Molecular details of phage phi6 RNA-dependent RNA synthesis

For most RNA viruses RNA-dependent RNA polymerases (RdRPs) encoded by the virus are responsible for the entire RNA metabolism. Thus, RdRPs are critical components in the viral life cycle. However, it is not fully understood how these important enzymes function during viral replication. Double-stranded RNA (dsRNA) viruses perform the synthesis of their RNA genome within a proteinacous viral particle containing an RdRP as a minor constituent. The phi6 bacteriophage is the best-studied dsRNA virus, providing an excellent background for studies of its RNA synthesis. The purified recombinant phi6 RdRP is highly active in vitro and it possesses both RNA replication and transcription activities. The crystal structure of the phi6 polymerase, solved in complex with a number of ligands, provides a working model for detailed in vitro studies of RNA-dependent RNA polymerization. In this thesis, the primer-independent initiation of the phi6 RdRP was studied in vitro using biochemical and structural methods. A C-terminal, four-amino-acid-long loop protruding into the central cavity of the phi6 RdRP has been suggested to stabilize the incoming nucleotides of the initiation complex formation through stacking interactions. A similar structural element has been found from several other viral RdRPs. In this thesis, this so-called initiation platform loop was subjected to site-directed mutagenesis to address its role in the initiation. It was found that the initiation mode of the mutants is primer-dependent, requiring either an oligonucleotide primer or a back-priming initiation mechanism for the RNA synthesis. The crystal structure of a mutant RdRP with altered initiation platform revealed a set of contacts important for primer-independent initiation. Since phi6 RdRP is structurally and functionally homologous to several viral RdRPs, among them the hepatitis C virus RdRP, these results provide further general insight to understand primer-independent initiation. In this study it is demonstrated that manganese phasing could be used as a practical tool for solving structures of large proteins with a bound manganese ion. The phi6 RdRP was used as a case study to obtain phases for crystallographic analysis. Manganese ions are naturally bound to the phi6 RdRP at the palm domain of the enzyme. In a crystallographic experiment, X-ray diffraction data from a phi6 RdRP crystal were collected at a wavelength of 1.89 Å, which is the K edge of manganese. With this data an automatically built model of the core region of the protein could be obtained. Finally, in this work terminal nucleotidyl transferase (TNTase) activity of the phi6 RdRP was documented in the isolated polymerase as well as in the viral particle. This is the first time that such an activity has been reported in a polymerase of a dsRNA virus. The phi6 RdRP used uridine triphosphates as the sole substrate in a TNTase reaction but could accept several heterologous templates. The RdRP was able to add one or a few non-templated nucleotides to the 3' end of the single- or double-stranded RNA substrate. Based on the results on particle-mediated TNTase activity and previous structural information of the polymerase, a model for termination of the RNA-dependent RNA synthesis is suggested in this thesis.

Interaction of alcohol and smoking in the pathogenesis of upper digestive tract cancers - possible chemoprevention with cysteine

Background: Alcohol consumption and smoking are the main causes of upper digestive tract cancers. These risk factors account for over 75% of all cases in developed countries. Epidemiological studies have shown that alcohol and tobacco interact in a multiplicative way to the cancer risk, but the pathogenetic mechanism behind this is poorly understood. Strong experimental and human genetic linkage data suggest that acetaldehyde is one of the major factors behind the carcinogenic effect. In the digestive tract, acetaldehyde is mainly formed by microbial metabolism of ethanol. Acetaldehyde is also a major constituent of tobacco smoke. Thus, acetaldehyde from both of these sources may have an interacting carcinogenic effect in the human upper digestive tract. Aims: The first aim of this thesis was to investigate acetaldehyde production and exposure in the human mouth resulting from alcohol ingestion and tobacco smoking in vivo. Secondly, specific L-cysteine products were prepared to examine their efficacy in the binding of salivary acetaldehyde in order to reduce the exposure of the upper digestive tract to acetaldehyde. Methods: Acetaldehyde levels in saliva were measured from human volunteers during alcohol metabolism, during tobacco smoking and during the combined use of alcohol and tobacco. The ability of L-cysteine to eliminate acetaldehyde during alcohol metabolism and tobacco smoking was also investigated with specifically developed tablets. Also the acetaldehyde production of Escherichia coli - an important member of the human microbiota - was measured in different conditions prevailing in the digestive tract. Results and conclusions: These studies established that smokers have significantly increased acetaldehyde exposure during ethanol consumption even when not actively smoking. Acetaldehyde exposure was dramatically further increased during active tobacco smoking. Thus, the elevated aerodigestive tract cancer risk observed in smokers and drinkers may be the result of the increased acetaldehyde exposure. Acetaldehyde produced in the oral cavity during ethanol challenge was significantly decreased by a buccal L-cysteine -releasing tablet. Also smoking-derived acetaldehyde could be totally removed by using a tablet containing L-cysteine. In conclusion, this thesis confirms the essential role of acetaldehyde in the pathogenesis of alcohol- and smoking-induced cancers. This thesis presents a novel experimental approach to decrease the local acetaldehyde exposure of the upper digestive tract with L-cysteine, with the eventual goal of reducting the prevalence of upper digestive tract cancers.

