pdbFun: mass selection and fast comparison of annotated PDB residues

pdbFun () is a web server for structural and functional analysis of proteins at the residue level. pdbFun gives fast access to the whole Protein Data Bank (PDB) organized as a database of annotated residues. The available data (features) range from solvent exposure to ligand binding ability, location in a protein cavity, secondary structure, residue type, sequence functional pattern, protein domain and catalytic activity. Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches. For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a dataset composed of many structures. The output is a list of aligned structural matches offered in tabular and also graphical format

SH3-Hunter: discovery of SH3 domain interaction sites in proteins

SH3-Hunter (http://cbm.bio.uniroma2.it/SH3-Hunter/) is a web server for the recognition of putative SH3 domain interaction sites on protein sequences. Given an input query consisting of one or more protein sequences, the server identifies peptides containing poly-proline binding motifs and associates them to a list of SH3 domains, in order to compose peptide–domain pairs. The server can accept a list of peptides and allows users to upload an input file in a proper format. An accurate selection of SH3 domains is available and users can also submit their own SH3 domain sequence

3dLOGO:a web server for the identification, analysis and use of conserved protein substructures

3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it

VirusMINT: a viral protein interaction database

Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network. The VirusMINT database (http://mint.bio.uniroma2.it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature. VirusMINT currently stores over 5000 interactions involving more than 490 unique viral proteins from more than 110 different viral strains. The whole data set can be easily queried through the search pages and the results can be displayed with a graphical viewer. The curation effort has focused on manuscripts reporting interactions between human proteins and proteins encoded by some of the most medically relevant viruses: papilloma viruses, human immunodeficiency virus 1, Epstein–Barr virus, hepatitis B virus, hepatitis C virus, herpes viruses and Simian virus 40

Inattività fisica tra società (post)moderna e stile di vita

Today’s society is characterized by inter-human relations network increasinglyglobalized; rapid transformation of everyday life dictated by new technologies;productivity and trade continues to increase. Everything generates a educationaldistance between generations whit the result of adults against the growing subjects.The latter are increasingly victims of consumerism and technology, withoutmaking movement, physical activity, sports. Consequently, society, perhaps because responsible for all this, finally wonders about issues related to such behaviors, as a result, produce physical inactivity, laziness, lack of exercise, overweight and obesity whit all associated pathological complications.La società odierna è caratterizzata da rete di rapporti interumani sempre più globalizzata;rapidità di trasformazione della vita quotidiana dettata dalle nuove tecnologie;produttività e scambi commerciali in continuo aumento. Tutto ciò generauna distanza pedagogico-educativa tra le generazioni con la conseguenza di disattenzionedegli adulti nei confronti dei soggetti in crescita. Questi ultimi risultanosempre più vittime del consumismo e della tecnologia, senza più praticare movimento,attività motoria, sport. Di conseguenza, la società, forse perché responsabiledi tutto questo, finalmente s’interroga su problematiche relative a tali comportamentiche, come esito, producono inattività fisica, pigrizia, sedentarietà,sovrappeso e obesità con tutte le complicanze patologiche connesse

Three-axial Fiber Bragg Grating Strain Sensor for Volcano Monitoring

Fiber optic and FBGs sensors have attained a large diffusion in the last years as cost-effective monitoring and diagnostic devices in civil engineering. However, in spite of their potential impact, these instruments have found very limited application in geophysics. In order to study earthquakes and volcanoes, the measurement of crustal deformation is of crucial importance. Stress and strain behaviour is among the best indicators of changes in the activity of volcanoes .. Deep bore-hole dilatometers and strainmeters have been employed for volcano monitoring. These instruments are very sensitive and reliable, but are not cost-effective and their installation requires a large effort. Fiber optic based devices offer low cost, small size, wide frequency band, easier deployment and even the possibility of creating a local network with several sensors linked in an array. We present the realization, installation and first results of a shallow-borehole (8,5 meters depth) three-axial Fiber Bragg Grating (FBG) strain sensor prototype. This sensor has been developed in the framework of the MED-SUV project and installed on Etna volcano, in the facilities of the Serra La Nave astrophysical observatory. The installation siteis about 7 Km South-West of the summit craters, at an elevation of about 1740 m. The main goal of our work is the realization of a three-axial device having a high resolution and accuracy in static and dynamic strain measurements, with special attention to the trade-off among resolution, cost and power consumption. The sensor structure and its read-out system are innovative and offer practical advantages in comparison with traditional strain meters. Here we present data collected during the first five months of operation. In particular, the very clear signals recorded in the occurrence of the Central Italy seismic event of October 30th demonstrate the performances of our device.PublishedWien7TM. Sviluppo e Trasferimento Tecnologic

Maquete tátil: explorando a paisagem por outro sentido

O projeto das maquetes táteis, desenvolvido na disciplina de Geomorfologia da PUC-Rio, nasceu da necessidade de ensinar geomorfologia para uma aluna DV que não é capaz de observar a paisagem por meio da visão e necessita de mecanismos que a auxiliem a entender a paisagem por meio de outro sentido. Para a compreensão do relevo e da sua dinâmica foram usados materiais de diferentes texturas, cada um representando um elemento geomorfológico da maquete, com o objetivo de fazer a aluna “enxergar”, através do tato, o funcionamento da encosta e os processos geomorfológicos envolvidos. As maquetes foram feitas sem muitos detalhes e com texturas bastante diversas, para proporcionar a distinção dos elementos com o toque. Espera-se que o contato com a maquete desenvolvida possibilite a abstração da aluna para a compreensão de outras paisagens

The ability of lumbar spine DXA and phalanx QUS to detect previous fractures in young thalassemic patients with hypogonadism, hypothyroidism, diabetes, and hepatitis-B: A 2-year subgroup analysis from the Taranto Area of Apulia Region.

BACKGROUND: Osteoporosis is a leading cause of morbidity in patients affected by β-thalassemia major or intermediate; we aimed to assess the association between demineralization observed in young thalassemic patients. METHODS: A total of 88 patients with β-thalassemia were recruited at Microcitemia Center of Taranto Hospital under the Prevention Osteoporosis and Fractures research project from 2008 to 2010. All the patients were screened with both dual energy x-ray absorptiometry (DXA) and quantitative ultrasound (QUS). T score and Z score values were obtained for each subject. RESULTS: The overall prevalence of demineralization was 84% with DXA and 70% with QUS, whereas normality was found in 16% of patients screened with DXA and in 30% of cases with QUS. Hypogonadism, hypothyroidism, diabetes mellitus, hepatitis-B, and the presence of previous fragility fractures were significantly associated with the demineralization status (lower T scores values) both with DXA and QUS. CONCLUSION: Our data confirm that DXA and QUS examinations are both useful for detecting bone demineralization in thalassemic patients

MINT, the molecular interaction database: 2009 update

MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals. Since its last report, MINT has grown considerably in size and evolved in scope to meet the requirements of its users. The main changes include a more precise definition of the curation policy and the development of an enhanced and user-friendly interface to facilitate the analysis of the ever-growing interaction dataset. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium