The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists

Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools

Solid-liquid separation of animal slurry in theory and practice: a review

International audienceAnimal slurry contains plant nutrients that are essential for crop production. However, intensive livestock production may lead to a surplus of plant nutrients on farms and, as a consequence, discharge or emission to the environment. In order to ensure that the slurry applied to fields matches the nutrient requirements of the crops, techniques have been developed to reduce the nutrient content of slurry by means of separation. This review discusses the separation technologies used for animal slurry treatment and the physical and chemical processes involved in separation. These processes need to be understood before efficient, reliable and cheap separation technologies that take into account the actual properties of slurry and the likely end-use of the separation products can be developed. A simple separation efficiency expression can be used to assess the efficiency of slurry separation. It is indeed important to measure the amount and composition of the slurry before treatment, the dry-matter-rich fraction and the liquid fraction. The separation efficiency of mechanical separators for the removal of dry matter and phosphorus (P) is ranked as follows: centrifugation > sedimentation > non-pressurized filtration > pressurized filtration. In general, the separation of total N and $\rm NH_{4}^{+}$ follows the same pattern, but the separation efficiency is lower than for dry matter and P. Treatment with a flocculant before separation improves separation efficiency significantly. Of the polyacrylamide polymers tested, high-molecular-weight, linear cationic polymers with a medium charge density (20-40 mol%) were found to be the most efficient flocculants. The best mechanical separation techniques for flocculated slurry are screens or filter belts. The separation efficiency of polyacrylamide-treated slurry can be improved by adding a multivalent ion to coagulate particles and for precipitation of phosphorus. Aluminium sulfate (Al2(SO4)3) or ferric chloride (FeCl3) seem to be very efficient for improving the mechanical separators. Alternatively, the mineral struvite (MgNH4PO4) may be formed by changing the slurry characteristics, such as by the addition of magnesium (Mg) or by increasing the pH to 9. The struvite crystals are removed during solid-liquid separation. The products of the solid-liquid separation may be further treated by evaporation, membrane filtration or ammonia stripping in order to obtain the desired end-products; however, low-maintenance and/or cost-efficient operation of these post-treatments has not yet been demonstrated. The separation should be developed as a whole-system approach, paying attention to parameters such as the value of end-products, environmental consequences and economy