Deriving structural information from non-coding ribonucleic acids by mass spectrometry

The purpose of this study is to describe the development of application of mass spectrometry for the structural analyses of non-coding ribonucleic acids during past decade. Mass spectrometric methods are compared of traditional gel electrophoretic methods, the characteristics of performance of mass spectrometric, analyses are studied and the future trends of mass spectrometry of ribonucleic acids are discussed. Non-coding ribonucleic acids are short polymeric biomolecules which are not translated to proteins, but which may affect the gene expression in all organisms. Regulatory ribonucleic acids act through transient interactions with key molecules in signal transduction pathways. Interactions are mediated through specific secondary and tertiary structures. Posttranscriptional modifications in the structures of molecules may introduce new properties to the organism, such as adaptation to environmental changes or development of resistance to antibiotics. In the scope of this study, the structural studies include i) determination of the sequence of nucleobases in the polymer chain, ii) characterisation and localisation of posttranscriptional modifications in nucleobases and in the backbone structure, iii) identification of ribonucleic acid-binding molecules and iv) probing of higher order structures in the ribonucleic acid molecule. Bacteria, archaea, viruses and HeLa cancer cells have been used as target organisms. Synthesised ribonucleic acids consisting of structural regions of interest have been frequently used. Electrospray ionisation (ESI) and matrix-assisted laser desorption ionisation (MALDI) have been used for ionisation of ribonucleic analytes. Ammonium acetate and 2-propanol are common solvents for ESI. Trihydroxyacetophenone is the optimal MALDI matrix for ionisation of ribonucleic acids and peptides. Ammonium salts are used in ESI buffers and MALDI matrices as additives to remove cation adducts. Reverse phase high performance liquid chromatography has been used for desalting and fractionation of analytes either off-line of on-line, coupled with ESI source. Triethylamine and triethylammonium bicarbonate are used as ion pair reagents almost exclusively. Fourier transform ion cyclotron resonance analyser using ESI coupled with liquid chromatography is the platform of choice for all forms of structural analyses. Time-of-flight (TOF) analyser using MALDI may offer sensitive, easy-to-use and economical solution for simple sequencing of longer oligonucleotides and analyses of analyte mixtures without prior fractionation. Special analysis software is used for computer-aided interpretation of mass spectra. With mass spectrometry, sequences of 20-30 nucleotides of length may be determined unambiguously. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Sequencing in conjunction with other structural studies enables accurate localisation and characterisation of posttranscriptional modifications and identification of nucleobases and amino acids at the sites of interaction. High throughput screening methods for RNA-binding ligands have been developed. Probing of the higher order structures has provided supportive data for computer-generated three dimensional models of viral pseudoknots. In conclusion. mass spectrometric methods are well suited for structural analyses of small species of ribonucleic acids, such as short non-coding ribonucleic acids in the molecular size region of 20-30 nucleotides. Structural information not attainable with other methods of analyses, such as nuclear magnetic resonance and X-ray crystallography, may be obtained with the use of mass spectrometry. Sequencing may be applied to quality control of short synthetic oligomers for analytical purposes. Ligand screening may be used in the search of possible new therapeutic agents. Demanding assay design and challenging interpretation of data requires multidisclipinary knowledge. The implement of mass spectrometry to structural studies of ribonucleic acids is probably most efficiently conducted in specialist groups consisting of researchers from various fields of science.

The Road to Hell Is Paved with Good Interventions : A Pragmatic Examination of Humanitarian Intervention with Special Reference to Kosovo

