Search for the B⁰s → η'φ decay and prospects for the study of selected charmless B decays at LHCb

This work explores charmless $B$ decays using the LHCb detector. LHCb is one of the four main experiments at the Large Hadron Collider (LHC) located at CERN, and is designed to perform CP violation measurements and to study rare decays of hadrons containing $b$ or $c$ quarks. Among charmless $B$ decays, the $B^0_s$ decay modes to final states with two light resonances ($\eta$, $\eta^{\prime}$, $\omega$, $\phi$) are particularly interesting in view of time-dependent CP violation studies. More specifically they can be used to measure the CP-violating phase difference between the $B^0_s$--$\bar{B}^0_s$ mixing amplitude and the $b\to s\bar{s}s$ decay amplitude. Among these, $B^0_s \to \phi\phi$ has been exploited by LHCb through an angular analysis of the vector-vector final state. The other modes have lower measured or expected event yields, but don't require an angular analysis. We present the results of a search for the yet unobserved $B^0_s \to \eta^{\prime} \phi$ decay using $3~\rm{fb}^{-1}$ of data collected by LHCb during the LHC Run 1 (2011--2012). The decay $B^{0}_{s} \to \eta^{\prime} \phi$ has been studied in several theoretical frameworks and the predictions for its branching fraction cover a wide range, typically from $0.05 \times 10^{-6}$ to $20 \times 10^{-6}$.\\ In the analysis presented in this thesis the $B^+ \to \eta^{\prime} K^+$ decay is used as normalisation in the computation of the branching fraction for the searched mode. The $B^{0}_{s} \to \eta^{\prime} \phi$ signal yield is obtained from a simultaneous two-dimensional fit of the reconstructed $B$ and $\eta^{\prime}$ invariant masses of the $B^{0}_{s} \to \eta^{\prime} \phi$ and $B^+ \to \eta^{\prime}K^+$ candidates in Run 1 data. No significant signal is found and, for the first time, an upper limit on the $B^{0}_{s} \to \eta^{\prime} \phi$ branching fraction is set: \begin{equation} {\cal B}(B^{0}_{s} \to \eta^{\prime} \phi)< 0.82\,(1.01)\times 10^{-6} \quad \mbox{at 90\% (95\%) CL}\,. \nonumber \end{equation} Although large theoretical uncertainties make most predictions compatible with the result of this analysis, the upper limit is significantly smaller than the central values of most of the predictions, which tends to favour the lower end of the range of predictions.\\ Furthermore, prospect studies using the Run~2 data collected in 2015 and 2016, are presented for $B^{0}_{s} \to \eta^{\prime} \phi$ and for two other decay modes already studied with Run 1 data, $B^{0}_{s} \to \eta^{\prime} \eta^{\prime}$ and $B^+ \to \phi\pi^+$. The $B^+ \to \eta^{\prime} K^+$} and $B^+ \to \phi K^+$ decay modes are used as normalisation channels. The study shows that at least the full Run 2 dataset, to be collected until the end of 2018, will be needed to aim at an observation of the $B^{0}_{s} \to \eta^{\prime} \phi$ and $B^+ \to \phi\pi^+$ decays, taking into account also the wide range of predictions for these modes, while for the already established $B^{0}_{s} \to \eta^{\prime} \eta^{\prime}$ decay the statistics collected by the end of Run 2 will allow a measurement of the $B^{0}_{s}$ lifetime

From milk to diet: feed recognition for milk authenticity.

The presence of plastidial DNA fragments of plant origin in animal milk samples has been confirmed. An experimental plan was arranged with 4 groups of goats, each provided with a different monophytic diet: 3 fresh forages (oats, ryegrass and X-triticosecale) and 1 two week-old silage (X-triticosecale). Feed-derived rubisco (ribulose bisphosphate carboxylase, rbcL) DNA fragments were detected in 100 % of the analyzed goat milk samples and the nucleotide sequence of the PCR amplified fragments was found to be 100 % identical to the corresponding fragments amplified from the plant species consumed in the diet. Two additional chloroplast-based molecular markers were used to set up an assay for distinctiveness, conveniently based on a simple polymerase chain reaction. In one case, differences in single nucleotides occurring within the gene encoding for plant maturase K (matK) were exploited. In the other, plant species recognition was based on the difference in the length of the intron present within the trnL gene. The presence of plastidial plant DNA, ascertained with the PCR-based amplification of the rbcL fragment, was also assessed in raw cow milk samples collected directly from stock farms or taken from milk sold in the commercial market. In this case the nucleotide sequence of the amplified DNA fragments reflected the multiple forages present in the diet fed to the animals

