Real-Time PCR : A Molecular Approach to Investigate the Role of Intestinal Microbiota in the Pathophysiology of Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is a common multifactorial functional intestinal disorder, the pathogenesis of which is not completely understood. Increasing scientific evidence suggests that microbes are involved in the onset and maintenance of IBS symptoms. The microbiota of the human gastrointestinal (GI) tract constitutes a massive and complex ecosystem consisting mainly of obligate anaerobic microorganisms making the use of culture-based methods demanding and prone to misinterpretation. To overcome these drawbacks, an extensive panel of species- and group-specific assays for an accurate quantification of bacteria from fecal samples with real-time PCR was developed, optimized, and validated. As a result, the target bacteria were detectable at a minimum concentration range of approximately 10 000 bacterial genomes per gram of fecal sample, which corresponds to the sensitivity to detect 0.000001% subpopulations of the total fecal microbiota. The real-time PCR panel covering both commensal and pathogenic microorganisms was assessed to compare the intestinal microbiota of patients suffering from IBS with a healthy control group devoid of GI symptoms. Both the IBS and control groups showed considerable individual variation in gut microbiota composition. Sorting of the IBS patients according to the symptom subtypes (diarrhea, constipation, and alternating predominant type) revealed that lower amounts of Lactobacillus spp. were present in the samples of diarrhea predominant IBS patients, whereas constipation predominant IBS patients carried increased amounts of Veillonella spp. In the screening of intestinal pathogens, 17% of IBS samples tested positive for Staphylococcus aureus, whereas no positive cases were discovered among healthy controls. Furthermore, the methodology was applied to monitor the effects of a multispecies probiotic supplementation on GI microbiota of IBS sufferers. In the placebo-controlled double-blind probiotic intervention trial of IBS patients, each supplemented probiotic strain was detected in fecal samples. Intestinal microbiota remained stable during the trial, except for Bifidobacterium spp., which increased in the placebo group and decreased in the probiotic group. The combination of assays developed and applied in this thesis has an overall coverage of 300-400 known bacterial species, along with the number of yet unknown phylotypes. Hence, it provides good means for studying the intestinal microbiota, irrespective of the intestinal condition and health status. In particular, it allows screening and identification of microbes putatively associated with IBS. The alterations in the gut microbiota discovered here support the hypothesis that microbes are likely to contribute to the pathophysiology of IBS. The central question is whether the microbiota changes described represent the cause for, rather than the effect of, disturbed gut physiology. Therefore, more studies are needed to determine the role and importance of individual microbial species or groups in IBS. In addition, it is essential that the microbial alterations observed in this study will be confirmed using a larger set of IBS samples of different subtypes, preferably from various geographical locations.

A modell of socially optimal hydro reservoir usage - yelding socially optimal outcomes in nordic electricity markets

