Distribution of non-biting midges (Diptera, Chironomidae) in subarctic lakes of Finnish Lapland applications in lake classification and palaeolimnology

Climate change contributes directly or indirectly to changes in species distributions, and there is very high confidence that recent climate warming is already affecting ecosystems. The Arctic has already experienced the greatest regional warming in recent decades, and the trend is continuing. However, studies on the northern ecosystems are scarce compared to more southerly regions. Better understanding of the past and present environmental change is needed to be able to forecast the future. Multivariate methods were used to explore the distributional patterns of chironomids in 50 shallow (≤ 10m) lakes in relation to 24 variables determined in northern Fennoscandia at the ecotonal area from the boreal forest in the south to the orohemiarctic zone in the north. Highest taxon richness was noted at middle elevations around 400 m a.s.l. Significantly lower values were observed from cold lakes situated in the tundra zone. Lake water alkalinity had the strongest positive correlation with the taxon richness. Many taxa had preference for lakes either on tundra area or forested area. The variation in the chironomid abundance data was best correlated with sediment organic content (LOI), lake water total organic carbon content, pH and air temperature, with LOI being the strongest variable. Three major lake groups were separated on the basis of their chironomid assemblages: (i) small and shallow organic-rich lakes, (ii) large and base-rich lakes, and (iii) cold and clear oligotrophic tundra lakes. Environmental variables best discriminating the lake groups were LOI, taxon richness, and Mg. When repeated, this kind of an approach could be useful and efficient in monitoring the effects of global change on species ranges. Many species of fast spreading insects, including chironomids, show a remarkable ability to track environmental changes. Based on this ability, past environmental conditions have been reconstructed using their chitinous remains in the lake sediment profiles. In order to study the Holocene environmental history of subarctic aquatic systems, and quantitatively reconstruct the past temperatures at or near the treeline, long sediment cores covering the last 10000 years (the Holocene) were collected from three lakes. Lower temperature values than expected based on the presence of pine in the catchment during the mid-Holocene were reconstructed from a lake with great water volume and depth. The lake provided thermal refuge for profundal, cold adapted taxa during the warm period. In a shallow lake, the decrease in the reconstructed temperatures during the late Holocene may reflect the indirect response of the midges to climate change through, e.g., pH change. The results from three lakes indicated that the response of chironomids to climate have been more or less indirect. However, concurrent shifts in assemblages of chironomids and vegetation in two lakes during the Holocene time period indicated that the midges together with the terrestrial vegetation had responded to the same ultimate cause, which most likely was the Holocene climate change. This was also supported by the similarity in the long-term trends in faunal succession for the chironomid assemblages in several lakes in the area. In northern Finnish Lapland the distribution of chironomids were significantly correlated with physical and limnological factors that are most likely to change as a result of future climate change. The indirect and individualistic response of aquatic systems, as reconstructed using the chironomid assemblages, to the climate change in the past suggests that in the future, the lake ecosystems in the north do not respond in one predictable way to the global climate change. Lakes in the north may respond to global climate change in various ways that are dependent on the initial characters of the catchment area and the lake.

