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  • Loukola, Anu-Maria (Helsingin yliopisto, 2000)
  • Seppälä, Anniina (2013)
    Montmorillonite is a layered swelling clay mineral that has the abilities to absorb water, causing the mineral to swell, and to exchange its structural cations, most commonly Na$^+$ and Ca$^{2+}$. These properties are applied in various fields including the nuclear waste management in Finland. Montmorillonite is the main component of bentonite clay which is planned to be used as a release barrier material in the final repository for spent nuclear fuel. The aim of this work was to study how water is absorbed into the interlayer spaces of Na-montmorillonite. Molecular dynamics simulations were performed on a 3-layered montmorillonite particle surrounded by free water. The amount of water initially present between the layers was varied from none to 1 and 2 water molecules per unit cell. The simulations were performed at two temperatures, 298 K and 323 K, applying CLAYFF force field. The evolution of water content showed practically no absorption at either temperature in the case of completely dry montmorillonite. For the other cases, montmorillonite with water initially present in the interlayers, absorption was observed and it was faster at the higher temperature. The evolution of interlayer thicknesses in each case showed a variation between the two interlayers of the system which was thought to result from the different placement of substitutions in the clay layers.
  • Ilinov, Andrey (Helsingin yliopisto, 2015)
    Nanotechnology became an emerging field during the last few decades. The possibility to create elements having sizes in the nanometer range provides new opportunities for medical applications, various sensors and detectors, and composite materials technologies. However, at the nanoscale the basic physical properties may change unexpectedly including chemical, mechanical, optical and electronic properties. There is still no clear understanding of all possible consequences of miniaturization on the behavior of nanostructures. This thesis is focused on the analysis of mechanical and structural (including sputtering under irradiation) properties of nanorods. By nanorods we imply structures like beams or rods, with their cross-sectional diameter measuring in nanometers and having a length several times larger than the diameter. At such sizes it becomes possible to simulate the structures atom by atom using the molecular dynamics (MD) method. In the first part of the thesis, we analyze the elastic properties of Si nanorods: how the variation in size may change the elastic moduli, the effects of oxidation and intrinsic stresses. We also check the validity of the classical continuum mechanics approach by modeling the same nanorods with the finite elements method (FEM). In the second part we investigate sputtering from Au nanorods under ion irradiation. Recent experiments had shown that there is a big enhancement of sputtering yields from Au nanorods in contrast with those from a flat surface. The yields can be as much as 1000 per individual impact. MD gives us an opportunity to analyze the sputtering process with a femtosecond resolution which is impossible by any of the existing experimental methods. We find that an explosive ejection of nanoclusters is the main factor causing such large sputtering yields.
  • Safi, Elnaz (2014)
    Beryllium (Be) is a strong candidate as plasma-facing material for the main wall of future fusion reactors. Thus, its erosion plays a key role in predicting the reactor's life-time and viability. MD simulations can be a powerful tool to study Be behavior under high plasma particle flux. In this work, beryllium sputtering due to D bombardment is studied using MD simulations. We have analyzed the fundamental mechanisms for Be erosion considering some important parameters that influence the outcome, such as particle flux and surface temperature. It is shown that the Be erosion yield is strongly dependent on the surface temperature and its dependency on the particle flux is negligible. We also show that different species of Be molecules can be sputtered from its surface, mainly due to swift chemical sputtering mechanism.
