Étude de la protéine sigma 1 de réovirus par génétique inverse.

Réovirus, connu sous le nom REOLYSIN®, est présentement à l'étude à titre d'agent oncolytique. Or, la spécificité du virus pour les cellules cancéreuses pourrait être optimisée par une modification au niveau de la protéine d'attachement σ1. La présente étude vise à démontrer qu'une telle amélioration est possible par l'utilisation de la méthode nouvellement décrite de génétique inverse. Par cette technique, il est possible d'ajouter un polypeptide d'une longueur de quarante acides aminés à l'extrémité C-terminale de σ1. Il est aussi possible d'engendrer des virus mutés en leur site d'activité mucinolytique. Les virus nouvellement créés démontrent une efficacité de réplication diminuée, mais demeurent infectieux. Contrairement aux méthodes traditionnellement utilisées avec réovirus, la méthode de génétique inverse permet de conserver les mutations engendrées, par substitution ou addition, au cours des cycles de réplication. Une telle étude démontre qu'il serait possible de modifier le tropisme de réovirus.

Type-1 error inflation in the traditional by-participant analysis to metamemory accuracy: a generalized mixed-effects model perspective

In order to examine metacognitive accuracy (i.e., the relationship between metacognitive judgment and memory performance), researchers often rely on by-participant analysis, where metacognitive accuracy (e.g., resolution, as measured by the gamma coefficient or signal detection measures) is computed for each participant and the computed values are entered into group-level statistical tests such as the t-test. In the current work, we argue that the by-participant analysis, regardless of the accuracy measurements used, would produce a substantial inflation of Type-1 error rates, when a random item effect is present. A mixed-effects model is proposed as a way to effectively address the issue, and our simulation studies examining Type-1 error rates indeed showed superior performance of mixed-effects model analysis as compared to the conventional by-participant analysis. We also present real data applications to illustrate further strengths of mixed-effects model analysis. Our findings imply that caution is needed when using the by-participant analysis, and recommend the mixed-effects model analysis.

Meta-analysis to integrate effect sizes within a paper: Possible misuse and Type-1 error inflation

In recent years an increasing number of papers have employed meta-analysis to integrate effect sizes of researchers’ own series of studies within a single paper (“internal meta-analysis”). Although this approach has the obvious advantage of obtaining narrower confidence intervals, we show that it could inadvertently inflate false-positive rates if researchers are motivated to use internal meta-analysis in order to obtain a significant overall effect. Specifically, if one decides whether to stop or continue a further replication experiment depending on the significance of the results in an internal meta-analysis, false-positive rates would increase beyond the nominal level. We conducted a set of Monte-Carlo simulations to demonstrate our argument, and provided a literature review to gauge awareness and prevalence of this issue. Furthermore, we made several recommendations when using internal meta-analysis to make a judgment on statistical significance.

Measurement of the ratio of inclusive cross sections sigma(p(p)over-bar -> Z plus b jet)/sigma(p(p)over-bar -> Z plus jet) at root s=1.96 TeV

Using the data collected with the D0 detector at root s=1.96 TeV, for integrated luminosities of about 180 pb(-1), we have measured the ratio of inclusive cross sections for p(p) over bar -> Z+b jet to p(p) over bar -> Z+jet production. The inclusive Z+b-jet reaction is an important background to searches for the Higgs boson in associated ZH production at the Fermilab Tevatron collider. Our measurement is the first of its kind, and relies on the Z -> e(+)e(-) and Z ->mu(+)mu(-) modes. The combined measurement of the ratio yields 0.021 +/- 0.005 for hadronic jets with transverse momenta p(T)> 20 GeV/c and pseudorapidities vertical bar eta vertical bar < 2.5, consistent with next-to-leading-order predictions of the standard model.

Measurement of sigma(p(p)over-bar -> Z)center dot Br(Z ->tau tau) at root s=1.96 TeV

We present a measurement of the cross section for Z production times the branching fraction to tau leptons, sigma.Br(Z ->tau(+)tau(-)), in p (p) over bar collisions at root s=1.96 TeV in the channel in which one tau decays into mu nu(mu)nu(tau), and the other into hadrons+nu(tau) or e nu(e)nu(tau). The data sample corresponds to an integrated luminosity of 226 pb(-1) collected with the D0 detector at the Fermilab Tevatron collider. The final sample contains 2008 candidate events with an estimated background of 55%. From this we obtain sigma.Br(Z ->tau(+)tau(-)) = 237 +/- 15(stat)+/- 18(sys)+/- 15(lum)pb, in agreement with the standard model prediction.