An extensive electricity transmission network facilitates electricity trading between Finland, Sweden, Norway and Denmark. Currently most of the area's power generation is traded at NordPool, where the trading volumes have steadily increased since the early 1990's, when the exchange was founded. The Nordic electricity is expected to follow the current trend and further integrate with the other European electricity markets. Hydro power is the source for roughly a half of the supply in the Nordic electricity market and most of the hydro is generated in Norway. The dominating role of hydro power distinguishes the Nordic electricity market from most of the other market places. Production of hydro power varies mainly due to hydro reservoirs and demand for electricity. Hydro reservoirs are affected by water inflows that differ each year. The hydro reservoirs explain remarkably the behaviour of the Nordic electricity markets. Therefore among others, Kauppi and Liski (2008) have developed a model that analyzes the behaviour of the markets using hydro reservoirs as explanatory factors. Their model includes, for example, welfare loss due to socially suboptimal hydro reservoir usage, socially optimal electricity price, hydro reservoir storage and thermal reservoir storage; that are referred as outcomes. However, the model does not explain the real market condition but rather an ideal situation. In the model the market is controlled by one agent, i.e. one agent controls all the power generation reserves; it is referred to as a socially optimal strategy. Article by Kauppi and Liski (2008) includes an assumption where an individual agent has a certain fraction of market power, e.g. 20 % or 30 %. In order to maintain the focus of this thesis, this part of their paper is omitted. The goal of this thesis is two-fold. Firstly we expand the results from the socially optimal strategy for years 2006-08, as the earlier study finishes in 2005. The second objective is to improve on the methods from the previous study. This thesis results several outcomes (SPOT-price and welfare loss, etc.) due to socially optimal actions. Welfare loss is interesting as it describes the inefficiency of the market. SPOT-price is an important output for the market participants as it often has an effect on end users' electricity bills. Another function is to modify and try to improve the model by means of using more accurate input data, e.g. by considering pollution trade rights effect on input data. After modifications to the model, new welfare losses are calculated and compared with the same results before the modifications. The hydro reservoir has the higher explanatory significance in the model followed by thermal power. In Nordic markets, thermal power reserves are mostly nuclear power and other thermal sources (coal, natural gas, oil, peat). It can be argued that hydro and thermal reservoirs determine electricity supply. Roughly speaking, the model takes into account electricity demand and supply, and several parameters related to them (water inflow, oil price, etc.), yielding finally the socially optimal outcomes. The author of this thesis is not aware of any similar model being tested before. There have been some other studies that are close to the Kauppi and Liski (2008) model, but those have a somewhat different focus. For example, a specific feature in the model is the focus on long-run capacity usage that differs from the previous studies on short-run market power. The closest study to the model is from California's wholesale electricity markets that, however, uses different methodology. Work is constructed as follows.

Dual-trap optical tweezers with real-time force clamp control

Single molecule force clamp experiments are widely used to investigate how enzymes, molecular motors, and other molecular mechanisms work. We developed a dual-trap optical tweezers instrument with real-time (200 kHz update rate) force clamp control that can exert 0–100 pN forces on trapped beads. A model for force clamp experiments in the dumbbell-geometry is presented. We observe good agreement between predicted and observed power spectra of bead position and force fluctuations. The model can be used to predict and optimize the dynamics of real-time force clamp optical tweezers instruments. The results from a proof-of-principle experiment in which lambda exonuclease converts a double-stranded DNA tether, held at constant tension, into its single-stranded form, show that the developed instrument is suitable for experiments in single molecule biology.

Field intercomparison of four methane gas analysers suitable for eddy covariance flux measurements

Eddy covariance (EC)-flux measurement technique is based on measurement of turbulent motions of air with accurate and fast measurement devices. For instance, in order to measure methane flux a fast methane gas analyser is needed which measures methane concentration at least ten times in a second in addition to a sonic anemometer, which measures the three wind components with the same sampling interval. Previously measurement of methane flux was almost impossible to carry out with EC-technique due to lack of fast enough gas analysers. However during the last decade new instruments have been developed and thus methane EC-flux measurements have become more common. Performance of four methane gas analysers suitable for eddy covariance measurements are assessed in this thesis. The assessment and comparison was performed by analysing EC-data obtained during summer 2010 (1.4.-26.10.) at Siikaneva fen. The four participating methane gas analysers are TGA-100A (Campbell Scientific Inc., USA), RMT-200 (Los Gatos Research, USA), G1301-f (Picarro Inc., USA) and Prototype-7700 (LI-COR Biosciences, USA). RMT-200 functioned most reliably throughout the measurement campaign and the corresponding methane flux data had the smallest random error. In addition, methane fluxes calculated from data obtained from G1301-f and RMT-200 agree remarkably well throughout the measurement campaign. The calculated cospectra and power spectra agree well with corresponding temperature spectra. Prototype-7700 functioned only slightly over one month in the beginning of the measurement campaign and thus its accuracy and long-term performance is difficult to assess.