Heavy-light mesons on a lattice

Several excited states of Ds and Bs mesons have been discovered in the last six years: BaBar, Cleo and Belle discovered the very narrow states D(s0)*(2317)+- and D(s1)(2460)+- in 2003, and CDF and DO Collaborations reported the observation of two narrow Bs resonances, B(s1)(5830)0 and B*(s2)(5840)0 in 2007. To keep up with experiment, meson excited states should be studied from the theoretical aspect as well. The theory that describes the interaction between quarks and gluons is quantum chromodynamics (QCD). In this thesis the properties of the meson states are studied using the discretized version of the theory - lattice QCD. This allows us to perform QCD calculations from first principles, and "measure" not just energies but also the radial distributions of the states on the lattice. This gives valuable theoretical information on the excited states, as we can extract the energy spectrum of a static-light meson up to D wave states (states with orbital angular momentum L=2). We are thus able to predict where some of the excited meson states should lie. We also pay special attention to the order of the states, to detect possible inverted spin multiplets in the meson spectrum, as predicted by H. Schnitzer in 1978. This inversion is connected to the confining potential of the strong interaction. The lattice simulations can also help us understand the strong interaction better, as the lattice data can be treated as "experimental" data and used in testing potential models. In this thesis an attempt is made to explain the energies and radial distributions in terms of a potential model based on a one-body Dirac equation. The aim is to get more information about the nature of the confining potential, as well as to test how well the one-gluon exchange potential explains the short range part of the interaction.

Applications of Gauge/Gravity Duality to QCD and Heavy Ion Collisions

The description of quarks and gluons, using the theory of quantum chromodynamics (QCD), has been known for a long time. Nevertheless, many fundamental questions in QCD remain unanswered. This is mainly due to problems in solving the theory at low energies, where the theory is strongly interacting. AdS/CFT is a duality between a specific string theory and a conformal field theory. Duality provides new tools to solve the conformal field theory in the strong coupling regime. There is also some evidence that using the duality, one can get at least qualitative understanding of how QCD behaves at strong coupling. In this thesis, we try to address some issues related to QCD and heavy ion collisions, applying the duality in various ways.

Molecular line and continuum studies of the early stages of star formation

New stars form in dense interstellar clouds of gas and dust called molecular clouds. The actual sites where the process of star formation takes place are the dense clumps and cores deeply embedded in molecular clouds. The details of the star formation process are complex and not completely understood. Thus, determining the physical and chemical properties of molecular cloud cores is necessary for a better understanding of how stars are formed. Some of the main features of the origin of low-mass stars, like the Sun, are already relatively well-known, though many details of the process are still under debate. The mechanism through which high-mass stars form, on the other hand, is poorly understood. Although it is likely that the formation of high-mass stars shares many properties similar to those of low-mass stars, the very first steps of the evolutionary sequence are unclear. Observational studies of star formation are carried out particularly at infrared, submillimetre, millimetre, and radio wavelengths. Much of our knowledge about the early stages of star formation in our Milky Way galaxy is obtained through molecular spectral line and dust continuum observations. The continuum emission of cold dust is one of the best tracers of the column density of molecular hydrogen, the main constituent of molecular clouds. Consequently, dust continuum observations provide a powerful tool to map large portions across molecular clouds, and to identify the dense star-forming sites within them. Molecular line observations, on the other hand, provide information on the gas kinematics and temperature. Together, these two observational tools provide an efficient way to study the dense interstellar gas and the associated dust that form new stars. The properties of highly obscured young stars can be further examined through radio continuum observations at centimetre wavelengths. For example, radio continuum emission carries useful information on conditions in the protostar+disk interaction region where protostellar jets are launched. In this PhD thesis, we study the physical and chemical properties of dense clumps and cores in both low- and high-mass star-forming regions. The sources are mainly studied in a statistical sense, but also in more detail. In this way, we are able to examine the general characteristics of the early stages of star formation, cloud properties on large scales (such as fragmentation), and some of the initial conditions of the collapse process that leads to the formation of a star. The studies presented in this thesis are mainly based on molecular line and dust continuum observations. These are combined with archival observations at infrared wavelengths in order to study the protostellar content of the cloud cores. In addition, centimetre radio continuum emission from young stellar objects (YSOs; i.e., protostars and pre-main sequence stars) is studied in this thesis to determine their evolutionary stages. The main results of this thesis are as follows: i) filamentary and sheet-like molecular cloud structures, such as infrared dark clouds (IRDCs), are likely to be caused by supersonic turbulence but their fragmentation at the scale of cores could be due to gravo-thermal instability; ii) the core evolution in the Orion B9 star-forming region appears to be dynamic and the role played by slow ambipolar diffusion in the formation and collapse of the cores may not be significant; iii) the study of the R CrA star-forming region suggests that the centimetre radio emission properties of a YSO are likely to change with its evolutionary stage; iv) the IRDC G304.74+01.32 contains candidate high-mass starless cores which may represent the very first steps of high-mass star and star cluster formation; v) SiO outflow signatures are seen in several high-mass star-forming regions which suggest that high-mass stars form in a similar way as their low-mass counterparts, i.e., via disk accretion. The results presented in this thesis provide constraints on the initial conditions and early stages of both low- and high-mass star formation. In particular, this thesis presents several observational results on the early stages of clustered star formation, which is the dominant mode of star formation in our Galaxy.

