Retrotransposon Tto1: functional analysis and engineering for insertional mutagenesis

Retrotransposons are genomic parasites activated by stress conditions that can be seriously detrimental for their host. In this work I demonstrate that Tto1, a typical plant LTR retrotransposon with insertion preference into genes can be turned into a synthetic molecular tool for gene tagging in plants and can be used to predict models for its replication steps. Although retrotransposons have been already used in plant mutagenesis, such application always required establishing protocols for tissue cultures and regeneration in vitro. Here, I show that sequence engineering of Tto1 provides the possibility to obtain transposition in vivo, with a simple screening method based on PCR and with the advantage to skip all in vitro manipulations. An artificial -estradiol inducible promoter has been used to obtain transposition “on demand” in Arabidopsis plants, which generates stable unlinked insertions that follow mendelian segregation in the progeny. Comparing serial deletions of 3’ LTR of the engineered inducible Tto1 (iTto1), I have mapped its two natural terminators and identified the “minimal” R (redundant) region required to achieve the complete reverse transcription of the genomic mRNA into a new cDNA copy. Interestingly, the transcripts ending at the major “early” terminator cannot support reverse transcription, suggesting a mechanism of natural control on the expression. Transcripts with a more extended termination point contain 100 essential nucleotides that define the active nucleus of the R region. This sequence promotes the formation of a stable hairpin structure that “kisses” a complementary identical hairpin on the cDNA and determines the formation of the characteristic cDNA/mRNA heteroduplex. Since the LTR is a repeated sequence the definition of a minimal redundant region has also the important implication to reduce the only possible target for sequence-based gene silencing, which should lead to an increase of the mutagenic efficiency of iTto1. Additional investigations have been carried out in attempt to identify points of improvement of iTto1 performances. By sequence alignment I identified different versions of the integrase that might have influence on insertion efficiency. Furthermore I tested the pOp6/LhGR-N system that will provide higher expression levels in different host plants. The final goal of my work is to extend the application of iTto1 to crop mutagenesis, therefore a big part of my work has been spent to develop Tto1 constructs with activity in barley. Transgenic plants have been obtained, however the constructs still need further experimentation

The GoSam package: an overview

The public code GOSAM for the computation of the one loop virtual corrections to scattering amplitudes in the Standard Model and beyond is presented. Particular emphasis is devoted to the interface with other public tools via the Binoth Les Houches Accord. We show with examples that doing LHC phenomenology including automatically Next to Leading Order QCD corrections is now handy.Comment: 8 pages, 4 figures, presented at the 11th DESY workshop "Loops and Legs in Quantum Field Theory", April 2012, Wernigerode, German

A structural view of microRNA-target recognition

It is well established that the correct identification of the messenger RNA targeted by a given microRNA (miRNA) is a difficult problem, and that available methods all suffer from low specificity. We hypothesize that the correct identification of the pairing should take into account the effect of the Argonaute protein (AGO), an essential catalyst of the recognition process. Therefore, we developed a strategy named MiREN for building and scoring three-dimensional models of the ternary complex formed by AGO, a miRNA and 22 nt of a target mRNA that putatively interacts with it. We show here that MiREN can be used to assess the likelihood that an RNA molecule is the target of a given miRNA and that this approach is more accurate than other existing methods, usually based on sequence or sequence-related features. Our results also suggest that AGO plays a relevant role in the selection of the miRNA targets. Our method can represent an additional step for refining predictions made by faster but less accurate classical methods for the identification of miRNA targets

Baryogenesis via leptogenesis in SO(10) models

We discuss the baryogenesis via leptogenesis mechanism within the supersymmetric and nonsupersymmetric SO(10) models. We find that the nonsupersymmetric model, endowed with an intermediate scale, is generally favoured, unless some fine tuning occurs in the supersymmetric case.Comment: 9 pages, RevTex, with 1 figur

Associated ZH production at hadron colliders: the fully differential NNLO QCD calculation

We consider Standard Model Higgs boson production in association with a Z boson in hadron collisions. We present a fully exclusive computation of QCD radiative corrections up to next-to-next-to-leading order (NNLO). Our calculation includes the Higgs boson decay to bottom quarks (b) in next-to-leading order QCD and the leptonic decay of the Z boson with finite-width effects and spin correlations. The computation is implemented in a parton level Monte Carlo program that makes possible to consider arbitrary kinematical cuts on the final-state leptons, the b jets and the associated QCD radiation, and to compute the corresponding distributions in the form of bin histograms. We assess the impact of QCD radiative effects in the boosted kinematics at the LHC and show that the inclusion of the NNLO corrections is crucial to control the pT spectrum of the Higgs boson candidate.Comment: 10 pages, 2 figure

Prediction of the permeability of neutral drugs inferred from their solvation properties

Determination of drug absorption is an important component of the drug discovery and development process in that it plays a key role in the decision to promote drug candidates to clinical trials. We have developed a method that, on the basis of an analysis of the dynamic distribution of water molecules around a compound obtained by molecular dynamics simulations, can compute a parameter-free value that correlates very well with the compound permeability measured using the human colon adenocarcinoma (Caco-2) cell line assay

Higher-order QCD effects for associated WH production and decay at the LHC

We consider Standard Model Higgs boson production in association with a W boson in hadron collisions. We supplement the fully exclusive perturbative computation of QCD radiative effects up to next-to-next-to-leading order (NNLO) with the computation of the decay of the Higgs boson into a bb pair at next-to-leading order (NLO). We consider the selection cuts that are typically applied in the LHC experimental analysis, and we compare our fixed-order predictions with the results obtained with the MC@NLO event generator. We find that NLO corrections to the H -> bb decay can be important to obtain a reliable pT spectrum of the Higgs boson, but that, in the cases of interest, their effect is well accounted for by the parton shower Monte Carlo. NNLO corrections to the production process typically decrease the cross section by an amount which depends on the detail of the applied cuts, but they have a mild effect on the shape of the Higgs pT spectrum. We also discuss the effect of QCD radiative corrections on the invariant mass distribution of the Higgs candidate.Comment: 18 pages, 7 figures. References and figure added. Version published on JHE

Wbbj production at NLO with POWHEG+MiNLO

We present a next-to-leading order plus parton-shower event generator for the production of a W boson plus two bottom quarks and a jet at hadron colliders, implemented in the POWHEG BOX framework. Bottom-mass effects and spin correlations of the decay products of the W boson are fully taken into account. The code has been automatically generated using the two available interfaces to MadGraph4 and GoSam, the last one updated to a new version. We have applied the MiNLO prescription to our Wbbj calculation, obtaining a finite differential cross section also in the limit of vanishing jet transverse momentum. Furthermore, we have compared several key distributions for Wbbj production with those generated with a next-to-leading order plus parton-shower event generator for Wbb production, and studied their factorization- and renormalization-scale dependence. Finally, we have compared our results with recent experimental data from the ATLAS and CMS Collaborations.Comment: Version as accepted for publication. Added references, one table and one figure. All the rest is the same as version

QCD corrections to J/psi and Upsilon production at hadron colliders

We calculate the cross section for hadroproduction of a pair of heavy quarks in a 3S1 color-singlet state at next-to-leading order in QCD. This corresponds to the leading contribution in the NRQCD expansion for J/psi and Upsilon production. The higher-order corrections have a large impact on the p_T distributions, enhancing the production at high p_T both at the Tevatron and at the LHC. The total decay rate of a 3S1 into hadrons at NLO is also computed, confirming for the first time the result obtained by Mackenzie and Lepage in 1981.Comment: 5 pages, 5 figure