To respond to rapidly-changing stresses in their environment, bacterial cells must be able to sense a variety of chemical cues and respond to them by activating the relevant genes. The lysine riboswitch is a short RNA motif, located just upstream of a gene encoding a lysine biosynthesis protein, that suppresses the expression of that gene when sufficient lysine is present in the cell. It acts by binding a lysine monomer in a region called the aptamer, which in turn rearranges an adjacent domain called the expression platform, sequestering the ‘start' sequence of the gene and preventing it from being transcribed. In this thesis, the lysine riboswitch's ligand-binding transition is studied using single-molecule fluorescence microscopy, optical tweezers, and a hybrid optical force/fluorescence technique. Förster Resonance Energy Transfer (FRET) is used with a fluorescently-labeled aptamer to show that it has a previously-undescribed, partially-folded structural state with enhanced ligand affinity compared to the unfolded structure. The Mg²⁺ dependence of the transition between these states is shown to resolve existing debates in the literature about the sensitivity of the riboswitch. The kinetics of the folding transition are explored using FRET, optical force, and hybrid ‘Fleezers' to map the free energy landscape of ligand binding and show that the ligand itself promotes transitions into the aptamer's folded state, a so-called ‘induced fit' mechanism rare among riboswitches. Finally, high-resolution optical tweezers are used to explore the link between the aptamer's secondary structure (the sequence of paired nucleotides) and its tertiary structure (three-dimensional folding) to illuminate the role of ligand binding in gene regulation, which depends on the equilibrium between competing secondary structures. Hybrid biophysical techniques like optical force/fluorescence microscopy are shown to be indispensable for addressing all the states in the reaction pathways of complex biomolecules like riboswitches and for discriminating between multiple levels of structure formation and interaction with the environment. Not only do the results presented here shed light on the RNA folding problem, particularly the role of tertiary structure in determining the minimum-energy configuration of an RNA sequence, but they could have implications for biomedical research, as the lysine riboswitch has already been shown to be a potential target for next-generation antibiotics.

Abstract Respiratory syncytial virus (RSV) infection may be associated with the development of asthma and atopy. The aim of the present study was to investigate this association and the related immunological mechanisms. Seventy-six children admitted to Oulu University Hospital in 1991–1994 for an RSV infection at an age of less than 12 months and healthy controls were called for a visit at the age of 6–10 years. Twenty subjects (26%) had asthma compared with 12 controls (16%) (difference 11%, 95% confidence interval (CI) –3% to 24%). Asthma had been diagnosed significantly earlier in the subjects. Eight per cent of the subjects had at least one positive skin prick test as compared with 43% of the controls (difference –35%, 95% CI –50% to –19%). Serum concentrations of interferon-γ and soluble intercellular adhesion molecule -1 were significantly higher among the subjects than among the controls and among the subjects with asthma or current wheezing than among the corresponding controls. All children born in Finland in 1986–1995 were arranged in birth cohorts by month and year of birth and grouped by exposure to an RSV epidemic at age 0–6 months, resulting in 97 exposed and 23 unexposed cohorts. The proportions of children taking asthma medication or receiving special reimbursement for asthma medication in 1995–2002 were similar in the unexposed and exposed cohorts. Altogether 47 children born between August and November 2001 with a cord blood sample taken were admitted to hospital (n = 26) or seen in an outpatient department (n = 21) for RSV infection before the age of six months. Twenty-eight children had some other respiratory viral infection and 84 children formed a group of healthy controls. High scores on a factor combining the cord blood interleukin-6 and interleukin-8 responses (as derived by factor analysis) were shown in logistic regression analysis to predict hospitalization for RSV infection by comparison with the healthy controls (odds ratio 2.29, 95% CI 1.21 to 4.33). We suggest that RSV does not induce asthma but inborn features of immunity affect the severity of RSV infection and the postinfectious development of asthma.

Abstract This thesis deals with infrared spectroscopy investigations on the linear DCCI molecule. The high resolution spectra between 200–5200 cm-1 were measured with the Fourier transform spectrometer at the University of Oulu. The spectra were analyzed taking into account various types of resonances between rovibrational energy levels. As a result, a set of molecular constants and resonance parameters describing the rotational and vibrational energy states of the molecule were obtained. From the resulting molecular constants, together with previous results from literature for HCCI, the structure of monoiodoacetylene was calculated. In addition, eight harmonic force constants with estimated uncertainties for monoiodoacetylene were determined.

