Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum

Protein-metabolite interactions play an important role in the cell's metabolism and many methods have been developed to screen them in vitro. However, few methods can be applied at a large scale and not alter biological state. Here we describe a proteometabolomic approach, using chromatography to generate cell fractions which are then analyzed with mass spectrometry for both protein and metabolite identification. Integrating the proteomic and metabolomic analyses makes it possible to identify protein-bound metabolites. Applying the concept to the thermophilic fungus Chaetomium thermophilum, we predict 461 likely protein-metabolite interactions, most of them novel. As a proof of principle, we experimentally validate a predicted interaction between the ribosome and isopentenyl adenine

Search for Λc+→pK+π−\Lambda_c^+ \to p K^+ \pi^- and Ds+→K+K+π−D_s^+ \to K^+ K^+ \pi^- Using Genetic Programming Event Selection

We apply a genetic programming technique to search for the double Cabibbo suppressed decays $\Lambda_c^+ \to p K^+ \pi^-$ and $D_s^+ \to K^+ K^+ \pi^-$. We normalize these decays to their Cabibbo favored partners and find $\text{BR}($\Lambda_c^+ \to p K^+ \pi^-$)/\text{BR}($\Lambda_c^+ \to p K^- \pi^+$) = (0.05 \pm 0.26 \pm 0.02)$ and $\text{BR}($D_s^+ \to K^+ K^+ \pi^-$)/\text{BR}($D_s^+ \to K^+ K^- \pi^+$) = (0.52\pm 0.17\pm 0.11)$ where the first errors are statistical and the second are systematic. Expressed as 90% confidence levels (CL), we find $< 0.46$ and $< 0.78$ respectively. This is the first successful use of genetic programming in a high energy physics data analysis.Comment: 10 page

Measurement of the D+ and Ds+ decays into K+K-K+

We present the first clear observation of the doubly Cabibbo suppressed decay D+ --> K-K+K+ and the first observation of the singly Cabibbo suppressed decay Ds+ --> K-K+K+. These signals have been obtained by analyzing the high statistics sample of photoproduced charm particles of the FOCUS(E831) experiment at Fermilab. We measure the following relative branching ratios: Gamma(D+ --> K-K+K+)/Gamma(D+ --> K-pi+pi+) = (9.49 +/- 2.17(statistical) +/- 0.22(systematic))x10^-4 and Gamma(Ds+ --> K-K+K+)/Gamma(Ds+ --> K-K+pi+) = (8.95 +/- 2.12(statistical) +2.24(syst.) -2.31(syst.))x10^-3.Comment: 10 pages, 8 figure

A Non-parametric Approach to the D+ to K*0bar mu+ nu Form Factors

Using a large sample of D+ -> K- pi+ mu+ nu decays collected by the FOCUS photoproduction experiment at Fermilab, we present the first measurements of the helicity basis form factors free from the assumption of spectroscopic pole dominance. We also present the first information on the form factor that controls the s-wave interference discussed in a previous paper by the FOCUS collaboration. We find reasonable agreement with the usual assumption of spectroscopic pole dominance and measured form factor ratios.Comment: 14 pages, 5 figures, and 2 tables. We updated the previous version by changing some words, removing one plot, and adding two tables. These changes are mostly stylisti

Measurements of Ξc+\Xi_c^{+} Branching Ratios

Using data collected by the fixed target Fermilab experiment FOCUS, we measure the branching ratios of the Cabibbo favored decays $\Xi_c^+ \to \Sigma^+K^-\pi^+$, $\Xi_c^+ \to \Sigma^+ \bar{K}^{*}(892)^0$, and $\Xi_c^+ \to \Lambda^0K^-\pi^+\pi^+$ relative to $\Xi_c^+ \to \Xi^-\pi^+\pi^+$ to be $0.91\pm0.11\pm0.04$, $0.78\pm0.16\pm0.06$, and $0.28\pm0.06\pm0.06$, respectively. We report the first observation of the Cabibbo suppressed decay $\Xi_c^+ \to \Sigma^+K^+K^-$ and we measure the branching ratio relative to $\Xi_c^+ \to \Sigma^+K^-\pi^+$ to be $0.16\pm0.06\pm0.01$. We also set 90% confidence level upper limits for $\Xi_c^+ \to \Sigma^+ \phi$ and $\Xi_c^+ \to \Xi^*(1690)^0(\Sigma^+ K^-) K^+$ relative to $\Xi_c^+ \to \Sigma^+K^-\pi^+$ to be 0.12 and 0.05, respectively. We find an indication of the decays $\Xi_c^+ \to \Omega^-K^{+}\pi^+$ and $\Xi_c^+ \to \Sigma^{*}(1385)^+ \bar{K}^0$ and set 90% confidence level upper limits for the branching ratios with respect to $\Xi_c^+ \to \Xi^-\pi^+\pi^+$ to be 0.12 and 1.72, respectively. Finally, we determine the 90% C.L. upper limit for the resonant contribution $\Xi_c^+ \to \Xi^{*}(1530)^0 \pi^+$ relative to $\Xi_c^+ \to \Xi^-\pi^+\pi^+$ to be 0.10.Comment: 14 pages, 8 figure

