N-Terminal myristoylation predictions by ensembles of neural networks

N-terminal myristoylation is a post-translational modification that causes the addition of a myristate to a glycine in the N-terminal end of the amino acid chain. This work presents neural network (NN) models that learn to discriminate myristoylated and nonmyristoylated proteins. Ensembles of 25 NNs and decision trees were trained on 390 positive sequences and 327 negative sequences. Experiments showed that NN ensembles were more accurate than decision tree ensembles. Our NN predictor evaluated by the leave-one-out procedure, obtained a false positive error rate equal to 2.1%. That was better than the PROSITE pattern for myristoylation for which the false positive error rate was 22.3%. On a recent version of Swiss-Prot (41.2), the NN ensemble predicted 876 myristoylated proteins, while 1150 proteins were predicted by the PROSITE pattern for myristoylation. Finally, compared to the well-known NMT predictor, the NN predictor gave similar results. Our tool is available under http://www.expasy.org/tools/myristoylator/myristoylator.html.     

Economic Impact of Gene Expression Profiling in Patients with Early-Stage Breast Cancer in France

Background and Aims

The heterogeneous nature of breast cancer can make decisions on adjuvant chemotherapy following surgical resection challenging. Oncotype DX is a validated gene expression profiling test that predicts the likelihood of adjuvant chemotherapy benefit in early-stage breast cancer. The aim of this study is to determine the costs of chemotherapy in private hospitals in France, and evaluate the cost-effectiveness of Oncotype DX from national insurance and societal perspectives.

Methods

A multicenter study was conducted in seven French private hospitals, capturing retrospective data from 106 patient files. Cost estimates were used in conjunction with a published Markov model to assess the cost-effectiveness of using Oncotype DX to inform chemotherapy decision making versus standard care. Sensitivity analyses were performed.

Results

The cost of adjuvant chemotherapy in private hospitals was estimated at EUR 8,218 per patient from a national insurance perspective and EUR 10,305 from a societal perspective. Cost-effectiveness analysis indicated that introducing Oncotype DX improved life expectancy (+0.18 years) and quality-adjusted life expectancy (+0.17 QALYs) versus standard care. Oncotype DX was found cost-effective from a national insurance perspective (EUR 2,134 per QALY gained) and cost saving from a societal perspective versus standard care. Inclusion of lost productivity costs in the modeling analysis meant that costs for eligible patients undergoing Oncotype DX testing were on average EUR 602 lower than costs for those receiving standard care.

Conclusions

As Oncotype DX was found both cost and life-saving from a societal perspective, the test was considered to be dominant to standard care. However, the delay in coverage has the potential to erode the quality of the French healthcare system, thus depriving patients of technologies that could improve clinical outcomes and allow healthcare professionals to better allocate hospital resources to improve the standard of care for all patients.     

Beta,but Not Gamma,Band Oscillations Index Visual Form-Motion Integration

Electrophysiological oscillations in different frequency bands co-occur with perceptual, motor and cognitive processes but their function and respective contributions to these processes need further investigations. Here, we recorded MEG signals and seek for percept related modulations of alpha, beta and gamma band activity during a perceptual form/motion integration task. Participants reported their bound or unbound perception of ambiguously moving displays that could either be seen as a whole square-like shape moving along a Lissajou''s figure (bound percept) or as pairs of bars oscillating independently along cardinal axes (unbound percept). We found that beta (15–25 Hz), but not gamma (55–85 Hz) oscillations, index perceptual states at the individual and group level. The gamma band activity found in the occipital lobe, although significantly higher during visual stimulation than during base line, is similar in all perceptual states. Similarly, decreased alpha activity during visual stimulation is not different for the different percepts. Trial-by-trial classification of perceptual reports based on beta band oscillations was significant in most observers, further supporting the view that modulation of beta power reliably index perceptual integration of form/motion stimuli, even at the individual level.     

New data on the Dyrosauridae (Crocodylomorpha) from the Paleocene of Togo

Following our fieldwork in Paleogene deposits of Togo, we herein report cranial as well as postcranial elements belonging to the family Dyrosauridae. This assemblage is dated to the Late Paleocene (Thanetian) from two quarries in southern Togo. The specimens include a partial skull presenting two large supratemporal fossae and a massive occipital condyle; long and slender isolated teeth; amphicoelous vertebrae including several articulated ones; and two osteoderms devoid of carina. The morphology of the partial skull reveals similarities with some African longirostrine forms such as Rhabdognathus spp., although this attribution cannot be confirmed. Longirostrine forms, known in the late Paleocene and early Eocene of the Iullemmeden basin (Nigeria, Niger, Mali, Algeria) and in the phosphates of Morocco and Tunisia, is only represented in Thanetian levels in Togo. Different palaeoenvironmental settings seem to have characterized the various African basins during the lower Eocene, with consequences for the geographic distribution of dyrosaurids. These dyrosaurid remains confirm the presence of the family in Togo during the Paleocene and underline the fossiliferous potential of the coastal sedimentary basin in Togo and in the bay of Benin.     