  • Magarkar, Aniket (Helsingin yliopisto, 2014)
    Drug delivery is a vital issue in pharmaceutical research; once a drug candidate molecule is identified, it must be delivered to the target area of the body where it can take effect. In addition, non-specific distribution of drug molecules to areas other than the drug target must be decreased to avoid unwanted side effects. To achieve this, nanotechnological drug delivery systems can be used. Nanotechnological drug delivery systems come in a wide variety of forms, including liposomes, dendrimers, nanoparticles, and polymeric micelles. Of these, our research is focused on drug delivery liposomes. Drug delivery liposomes are composed of a membrane that forms a closed spherical sack, with a diameter of approximately 100 nm that can contain drug molecules. The criteria for effectiveness of these drug delivery liposomes (DDLs) are structural stability, its lifetime in the bloodstream, the release rate of the encapsulated content and site specific targeting. Cholesterol is one of the crucial lipid components of the DDL known to increase its stability. They also can have a protective polymer coating such as polyethylene glycol (PEG) that protects the DDL from the body s defense mechanisms. Also the DDL can posses targeting moieties, able to direct the PEGylated liposomes to the specific target. In this study we have investigated surface structure of the DDL and its interactions with elements of the blood stream. While it is difficult to determine an accurate picture of the DDL surface and its interactions with ions and bloodstream proteins with atomistic resolution by experiments alone, computational molecular modelling techniques can provide insights into it. Hence, we have used computational modelling and molecular dynamics simulations to understand the role of each component of the DDL in its structure. The three of the five reported studies in this thesis (I, II, III) are focused on how surface charge plays an important role in the liposome, how it is affected by various components of the DDLs, and how the specific interactions of DDLs and ions present in the blood stream influence it. The chapter IV deals with understanding the properties by systematically varying components such as cholesterol and PEG. Also we have produced the first ever model of the first FDA approved drug delivery liposome (DOXIL ®) at atomistic resolution details. The last study (V) deals with the application of molecular dynamics in targeted drug delivery research. In this study we could identify the reason for failure of specific novel targeting peptide (AETP), which is used to functionalize the DDL, by identifying its interactions with the protective PEG polymer.
  • Ilmola, Roni (2015)
    Surface growth by using nanocluster deposition has attracted a lot of attention in recent years due to possibilities to affect electronic properties of the resulting thin films. Industry is interested in this method because with cluster deposition it is possible to manufacture thin films much faster than by using single atom deposition. In some cases, nanocluster deposition is the only method by which thin films have been able to be deposited successfully. I have studied Si20 cluster deposition on the Si(0 0 1) surface. I used molecular dynamics simulations to simulate epitaxial silicon growth at temperatures 300 K, 500 K, 700 K, 1000 K, 1300 K and 1600 K. I used two potential models to do this, the Tersoff and the Stillinger-Weber potentials. This work focuses on the differences in the results of these potential models at various temperatures. All the atoms in the cluster had 1 eV of energy. I observed that the growth is stronger with the Stillinger-Weber potential almost at every temperature. At 300 K no epitaxial growth was seen and at 1600 K the substrate melted. I observed almost complete epitaxial growth with the Stillinger-Weber potential, whereas with the Tersoff potential there was an amorphous layer on top of the crystalline region. The epitaxial growth didn’t originate from the diffusion as much as from the rearrangement of atoms at the amorphous-crystalline interface.
  • Julin, Jan (Helsingin yliopisto, 2011)
    Nucleation is the first step in a phase transition where small nuclei of the new phase start appearing in the metastable old phase, such as the appearance of small liquid clusters in a supersaturated vapor. Nucleation is important in various industrial and natural processes, including atmospheric new particle formation: between 20 % to 80 % of atmospheric particle concentration is due to nucleation. These atmospheric aerosol particles have a significant effect both on climate and human health. Different simulation methods are often applied when studying things that are difficult or even impossible to measure, or when trying to distinguish between the merits of various theoretical approaches. Such simulation methods include, among others, molecular dynamics and Monte Carlo simulations. In this work molecular dynamics simulations of the homogeneous nucleation of Lennard-Jones argon have been performed. Homogeneous means that the nucleation does not occur on a pre-existing surface. The simulations include runs where the starting configuration is a supersaturated vapor and the nucleation event is observed during the simulation (direct simulations), as well as simulations of a cluster in equilibrium with a surrounding vapor (indirect simulations). The latter type are a necessity when the conditions prevent the occurrence of a nucleation event in a reasonable timeframe in the direct simulations. The effect of various temperature control schemes on the nucleation rate (the rate of appearance of clusters that are equally able to grow to macroscopic sizes and to evaporate) was studied and found to be relatively small. The method to extract the nucleation rate was also found to be of minor importance. The cluster sizes from direct and indirect simulations were used in conjunction with the nucleation theorem to calculate formation free energies for the clusters in the indirect simulations. The results agreed with density functional theory, but were higher than values from Monte Carlo simulations. The formation energies were also used to calculate surface tension for the clusters. The sizes of the clusters in the direct and indirect simulations were compared, showing that the direct simulation clusters have more atoms between the liquid-like core of the cluster and the surrounding vapor. Finally, the performance of various nucleation theories in predicting simulated nucleation rates was investigated, and the results among other things highlighted once again the inadequacy of the classical nucleation theory that is commonly employed in nucleation studies.