Kansainvälisen oikeuden alaan kuuluvassa tutkielmassa käsitellään humanitaarisen intervention oikeutusta ja laillisuutta. Tutkimuskysymyksenä on, missä määrin humanitaarisilla näkökohdilla perusteltuja sotilaallisia toimia tai niillä uhkaamista voi pitää kansainvälisoikeudellisesti hyväksyttävänä ja millainen painoarvo ennakkotapauksena olisi annettava NATO-maiden Kosovossa toteuttamalle väliintulolle. Tutkielmassa perehdytään ihmisoikeusajattelun tiettyjen taustaoletusten kritiikkiin. Tarkastelun kohteena ovat erityisesti kannanotot, joiden mukaan ihmisoikeuksia ei voi pitää luonteeltaan universaaleina, sekä kyseiseen kritiikkiin liittyvät väitteet siitä, että ns. hegemonisessa asemassa olevat valtiot hyödyntävät ihmisoikeusargumentteja oikeuttaakseen voimankäyttönsä. Universaalisuuskritiikkiä voidaan pitää pitkälti perusteltuna, mutta nykyinen kansainvälinen yhteisö tarvitsee kuitenkin tietynlaisia yleismaailmallisia normeja voidakseen toimia tehokkaasti. Kritiikin ei voikaan katsoa pätevän humanitaarisen intervention kannalta keskeisiin ihmisoikeusnormeihin kuten kansanmurhan kieltoon, sillä kyseiset velvoitteet suojaavat kansainvälisen yhteisön toimivuutta ja uskottavuutta. Humanitaarisiin argumentteihin liittyy kuitenkin muita ongelmia: niillä on esimerkiksi aika ajoin pyritty oikeuttamaan sotilaallisia toimia, joissa ihmisoikeusnäkökohdat eivät välttämättä ole olleet etusijalla. Ihmisoikeuksille ei ole syytä antaa kansainvälisessä oikeudessa asemaa universaaleina "superargumentteina", jotka eivät olisi kyseenalaistettavissa. YK:n peruskirjan ja kansainvälisen tapaoikeuden näkökulmasta humanitaarisen intervention kaltaiseen voimankäyttöön vaaditaan turvallisuusneuvoston hyväksyntä, jota ei Kosovo-operaatioon saatu. Interventiota voi tässä suhteessa pitää yksiselitteisesti laittomana, sillä sen tueksi esitetyt oikeudelliset argumentit eivät ole vakuuttavia. Tapaukseen liittyvät ihmisoikeusnäkökohdat ovat kuitenkin siinä määrin merkittäviä, että ongelmaan ei ole perusteltua suhtautua tiukan legalistisesti. Operaation hyväksyminen moraaliargumenttien nojalla voisi kuitenkin johtaa nykyisten voimankäyttörajoitusten marginalisoitumiseen, mikä olisi yllä käsitellyn kritiikin valossa ongelmallista. Tutkielmassa nostetaan suositeltavaksi ratkaisuksi lähestymistapa, jossa Kosovon tapaus ymmärretään yksittäisenä oikeudenvastaisena mutta samalla oikeudenulkoisena poikkeustapauksena. Tällöin peruskirjan mukainen voimankäytön sääntely säilyy entisellään ilman että humanitaariset näkökohdat jäisivät tyystin huomiotta. Ratkaisu ei sulje pois mahdollisuutta suhtautua positiivisesti Kosovo-operaation mahdollisesti luomaan "poliittiseen normiin": suuren mittakaavan ihmisoikeusloukkaukset eivät jää Euroopassa seurauksitta. Ilman turvallisuusneuvoston suostumusta toteutettaviin humanitaarisiin interventioihin liittyvien käytännöllisten ja kansainvälisoikeudellisten riskien vuoksi niihin on kuitenkin aihetta suhtautua suurella varauksella.

