CatRAPID signature: identification of ribonucleoproteins and RNA-binding regions

Motivation: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ribonucleoproteins based on physico-chemical features instead of sequence similarity searches. The algorithm, trained on human proteins and tested on model organisms, calculates the overall RNA-binding propensity followed by the prediction of RNA-binding regions. catRAPID signature outperforms other algorithms in the identification of RNA-binding proteins and detection of non-classical RNA-binding regions. Results are visualized on a webpage and can be downloaded or forwarded to catRAPID omics for predictions of RNA targets

ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

SUMMARY: Here we introduce ccSOL omics, a webserver for large-scale calculations of protein solubility. Our method allows (i) proteome-wide predictions; (ii) identification of soluble fragments within each sequences; (iii) exhaustive single-point mutation analysis.RESULTS: Using coil/disorder, hydrophobicity, hydrophilicity, β-sheet and α-helix propensities, we built a predictor of protein solubility. Our approach shows an accuracy of 79% on the training set (36 990 Target Track entries). Validation on three independent sets indicates that ccSOL omics discriminates soluble and insoluble proteins with an accuracy of 74% on 31 760 proteins sharing <30% sequence similarity.AVAILABILITY AND IMPLEMENTATION: ccSOL omics can be freely accessed on the web at http://s.tartaglialab.com/page/ccsol_group. Documentation and tutorial are available at http://s.tartaglialab.com/static_files/shared/tutorial_ccsol_omics.html.CONTACT: [email protected] INFORMATION: Supplementary data are available at Bioinformatics online

Patient safety on the press in Italy, a preliminary investigation of the terms and trend

Patient safety is a public concern. In Italy, the wide majority of the citizens (97%) reported that medical errors are an important problem (Eurobarometer 241, 2006), but the proportion of those who reported to have suffered an adverse event (15%) is much below the EU average of 26% (Eurobarometer 3 27, 2010). Then we decided to systematically analyse the terms used on the press to report patient safety incidents and to look at eventual correlations between the trend of terms, catastrophic events occurred, regulations and practices to reduce risks

Malignancies and Biosensors: A Focus on Oral Cancer Detection through Salivary Biomarkers

Oral cancer is among the deadliest types of malignancy due to the late stage at which it is usually diagnosed, leaving the patient with an average five-year survival rate of less than 50%. The booming field of biosensing and point of care diagnostics can, in this regard, play a major role in the early detection of oral cancer. Saliva is gaining interest as an alternative biofluid for non-invasive diagnostics, and many salivary biomarkers of oral cancer have been proposed. While these findings are promising for the application of salivaomics tools in routine practice, studies on larger cohorts are still needed for clinical validation. This review aims to summarize the most recent development in the field of biosensing related to the detection of salivary biomarkers commonly associated with oral cancer. An introduction to oral cancer diagnosis, prognosis and treatment is given to define the clinical problem clearly, then saliva as an alternative biofluid is presented, along with its advantages, disadvantages, and collection procedures. Finally, a brief paragraph on the most promising salivary biomarkers introduces the sensing technologies commonly exploited to detect oral cancer markers in saliva. Hence this review provides a comprehensive overview of both the clinical and technological advantages and challenges associated with oral cancer detection through salivary biomarkers

Long non-coding RNA uc.291 controls epithelial differentiation by interfering with the ACTL6A/BAF complex.

The mechanisms that regulate the switch between epidermal progenitor state and differentiation are not fully understood. Recent findings indicate that the chromatin remodelling BAF complex (Brg1-associated factor complex or SWI/SNF complex) and the transcription factor p63 mutually recruit one another to open chromatin during epidermal differentiation. Here, we identify a long non-coding transcript that includes an ultraconserved element, uc.291, which physically interacts with ACTL6A and modulates chromatin remodelling to allow differentiation. Loss of uc.291 expression, both in primary keratinocytes and in three-dimensional skin equivalents, inhibits differentiation as indicated by epidermal differentiation complex genes down-regulation. ChIP experiments reveal that upon uc.291 depletion, ACTL6A is bound to the differentiation gene promoters and inhibits BAF complex targeting to induce terminal differentiation genes. In the presence of uc.291, the ACTL6A inhibitory effect is released, allowing chromatin changes to promote the expression of differentiation genes. Thus, uc.291 interacts with ACTL6A to modulate chromatin remodelling activity, allowing the transcription of late differentiation genes

A 3D non invasive assessment of the position of the occlusal plane

Introduction. The occlusal plane has a key-role in various dental and medical fields. Several methods have analyzed and measured the relative positions of the occlusal and facial planes; most of these investigations used 2D radiographic exams. Currently, 3D assessments may be performed overlapping CT reconstructions and digitized dental casts, but the method requires ionizing radiations, and it is not applicable in reference studies performed with healthy subjects. The efficacy of these measurements could be improved by a 3D, non invasive approach to the problem. Methods. 20 healthy subjects were selected to have their maxillary dental casts digitized by laser scanning, and their 3D facial soft tissue stereophotogrammetry acquisition merged in a single file. The digital 3D coordinates of three facial (right and left Tragus, Subnasale) and three dental landmarks (inter-incisor, tips of the mesio-vestibular cuspids of right and left first permanent molars), were obtained and exported in a 3D CAD (computed aided design) software for a geometrical analysis. The 3D orientation of the planes, referred to a Cartesian orthogonal reference system, was estimated calculating angular values between the sagittal midlines of the two planes. To evaluate the repeatability of the measurements the protocol was performed independently by two different operators. In total 120 measurements were obtained; descriptive statistics were calculated for each variable. To evaluate the method repeatability mean absolute difference between repeated measurements (MAD), technical error of measurement (REM) and Paired Student’s T tests (P<0.05) were computed. Results. In the frontal and horizontal projections, the occlusal plane resulted nearly parallel to Camper’s plane, with average inclinations of 1.5 (frontal) and 1.9 (horizontal) degrees. In the sagittal projection, the two planes had an average angle of 4.9 degrees, with the occlusal plane more anteriorly inclined than Camper’s plane. For all three projections, a fair inter-operator repeatability was found, with all MADs and TEMs slightly lower than 2 degrees. No systematic errors between repeated measurements were found (T test > 0.05). Conclusions. The current non-invasive method resulted appropriate to the aims. Camper’s and occlusal planes resulted almost parallel in the frontal and horizontal projections, while in the sagittal projection the occlusal plane was 5 degrees more anteriorly inclined than Camper’s plane

Intra-varietal variability of Romanesco variety (Vitis vinifera L.)

Most historical sources that describe the presence of Romanesco variety in vine-growing areas of Lazio Region (Italy) highlighted the variability of morphological traits within the variety. This partly justifies the presence of different synonyms, true or presumed, reported by many authors for this grape variety. With the aim of analysing this variability, eight accessions related to the variety, collected in Lazio Region and grown in the DAFNE grape germplasm collection, have been characterized over five productive seasons. The ampelographic description was carried out using 50 OIV morphological descriptors and ampelometric analyses were carried out on mature leaves by SuperAmpelo software. The DNA of the different accessions, extracted from young leaves, was analyzed using 14 microsatellite loci. Furthermore, at harvest, the grapes of each accession were sampled to assess main compositive characteristics. Results showed differences among accessions on some ampelographic descriptors of the mature leaf, of the bunch, and on phenological stages. Microsatellite profiles allowed for classification of the accessions into three distinct groups. Qualitative analysis of the berry skin showed differences among accessions in the content of the main classes of phenolic compounds