H . H EI N ON EN -TA NS K I, E. M . N IS K AN EN , P. SA L ME LA A ND E. L AN KI . 1998. Cattle and other animals infected by Salmonella can emit high numbers of these bacteria. To determine an effective means for reducing this bacterial group in animal slurry, samples were subjected to aeration in laboratory experiments and in farm-scale slurry tanks. A clear reduction in Salmonella levels was found in laboratory experiments at temperatures from 4 to 40°C. Aeration in farm-scale slurry tanks increased the temperature above the ambient temperatures (often less than 0°C) to maxima ranging between 19 and 40°C. Farm-scale aeration resulted in similar reductions in Salmonella as those achieved in laboratory experiments. Thus, reductions, ranging from greater than 99% of the initial number to no detectable Salmonella, could be reached after 2-5 weeks using aeration processes with cattle slurries contaminated by Salm. infantis or pig slurry contaminated by Salm. typhimurium. These results suggest that farmers can control the spread of Salmonella from slurry to agricultural fields. The reduction mechanisms remain unknown, though the increase in pH (to 7·6-9·0) found in slurries after aeration might exert a decreasing effect on these bacteria.

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BackgroundGraph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular network analysis platforms, such as Cytoscape, it remains poorly understood how well their solutions reflect the underlying biological processes that give rise to the network connectivity structure. Moreover, visualizations obtained using conventional layout algorithms, such as those based on the force-directed drawing approach, may become uninformative when applied to larger networks with dense or clustered connectivity structure.MethodsWe implemented a modified layout plug-in, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks. Using a wide variety of real life biological networks, we carried out a systematic evaluation of the method in comparison with other layout algorithms in Cytoscape.ResultsThe multilevel approach provided both biologically relevant and visually pleasant layout solutions in most network types, hence complementing the layout options available in Cytoscape. In particular, it could improve drawing of large-scale networks of yeast genetic interactions and human physical interactions. In more general terms, the biological evaluation framework developed here enables one to assess the layout solutions from any existing or future graph drawing algorithm as well as to optimize their performance for a given network type or structure.ConclusionsBy making use of the multilevel modular organization when visualizing biological networks, together with the biological evaluation of the layout solutions, one can generate convenient visualizations for many network biology applications.