Micro-CT X-rays do not fragment DNA in preserved bird skins

Abstract

Most zoological systematics studies are currently based on morphological features, molecular traits or a combination of both to reconstruct animals’ phylogenetic history. Increasingly, morphological studies of museum specimens are using X‐ray computed tomography to visualize internal morphology, because of its ‘non‐destructive’ nature. However, it is not known whether CT can fragment the size of DNA extracted from museum specimens, as has been demonstrated to occur in living cells. This question is of paramount importance for collections based research because X‐rays may reduce the amount of data obtainable from specimens. In our study, we tested whether exposure of museum bird skins to typical CT X‐ray energies (for visualization of the skeleton) increased DNA strand fragmentation, a key factor for the success of downstream molecular applications. For the present study, we extracted DNA from shavings of 24 prepared and dried bird skins (100+ years) footpads before and after CT scanning. The pre‐ and post‐CT fragmentation profiles were assessed using a capillary electrophoresis high‐precision instrument (Agilent Bioanalyzer). Comparison of the most common strand length in each DNA sample (relative mass) revealed no significant difference unexposed and exposed tissue (paired t‐test p = 0.463). In conclusion, we found no further quantifiable degradation of DNA strand length under standard X‐ray exposure obtained from our bird skins sample. Differences in museum preservation techniques probably had a greater effect on variation of pre‐CT DNA fragmentation.

Micro-computed tomography: Introducing new dimensions to taxonomy

“…Neither exposure to high energies nor repetitive exposure seems to have caused any mutations in this specific part of the molecular material. Previous studies attempting to determine whether exposure of preserved tissue to X-ray radiation causes a fragmentation of the DNA have reached contradicting conclusions (Götherstrom et al 1995, Grieshaber et al 2008, Paredes et al 2012). As Paredes et al (2012) point out, the findings of Götherstrom et al (1995) and Grieshaber et al (2008) might however be biased by the setup of the experiment.…”

“…Previous studies attempting to determine whether exposure of preserved tissue to X-ray radiation causes a fragmentation of the DNA have reached contradicting conclusions (Götherstrom et al 1995, Grieshaber et al 2008, Paredes et al 2012). As Paredes et al (2012) point out, the findings of Götherstrom et al (1995) and Grieshaber et al (2008) might however be biased by the setup of the experiment. Götherstrom et al (1995) examined the effect of X-ray radiation on the ability to amplify DNA fragments from pig bones, basing their conclusions on the results on the differences of PCR products brightness in an agarose gel.…”

“…Particularly, the imaging of soft tissues with micro-CT might require tissue staining (Metscher 2009a, b), but neither the effects of contrast-enhancing chemicals nor of ionising radiation upon the integrity of tissue and genetic material are yet fully understood. Although micro-CT radiation seems to negatively affect the genetic material of living tissue (Wolff 1971, Kersemans et al 2011), no fragmentation of the DNA could be detected in museum material of bird skins exposed to micro-CT scanning (Paredes et al 2012). The morphological and molecular integrity of scanned material is particularly important when valuable museum material is imaged, otherwise the material is rendered useless for further investigations.…”

The pros and cons of using micro-computed tomography in gross and microanatomical assessments of polychaetous annelids

“…Given that X-rays are a core tool for human medicine, this suggests that use of micro-CT may have limited impact on genetic material. Trials using bird specimens did not find any discernible effects (Paredes et al, 2012) and tests on polychaete material also failed to show any major impact, at least for the 16S rRNA gene (Faulwetter et al, 2013). These results indicate that -at least with commonly used scanning parameters -there should be no impediment to using this approach on specimens in museums.…”

Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in ‘Anthropocene’ Colombian Copal

“…Clearly, the better preserved a copal specimen is internally, then the more likely it is that DNA will survive. A recent study investigating the effects of CT scanning on aDNA recovery from c.100-year-old bird footpads has demonstrated that this technique has negligible impact on DNA integrity [37]. Hence, future studies may benefit from identifying specimens with preserved internal morphology prior to attempting aDNA extraction, assuming the X-ray energy levels required to scan the copal are maintained below a threshold at which DNA is damaged.…”