4,889 research outputs found
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
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
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
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
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
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
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