On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family

Background Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant diversity. Results Exploiting one of the most valuable features of TBP, that is the convenient and immediate application of the assay to groups of individuals that may belong to different taxa, we show that the TBP method can successfully discriminate different agricultural species and their crop wild relatives within the Papilionoideae subfamily. Detection of intraspecific variability is demonstrated by the genotyping of 27 different accessions of Phaseolus vulgaris. Conclusions These data illustrate TBP as a useful and versatile tool for plant genotyping. Since its potential has not yet been fully appreciated by the scientific community, we carefully report all the experimental details of a successful TBP protocol, while describing different applications, so that the method can be replicated in other laboratories

Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression

Thyroid cancer is the commonest endocrine malignancy. Mutation in the BRAF serine/threonine kinase is the most frequent genetic alteration in thyroid cancer. Target therapy for advanced and poorly differentiated thyroid carcinomas include BRAF pathway inhibitors. Here, we evaluated the role of MAP3K8 expression as a potential driver of resistance to BRAF inhibition in thyroid cancer. By analyzing Gene Expression Omnibus data repository, across all thyroid cancer histotypes, we found that MAP3K8 is up-regulated in poorly differentiated thyroid carcinomas and its expression is related to a stem cell like phenotype and a poorer prognosis and survival. Taken together these data unravel a novel mechanism for thyroid cancer progression and chemo-resistance and confirm previous results obtained in cultured thyroid cancer stem cellsComment: 5 page

The Inorganic Side of NGF: Copper(II) And Zinc(II) Affect the NGF Mimicking Signalling of the N-Terminus Peptides Encompassing the Recognition Domain of TrkA Receptor

The nerve growth factor (NGF) N-terminus peptide, NGF(1-14), and its acetylated form, Ac-NGF(1-14), were investigated to scrutinise the ability of this neurotrophin domain to mimic the whole protein. Theoretical calculations demonstrated that non-covalent forces assist the molecular recognition of TrkA receptor for both peptides. Combined parallel tempering/docking simulations discriminated the effect of the N-terminal acetylation on the recognition of NGF(1-14) towards the domain 5 of TrkA (TrkA-D5). Experimental findings demonstrated that both NGF(1-14) and Ac-NGF(1-14) activate TrkA signaling pathways essential for neuronal survival. The NGF-induced TrkA internalization was slightly inhibited in the presence of Cu2+ and Zn2+ ions, whereas the metal ions elicited the NGF(1-14)-induced internalization of TrkA and no significant differences were found in the weak Ac-NGF(1-14)-induced receptor internalization. The crucial role of the metals was confirmed by experiments with the metal-chelator bathocuproine disulfonic acid, which discriminated different levels of inhibitory effects in the signalling cascade, due to different metal affinity of NGF, the free amino and the acetylated peptides. The NGF signaling cascade, activated by NGF (1−14) and Ac-NGF(1-14), induced CREB phosphorylation, but the copper addition further stimulated the Akt, ERK and CREB phosphorylation only for NGF and NGF(1-14). A dynamic and quick influx of both peptides into PC12 cells was tracked by live cell imaging with confocal microscopy. A significant role of copper ions was found in the modulation of peptide sub-cellular localization, especially at the nuclear level. Furthermore, a strong copper ionophoric ability of NGF(1-14) was measured. The Ac-NGF(1-14) peptide, which binds copper ions with a lower stability constant than NGF(1-14), exhibited a lower nuclear localization with respect to the total cellular uptake. These findings were correlated to the metal-induced increase of CREB and BDNF expression upon NGF(1-14) stimulation. In summary, we here validate NGF(1-14) and Ac-NGF(1-14) as first examples of monomer and linear peptides able to activate the NGF-TrkA signaling cascade. Metal ions modulate the activity of both NGF protein and the NGF-mimicking peptides. Such findings demonstrate that NGF(1-14) sequence can reproduce the signal transduction of whole protein, therefore represent a very promising drug candidate for further preclinical studies

Correlations between isospin dynamics and Intermediate Mass Fragments emission time scales: a probe for the symmetry energy in asymmetric nuclear matter

