Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways.

Mediterranean rivers are characterized by the irregularity of flow, harsh hydrological fluctuations and a profound transformation as the result of human activity. In this study, we investigate the streamflow response of a Mediterranean temporary river in which different groundwater, agriculture and urban contributions play an important role. Streamflow was measured at three nested gauging stations installed along Na Borges River, a lowland agricultural catchment (319 km²) on the island of Mallorca. Based on two hydrological years (2004/05 and 2005/06), potential evapotranspiration and surface water–groundwater interaction generated a succession of four different hydrological periods playing an important role in baseflow dynamics. The runoff coefficients were very low (<5%). At the event scale, groundwater also controlled runoff response, being very different according to hydrogeology, antecedent conditions and human impacts. During dry seasons, wastewater and karstic spring discharges maintain an influent regime into some streams. As a result, intense rainstorms in late summer generated water volumes over the impervious urban surfaces involved, with the result that quickflow was significant because the hydrological pathways were active. Citation Estrany, J., Garcia, C. & Alberich, R. ( 2010 Estrany, J. , Garcia, C. and Batalla, R. J. 2010. Hydrological response of a small Mediterranean agricultural catchment. J. Hydrol., 380(1-2): 180–190. doi:10.1016/j.jhydrol.2009.10.035 [Crossref] [Google Scholar] ) Streamflow dynamics in a Mediterranean temporary river. Hydrol. Sci. J. 55(5), 717–736. View all notes

One of the most difficult problems difficult problem in systems biology is to discover protein-protein interactions as well as their associated functions. The analysis and alignment of protein-protein interaction networks (PPIN), which are the standard model to describe protein-protein interactions, has become a key ingredient to obtain functional orthologs as well as evolutionary conserved pathways and protein complexes. Several methods have been proposed to solve the PPIN alignment problem, aimed to match conserved subnetworks or functionally related proteins. However, the right balance between considering network topology and biological information is one of the most difficult and key points in any PPIN alignment algorithm which, unfortunately, remains unsolved. Therefore, in this work, we propose AligNet, a new method and software tool for the pairwise global alignment of PPIN that produces biologically meaningful alignments and more efficient computations than state-of-the-art methods and tools, by achieving a good balance between structural matching and protein function conservation as well as reasonable running times.

When a researcher uses a program to align two proteins and gets a score, one of her main concerns is how often the program gives a similar score to pairs that are or are not in the same fold. This issue was analysed in detail recently for the program TM-align with its associated TM-score. It was shown that because the TM-score is length independent, it allows a P-value and a hit probability to be defined depending only on the score. Also, it was found that the TM-scores of gapless alignments closely follow an Extreme Value Distribution (EVD). The program ProtDeform for structural protein alignment was developed recently and is characterised by the ability to propose different transformations of different protein regions. Our goal is to analyse its associated score to allow a researcher to have objective reasons to prefer one aligner over another, and carry out a better interpretation of the output. The study on the ProtDeform score reveals that it is length independent in a wider score range than TM-scores and that PD-scores of gapless (random) alignments also approximately follow an EVD. On the CASP8 predictions, PD-scores and TM-scores, with respect to native structures, are highly correlated (0.95), and show that around a fifth of the predictions have a quality as low as 99.5% of the random scores. Using the Gold Standard benchmark, ProtDeform has lower probabilities of error than TM-align both at a similar speed. The analysis is extended to homology discrimination showing that, again, ProtDeform offers higher hit probabilities than TM-align. Finally, we suggest using three different P-values according to the three different contexts: Gapless alignments, optimised alignments for fold discrimination and that for superfamily discrimination. In conclusion, PD-scores are at the very least as valuable for prediction scoring as TM-scores, and on the protein classification problem, even more reliable.