Compactifying the image of the Abel map

Let $\alpha_X^{\underline d}$ be the Abel map of multidegree $\underline d$ of a singular curve $X$ of genus $g$. We describe the closure of ${\rm Im}\alpha_X^{\underline d}$ inside Caporaso's compactified Jacobian $\bar{P_X^d}$ for irreducible curves, curves of compact type and binary curves

iSPOT: A web tool to infer the interaction specificity of families of protein modules

iSPOT (http://cbm.bio.uniroma2.it/ispot) is a web tool developed to infer the recognition specificity of protein module families; it is based on the SPOT procedure that utilizes information from position-specific contacts, derived from the available domain/ligand complexes of known structure, and experimental interaction data to build a database of residue-residue contact frequencies. iSPOT is available to infer the interaction specificity of PDZ, SH3 and WW domains. For each family of protein domains, iSPOT evaluates the probability of interaction between a query domain of the specified families and an input protein/peptide sequence and makes it possible to search for potential binding partners of a given domain within the SWISS-PROT database. The experimentally derived interaction data utilized to build the PDZ, SH3 and WW databases of residue-residue contact frequencies are also accessible. Here we describe the application to the WW family of protein modules

Geometry of tropical moduli spaces and linkage of graphs

We prove the following "linkage" theorem: two p-regular graphs of the same genus can be obtained from one another by a finite alternating sequence of one-edge-contractions; moreover this preserves 3-edge-connectivity. We use the linkage theorem to prove that various moduli spaces of tropical curves are connected through codimension one.Comment: Final version incorporating the referees correction

On the tropical Torelli map

AbstractWe construct the moduli spaces of tropical curves and tropical principally polarized abelian varieties, working in the category of (what we call) stacky fans. We define the tropical Torelli map between these two moduli spaces and we study the fibers (tropical Torelli theorem) and the image of this map (tropical Schottky problem). Finally we determine the image of the planar tropical curves via the tropical Torelli map and we use it to give a positive answer to a question raised by Namikawa on the compactified classical Torelli map

Alignment of protein structures in the presence of domain motions

Abstract Background Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of domains or subdomains with respect to each other. Such movements can impede the identification of structural equivalences when rigid aligners are used. Results We introduce a new method called RAPIDO (Rapid Alignment of Proteins in terms of Domains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences. Conclusion RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures.</p

iSPOT: A Web Tool for the Analysis and Recognition of Protein Domain Specificity

Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool (accessible at http://cbm.bio.uniroma2.it/iSPOT) developed for the prediction of protein-protein interaction mediated by families of peptide recognition modules. iSPOT accesses a database of position specific residue-residue interaction frequencies for members of the SH3 and PDZ protein domain families. The software utilises this database to provide a score for any potential domain peptide interaction

Development of Computational Tools for the Inference of Protein Interaction Specificity Rules and Functional Annotation Using Structural Information

Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry). Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods

Levels of vibration transmitted to the operator of the tractor equipped with front axle suspension

In recent years the comfort and the preservation of the health of the operators became central issues in the evolution of agricultural machinery and led to the introduction of devices aimed at improving working conditions. Thereby, for instance, the presence of air conditioner, soundproof cab and driver seat suspension became normal on agricultural tractors. The vibrations are one of the most complex issues to deal with, being determined by the characteristics and interaction of elements such as tyres, axles, mainframe, cab and seat suspension. In this respect, manufacturers are trying to improve their products, even integrating these elements with new devices such as the suspension on the front axle of the tractor, aimed at reducing the level of vibrations during the transfers at high speed. One of these underwent tests at CRA-ING. Since its purpose is to reduce the level of vibration transmitted to the driver, their measurements in different points of the tractor and in different operating conditions, were compared in order to evaluate the effectiveness of the device, expressed as time of exposure. The suspension system of the front axle is designed to absorb the oscillations (especially pitching) determined by irregularities in the road surface, allowing an increased control of the vehicle at high speed, as demonstrated by the test results and confirmed by the driving impressions outlined by the operator. The action of the device under these conditions results in an increase of the exposure time, important fact because of the relevance of the road transfer operations of tractors with mounted implements or trailers to tow and of the tendency to increase the speed limit for the road tractors (in Germany were brought to 50 km h–1 for several years). The action just described is less evident with increasing irregularity of the road surface and with the decrease of the travel speed. Nevertheless, in such conditions, the device appears to positively work along the other directions, in particular in the Z-axis, improving the action of the suspension of the driver seat