Plasmids and aromatic degradation in Sphingomonas for bioremediation : Aromatic ring cleavage genes in soil and rhizosphere

Microbial degradation pathways play a key role in the detoxification and the mineralization of polyaromatic hydrocarbons (PAHs), which are widespread pollutants in soil and constituents of petroleum hydrocarbons. In microbiology the aromatic degradation pathways are traditionally studied from single bacterial strains with capacity to degrade certain pollutant. In soil the degradation of aromatics is performed by a diverse community of micro-organisms. The aim of this thesis was to study biodegradation on different levels starting from a versatile aromatic degrader Sphingobium sp. HV3 and its megaplasmid, extending to revelation of diversity of key catabolic enzymes in the environment and finally studying birch rhizoremediation in PAH-polluted soil. To understand biodegradation of aromatics on bacterial species level, the aromatic degradation capacity of Sphingobium sp. HV3 and the role of the plasmid pSKY4, was studied. Toluene, m-xylene, biphenyl, fluorene, phenanthrene were detected as carbon and energy sources of the HV3 strain. Tn5 transposon mutagenesis linked the degradation capacity of toluene, m-xylene, biphenyl and naphthalene to the pSKY4 plasmid and qPCR expression analysis showed that plasmid extradiol dioxygenases genes (bphC and xylE) are inducted by phenanthrene, m-xylene and biphenyl whereas the 2,4-dichlorophenoxyacetic acid herbicide induced the chlorocatechol 1,2-dioxygenase gene (tfdC) from the ortho-pathway. A method to study upper meta-pathway extradiol dioxygenase gene diversity in soil was developed. The extradiol dioxygenases catalyse cleavage of the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage). A high diversity of extradiol dioxygenases were detected from polluted soils. The detected extradiol dioxygenases showed sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Five groups of extradiol dioxygenases contained sequences with no close homologues in the database, representing novel genes. In rhizoremediation experiment with birch (Betula pendula) treatment specific changes of extradiol dioxygenase communities were shown. PAH pollution changed the bulk soil extradiol dioxygenase community structure and birch rhizosphere contained a more diverse extradiol dioxygenase community than the bulk soil showing a rhizosphere effect. The degradation of pyrene in soil was enhanced with birch seedlings compared to soil without birch. The complete 280,923 kb nucleotide sequence of pSKY4 plasmid was determined. The open reading frames of pSKY4 were divided into putative conjugative transfer, aromatic degradation, replication/maintaining and transposition/integration function-encoding proteins. Aromatic degradation orfs shared high similarity to corresponding genes in pNL1, a plasmid from the deep subsurface strain Novosphingobium aromaticivorans F199. The plasmid backbones were considerably more divergent with lower similarity, which suggests that the aromatic pathway has functioned as a plasmid independent mobile genetic element. The functional diversity of microbial communities in soil is still largely unknown. Several novel clusters of extradiol dioxygenases representing catabolic bacteria, whose function, biodegradation pathways and phylogenetic position is not known were amplified with single primer pair from polluted soils. These extradiol dioxygenase communities were shown to change upon PAH pollution, which indicates that their hosts function in PAH biodegradation in soil. Although the degradation pathways of specific bacterial species are substantially better depicted than pathways in situ, the evolution of degradation pathways for the xenobiotic compounds is largely unknown. The pSKY4 plasmid contains aromatic degradation genes in putative mobile genetic element causing flexibility/instability to the pathway. The localisation of the aromatic biodegradation pathway in mobile genetic elements suggests that gene transfer and rearrangements are a competetive advantage for Sphingomonas bacteria in the environment.

Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.