Development of biogenic VOC emission inventories for the boreal forest

Luonnosta haihtuvat orgaaniset yhdisteet, joita pääsee ilmaan etenkin metsistä, voivat vaikuttaa paikalliseen ja alueelliseen ilmanlaatuun, koska ne reagoivat ilmakehässä. Niiden reaktiotuotteet voivat myös osallistua uusien hiukkasten muodostumiseen ja kasvuun, millä voi olla vaikutusta ilmakehän säteilytaseeseen ja tätä kautta myös ilmastoon. Hiukkaset absorboivat ja sirottavat auringon säteilyä ja maapallon lämpösäteilyä minkä lisäksi ne vaikuttavat pilvien säteilyominaisuuksiin, määrään ja elinikään. Koko maapallon mittakaavassa luonnosta tulevat hiilivetypäästöt ylittävät ihmistoiminnan aiheuttamat päästöt moninkertaisesti. Tämän vuoksi luonnon päästöjen arviointi on tärkeää kun halutaan kehittää tehokkaita ilmanlaatu- ja ilmastostrategioita. Tämä tutkimus käsittelee boreaalisen metsän hiilivetypäästöjä. Boreaalinen metsä eli pohjoinen havumetsä on suurin maanpäällinen ekosysteemi, ja se ulottuu lähes yhtenäisenä nauhana koko pohjoisen pallonpuoliskon ympäri. Sille on tyypillistä puulajien suhteellisen pieni kirjo sekä olosuhteiden ja kasvun voimakkaat vuodenaikaisvaihtelut. Työssä on tutkittu Suomen yleisimmän boreaalisen puun eli männyn hiilivetypäästöjen vuodenaikaisvaihtelua sekä päästöjen riippuvuutta lämpötilasta ja valosta. Saatuja tuloksia on käytetty yhdessä muiden boreaalisilla puilla tehtyjen päästömittaustulosten kanssa Suomen metsiä varten kehitetyssä päästömallissa. Malli perustuu lisäksi maankäyttötietoihin, suomen metsille kehitettyyn luokitukseen ja meteorologisiin tietoihin, joiden avulla se laskee metsien hiilivetypäästöt kasvukauden aikana. Suomen metsien päästöt koostuvat koko kasvukauden ajan suurelta osin alfa- ja beta-pineenistä sekä delta-kareenista. Kesällä ja syksyllä päästöissä on myös paljon sabineenia, jota tulee etenkin lehtipuista. Päästöt seuraavat lämpötilan keskimääräistä vaihtelua, ovat suurimmillaan maan eteläosissa ja laskevat tasaisesti pohjoiseen siirryttäessä. Metsän isopreenipäästö on suhteellisen pieni – Suomessa tärkein isopreeniä päästävä puu on vähäpäästöinen kuusi, koska runsaspäästöisten pajun ja haavan osuus metsän lehtimassasta on hyvin pieni. Tässä työssä on myös laskettu ensimmäinen arvio metsän seskviterpeenipäästöistä. Seskviterpeenipäästöt alkavat Juhannuksen jälkeen ja ovat kasvukauden aikana samaa suuruusluokkaa kuin isopreenipäästöt. Vuositasolla Suomen metsien hiilivetypäästöt ovat noin kaksinkertaiset ihmistoiminnasta aiheutuviin päästöihin verrattuna.

Effects of climate and morphology on temperature conditions of lakes

To a large extent, lakes can be described with a one-dimensional approach, as their main features can be characterized by the vertical temperature profile of the water. The development of the profiles during the year follows the seasonal climate variations. Depending on conditions, lakes become stratified during the warm summer. After cooling, overturn occurs, water cools and an ice cover forms. Typically, water is inversely stratified under the ice, and another overturn occurs in spring after the ice has melted. Features of this circulation have been used in studies to distinguish between lakes in different areas, as basis for observation systems and even as climate indicators. Numerical models can be used to calculate temperature in the lake, on the basis of the meteorological input at the surface. The simple form is to solve the surface temperature. The depth of the lake affects heat transfer, together with other morphological features, the shape and size of the lake. Also the surrounding landscape affects the formation of the meteorological fields over the lake and the energy input. For small lakes the shading by the shores affects both over the lake and inside the water body bringing limitations for the one-dimensional approach. A two-layer model gives an approximation for the basic stratification in the lake. A turbulence model can simulate vertical temperature profile in a more detailed way. If the shape of the temperature profile is very abrupt, vertical transfer is hindered, having many important consequences for lake biology. One-dimensional modelling approach was successfully studied comparing a one-layer model, a two-layer model and a turbulence model. The turbulence model was applied to lakes with different sizes, shapes and locations. Lake models need data from the lakes for model adjustment. The use of the meteorological input data on different scales was analysed, ranging from momentary turbulent changes over the lake to the use of the synoptical data with three hour intervals. Data over about 100 past years were used on the mesoscale at the range of about 100 km and climate change scenarios for future changes. Increasing air temperature typically increases water temperature in epilimnion and decreases ice cover. Lake ice data were used for modelling different kinds of lakes. They were also analyzed statistically in global context. The results were also compared with results of a hydrological watershed model and data from very small lakes for seasonal development.