Naudanlihan jalostusketjun hiilijalanjälki Suomessa

Kirjallisuustutkimuksen tavoitteena oli perehtyä kasvihuoneilmiön taustoihin ja kartoittaa aiempia tutkimuksia naudan- ja muiden lihatuotteiden kasvihuonekaasupäästöistä. Lisäksi kirjallisuustutkimuksessa perehdyttiin aiemmissa tutkimuksissa elintarvikkeiden hiilijalanjäljen laskemisessa sovellettuun elinkaarianalyysiin ISO 14040-standardin mukaisesti. Kokeellisen osion tavoitteena oli määrittää naudanlihan hiilijalanjälki Suomessa maatilan portilta kuluttajan ruokapöytään. Tavoitteena oli myös ymmärtää jalostusketjun päästöjen merkitys verrattuna koko naudanlihan tuotantoketjuun ja määrittää jalostusketjun vaiheiden merkitys ketjussa. Työn toiminnallisena yksikkönä toimi kilo naudanlihaa. Työ toteutettiin perehtymällä yksityiskohtaisesti yhteen naudanlihan jalostusketjuun Suomessa. Päästöt laskettiin todellisten yhteistyöyritykseltä saatujen prosessitietojen perusteella. Tiedot kerättiin tiedonkeruulomakkeella vierailemalla yhteistyöyrityksen kahdessa tuotantolaitoksessa ja täydentämällä tietoja haastatteluilla. Naudanlihan jalostusketjun päästöt olivat 1240 g CO2-ekv/lihakilo. Eniten päästöjä tuottivat jalostusvaihe (310 g CO2-ekv/lihakilo), teurastus (280 g CO2-ekv/lihakilo) ja lihatuotteiden kuljetus kuluttajalle (210 g CO2-ekv/lihakilo). Koko naudanlihan tuotantoketjusta jalostusketjun päästöt muodostivat alle 4 %, sillä syntymästä maatilan portille syntyviksi päästöiksi laskettiin kirjallisuuden perusteella yli 30 000 g CO2-ekv/lihakilo. Jatkossa naudanlihan hiilijalanjälkeä voitaisiin pääasiassa pienentää kehittämällä prosessia maatilan portille asti. Tämän työn tulokset olivat hyvin samansuuruiset verrattuna aiempaan tutkimukseen broilerin jalostusketjun päästöistä Suomessa (Katajajuuri ym. 2008). Tämä vastasi ennakko-odotuksia, sillä jalostusketjujen vaiheissa ei ollut merkittäviä eroja. Aiempia tutkimuksia naudanlihan jalostusketjun päästöistä ei ollut saatavilla.

Rapsista tuotetun biodieselin ja vehnästä tuotetun bioetanolin energiavirrat ja ympäristövaikutukset Euroopan unionissa