Quantum Space-Time and Noncommutative Gauge Field Theories

Arguments arising from quantum mechanics and gravitation theory as well as from string theory, indicate that the description of space-time as a continuous manifold is not adequate at very short distances. An important candidate for the description of space-time at such scales is provided by noncommutative space-time where the coordinates are promoted to noncommuting operators. Thus, the study of quantum field theory in noncommutative space-time provides an interesting interface where ordinary field theoretic tools can be used to study the properties of quantum spacetime. The three original publications in this thesis encompass various aspects in the still developing area of noncommutative quantum field theory, ranging from fundamental concepts to model building. One of the key features of noncommutative space-time is the apparent loss of Lorentz invariance that has been addressed in different ways in the literature. One recently developed approach is to eliminate the Lorentz violating effects by integrating over the parameter of noncommutativity. Fundamental properties of such theories are investigated in this thesis. Another issue addressed is model building, which is difficult in the noncommutative setting due to severe restrictions on the possible gauge symmetries imposed by the noncommutativity of the space-time. Possible ways to relieve these restrictions are investigated and applied and a noncommutative version of the Minimal Supersymmetric Standard Model is presented. While putting the results obtained in the three original publications into their proper context, the introductory part of this thesis aims to provide an overview of the present situation in the field.

Quantum Chemical Studies on Tropospheric Nucleation Mechanisms Involving Sulfuric Acid

Nucleation is the first step of the process by which gas molecules in the atmosphere condense to form liquid or solid particles. Despite the importance of atmospheric new-particle formation for both climate and health-related issues, little information exists on its precise molecular-level mechanisms. In this thesis, potential nucleation mechanisms involving sulfuric acid together with either water and ammonia or reactive biogenic molecules are studied using quantum chemical methods. Quantum chemistry calculations are based on the numerical solution of Schrödinger's equation for a system of atoms and electrons subject to various sets of approximations, the precise details of which give rise to a large number of model chemistries. A comparison of several different model chemistries indicates that the computational method must be chosen with care if accurate results for sulfuric acid - water - ammonia clusters are desired. Specifically, binding energies are incorrectly predicted by some popular density functionals, and vibrational anharmonicity must be accounted for if quantitatively reliable formation free energies are desired. The calculations reported in this thesis show that a combination of different high-level energy corrections and advanced thermochemical analysis can quantitatively replicate experimental results concerning the hydration of sulfuric acid. The role of ammonia in sulfuric acid - water nucleation was revealed by a series of calculations on molecular clusters of increasing size with respect to all three co-ordinates; sulfuric acid, water and ammonia. As indicated by experimental measurements, ammonia significantly assists the growth of clusters in the sulfuric acid - co-ordinate. The calculations presented in this thesis predict that in atmospheric conditions, this effect becomes important as the number of acid molecules increases from two to three. On the other hand, small molecular clusters are unlikely to contain more than one ammonia molecule per sulfuric acid. This implies that the average NH3:H2SO4 mole ratio of small molecular clusters in atmospheric conditions is likely to be between 1:3 and 1:1. Calculations on charged clusters confirm the experimental result that the HSO4- ion is much more strongly hydrated than neutral sulfuric acid. Preliminary calculations on HSO4- NH3 clusters indicate that ammonia is likely to play at most a minor role in ion-induced nucleation in the sulfuric acid - water system. Calculations of thermodynamic and kinetic parameters for the reaction of stabilized Criegee Intermediates with sulfuric acid demonstrate that quantum chemistry is a powerful tool for investigating chemically complicated nucleation mechanisms. The calculations indicate that if the biogenic Criegee Intermediates have sufficiently long lifetimes in atmospheric conditions, the studied reaction may be an important source of nucleation precursors.

Implications of Bohmian quantum ontology for psychopathology

This article discusses the prospects of quantum psychiatry from a Bohmian point of view, which provides an ontological interpretation of quantum theory, and extends such ontology to include mind. At first, we discuss the more general relevance of quantum theory to psychopathology. The basic idea is that because quantum theory emphasizes the role of wholeness, it might be relevant to psychopathology, where breakdown of unity in the mental domain is a key feature. We then discuss the role of information in psychopathology, and consider the connections with quantum theory in this area. In particular, we discuss David Bohm’s notion of active information, which arises in the ontological interpretation of quantum theory, and is suggested to play a fundamental role as the bridge between mind and matter. Some such bridge is needed if we are to understand how subtle mental properties are able to influence more manifest physical properties in the brain (all the way to the molecular and possibly microtubular level), and how changes in those possibly quantum‐level physical processes are able to influence higher cognitive functions. We also consider the implications of the notion of active information for psychopathology. The prospects of implementing the Bohmian scheme in neuroquantal terms are then briefly considered. Finally, we discuss some possible therapeutic implications of Bohm’s approach to information and the relation of mind and matter.