No description available.

Doctor of Philosophy / Department of Physics / Charles L. Cocke / An underlying goal of studying atomic or molecular dynamics with short laser pulses is to reach a time scale short enough to study the evolution of the system in the time domain. In this thesis, the strong field ionization of atoms and molecules has been investigated with the highly resolved technique known as cold target recoil momentum spectroscopy (COLTRIMS). The thesis can be divided into two parts: single and double ionization. In the first part, we studied the momentum vectors of low energy electrons generated by short laser pulses of wavelengths varying from 400 to 800 nm with atomic and molecular targets with intensities in the tunneling region. Most of the structures observed in the momentum spectra of atomic and molecular targets can be explained as due to above-threshold ionization, and Freeman resonances. The most significant structure in our observed spectra is the angular structure in the lowest part of the momentum image, and this is attributed to the diffraction pattern evolved by tunneling electrons. Surprisingly, we observed that the structure produced by the electrons from high Rydberg states is independent of the internal structure of the target atom and molecules. The same work is extended to aligned molecules. The basic idea of this part of the work is to see whether the angular distribution of electrons from aligned molecules resembles the orbital structures of the molecules. The rotational revival structure was used to align the molecules. We observed pronounced energy and angular structures of the momentum images which show a dependence on the alignment of the molecule. The last part of this work mainly focuses on double ionization, i.e. the removal of two electrons from the target atoms sequentially by a short laser pulse. Measuring the complete momentum vector of Ar2+ and Ne2+, we demonstrate that these can be used to extract the angular correlation between two electrons sequentially released in the circularly polarized pulse. We demonstrate how the measurement of full momentum vectors of the doubly ionized argon and neon ions can be used to extract the time gap of the two emissions.

No description available.

L'ARN s'est longtemps vu attribuer un simple role de transmission entre l'ADN, garant de l'information genetique, et les proteines, assurant les fonctions et donc la survie cellulaire. Ce n'est qu'avec les decouvertes des ARNs de transfert dans les annees 70, puis des ribozymes dans les annees 80, qu'il a ete realise que l'ARN pouvait assurer ces deux roles : l'information genetique est stockee dans sa sequence lineaire, et l'adoption de structures tridimensionnelles complexes rend possible une activite catalytique. Depuis, de nouvelles fonctions de l'ARN n'ont cesse d'etre decouvertes, a tous les niveaux de regulation de l'expression genique entre autres. La majorite de ces fonctions repose sur la structuration tridimensionnelle d'ARNs simple brin.Dans ce travail, differents aspects de la structuration de l'ARN sont abordes, toujours en utilisant la technique de mesure de forces sur molecules uniques par piegeage optique. Dans un premier temps, une etude comparative d'une structure secondaire modele, le hairpin dans ses formes ARN et ADN, a ete realisee. La question de l'interaction d'une structure secondaire avec une proteine helicase (DbpA) a ensuite ete abordee. Enfin, dans le cadre plus general d'une etude sur l'assemblage du ribosome, nous avons debute le developpement d'une nouvelle methode d'analyse des structures secondaires. Cette methode repose sur le suretirement d'un hybride ARN ribosomique / ADN. / Traditionally, RNA has been considered as a mere intermediate between DNA, keeper of the genetic information, and proteins, which assume cells self-sustenance. With the discoveries of the transfert RNA in the 70s, and of the ribozymes in the 80s, RNA took on both roles: it can store information in its linear sequence, and tridimensional structuration enables catalytic functions. Since then, numerous roles devoted to RNA have been discovered, particularly for gene expression regulation. Most of these functions rely on tridimensional structuration of single stranded RNA. In this work, we used an optical tweezers setup to study several aspects of RNA structuration by single molecule force measurement. In a first part, we compared the dynamic behaviour of a model secondary structure made of either RNA or DNA, the hairpin. Then we considered the interaction of a secondary structure with a protein, the RNA helicase DbpA. Finally, within a wider study of ribosome assembly, we worked on the development of a new method to study tridimensional structuration. This method relies on the overstretching of a hybrid ribosomal RNA / DNA molecule.