Formation of structure in dark energy cosmologies

Acceleration of the universe has been established but not explained. During the past few years precise cosmological experiments have confirmed the standard big bang scenario of a flat universe undergoing an inflationary expansion in its earliest stages, where the perturbations are generated that eventually form into galaxies and other structure in matter, most of which is non-baryonic dark matter. Curiously, the universe has presently entered into another period of acceleration. Such a result is inferred from observations of extra-galactic supernovae and is independently supported by the cosmic microwave background radiation and large scale structure data. It seems there is a positive cosmological constant speeding up the universal expansion of space. Then the vacuum energy density the constant describes should be about a dozen times the present energy density in visible matter, but particle physics scales are enormously larger than that. This is the cosmological constant problem, perhaps the greatest mystery of contemporary cosmology. In this thesis we will explore alternative agents of the acceleration. Generically, such are called dark energy. If some symmetry turns off vacuum energy, its value is not a problem but one needs some dark energy. Such could be a scalar field dynamically evolving in its potential, or some other exotic constituent exhibiting negative pressure. Another option is to assume that gravity at cosmological scales is not well described by general relativity. In a modified theory of gravity one might find the expansion rate increasing in a universe filled by just dark matter and baryons. Such possibilities are taken here under investigation. The main goal is to uncover observational consequences of different models of dark energy, the emphasis being on their implications for the formation of large-scale structure of the universe. Possible properties of dark energy are investigated using phenomenological paramaterizations, but several specific models are also considered in detail. Difficulties in unifying dark matter and dark energy into a single concept are pointed out. Considerable attention is on modifications of gravity resulting in second order field equations. It is shown that in a general class of such models the viable ones represent effectively the cosmological constant, while from another class one might find interesting modifications of the standard cosmological scenario yet allowed by observations. The thesis consists of seven research papers preceded by an introductory discussion.

Dimensional Reduction Near the Deconfinement Transition

When ordinary nuclear matter is heated to a high temperature of ~ 10^12 K, it undergoes a deconfinement transition to a new phase, strongly interacting quark-gluon plasma. While the color charged fundamental constituents of the nuclei, the quarks and gluons, are at low temperatures permanently confined inside color neutral hadrons, in the plasma the color degrees of freedom become dominant over nuclear, rather than merely nucleonic, volumes. Quantum Chromodynamics (QCD) is the accepted theory of the strong interactions, and confines quarks and gluons inside hadrons. The theory was formulated in early seventies, but deriving first principles predictions from it still remains a challenge, and novel methods of studying it are needed. One such method is dimensional reduction, in which the high temperature dynamics of static observables of the full four-dimensional theory are described using a simpler three-dimensional effective theory, having only the static modes of the various fields as its degrees of freedom. A perturbatively constructed effective theory is known to provide a good description of the plasma at high temperatures, where asymptotic freedom makes the gauge coupling small. In addition to this, numerical lattice simulations have, however, shown that the perturbatively constructed theory gives a surprisingly good description of the plasma all the way down to temperatures a few times the transition temperature. Near the critical temperature, the effective theory, however, ceases to give a valid description of the physics, since it fails to respect the approximate center symmetry of the full theory. The symmetry plays a key role in the dynamics near the phase transition, and thus one expects that the regime of validity of the dimensionally reduced theories can be significantly extended towards the deconfinement transition by incorporating the center symmetry in them. In the introductory part of the thesis, the status of dimensionally reduced effective theories of high temperature QCD is reviewed, placing emphasis on the phase structure of the theories. In the first research paper included in the thesis, the non-perturbative input required in computing the g^6 term in the weak coupling expansion of the pressure of QCD is computed in the effective theory framework at an arbitrary number of colors. The two last papers on the other hand focus on the construction of the center-symmetric effective theories, and subsequently the first non-perturbative studies of these theories are presented. Non-perturbative lattice simulations of a center-symmetric effective theory for SU(2) Yang-Mills theory show --- in sharp contrast to the perturbative setup --- that the effective theory accommodates a phase transition in the correct universality class of the full theory. This transition is seen to take place at a value of the effective theory coupling constant that is consistent with the full theory coupling at the critical temperature.

Simulations of dimensionally reduced effective theories of high temperature QCD

Quantum chromodynamics (QCD) is the theory describing interaction between quarks and gluons. At low temperatures, quarks are confined forming hadrons, e.g. protons and neutrons. However, at extremely high temperatures the hadrons break apart and the matter transforms into plasma of individual quarks and gluons. In this theses the quark gluon plasma (QGP) phase of QCD is studied using lattice techniques in the framework of dimensionally reduced effective theories EQCD and MQCD. Two quantities are in particular interest: the pressure (or grand potential) and the quark number susceptibility. At high temperatures the pressure admits a generalised coupling constant expansion, where some coefficients are non-perturbative. We determine the first such contribution of order g^6 by performing lattice simulations in MQCD. This requires high precision lattice calculations, which we perform with different number of colors N_c to obtain N_c-dependence on the coefficient. The quark number susceptibility is studied by performing lattice simulations in EQCD. We measure both flavor singlet (diagonal) and non-singlet (off-diagonal) quark number susceptibilities. The finite chemical potential results are optained using analytic continuation. The diagonal susceptibility approaches the perturbative result above 20T_c$, but below that temperature we observe significant deviations. The results agree well with 4d lattice data down to temperatures 2T_c.

Applications of dimensional reduction to electroweak and QCD matter

When heated to high temperatures, the behavior of matter changes dramatically. The standard model fields go through phase transitions, where the strongly interacting quarks and gluons are liberated from their confinement to hadrons, and the Higgs field condensate melts, restoring the electroweak symmetry. The theoretical framework for describing matter at these extreme conditions is thermal field theory, combining relativistic field theory and quantum statistical mechanics. For static observables the physics is simplified at very high temperatures, and an effective three-dimensional theory can be used instead of the full four-dimensional one via a method called dimensional reduction. In this thesis dimensional reduction is applied to two distinct problems, the pressure of electroweak theory and the screening masses of mesonic operators in quantum chromodynamics (QCD). The introductory part contains a brief review of finite-temperature field theory, dimensional reduction and the central results, while the details of the computations are contained in the original research papers. The electroweak pressure is shown to converge well to a value slightly below the ideal gas result, whereas the pressure of the full standard model is dominated by the QCD pressure with worse convergence properties. For the mesonic screening masses a small positive perturbative correction is found, and the interpretation of dimensional reduction on the fermionic sector is discussed.

Search for the Higgs boson produced in association with Z→ℓ+ℓ- using the matrix element method at CDF II

We present a search for associated production of the standard model (SM) Higgs boson and a $Z$ boson where the $Z$ boson decays to two leptons and the Higgs decays to a pair of $b$ quarks in $p\bar{p}$ collisions at the Fermilab Tevatron. We use event probabilities based on SM matrix elements to construct a likelihood function of the Higgs content of the data sample. In a CDF data sample corresponding to an integrated luminosity of 2.7 fb$^{-1}$ we see no evidence of a Higgs boson with a mass between 100 GeV$/c^2$ and 150 GeV$/c^2$. We set 95% confidence level (C.L.) upper limits on the cross-section for $ZH$ production as a function of the Higgs boson mass $m_H$; the limit is 8.2 times the SM prediction at $m_H = 115$ GeV$/c^2$.

