Also, when the laser power, HV and offset were increased with regard to DNA probe, LNA probe increased multifold in signal intensity and background (Additional
file 3: Figure S3C). The laser settings were then lowered for LNA probe to such an extent that even the lowest signal produced by LNA was detectable. Different probe concentrations LEE011 cell line were also tested for DNA and LNA in order for detecting Arsenophonus where 1 pmoles concentration showed good results. At lower probe concentration (0.6pmoles) that was used for detection of Portiera, DNA failed to produce any signal for Arsenophonus, even though non-specific background signals could still be detected (Additional file 4: Figure S4A). LNA probe produced low intensity signals at the same concentration (Additional file 4: Figure S4B). Figure 4 FISH staining of Arsenophonus 16 S rRNA in whole mount of whitefly Bemisia tabaci . (A.b) DNA probe stains Arsenophonus in the bacteriocytes; (B.b) at the same concentration (1.0 pmoles) LNA probe shows higher signal and a low background while staining for Arsenophonus. Arrows indicate the bacteriocytes. White arrowhead indicates the non-specific background in DNA samples. The images have been taken at best formamide
concentration for Arsenophonus DNA (30%) and LNA (70%) AZD1080 cell line probes separately. Both DNA and LNA panels also show merged and DIC images (as a and c respectively). We found that LNA probes produced very high signals when compared to the DNA probes (Figure 4) while detecting Arsenophonus.
We performed all the intensity measurements only after background correction. The LNA probe of had highest intensity values (>60,000) at 70% formamide concentration while the lowest (30,000) at 10%. DNA probe had highest intensity at 30% formamide concentration (39,000) and lowest at (16,000) 80% formamide concentration. At 10% formamide concentration, LNA signal was nearly as low as the DNA signal (Figure 5). The DNA probe gave an intensity which was similar to that of LNA probe at 0% formamide concentration. Similar to the earlier case of Portiera, 0% formamide gave high signal intensity as well as very high background noise. Therefore we did not consider it as an ideal concentration to eFT508 ic50 detect the difference between the probes. It was seen that DNA probe produced good signal only at very low formamide concentration unlike LNA probe. Negative controls did not show any signal for Arsenophonus (Additional file 1: Figure S1 & Additional file 2: Figure S2). Since high formamide concentration produces high stringency, false positive signals get negated while using LNA probes. Figure 5 Comparison between LNA and DNA probes for detecting endosymbiont of lower abundance ( Arsenophonus ). All specimens were processed using the procedure described for Portiera. However, the probe concentration used for Arsenophonus was 1.0 pmoles and kept identical for LNA and DNA.