This is a universal rule of law based on the principle of Bona Fides (Digest 1, 7, 25).
The assay principle is based on the ability of bona fide inflammatory agents to activate the transcription factor NF-κB in cultured cells.
"We can design better, bona fide treatments based on the biology of the worms that can be scaled up and manufactured without the complexities or safety issues that go along with administering live parasites".
The discovery of bona fide markers based on the comparison of HVC vs. the underlying nidopallial Shelf provides important support for our rationale that HVC constitutes a molecular specialization of the nidopallium that is the product of specific programs of gene regulation.
The comparison with random regions of the genome provided us with a cut-off for bona fide transcribed UCEs based on the RNA-Seq expression levels.
Thus, the notion that Runx3 is a bona fide TSG was based on the claim that it highly expressed in the normal healthy tissue.
Indeed, to assume that every single bound site must be functional is unlikely, however, importantly, our study does not rest on that assumption, only that the large majority of target genes are bona fide Hairy targets based on the criteria below.
Our searches identified bona fide TAS4 loci based on the production of phasiRNAs in several dicot species, including poplar (Populus trichocarpa), sweet orange (Citrus sinensis), grape (Vitis vinifera), tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), potato (S. tuberosum), and monkey flower (Mimulus guttatus) (Additional file 6).
The RS1615 and RS1046 environmental strains were also used, and were identified here as bona fide B. anthracis isolates based on the detection of chromosomal and/or virulence plasmid markers (Table S1).
Given this coincidence between the two antibodies, we are confident that we have identified the majority of Myc bound genes, and (based on the negative controls) that these genes represent bona fide Myc-binding sites.
