An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge.

14: Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al. , (2013), BMC Bioinformatics , (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al ., Nucleic Acids Res. 2016; , D385-D395) Rhea-a database of enzyme-catalysed reactions (Morgat, A., et al .,  Nucleic Acids Res.  2015; , D459-D464), Reactome-a database of biochemical pathways (Fabregat, A., et al ., Nucleic Acids Res. 2016;  , D481-D487), IntEnz-a resource with enzyme nomenclature information (Fleischmann, A., et al ., Nucleic Acids Res.  2004 , D434-D437) and ChEBI (Hastings, J., et al .,  Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al ., Nucleic Acids Res.  2014 , 1083-1090)-resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration.

Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants.

The formation of viscous foams on aeration basins and secondary clarifiers of activated sludge plants is a common and widespread problem. Foam formation is often attributed to the presence of mycolic acid-containing actinomycetes (mycolata). In order to examine the relationship between the number of mycolata and foam, we developed a group-specific probe targeting the 16S rRNA of the mycolata, a protocol to permeabilize mycolata, and a statistically robust quantification method. Statistical analyses showed that a lipase-based permeabilization method was quantitatively superior to previously described methods (P << 0.05). When mixed liquor and foam samples were examined, most of the mycolata present were rods or cocci, although filamentous mycolata were also observed. A nested analysis of variance showed that virtually all of the measured variance occurred between fields of view and not between samples. On this basis we determined that as few as five fields of view could be used to give a statistically meaningful sample. Quantitative fluorescent in situ hybridization (FISH) was used to examine the relationship between foaming and the concentration of mycolata in a 20-m(3) completely mixed activated sludge plant. Foaming occurred when the number of mycolata exceeded a certain threshold value. Baffling of the plant affected foaming without affecting the number of mycolata. We tentatively estimated that the threshold foaming concentration of mycolata was about 2 x 10(6) cells ml(-1) or 4 x 10(12) cells m(-2). We concluded that quantitative use of FISH is feasible and that quantification is a prerequisite for rational investigation of foaming in activated sludge.

Some unusual high speed responses to electrical stimulation in Nitella with microscopic observations of electromagnetically induced changes in the cytoplasm.

Nitella flexilis living in Surrey ponds shows an unusual response to external electrical stimulation. This response is shorter (250 milliseconds) than the normal response (5 seconds), nor does it seem to obey the all-or-none law; decreasing the level of stimulus introduces a delay in its appearance. Microelectrode studies suggest that this response though propagated down the length of the cell is a surface phenomenon as compared to the normal response which is generated across the membrane. Normasky interference microscopic observation of the cytoplasm of those cells exhibiting this response shows large vesicles whose contents rotate, as opposed to those cells showing a normal response which do not show these vesicles. This response is associated with local extinction of groups of Nitella flexilis from ponds in Surrey and a temporary reduction in numbers in certain areas of the New Forest. Electrical excitation itself induces vesicle formation and its associated response in Nitella flexilis, and to a far lesser degree in Nitella translucens. In Nitella translucens alternating electromagnetic fields of low strength induce the formation of vesicles whose contents actively rotate in some individual cells. These vesicles are always accompanied by distortions in electrical response to stimulation. In its response to electromagnetic fields, Nitella translucens is very variable. Nitella opaca exhibits the same response as Nitella flexilis including the same fragility of survival. Electrical studies may throw light on the contentious problem as to whether Nitella opaca is in reality a separate species from Nitella flexilis.