Measurements of Volatile Organic Compounds - from Biogenic Emissions to Concentrations in Ambient Air

Volatile organic compounds (VOCs) affect atmospheric chemistry and thereafter also participate in the climate change in many ways. The long-lived greenhouse gases and tropospheric ozone are the most important radiative forcing components warming the climate, while aerosols are the most important cooling component. VOCs can have warming effects on the climate: they participate in tropospheric ozone formation and compete for oxidants with the greenhouse gases thus, for example, lengthening the atmospheric lifetime of methane. Some VOCs, on the other hand, cool the atmosphere by taking part in the formation of aerosol particles. Some VOCs, in addition, have direct health effects, such as carcinogenic benzene. VOCs are emitted into the atmosphere in various processes. Primary emissions of VOC include biogenic emissions from vegetation, biomass burning and human activities. VOCs are also produced in secondary emissions from the reactions of other organic compounds. Globally, forests are the largest source of VOC entering the atmosphere. This thesis focuses on the measurement results of emissions and concentrations of VOCs in one of the largest vegetation zones in the world, the boreal zone. An automated sampling system was designed and built for continuous VOC concentration and emission measurements with a proton transfer reaction - mass spectrometer (PTR-MS). The system measured one hour at a time in three-hourly cycles: 1) ambient volume mixing-ratios of VOCs in the Scots-pine-dominated boreal forest, 2) VOC fluxes above the canopy, and 3) VOC emissions from Scots pine shoots. In addition to the online PTR-MS measurements, we determined the composition and seasonality of the VOC emissions from a Siberian larch with adsorbent samples and GC-MS analysis. The VOC emissions from Siberian larch were reported for the fist time in the literature. The VOC emissions were 90% monoterpenes (mainly sabinene) and the rest sesquiterpenes (mainly a-farnesene). The normalized monoterpene emission potentials were highest in late summer, rising again in late autumn. The normalized sesquiterpene emission potentials were also highest in late summer, but decreased towards the autumn. The emissions of mono- and sesquiterpenes from the deciduous Siberian larch, as well as the emissions of monoterpenes measured from the evergreen Scots pine, were well described by the temperature-dependent algorithm. In the Scots-pine-dominated forest, canopy-scale emissions of monoterpenes and oxygenated VOCs (OVOCs) were of the same magnitude. Methanol and acetone were the most abundant OVOCs emitted from the forest and also in the ambient air. Annually, methanol and mixing ratios were of the order of 1 ppbv. The monoterpene and sum of isoprene 2-methyl-3-buten-2-ol (MBO) volume mixing-ratios were an order of magnitude lower. The majority of the monoterpene and methanol emissions from the Scots-pinedominated forest were explained by emissions from Scots pine shoots. The VOCs were divided into three classes based on the dynamics of the summer-time concentrations: 1) reactive compounds with local biological, anthropogenic or chemical sources (methanol, acetone, butanol and hexanal), 2) compounds whose emissions are only temperaturedependent (monoterpenes), 3) long-lived compounds (benzene, acetaldehyde). Biogenic VOC (methanol, acetone, isoprene MBO and monoterpene) volume mixing-ratios had clear diurnal patterns during summer. The ambient mixing ratios of other VOCs did not show this behaviour. During winter we did not observe systematical diurnal cycles for any of the VOCs. Different sources, removal processes and turbulent mixing explained the dynamics of the measured mixing-ratios qualitatively. However, quantitative understanding will require longterm emission measurements of the OVOCs and the use of comprehensive chemistry models. Keywords: Hydrocarbons, VOC, fluxes, volume mixing-ratio, boreal forest