Eru Ilúvatar : Jumala J.R.R. Tolkienin legendariumissa

The purpose of my research is to inquire into the essence and activity of God in the legendarium of the English philologist and writer J.R.R. Tolkien (1892-1973). The legendarium, composed of Tolkien’s writings related to Middle-earth, was begun when he created two Elvish languages, Quenya based on Finnish, Sindarin based on Welsh. Tolkien developed his mythology inspired by Germanic myths and The Kalevala. It is a fictional ancient history set in our world. The legendarium is monotheistic: God is called Eru ‘The One’ and Ilúvatar ‘Father of All’. Eru is the same as the Christian God, for Tolkien wanted to keep his tales consistent with his faith. He said his works were Christian by nature, with the religious element absorbed into the story and the symbolism. In The Silmarillion, set in the primeval ages of Middle-earth, the theological aspects are more conspicuous, while in The Lord of the Rings, which brings the stories to an end, they are mostly limited to symbolic references. The legendarium is unified by its realistic outlook on creaturely abilities and hope expressing itself as humbly defiant resistance. ”The possibility of complexity or of distinctions in the nature of Eru” is a part of the legendarium. Eru Ilúvatar is Trinitarian, as per Tolkien’s faith. Without contextual qualifiers, Eru seems to refer to God the Father, like God in the Bible. Being the creator who dwells outside the world is attributed to Him. The Holy Spirit is the only Person of the Trinity bestown with names: the Flame Imperishable and the Secret Fire. When Eru creates the material world with His word, He sends the Flame Imperishable to burn at the heart of the world. The Secret Fire signifies the Creative Power that belongs to God alone, and is a part of Him. The Son, the Word, is not directly mentioned, but according to one writing Eru must step inside the world in order to save it from corruption, yet remain outside it at the same time. The inner structure of the legendarium refers to the need for a future salvation. The creative word of Eru, “Eä! Let these things Be!”, probably has a connection with the Logos in Christianity. Thus we can find three “distinctions” in Eru: a Creator who dwells outside the world, a Sustainer who dwells inside it and a Redeemer who shall step inside it. Some studies of Tolkien have claimed that Eru is distant and remote. This seems to hold water only partially. Ilúvatar, the Father of All, has a special relation with the Eruhíni, His Children, the immortal Elves and the mortal Men. He communicates with them directly only through the Valar, who resemble archangels. Nevertheless, only the Children of Eru can fight against evil, because their tragic fortunes turn evil into good. Even though religious activities are scarce among them, the fundamental faith and ultimate hope of the “Free Peoples” is directed towards Eru. He is present in the drama of history as the “Author of the Story”, who at times also interferes with its course through catastrophes and eucatastrophes, ‘good catastrophes’. Eru brings about a catastrophe when evil would otherwise bring good to an end, and He brings about a eucatasrophe when creaturely strength is not sufficent for victory. Victory over corruption is especially connected with mortal Men, of whom the most (or least) insignificant people are the Hobbits. However, because of the “primeval disaster” (that is, fall) of Mankind, ultimate salvation can only remain open, a hope for the far future.

Normalization and Charter 77 : Violence, Commitment and Resistance in Czechoslovakia

In Czechoslovakia, the occupation of 1968 denoted the beginning of normalization , a political and societal stagnation that lasted two decades. Dissident initiative Charter 77 emerged in 1977, demanding that the leaders of the country respect human rights. The Helsinki process provided a macro-level framework that influenced opposition and dissident activities throughout Eastern Europe. The study contributes a focused empirical analysis of the period of normalization and the dissident movement Charter 77. Dissent in general is seen as an existential attitude; it can be encapsulated as a morally rationalized critical stance as derived from shared experience or interpretation of injustice, which serves as a basis for a shared collective identity comprising oppositional consciousness as one unifying factor. The study suggests that normalization can be understood as a fundamentally violent process and discusses the structural and cultural manifestations of violence with relation to Charter 77. In general, the aim of the system was to passivize the society to such an extent that it would not constitute a potential threat to the hegemonic rule of the regime. Normalization caused societal stagnation and apoliticization, but it also benefited those who accepted the new political reality. The study, however, questions the image of Czechoslovakia s allegedly highly repressive rule by showing that there was also quite considerable tolerance of Charter 77 and consideration before severe repression was brought to bear against dissidents. Furthermore, the study provides understanding of the motives and impetuses behind dissent, the strategic shifts in Charter 77 activities, and the changes in the regime s policies toward Charter 77. The study also adds new perspective on the common image of Charter 77 as a non political initiative and suggests that Charter 77 was, in fact, a political entity, an actively political one in the latter half of the 1980s. Charter 77 was a de facto hybrid of a traditional dissident initiative and an oppositional actor. Charter 77 adopted a two-dimension approach: firstly, it still emphasized its role as a citizens initiative supporting human rights, but, secondly, at the same time, it was a directly political actor supporting and furthering the development of political opposition against the ruling power.