Measurement of sigma(p(p)over-bar -> Z plus X)Br(Z -> tau(+)tau(-)) at root s=1.96 TeV

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Measurement of three-jet differential cross sections d sigma(3jet)/dM(3jet) in p(p)over-bar collisions at root s=1.96 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Measurement of the ratio of inclusive cross sections sigma(p(p)over-bar -> Z plus b-quark jet)/sigma(p(p)over-bar -> Z plus jet) at root s=1.96 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Measurement of the differential cross section d sigma/dt in elastic p(p)over-bar scattering at root s=1.96 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Molecular analysis of Sigma-1 receptor modulation of the dopamine transporter

Sigma (σ) receptors are well established as a non-opioid, non-phencyclidine, and haloperidol-sensitive receptor family with its own binding profile and a characteristic distribution in the central nervous system (CNS) as well as in endocrine, immune, and some peripheral tissues. Two σ receptors subtypes, termed σ1 and σ2, have been pharmacologically characterized, but, to date, only the σ1 has also been cloned. Activation of σ1 receptors alter several neurotransmitter systems and dopamine (DA) neurotrasmission has been often shown to constitute an important target of σ receptors in different experimental models; however the exact role of σ1 receptor in dopaminergic neurotransmission remains unclear. The DA transporter (DAT) modulates the spatial and temporal aspects of dopaminergic synaptic transmission and interprer the primary mechanism by wich dopaminergic neurons terminate the signal transmission. For this reason present studies have been focused in understanding whether, in cell models, the human subtype of σ1 (hσ1) receptor is able to directly modulate the human DA transporter (hDAT). In the first part of this thesis, HEK-293 and SH-SY5Y cells were permanently transfected with the hσ1 receptor. Subsequently, they were transfected with another plasmid for transiently expressing the hDAT. The hDAT activity was estimated using the described [3H]DA uptake assay and the effects of σ ligands were evaluated by measuring the uptaken [3H]DA after treating the cells with known σ agonists and antagonists. Results illustrated in this thesis demonstrate that activation of overexpressed hσ1 receptors by (+)-pentazocine, the σ1 agonist prototype, determines an increase of 40% of the extracellular [3H]DA uptake, in comparison to non-treated controls and the σ1 antagonists BD-1047 and NE-100 prevent the positive effect of (+)-pentazocine on DA reuptake DA is likely to be considered a neurotoxic molecule. In fact, when levels of intracellular DA abnormally invrease, vescicles can’t sequester the DA which is metabolized by MAO (A and B) and COMT with consequent overproduction of oxygen reactive species and toxic catabolites. Stress induced by these molecules leads cells to death. Thus, for the second part of this thesis, experiments have been performed in order to investigate functional alterations caused by the (+)-pentazocine-mediated increase of DA uptake; particularly it has been investigated if the increase of intracellular [DA] could affect cells viability. Results obtained from this study demonstrate that (+)-pentazocine alone increases DA cell toxicity in a concentration-dependent manner only in cells co-expressing hσ1 and hDAT and σ1 antagonists are able to revert the (+)-pentazocine-induced increase of cell susceptibility to DA toxicity. In the last part of this thesis, the functional cross-talking between hσ1 receptor and hDAT has been further investigated using confocal microscopy. From the acquired data it could be suggested that, following exposure to (+)-pentazocine, the hσ1 receptors massively translocate towards the plasma membrane and colocalize with the hDATs. However, any physical interaction between the two proteins remains to be proved. In conclusion, the presented study shows for the first time that, in cell models, hσ1 receptors directly modulate the hDAT activity. Facilitation of DA uptake induced by (+)-pentazocine is reflected on the increased cell susceptibility to DA toxicity; these effects are prevented by σ1 selective antagonists. Since numerous compounds, including several drugs of abuse, bind to σ1 receptors and activating them could facilitate the damage of dopaminergic neurons, the reported protective effect showed by σ1 antagonists would represent the pharmacological basis to test these compounds in experimental models of dopaminergic neurodegenerative diseases (i.e. Parkinson’s Disease).

