A cell spot microarray method for high-throughput biology

High-throughput screening of cellular effects of RNA interference (RNAi) libraries is now being increasingly applied to explore the role of genes in specific cell biological processes and disease states. However, the technology is still limited to specialty laboratories, due to the requirements for robotic infrastructure, access to expensive reagent libraries, expertise in high-throughput screening assay development, standardization, data analysis and applications. In the future, alternative screening platforms will be required to expand functional large-scale experiments to include more RNAi constructs, allow combinatorial loss-of-function analyses (e.g. genegene or gene-drug interaction), gain-of-function screens, multi-parametric phenotypic readouts or comparative analysis of many different cell types. Such comprehensive perturbation of gene networks in cells will require a major increase in the flexibility of the screening platforms, throughput and reduction of costs. As an alternative for the conventional multi-well based high-throughput screening -platforms, here the development of a novel cell spot microarray method for production of high density siRNA reverse transfection arrays is described. The cell spot microarray platform is distinguished from the majority of other transfection cell microarray techniques by the spatially confined array layout that allow highly parallel screening of large-scale RNAi reagent libraries with assays otherwise difficult or not applicable to high-throughput screening. This study depicts the development of the cell spot microarray method along with biological application examples of high-content immunofluorescence and phenotype based cancer cell biological analyses focusing on the regulation of prostate cancer cell growth, maintenance of genomic integrity in breast cancer cells, and functional analysis of integrin protein-protein interactions in situ.

Sormijatketun rakennesahatavaran lujuuteen vaikuttavat tekijät puun jatkojalostuksessa

Diplomityö tehtiin Stora Enson Kiteen sahalla, tuotantokäytössä olevaa sormijatkoslinjaa tutkien. Tutkimuksen tavoitteena oli selvittää raaka-aineen keskikosteuden, kosteusgradientin, mitallistamishöyläyksen ja liitettävien aihioiden pituuden vaikutus jatketun tuotteen laatuun. Koekappaleita valmistettiin viisi höylättyä ja viisi sahapintaista luokkaa. Luokat valmistettiin eripituisista aihioista, puolen metrin jaolla. Koekappaleiden taivutuslujuus mitattiin nelipistetaivutuksella, standardin EN 408 mukaan. Taivutuskokeen jälkeen kappaleista mitattiin keskikosteus ja sahattiin koepalat kosteusgradientin mittaamiseksi. Koekappaleita valmistettiin yhteensä 37.8 m3. Tutkimuksissa selvisi, että kappaleiden keskikosteuden ja taivutuslujuuden välillä vallitsee heikko positiivinen riippuvuus. Kosteusgradientin ja taivutuslujuuden välillä riippuvuus on selkeämpi, kosteusgradientin kasvaessa myös taivutuslujuus lisääntyy. Tämä selittyy kappaleiden tiheyden vaihtelulla. Tiheämpiin kappaleisiin jää kuivauksessa suurempi kosteusgradientti. Aihioiden mitallistaminen pienentää taivutuslujuuden hajontaa ja vähentää raaka-aineen mittaheittojen aiheuttamia häiriöitä tuotannossa. Aihionpituus vaikuttaa murtumatyyppien jakaumiin ja aihioiden kierouteen. Sopivin aihionpituus on tässä tapauksessa 0.8-1.0 m. Puolet kappaleista murtui liitoksen ulkopuolelta, useimmiten oksan kohdalta. Paras tapa parantaa kappaleiden lujuutta on lujuuslajitella raaka-aine.

CO2 Laser Cutting of Particleboard, HDF and MDF

The purpose of this thesis is to reveal how the laser cutting parameters influence lasercutting of particleboard, HDF and MDF. The literature review introduces the basic principle of CO2 laser, CO2 laser equipment and its usage in cutting of wood-based materials. The experimental part focuses on the discussion and analysis ofthe test data and attempts to draw conclusions on the influence of various parameters, including laser power, focal length of the lens and cutting gas, on the cutting speed and kerf quality. The tested materials include various thicknesses of particleboard, HDF and MDF samples. A TRUMPF TLF2700 HQ laser equipment was used for the experiments. To obtain valid data, the test samples must be completely cut through without any bonding of wood fibre. The maximum cutting speed is linear dependent on the laser power in thecondition that the other parameters are constant. For each thickness of a specific material type, there is a minimum laser power for cutting. Normally, the topand bottom kerf widths increase with the enhancement of laser power. There may be a critical laser power which can generate the minimum cross-sectional kerf width. Lens of larger focal length may achieve higher cutting speed. As the focal length becomes larger, the top kerf width tends to increase while the bottom andcross-sectional kerf widths to the opposite. Of all cutting gases, oxygen can help achieve higher cutting speed. The gas pressure of nitrogen does not seem to have strong influence on the cutting result. Generally, 2 bar air is more preferable for higher cutting speed. For particleboard and MDF samples of larger thickness than 12 mm, 2 bar argon can be used to reach remarkably higher cutting speed than the 5 bar. Generally, the 190.5 mm lens can produce smallest total kerf width. The kerf sides of thicker samples are darker than the thinner ones. The sample darkness tends to be lower as laser power increased. 63.5 mm lens seemed tocause more darkness than other lens. 5 bar cutting gases can produce less dark side kerfs than 2 bar ones. Oxygen normally causes darker kerfs than other gases. No distinct differences were found between nitrogen and argon.