La protéine SRSF1, aussi appelée ASF/SF2, fait partie de la famille des protéines SR, une famille de protéines liant l’ARN très conservées. Ces protéines jouent un rôle régulateur de l’épissage, également lors de l’épissage alternatif. Une centaine d’ARN cible ont été décrits pour SRSF1 mais la manière dont SRSF1 sélectionne ses cibles parmi tous les pré-ARNm est mal comprise. Des études in vitro et in vivo ont montré que les protéines SR reconnaissent un petit motif dégénéré qui est souvent présent en plusieurs copies dans les ESE («enhancer splicing element »). Bien que les protéines SR lient ces motifs avec une faible spécificité, la définition des exons se fait avec une grande fidélité. Afin de mieux comprendre le mécanisme d’action de SRSF1, j’ai réalisé une étude cinétique des interactions SRSF1-ARN dans les cellules vivantes par des techniques de microscopies avancées. Grâce au système CRISPR, j’ai pu étiqueter la protéine SRSF1 avec la protéine Halo puis j’ai combiné une technique de photo-blanchiment (FRAP) et une technique de suivi de particule unique (« single particle tracking, SPT) pour mesurer la diffusion de SRSF1 et son affinité pour l’ARN. J’ai mesuré la durée de vie des événements de liaison individuellement aussi bien sur le pool global de pré-ARNm que sur des cibles spécifiques. Nos résultats indiquent que la liaison de SRSF1 ne dépasse pas quelques secondes, même sur les cibles de haute affinité. Cette cinétique rapide permet à SRSF1 d’être en contact avec l’ensemble des transcrits naissants qui est produit en permanence dans la cellule. De plus, mon travail apporte une analyse cinétique de la dynamique des snRNP à la résolution de la molécule unique dans le nucléoplasme des cellules vivantes. Nous avons déterminé les coefficients de diffusion des snRNP et la durée de leur association à l’ARN dans ces cellules. / SRSF1, formerly known as ASF/SF2, belongs to the SR protein family, which is a conserved family of RNA-binding protein that plays essential roles as regulators of both constitutive and alternative splicing. Hundreds of RNA targets have been described for SRSF1 but how SRSF1 selects its targets from the entire pool of cellular pre-mRNAs remains an open question. In vitro and in vivo studies have shown that SR proteins recognize short degenerated motifs often present in multiple copies at ESEs. Similar cryptic motifs are however frequently present in pre-mRNAs, and this low specificity of binding contrasts with the great fidelity of exon definition. To better understand the mechanism of action of SRSF1, I performed a kinetic study of SRSF1-RNA interactions in live cells using advanced microscopic techniques. Taking advantage by the CRISPR system, I tagged endogenous SRSF1 with Halo protein, and I combined photobleaching (FRAP) and single particle tracking (SPT) techniques to estimate diffusion and binding rates of SRSF1. I measured the duration of individual binding events, both on the cellular pool of pre-mRNAs and on specific targets. Our results indicate that binding of SRSF1 does not exceed few seconds, even on high-affinity targets. This rapid kinetics allows SRSF1 to rapidly sample the entire pool of nascent RNAs continuously produced in cells. Moreover, we provided a kinetic analysis of snRNP dynamics at a single-molecule resolution in the nucleoplasm of living cells. Our results enabled us to determine diffusion coefficients of snRNPs and their RNA binding duration in vivo.

Disruptions in the response of endothelial progenitor cells to changes in oxygen environment may present a possible mechanism behind multiple pediatric pulmonary disease models, such as bronchopulmonary dysplasia. Using high-throughput fixed single-cell protein and RNA imaging, we have created "stop-motion" movies of Thymosin. 4 (T beta 4) and Hypoxia Inducible Factor 1 alpha (HIF-1 alpha) protein expression and vascular endothelial growth factor (vegf) and endothelial nitric oxide synthase (eNOS) mRNA in human umbilical cord-derived endothelial colony-forming cells (ECFC). ECFC were grown in vitro under both room air and hyperoxia (50% O-2). We find elevated basal T beta 4 protein expression in ECFC derived from prematurely born infants versus full term infants. T beta 4 is a potent growth hormone that additionally acts as an actin sequestration protein and regulates the stability of HIF-1 alpha. This basal level increase of T beta 4 is associated with lower HIF1 alpha nuclear localization in preterm versus term ECFC upon exposure to hyperoxia. We find altered expression in the pro-angiogenic genes vegf and eNOS, two genes that HIF-1 alpha acts as a transcription factor for. This provides a potential link between a developmentally regulated protein and previously observed impaired function of preterm ECFC in response to hyperoxia.

No description available.