  • Sand, Andrea (Helsingin yliopisto, 2015)
    In the face of the world's increasing demand for energy, and the need to find sustainable and environmentally friendly ways of producing that energy, fusion power offers an attractive possibility. However, the harsh operating conditions of future fusion devices poses a significant challenge for materials development and engineering. Tungsten (W) and tungsten alloys are current candidate materials for both structural and plasma-facing components, due to favourable properties such as good thermal conductivity, high heat strength and stability, and resistance to erosion. However, fusion reactor components will be subjected to high neutron loads, and little is currently known of the effects of radiation on the mechanical properties of this intrinsically brittle metal. The extreme conditions in a future fusion reactor cannot be reproduced in existing experimental facilities, rendering simulation an invaluable tool in understanding the radiation damage processes. Multiscale methods are necessary to span the length and time scales involved, from the picosecond and nanometer scale of displacement cascades giving rise to the primary damage, to the evolution of the radiation induced microstructure over the seconds of typical in-situ ion irradiation experiments, and further to the years of a reactor component s life time. In order to implement a multiscale simulation method, information must be distilled and transferred from the smaller scale to the larger. Molecular dynamics (MD) simulations are ideal for studying the primary damage, but individual cascades vary greatly, and simulating high energy impacts in MD requires immense computer capacity. It is therefore not possible to simulate directly the whole variety of cascade outcomes. General laws deduced from the MD data can, however, be used to statistically generate varying cascades in the thousands. In this thesis we use MD simulations to study the primary damage in metals, with focus on tungsten. We identify aspects of the simulation methodology which affect the results, and validate our methods by direct comparison to experiments. Detailed analysis of the primary damage from high-energy cascades shows the formation of novel defects, confirming recent experimental observations. We also show that defect cluster sizes follow a general scaling law, which can be used to statistically generate cascade debris as input for microstructural evolution models, circumventing the need to directly simulate thousands of cascades.
  • Zhao, Junlei (2014)
    Metal-induced crystallization (MIC) has been investigated extensively as an alternative crystallization process in the silicon based photovoltaic industry. In this work, we simulate a nanoscale version of this process by using molecular dynamics simulation involving liquid Si nanoclusters inoculated with Ag atoms in Ar thermal bath. The simulations reveal that the energy released during coalescence of the silver silicide region is the main factor to remelt the surface of the Si nanocluster. In an earlier report, Ag nanoparticles is observed to induced crystallization in 12-15 nm- diameter silicon cluster, which upon further cooling results in nano-polycrystalline silicon core and segregated Ag sub-shells. The work focuses on the crucial conditions that influence the MIC process, such as (i) number of Ag atoms per unit volume, (ii) initial temperature of Si cluster, (iii) crystallization temperature and (iv) cooling rate of the Si cluster. The results presented in this study provide insight into the effect of the first three parameters. Also, the results suggest that the coalescence of eutectic phase is the essential step which induces the crystallization.
  • Samela, Juha (Helsingin yliopisto, 2008)
    This thesis concerns the dynamics of nanoparticle impacts on solid surfaces. These impacts occur, for instance, in space, where micro- and nanometeoroids hit surfaces of planets, moons, and spacecraft. On Earth, materials are bombarded with nanoparticles in cluster ion beam devices, in order to clean or smooth their surfaces, or to analyse their elemental composition. In both cases, the result depends on the combined effects of countless single impacts. However, the dynamics of single impacts must be understood before the overall effects of nanoparticle radiation can be modelled. In addition to applications, nanoparticle impacts are also important to basic research in the nanoscience field, because the impacts provide an excellent case to test the applicability of atomic-level interaction models to very dynamic conditions. In this thesis, the stopping of nanoparticles in matter is explored using classical molecular dynamics computer simulations. The materials investigated are gold, silicon, and silica. Impacts on silicon through a native oxide layer and formation of complex craters are also simulated. Nanoparticles up to a diameter of 20 nm (315000 atoms) were used as projectiles. The molecular dynamics method and interatomic potentials for silicon and gold are examined in this thesis. It is shown that the displacement cascade expansionmechanism and crater crown formation are very sensitive to the choice of atomic interaction model. However, the best of the current interatomic models can be utilized in nanoparticle impact simulation, if caution is exercised. The stopping of monatomic ions in matter is understood very well nowadays. However, interactions become very complex when several atoms impact on a surface simultaneously and within a short distance, as happens in a nanoparticle impact. A high energy density is deposited in a relatively small volume, which induces ejection of material and formation of a crater. Very high yields of excavated material