From interfacial ring-opening polymerization to melt processing of cellulose nanowhisker-filled polylactide-based nanocomposites

In the present work, cellulose nanowhiskers (CNWs), extracted from ramie fibers, were incorporated in polylactide (PLA)-based composites. Prior to the blending, PLA chains were chemically grafted on the surface of CNW to enhance the compatibilization between CNW and the hydrophobic polyester matrix. Ring-opening polymerization of l-lactide was initiated from the hydroxyl groups available at the CNW surface to yield CNW-g-PLA nanohybrids. PLA-based nanocomposites were prepared by melt blending to ensure a green concept of the study thereby limiting the use of organic solvents. The influence of PLA-grafted cellulose nanoparticles on the mechanical and thermal properties of the ensuing nanocomposites was deeply investigated. The thermal behavior and mechanical properties of the nanocomposites were determined using differential scanning calorimetry (DSC) and dynamical mechanical and thermal analysis (DMTA), respectively. It was clearly evidenced that the chemical grafting of CNW enhances their compatibility with the polymeric matrix and thus improves the final properties of the nanocomposites. Large modification of the crystalline properties such as the crystallization half-time was evidenced according to the nature of the PLA matrix and the content of nanofillers.     

Prognostic Value of PLAGL1-Specific CpG Site Methylation in Soft-Tissue Sarcomas

Soft tissue sarcomas (STS) are rare, complex tumors with a poor prognosis. The identification of new prognostic biomarkers is needed to improve patient management. Our aim was to determine the methylation status of the 118 CpG sites in the PLAGL1 tumor-suppressor gene P1 CpG island promoter and study the potential prognostic impact of PLAGL1 promoter methylation CpG sites in STS. Training cohorts constituted of 28 undifferentiated sarcomas (US) and 35 leiomyosarcomas (LMS) were studied. PLAGL1 mRNA expression was investigated by microarray analysis and validated by RT-qPCR. Pyrosequencing was used to analyze quantitative methylation of the PLAGL1 promoter. Associations between global promoter or specific CpG site methylation and mRNA expression were evaluated using Pearson’s product moment correlation coefficient. Cox univariate and multivariate proportional hazard models were used to assess the predictive power of CpG site methylation status. Sixteen CpG sites associated with PLAGL1 mRNA expression were identified in US and 6 in LMS. Statistical analyses revealed an association between CpG107 methylation status and both overall and metastasis-free survival in US, which was confirmed in a validation cohort of 37 US. The exhaustive study of P1 PLAGL1 promoter methylation identified a specific CpG site methylation correlated with mRNA expression, which was predictive for both metastasis-free and overall survival and may constitute the first US-specific biomarker. Such a biomarker may be relevant for identifying patients likely to derive greater benefit from treatment.     

Calmodulin antagonizes a calcium-activated SCF ubiquitin E3 ligase subunit, FBXL2, to regulate surfactant homeostasis

Calmodulin is a universal calcium-sensing protein that has pleiotropic effects. Here we show that calmodulin inhibits a new SCF (Skp1-Cullin-F-box) E3 ligase component, FBXL2. During Pseudomonas aeruginosa infection, SCF (FBXL2) targets the key enzyme, CCTα, for its monoubiquitination and degradation, thereby reducing synthesis of the indispensable membrane and surfactant component, phosphatidylcholine. P. aeruginosa triggers calcium influx and calcium-dependent activation of FBXL2 within the Golgi complex, where it engages CCTα. FBXL2 through its C terminus binds to the CCTα IQ motif. FBXL2 knockdown increases CCTα levels and phospholipid synthesis. The molecular interaction of FBXL2 with CCTα is opposed by calmodulin, which traffics to the Golgi complex, binds FBXL2 (residues 80 to 90) via its C terminus, and vies with the ligase for occupancy within the IQ motif. These observations were recapitulated in murine models of P. aeruginosa-induced surfactant deficiency, where calmodulin gene transfer reduced FBXL2 actions by stabilizing CCTα and lessening the severity of inflammatory lung injury. The results provide a unique model of calcium-regulated intermolecular competition between an E3 ligase subunit and an antagonist that is critically relevant to pneumonia and lipid homeostasis.