Road Dust from Pavement Wear and Traction Sanding

Vehicles affect the concentrations of ambient airborne particles through exhaust emissions, but particles are also formed in the mechanical processes in the tire-road interface, brakes, and engine. Particles deposited on or in the vicinity of the road may be re-entrained, or resuspended, into air through vehicle-induced turbulence and shearing stress of the tires. A commonly used term for these particles is road dust . The processes affecting road dust emissions are complex and currently not well known. Road dust has been acknowledged as a dominant source of PM10 especially during spring in the sub-arctic urban areas, e.g. in Scandinavia, Finland, North America and Japan. The high proportion of road dust in sub-arctic regions of the world has been linked to the snowy winter conditions that make it necessary to use traction control methods. Traction control methods include dispersion of traction sand, melting of ice with brine solutions, and equipping the tires with either metal studs (studded winter tires), snow chains, or special tire design (friction tires). Several of these methods enhance the formation of mineral particles from pavement wear and/or from traction sand that accumulate in the road environment during winter. When snow and ice melt and surfaces dry out, traffic-induced turbulence makes some of the particles airborne. A general aim of this study was to study processes and factors underlying and affecting the formation and emissions of road dust from paved road surfaces. Special emphasis was placed on studying particle formation and sources during tire road interaction, especially when different applications of traction control, namely traction sanding and/or winter tires were in use. Respirable particles with aerodynamic diameter below 10 micrometers (PM10) have been the main concern, but other size ranges and particle size distributions were also studied. The following specific research questions were addressed: i) How do traction sanding and physical properties of the traction sand aggregate affect formation of road dust? ii) How do studded tires affect the formation of road dust when compared with friction tires? iii) What are the composition and sources of airborne road dust in a road simulator and during a springtime road dust episode in Finland? iv) What is the size distribution of abrasion particles from tire-road interaction? The studies were conducted both in a road simulator and in field conditions. The test results from the road simulator showed that traction sanding increased road dust emissions, and that the effect became more dominant with increasing sand load. A high percentage of fine-grained anti-skid aggregate of overall grading increased the PM10 concentrations. Anti-skid aggregate with poor resistance to fragmentation resulted in higher PM levels compared with the other aggregates, and the effect became more significant with higher aggregate loads. Glaciofluvial aggregates tended to cause higher particle concentrations than crushed rocks with good fragmentation resistance. Comparison of tire types showed that studded tires result in higher formation of PM emissions compared with friction tires. The same trend between the tires was present in the tests with and without anti-skid aggregate. This finding applies to test conditions of the road simulator with negligible resuspension. Source and composition analysis showed that the particles in the road simulator were mainly minerals and originated from both traction sand and pavement aggregates. A clear contribution of particles from anti-skid aggregate to ambient PM and dust deposition was also observed in urban conditions. The road simulator results showed that the interaction between tires, anti-skid aggregate and road surface is important in dust production and the relative contributions of these sources depend on their properties. Traction sand grains are fragmented into smaller particles under the tires, but they also wear the pavement aggregate. Therefore particles from both aggregates are observed. The mass size distribution of traction sand and pavement wear particles was mainly coarse, but fine and submicron particles were also present.

Revision of the family Alycidae (Acariformes, Acari), with special reference to European species

The thesis provides a proposal to divide Alycidae G. Canestrini & Fanzago into two subfamilies and four tribes. This new hierarchy is based on a reassessment and reranking of new and previously known synapomorphies of the clusters concerned by cladistic analysis, using 60 morphological characters for 48 ingroup species. The basic characters of the taxa are illustrated either by SEM micrographs (Scanning Electron Microscopy) or by outline drawings. The presented classification includes the definitions of Alycini G. Canestrini & Fanzago new rank; Bimichaeliini Womersley new rank; Petralycini new rank; and the (re)descriptions of Alycus C.L. Koch, Pachygnathus Dugès, Amphialycus Zachvatkin, Bimichaelia Thor and Laminamichaelia gen. nov. The species described or redescribed are: Pachygnathus wasastjernae sp. nov. from Kvarken (Merenkurkku), Finland; Pachygnathus villosus Dugès (in Oken); Alycus roseus C.L. Koch; Alycus denasutus (Grandjean) comb. and stat. nov.; Alycus trichotus (Grandjean) comb. nov.; Alycus marinus (Schuster) comb. nov.; Amphialycus (Amphialycus) pentophthalmus Zachvatkin; Amphialycus (Amphialycus) leucogaster (Grandjean); and Amphialycus (Orthacarus) oblongus (Halbert) comb. nov.; Bimichaelia augustana (Berlese); Bimichaelia sarekensis Trägårdh; Laminamichaelia setigera (Berlese) comb. nov.; Laminamichelia arbusculosa (Grandjean) comb. nov.; Laminamichelia subnuda (Berlese) comb. nov. and Petralycus unicornis Grandjean. Fourteen nominal species were found to be junior synonymies. The importance of sensory organs in taxonomy is well recognized, but inclusion of the elaborate skin pattern seemed to improve essentially the usefulness of the prodorsal sensory area. The detailed pictures of the prodorsa of the European alycids could be used like passport photographs for the species. A database like this of prodorsa of other mite taxa as well might be an answer to future needs of species identification in soil zoology, ecology and conservation.