New Measurements of the D+ to K* mu nu Form Factor Ratios

Using a large sample of D+ to K- pi+ mu+ nu decays collected by the FOCUS photoproduction experiment at Fermilab, we present new measurements of two semileptonic form factor ratios: rv and r2. We find rv = 1.504 \pm 0.057 \pm 0.039 and r2 = 0.875 \pm 0.049 \pm 0.064. Our form factor results include the effects of the s-wave interference discussed in a previous paper.Comment: 12 pages, 5 figure

Study of the D^0 \to pi^-pi^+pi^-pi^+ decay

Using data from the FOCUS (E831) experiment at Fermilab, we present new measurements for the Cabibbo-suppressed decay mode $D^0 \to \pi^-\pi^+\pi^-\pi^+$. We measure the branching ratio $\Gamma(D^0 \to\pi^+\pi^- \pi^+\pi^-)/\Gamma(D^0 \to K^-\pi^+\pi^-\pi^+) = 0.0914 \pm 0.0018 \pm 0.0022$. An amplitude analysis has been performed, a first for this channel, in order to determine the resonant substructure of this decay mode. The dominant component is the decay $D^0 \to a_1(1260)^+ \pi^-$, accounting for 60% of the decay rate. The second most dominant contribution comes from the decay $D^0 \to \rho(770)^0\rho(770)^0$, with a fraction of 25%. We also study the $a_1(1260)$ line shape and resonant substructure. Using the helicity formalism for the angular distribution of the decay $D^0 \to \rho(770)^0\rho(770)^0$, we measure a longitudinal polarization of $P_L = (71 \pm 4\pm 2)$%.Comment: 38 pages, 8 figures. accepted for publication in Physical Review

Study of Hadronic Five-Body Decays of Charmed Mesons

We study the decay of D+ and Ds+ mesons into charged five body final states, and report the discovery of the decay mode D+ -> K+K-Pi+Pi+Pi-, as well as measurements of the decay modes D+ -> K-Pi+Pi+Pi+Pi-, Ds+ -> K+K-Pi+Pi+Pi-, Ds+ -> PhiPi+Pi+Pi- and D+/Ds+ -> Pi+Pi+Pi+Pi-Pi-. An analysis of the resonant substructure is also included, with evidence suggesting that both decays proceed primarily through an a1 vector resonance.Comment: 11 pages, 3 figure

Dalitz plot analysis of D_s+ and D+ decay to pi+pi-pi+ using the K-matrix formalism

FOCUS results from Dalitz plot analysis of D_s+ and D+ to pi+pi-pi+ are presented. The K-matrix formalism is applied to charm decays for the first time to fully exploit the already existing knowledge coming from the light-meson spectroscopy experiments. In particular all the measured dynamics of the S-wave pipi scattering, characterized by broad/overlapping resonances and large non-resonant background, can be properly included. This paper studies the extent to which the K-matrix approach is able to reproduce the observed Dalitz plot and thus help us to understand the underlying dynamics. The results are discussed, along with their possible implications on the controversial nature of the sigma meson.Comment: To be submitted to Phys.Lett.B A misprint corrected in formula

Measurement of the branching ratio of the decay D^0 -> \pi^-\mu^+\nu relative to D^0 -> K^-\mu^+\nu

We present a new measurement of the branching ratio of the Cabibbo suppressed decay D^0\to \pi^-\mu^+\nu relative to the Cabibbo favored decay D^0\to K^-\mu^+\nu and an improved measurement of the ratio |\frac{f_+^{\pi}(0)}{f_+^{K}(0)}|. Our results are 0.074 \pm 0.008 \pm 0.007 for the branching ratio and 0.85 \pm 0.04 \pm 0.04 \pm 0.01 for the form factor ratio, respectively.Comment: 13pages, 3 figure