Implications of Bohmian quantum ontology for psychopathology

This article discusses the prospects of quantum psychiatry from a Bohmian point of view, which provides an ontological interpretation of quantum theory, and extends such ontology to include mind. At first, we discuss the more general relevance of quantum theory to psychopathology. The basic idea is that because quantum theory emphasizes the role of wholeness, it might be relevant to psychopathology, where breakdown of unity in the mental domain is a key feature. We then discuss the role of information in psychopathology, and consider the connections with quantum theory in this area. In particular, we discuss David Bohm’s notion of active information, which arises in the ontological interpretation of quantum theory, and is suggested to play a fundamental role as the bridge between mind and matter. Some such bridge is needed if we are to understand how subtle mental properties are able to influence more manifest physical properties in the brain (all the way to the molecular and possibly microtubular level), and how changes in those possibly quantum‐level physical processes are able to influence higher cognitive functions. We also consider the implications of the notion of active information for psychopathology. The prospects of implementing the Bohmian scheme in neuroquantal terms are then briefly considered. Finally, we discuss some possible therapeutic implications of Bohm’s approach to information and the relation of mind and matter.

AC transport at holographic quantum hall transitions

We compute AC electrical transport at quantum Hall critical points, as modeled by intersecting branes and gauge/gravity duality. We compare our results with a previous field theory computation by Sachdev, and find unexpectedly good agreement. We also give general results for DC Hall and longitudinal conductivities valid for a wide class of quantum Hall transitions, as well as (semi)analytical results for AC quantities in special limits. Our results exhibit a surprising degree of universality; for example, we find that the high frequency behavior, including subleading behavior, is identical for our entire class of theories.

Coherent quantum Boltzmann equations from cQPA

We reformulate and extend our recently introduced quantum kinetic theory for interacting fermion and scalar fields. Our formalism is based on the coherent quasiparticle approximation (cQPA) where nonlocal coherence information is encoded in new spectral solutions at off-shell momenta. We derive explicit forms for the cQPA propagators in the homogeneous background and show that the collision integrals involving the new coherence propagators need to be resummed to all orders in gradient expansion. We perform this resummation and derive generalized momentum space Feynman rules including coherent propagators and modified vertex rules for a Yukawa interaction. As a result we are able to set up self-consistent quantum Boltzmann equations for both fermion and scalar fields. We present several examples of diagrammatic calculations and numerical applications including a simple toy model for coherent baryogenesis.

Word order and tonal shape in the production of focus in short Finnish utterances

This paper presents results from a study on the production of Finnish prosody. The effect of word order and the tonal shape in the production of Finnish prosody was studied as produced by 8 native Finnish speakers. Predictions formulated with regard to results from an earlier study pertaining to the perception of promi- nence were tested. These predictions had to do with the tonal shape of the utterances in the form of a flat hat pattern and the effect of word order on the so called top-line declination within an adver- bial phrase in the utterances. The results from the experiment give support to the following claims: the temporal domain of prosodic focus is the whole utterance, word order reversal from unmarked to marked has an effect on the production of prosody, and the pro- duction of the tonal aspects of focus in Finnish follows a basic flat hat pattern. That is the prominence of a word can be produced by an f 0 rise or a fall, depending on the location of the word in an utterance. The basic accentual shape of a Finnish word is then not a pointed rise/fall hat shape as claimed before since it can vary depending on the syllable structure and the position within an ut- terance.