are observed experimentally. In addition, the yields scale nonlinearly with the cluster size and impact energy at small cluster sizes, whereas in macroscopic hypervelocity impacts, the scaling 2 is linear. The aim of this thesis is to explore the atomistic mechanisms behind the nonlinear scaling at small cluster sizes. It is shown here that the nonlinear scaling of ejected material yield disappears at large impactor sizes because the stopping mechanism of nanoparticles gradually changes to the same mechanism as in macroscopic hypervelocity impacts. The high yields at small impactor size are due to the early escape of energetic atoms from the hot region. In addition, the sputtering yield is shown to depend very much on the spatial initial energy and momentum distributions that the nanoparticle induces in the material in the first phase of the impact. At the later phases, the ejection of material occurs by several mechanisms. The most important mechanism at high energies or at large cluster sizes is atomic cluster ejection from the transient liquid crown that surrounds the crater. The cluster impact dynamics detected in the simulations are in agreement with several recent experimental results. In addition, it is shown that relatively weak impacts can induce modifications on the surface of an amorphous target over a larger area than was previously expected. This is a probable explanation for the formation of the complex crater shapes observed on these surfaces with atomic force microscopy. Clusters that consist of hundreds of thousands of atoms induce long-range modifications in crystalline gold.
  • Berzins, Aivars (Helsingin yliopisto, 2010)
    The prevalence, contamination and heat resistance of Listeria monocytogenes were investigated in meat products and meat-processing plants. Moreover, trends of human listeriosis in Latvia were studied over a 10-year period from 1998 to 2007. A high prevalence (40%) of L. monocytogenes was found in cold-smoked meat products compared with other heat-treated ready-to-eat meat products (0.7%) available in retail markets in Latvia. Pulsed-field gel electrophoresis (PFGE) and serotyping were applied to analyse the diversity of L. monocytogenes isolates present in ready-to-eat (RTE) meat products and meat-processing plants. A high genetic diversity was seen among L. monocytogenes isolates from cold-smoked meat products, suggesting the existence of various sources of contamination at different production stages in the meat-processing environment. The manufacture of cold-smoked meat products involves no processing steps to eliminate L. monocytogenes, thus, contamination of the raw meat and contamination during processing can both contribute to L. monocytogenes in the finished product. Logistic multivariable regression model was successfully applied to identify the main factors associated with L. monocytogenes contamination during the manufacturing of cold-smoked pork products. Meat brining by injections was a significant factor (odds ratio 10.66; P<0.05) for contamination of products with L. monocytogenes. Of the cold-smoked meat-processing plant environmental samples, most contaminated sites were associated with brining machine and brining area. Long cold-smoking times (≥ 12 h) also had a significant predictive value (odds ratio 24.38; P<0.014) for a sample testing positive for L. monocytogenes. A genetically diverse population of L. monocytogenes entered the meat-processing plant, where only some of the strains colonized and established a persistent microbial community within the plant over a 5-year period. L. monocytogenes PFGE types belonging to serotypes 1/2a and 4b were isolated from imported, defrosted, raw pork from Germany and Belgium in meat-processing plant B. In total, two L. monocytogenes PFGE types originating from raw meat were found also in finished RTE cold-smoked pork products, whereas one PFGE type was recovered later only from the meat-processing environment. One of the L. monocytogenes PFGE types, belonging to serotype 1/2c, was isolated from RTE cold-smoked meat products and from the feeding teeth of the brining machine, thus showing that improper cleaning, disinfection and poor hygiene design of the brining machine may cause L. monocytogenes contamination over time. Post-package pasteurization of high- and low-fat content cooked sausages at temperatures higher than 55°C was found to be an effective method of post-process thermal treatment to reduce contamination of L. monocytogenes. However, heating to 55°C, 60°C and 62.5°C may not be practical in the meat industry because the process takes too long to reach a 3-log reduction. The formulation of high-fat content RTE cooked sausages may require modification to maintain product quality. During the 10-year study period the overall incidence of listeriosis in Latvia was 0.4 per 100 000 population, with the highest incidences recorded in 2000 and 2002 (1.5 and 0.7 per 100 000 population, respectively). The highest incidence of listeriosis in Latvia was observed in 2000, which significantly exceeded incidence levels in all Baltic and Nordic countries, and was the highest among all EU member states during the same period. A marked clustering of human listeriosis cases was observed from September to December 2000, possibly indicating one large outbreak. The lack of serotyping and molecular typing methods for subtyping of L. monocytogenes isolates in the present surveillance system is one of the main reasons why there have been no officially documented listeriosis outbreaks in Latvia to date. Measures to allow the application of appropriate actions at the food industry level need to be implemented to prevent or significantly reduce the real burden of foodborne listeriosis in Latvia.
