A defective interfering particle (DIP) in the context of influenza A is a virion with a significantly shortened RNA segment substituting one of eight full-length parent RNA segments, such that it is preferentially amplified. Hence, a cell co-infected with DIPs will produce mainly DIPs, suppressing infectious virus yields, and affecting infection kinetics. Unfortunately, the quantification of DIPs contained in a sample is difficult since they are indistinguishable from standard virus. Using a mathematical model, we investigated the standard experimental method for counting DIPs based on the reduction in infectious virus yield (Bellett and Cooper, 1959). We found the method is valid for counting DIPs provided that: (1) a cell’s co-infection window is approximately half its eclipse phase (it blocks infection by other virions before it begins producing progeny virions); (2) a cell co-infected by virus and DIP produces less than 1 infectious virus per 1,000 DIPs; and (3) highly concentrated virus stock (>4 PFU/cell) is used to perform the assay. Prior work makes no mention of these criteria such that the method has been applied incorrectly in several publications discussed herein. We determined influenza A virus meets these criteria, making the method suitable for counting influenza A DIPs.

The shade avoidance syndrome (SAS) is one of the best-studied forms of plant phenotypic plasticity. Petiole elongation and hyponasty (leaf angle increase) are the two most important responses for Arabidopsis thaliana. These responses are both induced by the perception of low R:FR light, however physiological experiments showed that the place of perception is different. With a virtual model we explored the role of the place of perception for plants growing with or without neighbours.