Diffusive and ship-mediated spread of dinoflagellates in the Baltic Sea with Prorocentrum minimum as a special case

In this thesis the role played by expansive and introduced species in the phytoplankton ecology of the Baltic Sea was investigated. The aims were threefold. First, the studies investigated the resting stages of dinoflagellates, which were transported into the Baltic Sea via shipping and were able to germinate under the ambient, nutrient-rich, brackish water conditions. The studies also estimated which factors favoured the occurrence and spread of P. minimum in the Baltic Sea and discussed the identification of this morphologically variable species. In addition, the classification of phytoplankton species recently observed in the Baltic Sea was discussed. Incubation of sediments from four Finnish ports and 10 ships ballast tanks revealed that the sediments act as sources of living dinoflagellates and other phytoplankton. Dinoflagellates germinated from all ports detected and from 90% of ballast tanks. The concentrations of cells germinating from ballast tank sediments were mostly low compared with the acceptable cell concentrations set by the International Maritime Organization s (IMO s) International Convention for the Control and Management of Ships Ballast Water and Sediments. However, the IMO allows such high concentrations of small cells in the discharged ballast water that the total number of cells in large ballast water tanks can be very high. Prorocentrum minimum occurred in the Baltic Sea annually but with no obvious trend in the 10-year timespan from 1993 to 2002. The species occurred under wide ranges of temperatures and salinities and the abundance of the species was positively related especially to the presence of organic nitrogen and phosphorus. This indicated that the species was favoured by increased organic nutrient loading and runoff from land and rivers. The cell shape of P. minimum varied from triangular to oval-round, but morphological fine details indicated that only one morphospecies was present. P. minimum also is, according to present knowledge, the only potentially harmful phytoplankton species that has recently expanded widely into new areas of the Baltic Sea.

The effect of lignin content and lignin modification on Norway spruce wood properties and decay resistance

Three different Norway spruce cutting clones growing in three environments with different soil and climatic conditions were studied. The purpose was to follow variation in the radial growth rate, wood properties and lignin content and to modify wood lignin with a natural monolignol, coniferyl alcohol, by making use of inherent wood peroxidases. In addition, the incorporation of chlorinated anilines into lignin was studied with synthetic model compounds and synthetic lignin preparations to show whether unnatural compounds originating from pesticides could be bound in the lignin polymer. The lignin content of heartwood, sapwood and earlywood was determined by applying Fourier transform infrared (FTIR) spectroscopy and a principal component regression (PCR) technique. Wood blocks were treated with coniferyl alcohol by using a vacuum impregnation method. The effect of impregnation was assessed by FTIR and by a fungal decay test. Trees from a fertile site showed the highest growth rate and sapwood lignin content and the lowest latewood proportion, weight density and modulus of rupture (MOR). Trees from a medium fertile site had the lowest growth rate and the highest latewood proportion, weight density, modulus of elasticity (MOE) and MOR. The most rapidly growing clone showed the lowest latewood proportion, weight density, MOE and MOR. The slowest growing clone had the lowest sapwood lignin content and the highest latewood proportion, weight density, MOE and MOR. Differences between the sites and clones were small, while fairly large variation was found between the individual trees and growing seasons. The cutting clones maintained clone-dependent wood properties in the different growing sites although variation between trees was high and climatic factors affected growth. The coniferyl alcohol impregnation increased the content of different lignin-type phenolic compounds in the wood as well as wood decay resistance against a white-rot fungus, Coriolus versicolor. During the synthetic lignin preparation 3,4-dichloroaniline became bound by a benzylamine bond to β-O-4 structures in the polymer and it could not be released by mild acid hydrolysis. The natural monolignol, coniferyl alcohol, and chlorinated anilines could be incorporated into the lignin polymer in vivo and in vitro, respectively.