  • Savolainen-Kopra, Carita (Helsingin yliopisto, 2006)
    The first part of this work investigates the molecular epidemiology of a human enterovirus (HEV), echovirus 30 (E-30). This project is part of a series of studies performed in our research team analyzing the molecular epidemiology of HEV-B viruses. A total of 129 virus strains had been isolated in different parts of Europe. The sequence analysis was performed in three different genomic regions: 420 nucleotides (nt) in the VP4/VP2 capsid protein coding region, the entire VP1 capsid protein coding gene of 876 nt, and 150 nt in the VP1/2A junction region. The analysis revealed a succession of dominant sublineages within a major genotype. The temporally earlier genotypes had been replaced by a genetically homogenous lineage that has been circulating in Europe since the late 1970s. The same genotype was found by other research groups in North America and Australia. Globally, other cocirculating genetic lineages also exist. The prevalence of a dominant genotype makes E-30 different from other previously studied HEVs, such as polioviruses and coxsackieviruses B4 and B5, for which several coexisting genetic lineages have been reported. The second part of this work deals with molecular epidemiology of human rhinoviruses (HRVs). A total of 61 field isolates were studied in the 420-nt stretch in the capsid coding region of VP4/VP2. The isolates were collected from children under two years of age in Tampere, Finland. Sequences from the clinical isolates clustered in the two previously known phylogenetic clades. Seasonal clustering was found. Also, several distinct serotype-like clusters were found to co-circulate during the same epidemic season. Reappearance of a cluster after disappearing for a season was observed. The molecular epidemiology of the analyzed strains turned out to be complex, and we decided to continue our studies of HRV. Only five previously published complete genome sequences of HRV prototype strains were available for analysis. Therefore, all designated HRV prototype strains (n=102) were sequenced in the VP4/VP2 region, and the possibility of genetic typing of HRV was evaluated. Seventy-six of the 102 prototype strains clustered in HRV genetic group A (HRV-A) and 25 in group B (HRV-B). Serotype 87 clustered separately from other HRVs with HEV species D. The field strains of HRV represented as many as 19 different genotypes, as judged with an approximate demarcation of a 20% nt difference in the VP4/VP2 region. The interserotypic differences of HRV were generally similar to those reported between different HEV serotypes (i.e. about 20%), but smaller differences, less than 10%, were also observed. Because some HRV serotypes are genetically so closely related, we suggest that the genetic typing be performed using the criterion "the closest prototype strain". This study is the first systematic genetic characterization of all known HRV prototype strains, providing a further taxonomic proposal for classification of HRV. We proposed to divide the genus Human rhinoviruses into HRV-A and HRV-B. The final part of the work comprises a phylogenetic analysis of a subset (48) of HRV prototype strains and field isolates (12) in the nonstructural part of the genome coding for the RNA-dependent RNA polymerase (3D). The proposed division of the HRV strains in the species HRV-A and HRV-B was also supported by 3D region. HRV-B clustered closer to HEV species B, C, and also to polioviruses than to HRV-A. Intraspecies variation within both HRV-A and HRV-B was greater in the 3D coding region than in the VP4/VP2 coding region, in contrast to HEV. Moreover, the diversity of HRV in 3D exceeded that of HEV. One group of HRV-A, designated HRV-A', formed a separate cluster outside other HRV-A in the 3D region. It formed a cluster also in the capsid region, but located within HRV-A. This may reflect a different evolutionary history of distinct genomic regions among HRV-A. Furthermore, the tree topology within HRV-A in the 3D region differed from that in the VP4/VP2, suggesting possible recombination events in the evolution of the strains. No conflicting phylogenies were observed in any of the 12 field isolates. Possible recombination was further studied using the Similarity and Bootscanning analyses of the complete genome sequences of HRV available in public databases. Evidence for recombination among HRV-A was found, as HRV2 and HRV39 showed higher similarity in the nonstructural part of the genome. Whether HRV2 and HRV39 strains - and perhaps also some other HRV-A strains not yet completely sequenced - are recombinants remains to be determined.