Tiivispaperin rasvanläpäisyn luonnehtiminen

Työn tavoitteena oli kehittää Metsä Tissue Oyj:n Mäntän tehtaille uusi testimenetelmä leivinpaperin rasvanläpäisyn mittaamiseen. Uudella testimenetelmällä korvataan kaksi nykyisistä testimenetelmistä, jotka ovat aikaa vieviä ja epäluotettavia. Uudelta menetelmältä vaaditaan lyhyttä kestoa, hyvää toistettavuutta ja luotettavuutta sekä korreloivuutta nykyisiin testimenetelmiin. Nykyisissä testeissä leivinpaperilla paistetaan sikaa ja kanaa uunissa, jonka jälkeen tarkastetaan leivinpaperin läpäisseen rasvan määrää leivinpaperin alla olleen lautasen puhtauden perusteella. Sikatesti on huomattavasti kriittisempi kuin kanatesti, joten tässä työssä keskitytään sikatestin korvaamiseen uudella testimenetelmällä. Työn kirjallisuusosassa perehdyttiin rasvatiiviisiin papereihin, niiden valmistukseen ja ominaisuuksiin. Lähinnä keskityttiin tiivispaperin valmistukseen ja sen silikonointiin. Lisäksi esitettiin rasvanläpäisyn mekanismeja ja niihin vaikuttavia tekijöitä sekä rasvanläpäisyn mittaamiseen kehitettyjä menetelmiä. Kokeellisen osan alussa tehtiin esikokeita olemassa olevilla testeillä, kuten Helga- ja Tappi-rasvatiiveystestillä, DIN 53116 standardin mukaisella menetelmällä sekä DPM menetelmällä. Esikokeiden tarkoituksena oli selvittää missä määrin sikatesti korreloi muiden testimenetelmien kanssa. Näistä menetelmistä ei löydetty korrelaatiota sikatestiin, joten kehitettiin aivan uusi testimenetelmä. Kokeellisessa osassa tutkittiin sikatestissä leivinpaperin pidättämiä ja läpäisemiä aineita. Testeissä huomattiin, että leivinpaperin läpäisseet aineet olivat pääosin vesiliukoisia proteiineja. Leivinpaperin pidättämässä aineessa oli vettä, vesiliukoista proteiineja ja rasvaa, siasta riippuen hyvinkin erilaisissa suhteissa. Täten todettiin sikatestin huono toistettavuus ja luotettavuus. Uudessa testimenetelmässä leivinpaperia ja sen päällä olevaa koeainetta puristetaan määrätyllä paineella määrätyssä lämpötilassa, jonka jälkeen leivinpaperin läpäissyt rasva havainnoidaan leivinpaperin alla olevasta indikaattoripaperista. Lopuksi lasketaan tietynkokoisten läpimenotahrojen lukumäärän perusteella näytteelle rasvan läpäisyindeksi. Uusi menetelmä korreloi sekä sika- että kanatestin kanssa.

Structural and optical properties of InAs/GaAs quantum structures

The goal of the thesis was to study fundamental structural and optical properties of InAs islands and In(Ga)As quantum rings. The research was carried out at the Department of Micro and Nanosciences of Helsinki University of Technology. A good surface quality can be essential for the potential applications in optoelectronic devices. For such device applications it is usually necessary to control size, density and arrangement of the islands. In order to study the dependence of the structural properties of the islands and the quantum rings on growth conditions, atomic force microscope was used. Obtained results reveal that the size and the density of the In(Ga)As quantum rings strongly depend on the growth temperature, the annealing time and the thickness of the partial capping layer. From obtained results it is possible to conclude that to get round shape islands and high density one has to use growth temperature of 500 ̊C. In the case of formation of In(Ga)As quantum rings the effect of mobility anisotropy is observed that so the shape of the rings is not symmetric. To exclude this effect it is preferable to use a higher annealing temperature of 570 ̊C. Optical properties were characterized by PL spectroscopy. PL emission was observed from buried InAs quantum dots and In(Ga)As quantum rings grown with different annealing time and temperature and covered with a various thickness of the partial capping layer.