Simulations of dimensionally reduced effective theories of high temperature QCD

Quantum chromodynamics (QCD) is the theory describing interaction between quarks and gluons. At low temperatures, quarks are confined forming hadrons, e.g. protons and neutrons. However, at extremely high temperatures the hadrons break apart and the matter transforms into plasma of individual quarks and gluons. In this theses the quark gluon plasma (QGP) phase of QCD is studied using lattice techniques in the framework of dimensionally reduced effective theories EQCD and MQCD. Two quantities are in particular interest: the pressure (or grand potential) and the quark number susceptibility. At high temperatures the pressure admits a generalised coupling constant expansion, where some coefficients are non-perturbative. We determine the first such contribution of order g^6 by performing lattice simulations in MQCD. This requires high precision lattice calculations, which we perform with different number of colors N_c to obtain N_c-dependence on the coefficient. The quark number susceptibility is studied by performing lattice simulations in EQCD. We measure both flavor singlet (diagonal) and non-singlet (off-diagonal) quark number susceptibilities. The finite chemical potential results are optained using analytic continuation. The diagonal susceptibility approaches the perturbative result above 20T_c$, but below that temperature we observe significant deviations. The results agree well with 4d lattice data down to temperatures 2T_c.

Carbon dioxide and methane exchange between a boreal pristine lake and the atmosphere

Lakes serve as sites for terrestrially fixed carbon to be remineralized and transferred back to the atmosphere. Their role in regional carbon cycling is especially important in the Boreal Zone, where lakes can cover up to 20% of the land area. Boreal lakes are often characterized by the presence of a brown water colour, which implies high levels of dissolved organic carbon from the surrounding terrestrial ecosystem, but the load of inorganic carbon from the catchment is largely unknown. Organic carbon is transformed to methane (CH4) and carbon dioxide (CO2) in biological processes that result in lake water gas concentrations that increase above atmospheric equilibrium, thus making boreal lakes as sources of these important greenhouse gases. However, flux estimates are often based on sporadic sampling and modelling and actual flux measurements are scarce. Thus, the detailed temporal flux dynamics of greenhouse gases are still largely unknown. ----- One aim here was to reveal the natural dynamics of CH4 and CO2 concentrations and fluxes in a small boreal lake. The other aim was to test the applicability of a measuring technique for CO2 flux, i.e. the eddy covariance (EC) technique, and a computational method for estimation of primary production and community respiration, both commonly used in terrestrial research, in this lake. Continuous surface water CO2 concentration measurements, also needed in free-water applications to estimate primary production and community respiration, were used over two open water periods in a study of CO2 concentration dynamics. Traditional methods were also used to measure gas concentration and fluxes. The study lake, Valkea-Kotinen, is a small, humic, headwater lake within an old-growth forest catchment with no local anthropogenic disturbance and thus possible changes in gas dynamics reflect the natural variability in lake ecosystems. CH4 accumulated under the ice and in the hypolimnion during summer stratification. The surface water CH4 concentration was always above atmospheric equilibrium and thus the lake was a continuous source of CH4 to the atmosphere. However, the annual CH4 fluxes were small, i.e. 0.11 mol m-2 yr-1, and the timing of fluxes differed from that of other published estimates. The highest fluxes are usually measured in spring after ice melt but in Lake Valkea-Kotinen CH4 was effectively oxidised in spring and highest effluxes occurred in autumn after summer stratification period. CO2 also accumulated under the ice and the hypolimnetic CO2 concentration increased steadily during stratification period. The surface water CO2 concentration was highest in spring and in autumn, whereas during the stable stratification it was sometimes under atmospheric equilibrium. It showed diel, daily and seasonal variation; the diel cycle was clearly driven by light and thus reflected the metabolism of the lacustrine ecosystem. However, the diel cycle was sometimes blurred by injection of hypolimnetic water rich in CO2 and the surface water CO2 concentration was thus controlled by stratification dynamics. The highest CO2 fluxes were measured in spring, autumn and during those hypolimnetic injections causing bursts of CO2 comparable with the spring and autumn fluxes. The annual fluxes averaged 77 (±11 SD) g C m-2 yr-1. In estimating the importance of the lake in recycling terrestrial carbon, the flux was normalized to the catchment area and this normalized flux was compared with net ecosystem production estimates of -50 to 200 g C m-2 yr-1 from unmanaged forests in corresponding temperature and precipitation regimes in the literature. Within this range the flux of Lake Valkea-Kotinen yielded from the increase in source of the surrounding forest by 20% to decrease in sink by 5%. The free water approach gave primary production and community respiration estimates of 5- and 16-fold, respectively, compared with traditional bottle incubations during a 5-day testing period in autumn. The results are in parallel with findings in the literature. Both methods adopted from the terrestrial community also proved useful in lake studies. A large percentage of the EC data was rejected, due to the unfulfilled prerequisites of the method. However, the amount of data accepted remained large compared with what would be feasible with traditional methods. Use of the EC method revealed underestimation of the widely used gas exchange model and suggests simultaneous measurements of actual turbulence at the water surface with comparison of the different gas flux methods to revise the parameterization of the gas transfer velocity used in the models.

