiation is studied. Surface curvature and the size of metal nanoparticles is demonstrated to determine the local carbon solubility in these particles. As for nanotube-metal contacts, previous experiments have proved the possibility to create junctions between carbon nanotubes and metal nanoparticles under irradiation in a transmission electron microscope. In this thesis, the microscopic mechanism of junction formation is studied by atomistic simulations carried out at various levels of sophistication. It is shown that structural defects created by the electron beam and efficient reconstruction of the nanotube atomic network, inherently related to the nanometer size and quasi-one dimensional structure of nanotubes, are the driving force for junction formation. Thus, the results of this thesis not only address practical aspects of irradiation-mediated engineering of nanosystems, but also contribute to our understanding of the behaviour of point defects in low-dimensional nanoscale materials.