Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

Background: The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartments such as nucleus, cytoplasm or organelles. However, many organelles, like mitochondria, have their own internal compartmentalization. Knowing the precise location of a protein inside mitochondria is crucial for its accurate functional characterization. We recently developed DeepMito, a new method based on a 1-Dimensional Convolutional Neural Network (1D-CNN) architecture outperforming other similar approaches available in literature. Results: Here, we explore the adoption of DeepMito for the large-scale annotation of four sub-mitochondrial localizations on mitochondrial proteomes of five different species, including human, mouse, fly, yeast and Arabidopsis thaliana. A significant fraction of the proteins from these organisms lacked experimental information about sub-mitochondrial localization. We adopted DeepMito to fill the gap, providing complete characterization of protein localization at sub-mitochondrial level for each protein of the five proteomes. Moreover, we identified novel mitochondrial proteins fishing on the set of proteins lacking any subcellular localization annotation using available state-of-the-art subcellular localization predictors. We finally performed additional functional characterization of proteins predicted by DeepMito as localized into the four different sub-mitochondrial compartments using both available experimental and predicted GO terms. All data generated in this study were collected into a database called DeepMitoDB (available at http://busca.biocomp.unibo.it/deepmitodb), providing complete functional characterization of 4307 mitochondrial proteins from the five species. Conclusions: DeepMitoDB offers a comprehensive view of mitochondrial proteins, including experimental and predicted fine-grain sub-cellular localization and annotated and predicted functional annotations. The database complements other similar resources providing characterization of new proteins. Furthermore, it is also unique in including localization information at the sub-mitochondrial level. For this reason, we believe that DeepMitoDB can be a valuable resource for mitochondrial research

Observation of the rare decay K_S -> pi^0mu^+mu^-

A search for the decay K_S -> pi^0mu^+mu^- has been made by the NA48/1 Collaboration at the CERN SPS accelerator. The data were collected during 2002 with a high-intensity K_S beam. Six events were found with a background expectation of 0.22^+0.18_-0.11 event. Using a vector matrix element and unit form factor, the measured branching ratio is B(K_S -> pi^0mu^+mu^-)=[2.9^+1.5_-1.2(stat)+/-0.2(syst)]x10^{-9}.Comment: 19 pages, 8 figures, 4 tables. To be published in Physics Letters

First Observation and Measurement of the Decay K+- -> pi+- e+ e- gamma

Using the full data set of the NA48/2 experiment, the decay K+- -> pi+- e+ e- gamma is observed for the first time, selecting 120 candidates with 7.3 +- 1.7 estimated background events. With K+- -> pi+- pi0D as normalisation channel, the branching ratio is determined in a model-independent way to be Br(K+- -> pi+- e+ e- gamma, m_eegamma > 260 MeV/c^2) = (1.19 +- 0.12_stat +- 0.04_syst) x 10^-8. This measured value and the spectrum of the e+ e- gamma invariant mass allow a comparison with predictions of Chiral Perturbation Theory.Comment: 13 pages, 3 figures. Accepted for publication in Phys.Lett.

First observation of the KS->pi0 gamma gamma decay

Using the NA48 detector at the CERN SPS, 31 KS->pi0 gamma gamma candidates with an estimated background of 13.7 +- 3.2 events have been observed. This first observation leads to a branching ratio of BR(KS->pi0 gamma gamma) = (4.9 +- 1.6(stat) +- 0.9(syst)) x 10^-8 in agreement with Chiral Perturbation theory predictions.Comment: 10 pages, 4 figures submitted to Phys. Lett.

Search for CP violation in K0 -> 3 pi0 decays

Using data taken during the year 2000 with the NA48 detector at the CERN SPS, a search for the CP violating decay K_S -> 3 pi0 has been performed. From a fit to the lifetime distribution of about 4.9 million reconstructed K0/K0bar -> 3 pi0 decays, the CP violating amplitude eta_000 = A(K_S -> 3 pi0)/A(K_L -> 3 pi0) has been found to be Re(eta_000) = -0.002 +- 0.011 +- 0.015 and Im(eta_000) = -0.003 +- 0.013 +- 0.017. This corresponds to an upper limit on the branching fraction of Br(K_S -> 3 pi0) < 7.4 x 10^-7 at 90% confidence level. The result is used to improve knowledge of Re(epsilon) and the CPT violating quantity Im(delta) via the Bell-Steinberger relation.Comment: 18 pages, 7 figures, submitted to Phys. Lett.