The aim of this thesis was to study the crops currently used for biofuel production from the following aspects: 1. what should be the average yield/ ha to reach an energy balance at least 0 or positive 2. what are the shares of the primary and secondary energy flows in agriculture, transport, processing and usage, and 3. overall effects of biofuel crop cultivation, transport, processing and usage. This thesis concentrated on oilseed rape biodiesel and wheat bioethanol in the European Union, comparing them with competing biofuels, such as corn and sugarcane-based ethanol, and the second generation biofuels. The study was executed by comparing Life Cycle Assessment-studies from the EU-region and by analyzing them thoroughly from the differences viewpoint. The variables were the following: energy ratio, hectare yield (l/ha), impact on greenhouse gas emissions (particularly CO2), energy consumption in crop growing and processing one hectare of a particular crop to biofuel, distribution of energy in processing and effects of the secondary energy flows, like e.g. wheat straw. Processing was found to be the most energy consuming part in the production of biofuels. So if the raw materials will remain the same, the development will happen in processing. First generation biodiesel requires esterification, which consumes approximately one third of the process energy. Around 75% of the energy consumed in manufacturing the first generation wheat-based ethanol is spent in steam and electricity generation. No breakthroughs are in sight in the agricultural sector to achieve significantly higher energy ratios. It was found out that even in ideal conditions the energy ratio of first generation wheat-based ethanol will remain slightly under 2. For oilseed rape-based biodiesel the energy ratios are better, and energy consumption per hectare is lower compared to wheat-based ethanol. But both of these are lower compared to e.g. sugarcane-based ethanol. Also the hectare yield of wheat-based ethanol is significantly lower. Biofuels are in a key position when considering the future of the world’s transport sector. Uncertainties concerning biofuels are, however, several, like the schedule of large scale introduction to consumer markets, technologies used, raw materials and their availability and - maybe the biggest - the real production capacity in relation to the fuel consumption. First generation biofuels have not been the expected answer to environmental problems. Comparisons made show that sugarcane-based ethanol is the most prominent first generation biofuel at the moment, both from energy and environment point of view. Also palmoil-based biodiesel looks promising, although it involves environmental concerns as well. From this point of view the biofuels in this study - wheat-based ethanol and oilseed rape-based biodiesel - are not very competitive options. On the other hand, crops currently used for fuel production in different countries are selected based on several factors, not only based on thier relative general superiority. It is challenging to make long-term forecasts for the biofuel sector, but it can be said that satisfying the world's current and near future traffic fuel consumption with biofuels can only be regarded impossible. This does not mean that biofuels shoud be rejected and their positive aspects ignored, but maybe this reality helps us to put them in perspective. To achieve true environmental benefits through the usage of biofuels there must first be a significant drop both in traffic volumes and overall fuel consumption. Second generation biofuels are coming, but serious questions about their availability and production capacities remain open. Therefore nothing can be taken for granted in this issue, expect the need for development.

Jatrophanviljely ja maankäyttö Vietnamissa

Biofuels are under discussion all over the world today. There are fears that the farming of biofuel plants hurts food production and weakens the food security of the poor. On the other hand, biofuel production could lessen the green house gas emissions caused by transportation, and it could also spread the profits from fuel markets more evenly between countries. The aim of this thesis is to find out how an oil plant called jatropha curcas L., which is used for biodiesel production, can affect the sustainability of livelihoods in Vietnam from the point of view of land use. Special attention is given to the effects of jatropha farming on food production, land productivity, natural resources of livelihoods and global livelihood. Jatropha belongs to the family Euphorbiaceae, and it grows naturally in tropical and subtropical areas. It can be grown on poor soils, its seeds have high oil content, and it cannot be eaten due to its toxicity. The plant grows naturally in Vietnam, and during the past few years it has also begun to be farmed for making biodiesel. Population growth in Vietnam has slowed down, but the population's standard of living and energy consumption are still rising quickly. An interest in the international biodiesel markets has awoken following Vietnam's opening up to international trade. Jatropha diesel plays a significant part in Vietnam’s clean fuel strategy, and many companies have set up jatropha plantations to produce raw material for biodiesel. Diesel made from jatropha is planned to be used both locally and for export. This thesis uses a theoretical concept of sustainable livelihoods. According to the theory, the resources that people have shape their livelihood possibilities. Farming of jatropha affects the livelihoods of people especially through land use, as land use changes have effects on many of the livelihood resources. In addition to the written sources, the material of the thesis is based on 14 interviews in Vietnam and Finland, and on observation during a field trip to Northern Vietnam in the spring of 2008. The results of the thesis show that jatropha diesel can support the sustainability of livelihoods at different scales if it is produced with deliberation. However, positive results are only possible if decisions are made carefully and more experience is collected. The possibilities of sustainable jatropha farming depend mainly on the previous land use methods and ways of production. Farming of jatropha does not threaten food production in Vietnam if the farming plans are implemented as planned. Jatropha may take some land from cassava, but at the same time, food production can be increased if mixed farming is used on some farms. Plenty of new research information and practical experiences on jatropha farming has to be collected before results of the real sustainability of the farming are ready. Carefully considered continuation and documentation of present and future projects would help to understand the possibilities of jatropha diesel in Vietnam and elsewhere.