Engineering the pentose phosphate pathway of Saccharomyces cerevisiae for production of ethanol and xylitol

The baker s yeast Saccharomyces cerevisiae has a long tradition in alcohol production from D-glucose of e.g. starch. However, without genetic modifications it is unable to utilise the 5-carbon sugars D-xylose and L arabinose present in plant biomass. In this study, one key metabolic step of the catabolic D-xylose pathway in recombinant D-xylose-utilising S. cerevisiae strains was studied. This step, carried out by xylulokinase (XK), was shown to be rate-limiting, because overexpression of the xylulokinase-encoding gene XKS1 increased both the specific ethanol production rate and the yield from D xylose. In addition, less of the unwanted side product xylitol was produced. Recombinant D-xylose-utilizing S. cerevisiae strains have been constructed by expressing the genes coding for the first two enzymes of the pathway, D-xylose reductase (XR) and xylitol dehydrogenase (XDH) from the D-xylose-utilising yeast Pichia stipitis. In this study, the ability of endogenous genes of S. cerevisiae to enable D-xylose utilisation was evaluated. Overexpression of the GRE3 gene coding for an unspecific aldose reductase and the ScXYL2 gene coding for a xylitol dehydrogenase homologue enabled growth on D-xylose in aerobic conditions. However, the strain with GRE3 and ScXYL2 had a lower growth rate and accumulated more xylitol compared to the strain with the corresponding enzymes from P. stipitis. Use of the strictly NADPH-dependent Gre3p instead of the P. stipitis XR able to utilise both NADH and NADPH leads to a more severe redox imbalance. In a S. cerevisiae strain not engineered for D-xylose utilisation the presence of D-xylose increased xylitol dehydrogenase activity and the expression of the genes SOR1 or SOR2 coding for sorbitol dehydrogenase. Thus, D-xylose utilisation by S. cerevisiae with activities encoded by ScXYL2 or possibly SOR1 or SOR2, and GRE3 is feasible, but requires efficient redox balance engineering. Compared to D-xylose, D-glucose is a cheap and readily available substrate and thus an attractive alternative for xylitol manufacture. In this study, the pentose phosphate pathway (PPP) of S. cerevisiae was engineered for production of xylitol from D-glucose. Xylitol was formed from D-xylulose 5-phosphate in strains lacking transketolase activity and expressing the gene coding for XDH from P. stipitis. In addition to xylitol, ribitol, D-ribose and D-ribulose were also formed. Deletion of the xylulokinase-encoding gene increased xylitol production, whereas the expression of DOG1 coding for sugar phosphate phosphatase increased ribitol, D-ribose and D-ribulose production. Strains lacking phosphoglucose isomerase (Pgi1p) activity were shown to produce 5 carbon compounds through PPP when DOG1 was overexpressed. Expression of genes encoding glyceraldehyde 3-phosphate dehydrogenase of Bacillus subtilis, GapB, or NAD-dependent glutamate dehydrogenase Gdh2p of S. cerevisiae, altered the cellular redox balance and enhanced growth of pgi1 strains on D glucose, but co-expression with DOG1 reduced growth on higher D-glucose concentrations. Strains lacking both transketolase and phosphoglucose isomerase activities tolerated only low D-glucose concentrations, but the yield of 5-carbon sugars and sugar alcohols on D-glucose was about 50% (w/w).

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.

Plant secondary compounds and soil microbial processes in carbon and nitrogen cycling in relation to tree species

The aim of this study was to explore soil microbial activities related to C and N cycling and the occurrence and concentrations of two important groups of plant secondary compounds, terpenes and phenolic compounds, under silver birch (Betula pendula Roth), Norway spruce (Picea abies (L.) Karst) and Scots pine (Pinus sylvestris L.) as well as to study the effects of volatile monoterpenes and tannins on soil microbial activities. The study site, located in Kivalo, northern Finland, included ca. 70-year-old adjacent stands dominated by silver birch, Norway spruce and Scots pine. Originally the soil was very probably similar in all three stands. All forest floor layers (litter (L), fermentation layer (F) and humified layer (H)) under birch and spruce showed higher rates of CO2 production, greater net mineralisation of nitrogen and higher amounts of carbon and nitrogen in microbial biomass than did the forest floor layers under pine. Concentrations of mono-, sesqui-, di- and triterpenes were higher under both conifers than under birch, while the concentration of total water-soluble phenolic compounds as well as the concentration of condensed tannins tended to be higher or at least as high under spruce as under birch or pine. In general, differences between tree species in soil microbial activities and in concentrations of secondary compounds were smaller in the H layer than in the upper layers. The rate of CO2 production and the amount of carbon in the microbial biomass correlated highly positively with the concentration of total water-soluble phenolic compounds and positively with the concentration of condensed tannins. Exposure of soil to volatile monoterpenes and tannins extracted and fractionated from spruce and pine needles affected carbon and nitrogen transformations in soil, but the effects were dependent on the compound and its molecular structure. Monoterpenes decreased net mineralisation of nitrogen and probably had a toxic effect on part of the microbial population in soil, while another part of the microbes seemed to be able to use monoterpenes as a carbon source. With tannins, low-molecular-weight compounds (also compounds other than tannins) increased soil CO2 production and nitrogen immobilisation by soil microbes while the higher-molecular-weight condensed tannins had inhibitory effects. In conclusion, plant secondary compounds may have a great potential in regulation of C and N transformations in forest soils, but the real magnitude of their significance in soil processes is impossible to estimate.