Novel Molecular Mechanisms of Arabidopsis Disease Resistance

Plants are capable of recognizing phytopathogens through the perception of pathogen-derived molecules or plant cell-wall degradation products due to the activities of pathogen-secreted enzymes. Such elicitor recognition events trigger an array of inducible defense responses involving signal transduction networks and massive transcriptional re-programming. The outcome of a pathogen infection relies on the balance between different signaling pathways, which are integrated by regulatory proteins. This thesis characterized two key regulatory components: a damage control enzyme, chlorophyllase 1 (AtCHL1), and a transcription factor, WRKY70. Their roles in defense signaling were then investigated. The Erwinia-derived elicitors rapidly activated the expression of AtCLH1 and WRKY70 through different signaling pathways. The expression of the AtCHL1 gene was up-regulated by jasmonic acid (JA) but down-regulated by salicylic acid (SA), whereas WRKY70 was activated by SA and repressed by JA. In order to elucidate the functions of AtCLH1 and WRKY70 in plant defense, stable transgenic lines were produced where these genes were overexpressed or silenced. Additionally, independent knockout lines were also characterized. Bacterial and fungal pathogens were then used to assess the contribution of these genes to the Arabidopsis disease resistance. The transcriptional modulation of AtCLH1 by either the constitutive over-expression or RNAi silencing caused alterations in the chlorophyll-to-chlorophyllide ratio, supporting the claim that chlorophyllase 1 has a role in the chlorophyll degradation pathway. Silencing of this gene led to light-dependent over-accumulation of the reactive oxygen species (ROS) in response to infection by Erwinia carotovora subsp. carotovora SCC1. This was followed by an enhanced induction of SA-dependent defense genes and an increased resistance to this pathogen. Interestingly, little effect on the pathogen-induced SA accumulation at the early infection was observed, suggesting that action of ROS might potentiate SA signaling. In contrast, the pathogen-induced JA production was significantly reduced in the RNAi silenced plants. Moreover, JA signaling and resistance to Alternaria brassicicola were impaired. These observations provide support for the argument that the ROS generated in chloroplasts might have a negative impact on JA signaling. The over-expression of WRKY70 resulted in an enhanced resistance to E. carotovora subsp. carotovora SCC1, Pseudomonas syringae pv. tomato DC3000 and Erysiphe cichoracearum UCSC1, whilst an antisense suppression or an insertional inactivation of WRKY70 led to a compromised resistance to E. carotovora subsp. carotovora SCC1 and to E. cichoracearum UCSC1 but not to P. syringae pv. tomato DC3000. Gene expression analysis revealed that WRKY70 activated many known defense-related genes associated with the SAR response but suppressed a subset of the JA-responsive genes. In particular, I was able to show that both the basal and the induced expression of AtCLH1 was enhanced by the antisense silencing or the insertional inactivation of WRKY70, whereas a reduction in AtCLH1 expression was observed in the WRKY70 over-expressors following an MeJA application or an A. brassicicola infection. Moreover, the SA-induced suppression of AtCLH1 was relieved in wrky70 mutants. These results indicate that WRKY70 down-regulates AtCLH1. An epistasis analysis suggested that WRKY70 functions downstream of the NPR1 in an SA-dependent signaling pathway. When challenged with A. brassicicola, WRKY70 over-expressing plants exhibited a compromised disease resistance while wrky70 mutants had the opposite effect. These results confirmed the WRKY70-mediated inhibitory effects on JA signaling. Furthermore, the WRKY70-controlled suppression of A. brassicicola resistance was mainly through an NPR1-dependent mechanism. Taking all the data together, I suggest that the pathogen-responsive transcription factor WRKY70 is a common component in both SA- and JA-dependent pathways and plays a crucial role in the SA-mediated suppression of JA signaling.