  • Maunula, Leena (Helsingin yliopisto, 2001)
  • Fredriksson-Ahomaa, Maria (Helsingin yliopisto, 2001)
  • Suomalainen, Marjo (Helsingin yliopisto, 2014)
    Omptins are a family of conserved, integral outer membrane proteases and widely distributed within Gram-negative bacterial species. The family offers a good example of the evolution and the adaptation of a protein to novel functions and to differing pathogenic bacterial life-styles. This work investigates three different omptins: Pla of Yersinia pestis, PgtE of Salmonella enterica and OmpT of Escherichia coli. The omptin proteases differ in substrate specificity and need lipopolysaccharide (LPS) for activity. My thesis work addressed two main questions in omptin function: what is the molecular basis of the dissimilar substrate selectivity in the structurally very similar omptins; and what are the structural features in LPS that affect omptin activity. I studied the LPS dependency of omptins by expressing the proteins in bacterial cells that differ in LPS structure and by reconstituting purified, detergent-solubilized omptin protein with characterized, purified LPS molecules. Y. pestis alters its LPS structure in response to change of temperature from 20°C to 37°C, which reflects the transfer from a flea to a mammalian host. I found that the activity of Pla in cells from 20°C was very low, whereas cells from 37°C expressed high activity. I reconstituted detergent-purified His6-Pla protein with various model LPS structures and with LPSs of Y. pestis grown at different temperatures. Adding Y. pestis LPS from 37°C to the nonfunctional Pla protein induced high proteolytic activity, whereas 20°C-LPS gave very low activity, indicating that the activity of Pla is controlled by LPS. Similarly, I found that the activity of PgtE was high with rough LPS and low with smooth LPS; the difference mimics the LPS of intracellular (rough) and extracellular (smooth) S. enterica. Thus, in both bacterial species the omptin activity is controlled by the LPS type that the bacteria express during infection in mammals. I further studied the fine structure of Y. pestis LPS that affects Pla activity. This was done by reconstituting Pla activity with various structurally characterized Y. pestis and E. coli LPSs. I found that lower levels of lipid A acylation and phosphate substitution by aminoarabinose, are important for Pla activity, these features are characteristic for Y. pestis LPS from 37°C. A common and conserved feature in omptin structure is the presence of LPS-binding motif in protein barrel. Disrupting of the lipid A-binding motifs in PgtE and Pla abolished their proteolytic activity, emphasizing the importance of the LPS binding site for omptin activity. Omptins have a highly spatically conserved active center and catalytic domains but express functional heterogeneity. The omptin transmembrane barrel contains five surface-exposed loops that show slightly higher sequence variation than the transmembrane protein regions. To study the effect of loop structures in omptin proteolytic specificity, I changed OmpT of E. coli to a Pla-like enzyme by a stepwise substitution of the loop areas. The proteins were characterized by their ability to activate the human protease precursor plasminogen(Plg) to the active serine protease plasmin and to inactivate the main plasmin inhibitor, α2-antiplasmin(α2AP); both functions are important for bacterial virulence. Pla cleaves very efficiently both substrates, whereas OmpT is only poorly active with them. I showed that OmpT could be converted into a Pla-like enzyme by cumulative substitutions at the loop areas, especially the loops L3-L5 were important. The successful conversion of OmpT towards Pla indicates that the loop structures are critical for omptin activity by allowing correct recognition of the polypeptide substrate. More detailed substitution analysis was taken to identify the catalytic residues in Pla. My thesis demonstrates that the omptin proteolytic activity depends on two things: their specific interaction with LPS and the structure of their surface-exposed loops. The thesis offers an example of omptins extensive evolvability and of how they adapt to the lifestyle of their host bacterium.