Magnetic Resonance Experiments with Atomic Hydrogen

In this thesis three experiments with atomic hydrogen (H) at low temperatures T<1 K are presented. Experiments were carried out with two- (2D) and three-dimensional (3D) H gas, and with H atoms trapped in solid H2 matrix. The main focus of this work is on interatomic interactions, which have certain specific features in these three systems considered. A common feature is the very high density of atomic hydrogen, the systems are close to quantum degeneracy. Short range interactions in collisions between atoms are important in gaseous H. The system of H in H₂ differ dramatically because atoms remain fixed in the H₂ lattice and properties are governed by long-range interactions with the solid matrix and with H atoms. The main tools in our studies were the methods of magnetic resonance, with electron spin resonance (ESR) at 128 GHz being used as the principal detection method. For the first time in experiments with H in high magnetic fields and at low temperatures we combined ESR and NMR to perform electron-nuclear double resonance (ENDOR) as well as coherent two-photon spectroscopy. This allowed to distinguish between different types of interactions in the magnetic resonance spectra. Experiments with 2D H gas utilized the thermal compression method in homogeneous magnetic field, developed in our laboratory. In this work methods were developed for direct studies of 3D H at high density, and for creating high density samples of H in H₂. We measured magnetic resonance line shifts due to collisions in the 2D and 3D H gases. First we observed that the cold collision shift in 2D H gas composed of atoms in a single hyperfine state is much smaller than predicted by the mean-field theory. This motivated us to carry out similar experiments with 3D H. In 3D H the cold collision shift was found to be an order of magnitude smaller for atoms in a single hyperfine state than that for a mixture of atoms in two different hyperfine states. The collisional shifts were found to be in fair agreement with the theory, which takes into account symmetrization of the wave functions of the colliding atoms. The origin of the small shift in the 2D H composed of single hyperfine state atoms is not yet understood. The measurement of the shift in 3D H provides experimental determination for the difference of the scattering lengths of ground state atoms. The experiment with H atoms captured in H2 matrix at temperatures below 1 K originated from our work with H gas. We found out that samples of H in H2 were formed during recombination of gas phase H, enabling sample preparation at temperatures below 0.5 K. Alternatively, we created the samples by electron impact dissociation of H₂ molecules in situ in the solid. By the latter method we reached highest densities of H atoms reported so far, 3.5(5)x10¹⁹ cm^-3. The H atoms were found to be stable for weeks at temperatures below 0.5 K. The observation of dipolar interaction effects provides a verification for the density measurement. Our results point to two different sites for H atoms in H2 lattice. The steady-state nuclear polarizations of the atoms were found to be non-thermal. The possibility for further increase of the impurity H density is considered. At higher densities and lower temperatures it might be possible to observe phenomena related to quantum degeneracy in solid.

Environments of Acitive Galaxies

This dissertation presents studies on the environments of active galaxies. Paper I is a case study of a cluster of galaxies containing BL Lac object RGB 1745+398. We measured the velocity dispersion, mass, and richness of the cluster. This was one of the most thorough studies of the environments of a BL Lac object. Methods used in the paper could be used in the future for studying other clusters as well. In Paper II we studied the environments of nearby quasars in the Sloan Digital Sky Survey (SDSS). We found that quasars have less neighboring galaxies than luminous inactive galaxies. In the large-scale structure, quasars are usually located at the edges of superclusters or even in void regions. We concluded that these low-redshift quasars may have become active only recently because the galaxies in low-density environments evolve later to the phase where quasar activity can be triggered. In Paper III we extended the analysis of Paper II to other types of AGN besides quasars. We found that different types of AGN have different large-scale environments. Radio galaxies are more concentrated in superclusters, while quasars and Seyfert galaxies prefer low-density environments. Different environments indicate that AGN have different roles in galaxy evolution. Our results suggest that activity of galaxies may depend on their environment on the large scale. Our results in Paper III raised questions of the cause of the environment-dependency in the evolution of galaxies. Because high-density large-scale environments contain richer groups and clusters than the underdense environments, our results could reflect smaller-scale effects. In Paper IV we addressed this problem by studying the group and supercluster scale environments of galaxies together. We compared the galaxy populations in groups of different richnesses in different large-scale environments. We found that the large-scale environment affects the galaxies independently of the group richness. Galaxies in low-density environments on the large scale are more likely to be star-forming than those in superclusters even if they are in groups with the same richness. Based on these studies, the conclusion of this dissertation is that the large-scale environment affects the evolution of galaxies. This may be caused by different “speed” of galaxy evolution in low and high-density environments: galaxies in dense environments reach certain phases of evolution earlier than galaxies in underdense environments. As a result, the low-density regions at low redshifts are populated by galaxies in earlier phases of evolution than galaxies in high-density regions.