Messung der semileptonischen Ξ°-Zerfälle mit dem NA48/1-Detektor

Im Jahre 2002 wurde mit dem NA48/1-Detektor eine Datennahme mit hoher Intensität von K_S-Mesonen und neutralen Hyperonen durchgeführt, bei der unter anderem etwa 10^9 Xi^0-Zerfallskandidaten aufgezeichnet wurden. Im Rahmen dieser Arbeit wurden aus diesem Datensatz 6657 Xi^0 -> Sigma^+ e^- Anti-nü und 581 Anti-Xi^0 -> Anti-Sigma^+ e^+ nü-Ereignisse ausgewählt und damit die Verzweigungsverhältnisse BR1(Gamma(Xi^0 -> Sigma^+ e^- Anti-nü)/Gamma(Xi^0 total))=( 2.533 +-0.032(stat) -0.076+0.089(syst) )10^-4 und BR2(Gamma(Anti-Xi^0 -> Anti-Sigma^+ e^+ nü)/Gamma(Anti-Xi^0 total))= ( 2.57 +-0.12(stat) -0.09+0.10(syst) )10^-4 bestimmt. Dieses Ergebnis für BR1 ist etwa 3.5-mal genauer als die bisher veröffentlichte Messung. Die Analyse der Anti-Xi^0-Beta-Zerfälle stellt die erste Messung von BR2 dar. Beide Ergebnisse stimmen mit der theoretischen Vorhersage von 2.6*10^-4 überein. Aus dem Xi^0-Beta-Verzweigungsverhältnis folgt unter Verwendung des experimentellen Wertes des Formfaktorverhältnisses g1/f1 für das CKM-Matrixelement |Vus| = 0.209 +- 0.004(exp) +- 0.026(syst), wobei die dominierende Unsicherheit von g1/f1 herrührt. Außerdem wurden in dieser Arbeit 99 Xi^0 -> Sigma^+ mu^- Anti-nü Zerfallskandidaten mit einem abgeschätzten Untergrund von 30 Ereignissen rekonstruiert und daraus ebenfalls das Verzweigungsverhältnis extrahiert: BR3(Gamma(Xi^0 -> Sigma^+ mu^- Anti-nü)/Gamma(Xi^0 total)) = ( 2.11 +- 0.31(stat) +- 0.15(syst) )10^-6.

Messung der Zerfallsasymmetrien der radiativen Hyperonzerfälle Xi 0 Lambda gamma und Xi 0 Sigma 0 gamma mit dem NA48/1-Experiment

Der radiative Zerfall eines Hyperons in ein leichteres Hyperon und ein Photon erlaubt eine Untersuchung der Struktur der elektroschwachen Wechselwirkung von Hadronen. Dazu wird die Zerfallsasymmetrie $alpha$ betrachtet. Sie beschreibt die Verteilung des Tochterhyperons bezüglich der Polarisation $vec{P}$ des Mutterhyperons mit $dN / d cos(Theta) propto 1 + alpha |vec{P}| cos(Theta)$, wobei $Theta$ der Winkel zwischen $vec{P}$ und dem Impuls des Tochterhyperons ist. Von besonderem Interesse ist der radiative Zerfall $Xi^0 to Lambda gamma$, für den alle Rechnungen auf Quarkniveau eine positive Asymmetrie vorhersagen, wohingegen bisher eine negative Asymmetrie von $alpha_{Lambda gamma} = -0,73 +- 0,17$ gemessen wurde. Ziel dieser Arbeit war es, die bisherigen Messungen zu überprüfen und die Asymmetrie mit einer deutlich höheren Präzision zu bestimmen. Ferner wurden die Zerfallsasymmetrie des radiativen Zerfalls $Xi^0 to Sigma^0 gamma$ ermittelt und zum Test der angewandten Analysemethode der gut bekannte Zerfall $Xi^0 to Lambda pi^0$ herangezogen. Während der Datennahme im Jahr 2002 zeichnete das NA48/1-Experiment am CERN gezielt seltene $K_S$- und Hyperonzerfälle auf. Damit konnte der weltweit größte Datensatz an $Xi^0$-Zerfällen gewonnen werden, aus dem etwa 52.000 $Xi^0 to Lambda gamma$-Zerfälle, 15.000 $Xi^0 to Sigma^0 gamma$-Zerfälle und 4 Mill. $Xi^0 to Lambda pi^0$-Zerfälle mit nur geringem Untergrund extrahiert wurden. Ebenso wurden die entsprechenden $antiXi$-Zerfälle mit etwa einem Zehntel der obigen Ereigniszahlen registriert. Die Bestimmung der Zerfallsasymmetrien erfolgte durch den Vergleich der gemessene Daten mit einer detaillierten Detektorsimulation und führte zu den folgenden Resultaten dieser Arbeit: $alpha_{Lambda gamma} = -0,701 +- 0,019_{stat} +- 0,064_{sys}$, $alpha_{Sigma^0 gamma} = -0,683 +- 0,032_{stat} +- 0,077_{sys}$, $alpha_{Lambda pi^0} = -0,439 +- 0,002_{stat} +- 0,056_{sys}$, $alpha_{antiLambda gamma} = 0,772 +- 0,064_{stat} +- 0,066_{sys}$, $alpha_{antiSigma^0 gamma} = 0,811 +- 0,103_{stat} +- 0,135_{sys}$, $alpha_{antiLambda pi^0} = 0,451 +- 0,005_{stat} +- 0,057_{sys}$. Somit konnte die Unsicherheit der $Xi^0 to Lambda gamma$-Zerfallsasymmetrie auf etwa ein Drittel reduziert werden. Ihr negatives Vorzeichen und damit der Widerspruch zu den Vorhersagen der Quarkmodellrechnungen ist so zweifelsfrei bestätigt. Mit den zum ersten Mal gemessenen $antiXi$-Asymmetrien konnten zusätzlich Grenzen auf eine mögliche CP-Verletzung in den $Xi^0$-Zerfällen, die $alpha_{Xi^0} neq -alpha_{antiXi}$ zur Folge hätte, bestimmt werden.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Next-generation sequencing (NGS) is a valuable tool for the detection and quantification of HIV-1 variants in vivo. However, these technologies require detailed characterization and control of artificially induced errors to be applicable for accurate haplotype reconstruction. To investigate the occurrence of substitutions, insertions, and deletions at the individual steps of RT-PCR and NGS, 454 pyrosequencing was performed on amplified and non-amplified HIV-1 genomes. Artificial recombination was explored by mixing five different HIV-1 clonal strains (5-virus-mix) and applying different RT-PCR conditions followed by 454 pyrosequencing. Error rates ranged from 0.04-0.66% and were similar in amplified and non-amplified samples. Discrepancies were observed between forward and reverse reads, indicating that most errors were introduced during the pyrosequencing step. Using the 5-virus-mix, non-optimized, standard RT-PCR conditions introduced artificial recombinants in a fraction of at least 30% of the reads that subsequently led to an underestimation of true haplotype frequencies. We minimized the fraction of recombinants down to 0.9-2.6% by optimized, artifact-reducing RT-PCR conditions. This approach enabled correct haplotype reconstruction and frequency estimations consistent with reference data obtained by single genome amplification. RT-PCR conditions are crucial for correct frequency estimation and analysis of haplotypes in heterogeneous virus populations. We developed an RT-PCR procedure to generate NGS data useful for reliable haplotype reconstruction and quantification.

