Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton

Background  

The genesis of the eukaryotes was a pivotal event in evolution and was accompanied by the acquisition of numerous new cellular features including compartmentalization by cytoplasmic organelles, mitosis and meiosis, and ciliary motility. Essential for the development of these features was the tubulin cytoskeleton and associated motors. It is therefore possible to map ancient cell evolution by reconstructing the evolutionary history of motor proteins. Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA).     

Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy

Background  

Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.     

Nitrogenase activity in composting horse bedding and leaves

To date little or no nitrogen fixation has been found in composting materials. However, some materials have high C:N ratios and thus might be expected to support nitrogen fixation. We examined windrows of composting horse bedding and leaves for nitrogenase activity via acetylene reduction and used carbon monoxide controls to differentiate ethylene evolved by nitrogenase from that evolved by endogenous processes. In both piles temperatures were substantially elevated and partial pressures of oxygen greatly reduced thus indicating vigorous microbial activity. In the horse bedding, there were only low rates of ethylene evolution and little of this was due to nitrogen fixation. In contrast, much higher rates of ethylene evolution were measured in the leaf pile and 94% of this was due to nitrogenase activity. We estimate that the leaf pile fixed approximately 0.062 mg N/g leaves during a 5-week period.