Differences in marginal distributions of ratings by the two observers are visualized by focusing on the 'path or rectangles'.
DOI: http://dx.doi.org/10.7554/eLife.08287.023 Our model further suggests that only those DSBs that recruit sufficient Vilya to form foci are converted into crossovers and can be visualized by the discrete prominent foci seen in early/mid pachytene.
Telomere disruption leads to a DNA damage response, which includes the recruitment of 53BP1 to, and phosphorylation of H2AX at, telomeres; this process can be visualized by the presence of foci, referred to as telomere-dysfunction- induced foci (TIF), that represent colocalization of 53BP1 or γH2AX with shelterin components such as TRF2 or TIN2 [ 83, 84].
This can be visualized by looking for the formation of foci of a green fluorescent protein tagged version of LC3 (GFP-LC3) (23).
However, TEV-GUS inoculated on leaves of C24, a susceptible ecotype, forms foci that can be visualized by GUS staining not only on inoculated leaves but also on uninoculated floral tissue by 10 days post inoculation (dpi).
This phosphorylated form of H2AX, termed γH2AX, can be visualized by immunofluorescence analysis and form discrete nuclear foci, which co-localize with other repair factors such MDC1 (mediator of DNA damage checkpoint protein 1) or 53BP1 (p53 binding protein 1) and reflect sites of DSBs [2], [3].
Replication foci or 'factories' can be visualized by immuno-detection of replication enzymes, or by following incorporation of nucleotide analogues into nascent DNA.
Following DNA damage, the recruitment of RPA to DNA repair centers is revealed by the formation of repair-associated foci, a process that can be visualized by immunofluorescence.
Sprouting was allowed to proceed for 5 days, whereupon sprouting cells were visualized by carefully focusing a 20X objective just above the plane of quiescent endothelium to identify cells that sprouted from the monolayer and entered the collagen matrix.