The role of conserved region 1 of Escherichia coli sigma-70 in transcription initiation

The sigma (σ) subunit of eubacterial RNA polymerase is essential for initiation of transcription at promoter sites. σ factor directs the RNA polymerase core subunits ( a2bb′ ) to the promoter consensus elements and thereby confers selectivity for transcription initiation. The N-terminal domain (region 1.1) of Escherichia coli σ70 has been shown to inhibit DNA binding by the C-terminal DNA recognition domains when σ is separated from the core subunits. Since DNA recognition by RNA polymerase is the first step in transcription, it seemed plausible that region 1 might also influence initiation processes subsesquent to DNA binding. This study explores the functional roles of regions 1.1 and 1.2 of σ70 in transcription initiation. Analysis in vitro of the transcriptional properties of a series of N-terminally truncated σ70 derivates revealed a critical role for region 1.1 at several key stages of initiation. Deletion of the first 75 to 100 amino acids of σ70 (region 1.1) resulted in both a slow rate of transition from a closed promoter complex to a DNA-strand-separated open complex, as well as a reduced efficiency of transition from the open complex to a transcriptionally active open complex. These effects were partially reversed by addition of a polypeptide containing region 1.1 in trans. Therefore, region 1.1 not only modulates DNA binding but is important for efficient transcription initiation, once a closed complex has formed. A deletion of the first 133 amino acids which removes both regions 1.1 and 1.2 resulted in arrest of initiation at the earliest closed complex, suggesting that region 1.2 is required for open complex formation. Mutagenesis of region 1.1 uncovered a mechanistically important role for isoleucine at position 53 (I53). Substitution of I53 with alanine created a σ factor that associated with the core subunits to form holoenzyme, but the holoenzyme was severely deficient for promoter binding. The I53A phenotype was suppressed in vivo by truncation of five amino acids from the C-terminus of σ 70. These observations are consistent with a model in which σ 70I53A fails to undergo a critical conformational change upon association with the core subunits, which is needed to expose the DNA-binding domains and confer promoter recognition capability upon holoenzyme. To understand the basis of the autoinhibitory properties of the σ70 N-terminal domain, in the absence of core RNA polymerase, a preliminary physical assessment of the interdomain interactions within the σ70 subunit was launched. Results support a model in which N-terminal amino acids are in close proximity to residues in the C-terminus of the σ 70 polypeptide. ^