We show new data from the $^{64}$Ni+$^{124}$Sn and $^{58}$Ni+$^{112}$Sn reactions studied in direct kinematics with the CHIMERA detector at INFN-LNS and compared with the reverse kinematics reactions at the same incident beam energy (35 A MeV). Analyzing the data with the method of relative velocity correlations, fragments coming from statistical decay of an excited projectile-like (PLF) or target-like (TLF) fragments are discriminated from the ones coming from dynamical emission in the early stages of the reaction. By comparing data of the reverse kinematics experiment with a stochastic mean field (SMF) + GEMINI calculations our results show that observables from neck fragmentation mechanism add valuable constraints on the density dependence of symmetry energy. An indication is found for a moderately stiff symmetry energy potential term of EOS.Comment: Talk given by E. De Filippo at the 11th International Conference on Nucleus-Nucleus Collisions (NN2012), San Antonio, Texas, USA, May 27-June 1, 2012. To appear in the NN2012 Proceedings in Journal of Physics: Conference Series (JPCS

Kinematical coincidence method in transfer reactions

A new method to extract high resolution angular distributions from kinematical coincidence measurements in binary reactions is presented. Kinematic is used to extract the center of mass angular distribution from the measured energy spectrum of light particles. Results obtained in the case of 10Be+p-->9Be+d reaction measured with the CHIMERA detector are shown. An angular resolution of few degrees in the center of mass is obtained.Comment: 6 Page 10 Figures submitted to Nuclear Instruments and Methods

Traceability of Plant Diet Contents in Raw Cow Milk Samples

The use of molecular marker in the dairy sector is gaining large acceptance as a reliable diagnostic approach for food authenticity and traceability. Using a PCR approach, the rbcL marker, a chloroplast-based gene, was selected to amplify plant DNA fragments in raw cow milk samples collected from stock farms or bought on the Italian market. rbcL-specific DNA fragments could be found in total milk, as well as in the skimmed and the cream fractions. When the PCR amplified fragments were sent to sequence, the nucleotide composition of the chromatogram reflected the multiple contents of the polyphytic diet

Testing the IMEter on rice introns and other aspects of intron-mediated enhancement of gene expression

In many eukaryotes, spliceosomal introns are able to influence the level and site of gene expression. The mechanism of this Intron Mediated Enhancement (IME) has not yet been elucidated, but regulation of gene expression is likely to occur at several steps during and after transcription. Different introns have different intrinsic enhancing properties, but the determinants of these differences remain unknown. Recently, an algorithm called IMEter, which is able to predict the IME potential of introns without direct testing, has been proposed. A computer program was developed for Arabidopsis thaliana and rice (Oryza sativa L.), but was only tested experimentally in Arabidopsis by measuring the enhancement effect on GUS expression of different introns inserted within otherwise identical plasmids. To test the IMEter potential in rice, a vector bearing the upstream regulatory sequence of a rice β-tubulin gene (OsTub6) fused to the GUS reporter gene was used. The enhancing intron interrupting the OsTub6 5′-UTR was precisely replaced by seven other introns carrying different features. GUS expression level in transiently transformed rice calli does not significantly correlate with the calculated IMEter score. It was also found that enhanced GUS expression was mainly due to a strong increase in the mRNA steady-state level and that mutations at the splice recognition sites almost completely abolished the enhancing effect. Splicing also appeared to be required for IME in Arabidopsis cell cultures, where failure of the OsTub6 5′ region to drive high level gene expression could be rescued by replacing the poorly spliced rice intron with one from Arabidopsis

Observation of two new Ξb−\Xi_b^- baryon resonances

Two structures are observed close to the kinematic threshold in the $\Xi_b^0 \pi^-$ mass spectrum in a sample of proton-proton collision data, corresponding to an integrated luminosity of 3.0 fb$^{-1}$ recorded by the LHCb experiment. In the quark model, two baryonic resonances with quark content $bds$ are expected in this mass region: the spin-parity $J^P = \frac{1}{2}^+$ and $J^P=\frac{3}{2}^+$ states, denoted $\Xi_b^{\prime -}$ and $\Xi_b^{*-}$. Interpreting the structures as these resonances, we measure the mass differences and the width of the heavier state to be $m(\Xi_b^{\prime -}) - m(\Xi_b^0) - m(\pi^{-}) = 3.653 \pm 0.018 \pm 0.006$ MeV$/c^2$, $m(\Xi_b^{*-}) - m(\Xi_b^0) - m(\pi^{-}) = 23.96 \pm 0.12 \pm 0.06$ MeV$/c^2$, $\Gamma(\Xi_b^{*-}) = 1.65 \pm 0.31 \pm 0.10$ MeV, where the first and second uncertainties are statistical and systematic, respectively. The width of the lighter state is consistent with zero, and we place an upper limit of $\Gamma(\Xi_b^{\prime -}) < 0.08$ MeV at 95% confidence level. Relative production rates of these states are also reported.Comment: 17 pages, 2 figure