Studies of new inorganic species using relativistic quantum chemistry

In the present work the methods of relativistic quantum chemistry have been applied to a number of small systems containing heavy elements, for which relativistic effects are important. First, a thorough introduction of the methods used is presented. This includes some of the general methods of computational chemistry and a special section dealing with how to include the effects of relativity in quantum chemical calculations. Second, after this introduction the results obtained are presented. Investigations on high-valent mercury compounds are presented and new ways to synthesise such compounds are proposed. The methods described were applied to certain systems containing short Pt-Tl contacts. It was possible to explain the interesting bonding situation in these compounds. One of the most common actinide compounds, uranium hexafluoride was investigated and a new picture of the bonding was presented. Furthermore the rareness of uranium-cyanide compounds was discussed. In a foray into the chemistry of gold, well known for its strong relativistic effects, investigations on different gold systems were performed. Analogies between Au$^+$ and platinum on one hand and oxygen on the other were found. New systems with multiple bonds to gold were proposed to experimentalists. One of the proposed systems was spectroscopically observed shortly afterwards. A very interesting molecule, which was theoretically predicted a few years ago is WAu$_{12}$. Some of its properties were calculated and the bonding situation was discussed. In a further study on gold compounds it was possible to explain the substitution pattern in bis[phosphane-gold(I)] thiocyanate complexes. This is of some help to experimentalists as the systems could not be crystallised and the structure was therefore unknown. Finally, computations on one of the heaviest elements in the periodic table were performed. Calculation on compounds containing element 110, darmstadtium, showed that it behaves similarly as its lighter homologue platinum. The extreme importance of relativistic effects for these systems was also shown.

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.

The role of lakes in carbon cycling in boreal catchments

Lakes are an important component of ecosystem carbon cycle through both organic carbon sequestration and carbon dioxide and methane emissions, although they cover only a small fraction of the Earth's surface area. Lake sediments are considered to be one of rather perma-nent sinks of carbon in boreal regions and furthermore, freshwater ecosystems process large amounts of carbon originating from terrestrial sources. These carbon fluxes are highly uncer-tain especially in the changing climate. -- The present study provides a large-scale view on carbon sources and fluxes in boreal lakes situated in different landscapes. We present carbon concentrations in water, pools in lake se-diments, and carbon gas (CO2 and CH4) fluxes from lakes. The study is based on spatially extensive and randomly selected Nordic Lake Survey (NLS) database with 874 lakes. The large database allows the identification of the various factors (lake size, climate, and catchment land use) determining lake water carbon concentrations, pools and gas fluxes in different types of lakes along a latitudinal gradient from 60oN to 69oN. Lakes in different landscapes vary in their carbon quantity and quality. Carbon (C) content (total organic and inorganic carbon) in lakes is highest in agriculture and peatland dominated areas. In peatland rich areas organic carbon dominated in lakes but in agricultural areas both organic and inorganic C concentrations were high. Total inorganic carbon in the lake water was strongly dependent on the bedrock and soil quality in the catchment, especially in areas where human influence in the catchment is low. In inhabited areas both agriculture and habitation in the catchment increase lake TIC concentrations, since in the disturbed soils both weathering and leaching are presumably more efficient than in pristine areas. TOC concentrations in lakes were related to either catchment sources, mainly peatlands, or to retention in the upper watercourses. Retention as a regulator of the TOC concentrations dominated in southern Finland, whereas the peatland sources were important in northern Finland. The homogeneous land use in the north and the restricted catchment sources of TOC contribute to the close relationship between peatlands and the TOC concentrations in the northern lakes. In southern Finland the more favorable climate for degradation and the multiple sources of TOC in the mixed land use highlight the importance of retention. Carbon processing was intensive in the small lakes. Both CO2 emission and the Holocene C pool in sediments per square meter of the lake area were highest in the smallest lakes. How-ever, because the total area of the small lakes on the areal level is limited, the large lakes are important units in C processing in the landscape. Both CO2 and CH4 concentrations and emissions were high in eutrophic lakes. High availability of nutrients and the fresh organic matter enhance degradation in these lakes. Eutrophic lakes are often small and shallow, enabling high contact between the water column and the sediment. At the landscape level, the lakes in agricultural areas are often eutrophic due to fertile soils and fertilization of the catchments, and therefore they also showed the highest CO2 and CH4 concentrations. Export from the catchments and in-lake degradation were suggested to be equally important sources of CO2 and CH4 in fall when the lake water column was intensively mixed and the transport of sub-stances from the catchment was high due to the rainy season. In the stagnant periods, especially in the winter, in-lake degradation as a gas source was highlighted due to minimal mixing and limited transport of C from the catchment. The strong relationship between the annual CO2 level of lakes and the annual precipitation suggests that climate change can have a major impact on C cycling in the catchments. Increase in precipitation enhances DOC export from the catchments and leads to increasing greenhouse gas emissions from lakes. The total annual CO2 emission from Finnish lakes was estimated to be 1400 Gg C a-1. The total lake sediment C pool in Finland was estimated to be 0.62 Pg, giving an annual sink in Finnish lakes of 65 Gg C a-1.