Suokasvillisuuden vaste muuttuvaan ilmastoon: kokeellinen tutkimus kuivumisen vaikutuksesta

Soilla on merkittävä rooli ilmastonmuutoksen hillitsemisessä suuren hiilivarastonsa sekä ekosysteemin ja ilmakehän välisen kaasunvaihdon ansiosta. Ilmastonmuutoksen ennustetaan vaikuttavan suokasvillisuuteen ja suon toimintaan epäsuorasti. Vedenpinnan ennustetaan laskevan 14–21 cm johtuen kasveista ja avoimilta pinnoilta tapahtuvan haihdunnan lisääntymisestä lämpötilan noustessa, mikäli sadanta ei lisäänny. Aiemmat vedenpinnan laskun jälkeistä kasvillisuutta seuranneet tutkimukset ovat osoittaneet, että putkilokasvit hyötyvät alhaisemmasta vedenpinnan tasosta ja että kuljuun sopeutuneet rahkasammalet kärsivät kuivuneista oloista. Kasvillisuuden runsaussuhteiden muuttumisen lisäksi kasviyhteisöjen monimuotoisuus vähenee. Erityisen herkkiä vedenpinnan laskulle ovat olleet välipinta- ja kuljurahkasammalet ja sarat. Funktionaalisten kasviryhmien vasteiden selvittämiksesi käytettiin BACI (before-after-control-impact) –tutkimusotetta. Tutkimuksessa oli kolme verrokkialaa ja kolme käsittelyalaa, joissa vedenpintaa oli laskettu 14–21 senttimetriin. Lisäksi vertailukohdaksi tutkimuksessa oli mukana kolme alaa, joissa oli tehty metsäojitus n. 50 vuotta sitten. Nämä toistot sijaitsivat meso-, oligo ombrotrofisilla suotyypeillä Oriveden Lakkasuolla. Kasvillisuus kartoitettiin ja vedenpinnat mitattiin aloilta ennen käsittelyä vuonna 2000 sekä vuosina 2001–2003 ja 2009. Aineisto analysoitiin TWINSPAN- (PC-Ord), PRC ja DCA (CANOCO)-monimuuttujamenetelmillä. Tulokset osoittivat, että verrokki- ja käsittelyalat olivat samanlaisia lähtökohdiltaan, joten niitä voitiin käsittelyn jälkeen verrata toisiinsa. Kasvillisuuden rakenne vaihteli vuosien välillä myös verrokkialoilla, mikä osoittaa kasvien sopeutumiskyvyn muuttuviin sääoloihin (lämpötila, sademäärä). Vuosi 2003 erottui tutkimuksessa alhaisella vedenpinnantasolla, mutta toisaalta myös ainavihantien varpujen suuren peittävyyden osalta. Vuoteen 2009 mennessä kasvillisuuden erityisesti sarojen peittävyys väheni. Ravinteikkaimmilla toistoilla kasvillisuuden vasteet vaikuttivat olevan vahvemmat kuin vähäravinteisilla toistoilla. Kasviryhmistä kulju- ja välipintasammalilla oli vahvimmat vasteetvedenpinnan laskuun ja mätäslajeilla heikoimmat. Tulosten mukaan kasviryhmien vasteet vaihtelevat riippuen tarkasteltavasta aikajaksosta: ensimmäiset kolme vuotta käsittelyn jälkeen suo oli häiriötilassa ja vasta sen jälkeen kasvillisuus sopeutui muuttuneisiin oloihin.