  • Österman, Janina (Helsingin yliopisto, 2015)
    Nitrogen is an indispensable element for plants and animals to be able to synthesise essential biological compounds such as amino acids and nucleotides. Although there is plenty of nitrogen in the form of nitrogen gas (N2) in the Earth s atmosphere, it is not readily available to plants but needs to be converted (fixed) into ammonia before it can be utilised. Nitrogen-fixing bacteria living freely in the soil or in symbiotic association with legume plants, fix N2 into ammonia used by the plants. This is known as biological nitrogen fixation (BNF). In contrast to industrial nitrogen fixation, an energy-demanding process using high temperature and pressure to produce chemical fertilizers, BNF makes use of solar energy alone to complete the same reaction. However, the requirements on compatibility of plants and nitrogen-fixing micro-organism, the rate of conversion and the ability of the micro-organisms to survive in stressful environments are limiting factors of this system. The current demand for more sustainable food production makes BNF an attractive alternative. However, optimization of existing BNF systems as well as development of new highly productive ones is necessary, to be able to replace the use of chemical fertilisers. In order to develop new alternatives, we need to gain more knowledge on the requirements set by both plants and micro-organisms for successful and efficient nitrogen fixation to occur. In this thesis, the nitrogen-fixing legume host Galega (goat s rue) and its symbiotic microbial partner Neorhizobium galegae were used as a model system to investigate the features defining good symbiotic nitrogen fixation. Studies of genetic diversity within the host plant showed that there are genetic traits making a distinction between the two species G. orientalis and G. officinalis, both at a whole-genome level and at the level of specific symbiosis-related genes. Genome sequencing of ten strains of N. galegae provided a useful dataset for studying i) the genomic features separating N. galegae from related nitrogen-fixing bacteria (rhizobia) and ii) the genetically encoded characteristics that divide strains of N. galegae into two separate symbiovars (symbiotic variants that show different phenotypes on the two different Galega host plant species). These studies provided new information on genes possibly involved in determining host specificity and efficiency of nitrogen fixation. In addition, previously unrecognised genetic contents provided insight into the ecology of N. galegae. Most importantly, genome sequencing enabled identification of the noeT gene, responsible for acetylation of the N. galegae Nod factor (signal molecule required for symbiosis). Although the noeT gene did not turn out to be the crucial determinant enabling nodulation of Galega spp. as previously anticipated, these results are important for future studies on mechanisms behind the selectiveness (host specificity) observed in nitogen-fixing symbioses between Galega and N. galegae.
  • Österman, Janina (Helsingin yliopisto, 2015)
    Nitrogen is an indispensable element for plants and animals to be able to synthesise essential biological compounds such as amino acids and nucleotides. Although there is plenty of nitrogen in the form of nitrogen gas (N2) in the Earth s atmosphere, it is not readily available to plants but needs to be converted (fixed) into ammonia before it can be utilised. Nitrogen-fixing bacteria living freely in the soil or in symbiotic association with legume plants, fix N2 into ammonia used by the plants. This is known as biological nitrogen fixation (BNF). In contrast to industrial nitrogen fixation, an energy-demanding process using high temperature and pressure to produce chemical fertilizers, BNF makes use of solar energy alone to complete the same reaction. However, the requirements on compatibility of plants and nitrogen-fixing micro-organism, the rate of conversion and the ability of the micro-organisms to survive in stressful environments are limiting factors of this system. The current demand for more sustainable food production makes BNF an attractive alternative. However, optimization of existing BNF systems as well as development of new highly productive ones is necessary, to be able to replace the use of chemical fertilisers. In order to develop new alternatives, we need to gain more knowledge on the requirements set by both plants and micro-organisms for successful and efficient nitrogen fixation to occur. In this thesis, the nitrogen-fixing legume host Galega (goat s rue) and its symbiotic microbial partner Neorhizobium galegae were used as a model system to investigate the features defining good symbiotic nitrogen fixation. Studies of genetic diversity within the host plant showed that there are genetic traits making a distinction between the two species G. orientalis and G. officinalis, both at a whole-genome level and at the level of specific symbiosis-related genes. Genome sequencing of ten strains of N. galegae provided a useful dataset for studying i) the genomic features separating N. galegae from related nitrogen-fixing bacteria (rhizobia) and ii) the genetically encoded characteristics that divide strains of N. galegae into two separate symbiovars (symbiotic variants that show different phenotypes on the two different Galega host plant species). These studies provided new information on genes possibly involved in determining host specificity and efficiency of nitrogen fixation. In addition, previously unrecognised genetic contents provided insight into the ecology of N. galegae. Most importantly, genome sequencing enabled identification of the noeT gene, responsible for acetylation of the N. galegae Nod factor (signal molecule required for symbiosis). Although the noeT gene did not turn out to be the crucial determinant enabling nodulation of Galega spp. as previously anticipated, these results are important for future studies on mechanisms behind the selectiveness (host specificity) observed in nitogen-fixing symbioses between Galega and N. galegae.