Feasibility of ASH DEC‐ process in treating sewage sludge and manure ash in Finland

In Finland the thermal treatment of sewage sludge has been moderate in 21th century. The reason has been the high moisture content of sludge. During 2005-2008, 97-99% of sewage sludge was utilized in landscaping and agriculture. However agricultural use has been during 2005-2007 less than 3 %. The aim of national waste management plan is that by 2016 100% of sludge is used either as soil amendment or energy. The most popular utilization method for manure is spreading it on arable land. The dry manures such as poultry manure and horse manure could also be used in incineration. The ashes could be used as fertilizers and while it is not suitable as a starter fertilizer, it is suitable in maintaining P levels in the soil. One of the main drivers for more efficient nutrient management is the eutrophication in lakes and the Baltic See. ASH DEC process can be used in concentrating phosphorus rich ashes while separating the heavy metals that could be included. ASH DEC process uses thermochemical treatment to produce renewable phosphate for fertilizer production. The process includes mixing of ashes and chlorine donors and subsequent treatment in rotary kiln for 20 min in temperature of 900 – 1 050 oC. The heavy metals evaporate and P-rich product is obtained. The toxic substances are retained in air pollution control system in form of mixed metal hydroxides. The aim of conducting this study is to estimate the potential of ASH DEC process in treating phosphorus rich ashes in Finland. The masses considered in are sewage sludge, dry manure from horses, and poultry and liquid pig manure. To date the usual treatment method for sewage sludge in Finland is composting or anaerobic digestion. Part of the amount of produced sewage sludge (800 kt/a fresh mass and 160 kt/a TS) could also be incinerated and the residual ashes used in ASH DEC process. Incinerating only manure can be economically difficult to manage because the incineration of manure is in Finland considered as waste incineration. Getting a permit for waste incineration is difficult and also small scale waste incineration is too expensive. The manure could act as an additional feedstock in counties with high density of animal husbandry where the land area might not be enough for spreading of manure. Now when the manure acts as a supplementary feedstock beside sludge, the ash can’t be used directly as fertilizer. Then it could be used in ASH DEC process. The perquisite is that the manure producers could pay for the incineration, which might prove problematic.

The nature of communication structures of university students in an international web-based computer-supported collaborative learning (CSCL) course

Communication, the flow of ideas and information between individuals in a social context, is the heart of educational experience. Constructivism and constructivist theories form the foundation for the collaborative learning processes of creating and sharing meaning in online educational contexts. The Learning and Collaboration in Technology-enhanced Contexts (LeCoTec) course comprised of 66 participants drawn from four European universities (Oulu, Turku, Ghent and Ramon Llull). These participants were split into 15 groups with the express aim of learning about computer-supported collaborative learning (CSCL). The Community of Inquiry model (social, cognitive and teaching presences) provided the content and tools for learning and researching the collaborative interactions in this environment. The sampled comments from the collaborative phase were collected and analyzed at chain-level and group-level, with the aim of identifying the various message types that sustained high learning outcomes. Furthermore, the Social Network Analysis helped to view the density of whole group interactions, as well as the popular and active members within the highly collaborating groups. It was observed that long chains occur in groups having high quality outcomes. These chains were also characterized by Social, Interactivity, Administrative and Content comment-types. In addition, high outcomes were realized from the high interactive cases and high-density groups. In low interactive groups, commenting patterned around the one or two central group members. In conclusion, future online environments should support high-order learning and develop greater metacognition and self-regulation. Moreover, such an environment, with a wide variety of problem solving tools, would enhance interactivity.