Search for the associated production of the standard-model Higgs boson in the all-hadronic channel

"We report on a search for the standard-model Higgs boson in pp collisions at s=1.96 TeV using an integrated luminosity of 2.0 fb(-1). We look for production of the Higgs boson decaying to a pair of bottom quarks in association with a vector boson V (W or Z) decaying to quarks, resulting in a four-jet final state. Two of the jets are required to have secondary vertices consistent with B-hadron decays. We set the first 95% confidence level upper limit on the VH production cross section with V(-> qq/qq('))H(-> bb) decay for Higgs boson masses of 100-150 GeV/c(2) using data from run II at the Fermilab Tevatron. For m(H)=120 GeV/c(2), we exclude cross sections larger than 38 times the standard-model prediction."

Search for Maximal Flavor Violating Scalars in Same-Charge Lepton Pairs in pp̅ Collisions at √s=1.96 TeV

Models of Maximal Flavor Violation (MxFV) in elementary particle physics may contain at least one new scalar SU$(2)$ doublet field $\Phi_{FV} = (\eta^0,\eta^+)$ that couples the first and third generation quarks ($q_1,q_3$) via a Lagrangian term $\mathcal{L}_{FV} = \xi_{13} \Phi_{FV} q_1 q_3$. These models have a distinctive signature of same-charge top-quark pairs and evade flavor-changing limits from meson mixing measurements. Data corresponding to 2 fb$^{-1}$ collected by the CDF II detector in $p\bar{p}$ collisions at $\sqrt{s} = 1.96$ TeV are analyzed for evidence of the MxFV signature. For a neutral scalar $\eta^0$ with $m_{\eta^0} = 200$ GeV/$c^2$ and coupling $\xi_{13}=1$, $\sim$ 11 signal events are expected over a background of $2.1 \pm 1.8$ events. Three events are observed in the data, consistent with background expectations, and limits are set on the coupling $\xi_{13}$ for $m_{\eta^0} = 180-300$ GeV/$c^2$.

First Measurement of the b-Jet Cross Section in Events with a W Boson in pp̅ Collisions at √s=1.96 TeV

The cross section for jets from b quarks produced with a W boson has been measured in ppbar collision data from 1.9/fb of integrated luminosity recorded by the CDF II detector at the Tevatron. The W+b-jets process poses a significant background in measurements of top quark production and prominent searches for the Higgs boson. We measure a b-jet cross section of 2.74 +- 0.27(stat.) +- 0.42(syst.) pb in association with a single flavor of leptonic W boson decay over a limited kinematic phase space. This measured result cannot be accommodated in several available theoretical predictions.

Search for Technicolor Particles Produced in Association with a W Boson at CDF

We present a search for the technicolor particles $\rho_{T}$ and $\pi_{T}$ in the process $p\bar{p} \to \rho_{T} \to W\pi_{T}$ at a center of mass energy of $\sqrt{s}=1.96 \mathrm{TeV}$. The search uses a data sample corresponding to approximately $1.9 \mathrm{fb}^{-1}$ of integrated luminosity accumulated by the CDF II detector at the Fermilab Tevatron. The event signature we consider is $W\to \ell\nu$ and $\pi_{T} \to b\bar{b}, b\bar{c}$ or $b\bar{u}$ depending on the $\pi_{T}$ charge. We select events with a single high-$p_T$ electron or muon, large missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with multiple $b$-tagging algorithms. The observed number of events and the invariant mass distributions are consistent with the standard model background expectations, and we exclude a region at 95% confidence level in the $\rho_T$-$\pi_T$ mass plane. As a result, a large fraction of the region $m(\rho_T) = 180$ - $250 \mathrm{GeV}/c^2$ and $m(\pi_T) = 95$ - $145 \mathrm{GeV}/c^2$ is excluded.

Search for the associated production of the standard-model Higgs boson in the all-hadronic channel

"We report on a search for the standard-model Higgs boson in pp collisions at s=1.96 TeV using an integrated luminosity of 2.0 fb(-1). We look for production of the Higgs boson decaying to a pair of bottom quarks in association with a vector boson V (W or Z) decaying to quarks, resulting in a four-jet final state. Two of the jets are required to have secondary vertices consistent with B-hadron decays. We set the first 95% confidence level upper limit on the VH production cross section with V(-> qq/qq('))H(-> bb) decay for Higgs boson masses of 100-150 GeV/c(2) using data from run II at the Fermilab Tevatron. For m(H)=120 GeV/c(2), we exclude cross sections larger than 38 times the standard-model prediction."