Photosynthesis of ground vegetation in boreal Scots pine forests

Research on carbon uptake in boreal forests has mainly focused on mature trees, even though ground vegetation species are effective assimilators and can substantially contribute to the CO2 uptake of forests. Here, I examine the photosynthesis of the most common species of ground vegetation in a series of differently aged Scots pine stands, and at two clear-cut sites with substantial differences in fertility. In general, the biomass of evergreen species was highest at poor sites and below canopies, whereas grasses and herbs predominated at fertile sites and open areas. Unlike mosses, the measured vascular species showed clear annual cycles in their photosynthetic activity, which increased earlier and decreased later in evergreen vascular species than in deciduous species. However, intraspecific variation and self-shading create differences in the overall level of photosynthesis. Light, temperature history, soil moisture and recent possible frosts could explain the changes in photosynthesis of low shrubs and partially also some changes in deciduous species. Light and the occurrence of rain events explained most of the variation in the photosynthesis of mosses. The photosynthetic production of ground vegetation was first upscaled, using species-specific and mass-based photosynthetic activities and average biomass of the site, and then integrated over the growing season, using changes in environmental factors. Leaf mass-based photosynthesis was highest in deciduous species, resulting in notably higher photosynthetic production at fertile sites than at poor clear-cut sites. The photosynthetic production decreased with stand age, because flora changed towards evergreen species, and light levels diminished below the canopy. In addition, the leaf mass-based photosynthetic activity of some low shrubs declined with the age of the surrounding trees. Different measuring methods led to different momentary rate of photosynthesis. Therefore, the choice of measuring method needs special attention.

High-precision diode-laser-based temperature measurement for air refractive index compensation

We present a laser-based system to measure the refractive index of air over a long path length. In optical distance measurements it is essential to know the refractive index of air with high accuracy. Commonly, the refractive index of air is calculated from the properties of the ambient air using either Ciddor or Edlén equations, where the dominant uncertainty component is in most cases the air temperature. The method developed in this work utilises direct absorption spectroscopy of oxygen to measure the average temperature of air and of water vapor to measure relative humidity. The method allows measurement of temperature and humidity over the same beam path as in optical distance measurement, providing spatially well matching data. Indoor and outdoor measurements demonstrate the effectiveness of the method. In particular, we demonstrate an effective compensation of the refractive index of air in an interferometric length measurement at a time-variant and spatially non-homogenous temperature over a long time period. Further, we were able to demonstrate 7 mK RMS noise over a 67 m path length using 120 s sample time. To our knowledge, this is the best temperature precision reported for a spectroscopic temperature measurement.