Hiilinanojohteiden makroskooppinen johtavuus

Hiilinanojohteet ovat sähkönjohteita, joiden valmistuksessa on käytetty hiilinanoputkia, eli yhden atomikerroksen paksuisesta hiiliatomiverkosta koostuvia rakenteita. Hiilinanoputket ovat viime vuosina keränneet suurta mielenkiintoa erinomaisten fysikaalisten ominaisuuksiensa ansiosta. Tämän työn tavoitteena on selvittää, voitaisiinko hiilinanojohteiden sähkönjohtavuus saada riittävälle tasolle, jotta niillä saatettaisiin korvata nykyisiä kuparista valmistettuja johteita. Vaikka kuparilla on erinomainen johtavuus, sen käytöllä on omat heikkoutensa, kuten korkea hinta, virran ahtautuminen, suuri tiheys ja heikko mekaaninen kestävyys. Hiilinanojohteet voisivat olla yksi osa-alue kehitettäessä uusia energiatehokkaita ja ympäristöystävällisiä laitteita nyky-yhteiskunnan tarpeisiin. Työn tulosten perusteella voidaan todeta, että nykyisten hiilinanojohteiden sähkönjohtavuus on yhä liian pieni laajamittaiseen käyttöön. Johtavuus on kuitenkin lisääntynyt jatkuvasti viime vuosina. Kehitystyön avulla hiilimateriaalin potentiaalia saadaan hyödynnettyä koko ajan enemmän, ja ajan myötä hiilijohteista voi tulla varteenotettava kilpailija perinteisille johdemateriaaleille. Hiilinanojohteet tulevat luultavasti aluksi yleistymään käyttökohteissa, joissa niiden muut ominaisuudet täydentävät hyvin sähkönjohtavuutta.

Cholesterol, cardiovascular disease and statin use in older persons

Older age increases the risk of developing a chronic atherosclerotic cardiovascular disease (CVD), such as coronary heart disease. Complications of CVDs, myocardial infarction or stroke often lead to loss of functional capacity or premature death. Dyslipidemia, high serum levels of total or low-density lipoprotein cholesterol (LDL-c) and low levels of high-density lipoprotein cholesterol (HDL-c), is among the most important modifiable risk factors for CVDs; it can be treated with lifestyle modifications, and with lipid-lowering drugs, primarily statins. In older persons, however, the association of cholesterol levels with cardiovascular and all-cause mortality has been inconsistent in previous studies. Furthermore, the beneficial effects of statins in older persons without previous CVD are still somewhat unclear, and older persons are more prone to adverse effects from statins. This thesis presents a prospective cohort study (TUVA), exploring associations of cholesterol levels with mortality and the changes in cholesterol levels of a 70-year-old population in long-term follow-up. Further, prevalence of CVDs, risk factors and preventive medication use in the TUVA cohort is compared with respective prevalences in another age-matched cohort (UTUVA) 20 years later in order to examine the changes in cardiovascular risk over time. Additionally, to evaluate statin use patterns among older persons, an observational register study was conducted covering the total Finnish population aged 70 and older during 2000-2008. Based on individual-level data retrieved from national health registries, the population was classified into low, moderate and high risk groups according to estimated CVD risk. The prevalence, incidence and persistence of statin use among the risk groups was then evaluated based upon yearly statin purchases tracked from the Prescription Register. The prospective cohort study demonstrated that low total cholesterol, LDL-c and HDL-c were associated with higher mortality in a cohort of home-dwelling 70-year-olds. However, after adjusting for traditional cardiovascular risk factors and cancer this association disappeared. Further, low total cholesterol seemed to be protective, whereas low HDL-c strongly predicted increased risk of CVD death. Cholesterol levels of those elderly who remained available for follow-up and were still home-dwelling at the age of 85 seemed to improve with advancing age. Compared to the TUVA cohort, the later born UTUVA cohort had less CVDs and their risk factors were better controlled, which was reflected in the higher use of preventive medications such as statins and antihypertensives. The register studies confirmed that statin use has increased significantly during 2000-2008 among older persons, especially among the oldest (80+) age groups and among those at high risk for cardiovascular events. Two-thirds of new statin users persisted with their use during the four years of follow-up; the most discontinuations were made during the first year of use. In conclusion, statins are commonly used among older age groups in Finland. Most of the older statin users had a high cardiovascular event risk, indicating that the treatment is well directed towards those who are likely to benefit from it the most. No age-limits should be put on the screening and treatment of dyslipidemia in older persons, but the benefits and adverse effects of statin treatment should be carefully weighed based on an individual assessment of the person’s general health status and functional capacity. Physicians should pay more attention to medication adherence, especially when prescribing preventive medications.