Biology subjects

Richardson, J. S.

Publications and source records attributed to Richardson, J. S..

2 recordsLinked to original sources

bioRxiv2018

Priming of leaf litter decomposition by algae seems of minor importance in natural streams during autumn

Allochthonous detritus from terrestrial origin is one of the main energy sources in forested headwater streams, but its poor nutritional quality makes it difficult to use by heterotrophs. It has been suggested that algae growing on this detritus can enhance its nutritional quality and promote decomposition. So far, most evidence of this \"priming\" effect is derived from laboratory or mesocosm experiments, and it is unclear what its importance is under natural conditions. We measured accrual of algae, phosphorus uptake capacity, and decomposition of poplar leaves in autumn in open- and closed-canopy reaches in 3 forest and 3 agricultural streams. Chlorophyll a abundance did not change significantly neither with stream type nor with canopy cover, although some between open and closed reaches, although in some agricultural streams it was higher in open than in closed canopy reaches. Canopy cover did not affect either phosphate uptake capacity or microbial decomposition. On the other hand, although there was no effect of canopy cover on invertebrate fragmentation rate, a significant interaction between canopy cover and stream suggests priming occurs at least in some streams. Overall, the results point to a weak effect of algae on litter decomposition in natural streams during autumn.

ecology↗

bioRxiv2018

Cis-nonPro Peptides: Genuine Occurrences and their Functional Roles

While cis peptides preceding proline can occur about 5% of the time, cis peptides preceding any other residue ("cis-nonPro" peptides) are an extremely rare feature in protein structures, of considerable importance for two opposite reasons. On one hand, their genuine occurrences are mostly found at sites critical to biological function, from the active sites of carbohydrate enzymes to rare adjacent-residue disulfide bonds. On the other hand, a cis-nonPro can easily be misfit into weak or ambiguous electron density, which led to a high incidence of unjustified cis-nonPro over the 2006-2015 decade. This paper uses high-resolution crystallographic data and especially stringent quality-filtering at the residue level to identify genuine occurrences of cis-nonPro, and to survey both individual examples and broad patterns of their functionality. We explain the procedure developed to identify genuine cis-nonPro examples with almost no false positives. We then survey a large sample of the varied functional roles and structural contexts of cis-nonPro, including the uses of specific amino acids for particular purposes. We emphasize aspects not previously covered: that cis-nonPro always (except for vicinal disulfides) occur in highly ordered structure, and especially the great concentration of occurrence in proteins that process or bind carbohydrates (identified by occurrence on the CAZy website).

biochemistry↗