Temperature-Sensitive Src-Transformed Mdck Cells nn 3d Cultures as a Model of Malignant Transformation of Epithelial Cells

The equilibrium between cell proliferation, differentiation, and apoptosis is crucial for maintaining homeostasis in epithelial tissues. In order for the epithelium to function properly, individual cells must gain normal structural and functional polarity. The junctional proteins have an important role both in binding the cells together and in taking part in cell signaling. Cadherins form adherens junctions. Cadherins initiate the polarization process by first recognizing and binding the neighboring cells together, and then guiding the formation of tight junctions. Tight junctions form a barrier in dividing the plasma membranes to apical and basolateral membrane domains. In glandular tissues, single layered and polarized epithelium is folded into tubes or spheres, in which the basal side of the epithelial layer faces the outer basal membrane, and the apical side the lumen. In carcinogenesis, the differentiated architecture of an epithelial layer is disrupted. Filling of the luminal space is a hallmark of early epithelial tumors in tubular and glandular structures. In order for the transformed tumor cells to populate the lumen, enhanced proliferation as well as inhibition of apoptosis is required. Most advances in cancer biology have been achieved by using two-dimensional (2D) cell culture models, in which the cells are cultured on flat surfaces as monolayers. However, the 2D cultures are limited in their capacity to recapitulate the structural and functional features of tubular structures and to represent cell growth and differentiation in vivo. The development of three-dimensional (3D) cell culture methods enables the cells to grow and to be studied in a more natural environment. Despite the wide use of 2D cell culture models and the development of novel 3D culture methods, it is not clear how the change of the dimensionality of culture conditions alters the polarization and transformation process and the molecular mechanisms behind them. Src is a well-known oncogene. It is found in focal and adherens junctions of cultured cells. Active src disrupts cell-cell junctions and interferes with cell-matrix binding. It promotes cell motility and survival. Src transformation in 2D disrupts adherens junctions and the fibroblastic phenotype of the cells. In 3D, the adherens junctions are weakened, and in glandular structures, the lumen is filled with nonpolarized vital cells. Madin-Darby canine kidney (MDCK) cells are an epithelial cell type commonly used as a model for cell polarization. Its-src-transformed variants are useful model systems for analyzing the changes in cell morphology, and they play a role in src-induced malignant transformation. This study investigates src-transformed cells in 3D cell cultures as a model for malignant transformation. The following questions were posed. Firstly: What is the role of the composition and stiffness of the extracellular matrix (ECM) on the polarization and transformation of ts v-src MDCK cells in 3D cell cultures? Secondly: How do the culture conditions affect gene expression? What is the effect of v-src transformation in 2D and in 3D cell models? How does the shift from 2D to 3D affect cell polarity and gene expression? Thirdly: What is the role of survivin and its regulator phosphatase and tensin homolog protein (PTEN) in cell polarization and transformation, and in determining cell fate? How does their expression correlate with impaired mitochondrial function in transformed cells? In order to answer the above questions, novel methods of culturing and monitoring cells had to be created: novel 3D methods of culturing epithelial cells were engineered, enabling real time monitoring of a polarization and transformation process, and functional testing of 3D cell cultures. Novel 3D cell culture models and imaging techniques were created for the study. Attention was focused especially on confocal microscopy and live-cell imaging. Src-transformation disturbed the polarization of the epithelium by disrupting cell adhesion, and sensitized the cells to their environment. With active src, the morphology of the cell cluster depended on the composition and stiffness of the matrix. Gene expression studies revealed a broader impact of src transformation than mere continuous activity of src-kinase. In 2D cultures, src transformation altered the expression of immunological, actin cytoskeleton and extracellular matrix (ECM). In 3D, the genes regulating cell division, inhibition of apoptosis, cell metabolism, mitochondrial function, actin cytoskeleton and mechano-sensing proteins were altered. Surprisingly, changing the culture conditions from 2D to 3D affected also gene expression considerably. The microarray hit survivin, an inhibitor of apoptosis, played a crucial role in the survival and proliferation of src-transformed cells.

Seasonal and short-term variation in denitrification and anammox at a coastal station on the Gulf of Finland, Baltic Sea

Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research.