A precision measurement of direct CP violation in the decay of neutral kaons into two pions

The direct CP violation parameter Re(epsilon'/epsilon) has been measured from the decay rates of neutral kaons into two pions using the NA48 detector at the CERN SPS. The 2001 running period was devoted to collecting additional data under varied conditions compared to earlier years (1997-99). The new data yield the result: Re(epsilon'/epsilon) = (13.7 +/- 3.1) times 10^{-4}. Combining this result with that published from the 1997, 98 and 99 data, an overall value of Re(epsilon'/epsilon) = (14.7 +/- 2.2) times 10^{-4} is obtained from the NA48 experiment.Comment: 19 pages, 5 figures, to be published in Physics Letters

Measurement of the Ratio Gamma(KL -> pi+ pi-)/Gamma(KL -> pi e nu) and Extraction of the CP Violation Parameter |eta+-|

We present a measurement of the ratio of the decay rates Gamma(KL -> pi+ pi-)/Gamma(KL -> pi e nu), denoted as Gamma(K2pi)/Gamma(Ke3). The analysis is based on data taken during a dedicated run in 1999 by the NA48 experiment at the CERN SPS. Using a sample of 47000 K2pi and five million Ke3 decays, we find Gamma(K2pi)/Gamma(Ke3) = (4.835 +- 0.022(stat) +- 0.016(syst)) x 10^-3. From this we derive the branching ratio of the CP violating decay KL -> pi+ pi- and the CP violation parameter |eta+-|. Excluding the CP conserving direct photon emission component KL -> pi+ pi- gamma, we obtain the results BR(KL -> pi+ pi-) = (1.941 +- 0.019) x 10^-3 and |eta+-| = (2.223 +- 0.012) x 10^-3.Comment: 20 pages, 7 figures, accepted by Phys. Lett.

Search for direct CP-violation in K+- --> pi+-pi0pi0 decays

A search for direct CP-violation in K+- --> pi+-pi0pi0 decays based on 47.14 million events has been performed by the NA48/2 experiment at the CERN SPS. The asymmetry in the Dalitz plot linear slopes A_g=(g^+ - g^-)/(g^+ + g^-) is measured to be A_g=(1.8 +- 2.6).10^{-4}. The design of the experiment and the method of analysis provide good control of instrumental charge asymmetries in this measurement. The precision of the result is limited by statistics and is almost one order of magnitude better than that of previous measurements by other experiments.Comment: 14 page

Measurement of K^0_e3 form factors

The semileptonic decay of the neutral K meson, KL -> pi e nu (Ke3), was used to study the strangeness-changing weak interaction of hadrons. A sample of 5.6 million reconstructed events recorded by the NA48 experiment was used to measure the Dalitz plot density. Admitting all possible Lorentz-covariant couplings, the form factors for vector (f_+(q^2)), scalar (f_S) and tensor (f_T) interactions were measured. The linear slope of the vector form factor lambda_+ = 0.0284+-0.0007+-0.0013 and values for the ratios |f_S/f_+(0)| = 0.015^{+0.007}_{-0.010}+-0.012 and |f_T/f_+(0)| = 0.05^{+0.03}_{-0.04}+-0.03 were obtained. The values for f_S and f_T are consistent with zero. Assuming only Vector-Axial vector couplings, lambda_+ = 0.0288+-0.0004+-0.0011 and a good fit consistent with pure V-A couplings were obtained. Alternatively, a fit to a dipole form factor yields a pole mass of M = 859+-18 MeV, consistent with the K^*(892) mass.Comment: 16 pages, 7 figures. submitted to Phys. Lett.

Measurement of the branching ratio of the decay KL -> pi e nu and extraction of the CKM parameter |Vus|

We present a new measurement of the branching ratio R of the decay KL -> pi e nu (Ke3), relative to all charged KL decays with two tracks, based on data taken with the NA48 detector at the CERN SPS. We measure R = 0.4978 +- 0.0035. From this we derive the Ke3 branching fraction and the weak coupling parameter |Vus| in the CKM matrix. We obtain |Vus|f+(0) = 0.2146 +- 0.0016, where f+(0) is the vector form factor in the Ke3 decay.Comment: 18 pages, 8 figures. accepted by Phys Lett.