Mycorrhizal fungi and nitrogen dynamics in drained peatland

Fungi have a fundamental role in carbon and nutrient transformations in the acids soils of boreal regions, such as peatlands, where high amounts of carbon (C) and nutrients are stored in peat, the pH is relatively low and the nutrient uptake of trees is highly dependent on mycorrhizae. In this thesis, the aim was to examine nitrogen (N) transformations and the availability of dissolved N compounds in forestry-drained peatlands, to compare the fungal community biomass and structure at various peat N levels, to investigate the growth of ectomycorrhizal fungi with variable P and K availability and to assess how the ectomycorrhizal fungi (ECM) affect N transformations. Both field and laboratory experiments were carried out. The peat N concentration did not affect the soil fungal community structure within a site. Phosphorus (P) and potassium (K) deficiency of the trees as well as the degree of decomposition and dissolved organic nitrogen (DON) concentration of the peat were shown to affect the fungal community structure and biomass of ECMs, highlighting the complexity of the below ground system on drained peatlands. The biomass of extrametrical mycorrhizal mycelia (EMM) was enhanced by P and/or K deficiency of the trees, and ECM biomass in the roots was increased by P deficiency. Thus, PK deficiency in drained peatlands may increase the allocation of C by the tree to ECMs. It was also observed that fungi can alter N mineralization processes in the rhizosphere but variously depending on fungal species and fertility level of peat. Gross N mineralization did not vary but the net N mineralization rate significantly increased along the N gradient in both field and laboratory experiments. Gross N immobilization also significantly increased when the peat N concentration increased. Nitrification was hardly detectable in either field or laboratory experiments. During the growing season, dissolved inorganic N (DIN) fluctuated much more than the relatively stable DON. Special methodological challenges associated with sampling and analysis in microbial studies on peatlands are discussed.

On the homogeneous and heterogeneous nucleation of some organic compounds

The conversion of a metastable phase into a thermodynamically stable phase takes place via the formation of clusters. Clusters of different sizes are formed spontaneously within the metastable mother phase, but only those larger than a certain size, called the critical size, will end up growing into a new phase. There are two types of nucleation: homogeneous, where the clusters appear in a uniform phase, and heterogeneous, when pre-existing surfaces are available and clusters form on them. The nucleation of aerosol particles from gas-phase molecules is connected not only with inorganic compounds, but also with nonvolatile organic substances found in atmosphere. The question is which ones of the myriad of organic species have the right properties and are able to participate in nucleation phenomena. This thesis discusses both homogeneous and heterogeneous nucleation, having as theoretical tool the classical nucleation theory (CNT) based on thermodynamics. Different classes of organics are investigated. The members of the first class are four dicarboxylic acids (succinic, glutaric, malonic and adipic). They can be found in both the gas and particulate phases, and represent good candidates for the aerosol formation due to their low vapor pressure and solubility. Their influence on the nucleation process has not been largely investigated in the literature and it is not fully established. The accuracy of the CNT predictions for binary water-dicarboxylic acid systems depends significantly on the good knowledge of the thermophysical properties of the organics and their aqueous solutions. A large part of the thesis is dedicated to this issue. We have shown that homogeneous and heterogeneous nucleation of succinic, glutaric and malonic acids in combination with water is unlikely to happen in atmospheric conditions. However, it seems that adipic acid could participate in the nucleation process in conditions occurring in the upper troposphere. The second class of organics is represented by n-nonane and n-propanol. Their thermophysical properties are well established, and experiments on these substances have been performed. The experimental data of binary homogeneous and heterogeneous nucleation have been compared with the theoretical predictions. Although the n-nonane - n-propanol mixture is far from being ideal, CNT seems to behave fairly well, especially when calculating the cluster composition. In the case of heterogeneous nucleation, it has been found that better characterization of the substrate - liquid interaction by means of line tension and microscopic contact angle leads to a significant improvement of the CNT prediction. Unfortunately, this can not be achieved without well defined experimental data.

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.