Is phototoxicity compromising experimental results?


Light-induced damage to biological samples during fluorescence imaging is known to occur but receives too little attention by researchers.

The December Technology Feature in Nature Methods asks if super-resolution microscopy is right for you and a point that comes up repeatedly from the researchers we interviewed is the danger of phototoxicity and photodamage caused by the high irradiation intensities needed for the illuminating light. This has long been a concern with these methods and many of the papers describing them mention it.

But as discussed in the December Editorial, even fluorescence microscopy with low irradiation intensities can cause dangerous levels of phototoxicity that permanently damage the sample. Microscopists are aware of these concerns but there has been little effort to implement processes intended to reduce the likelihood of it compromising research study results. Dave Piston, Director of the Biophotonics Institute at Vanderbilt University School of Medicine, laments that while phototoxicity is a big deal he has gotten zero traction with NIH reviewers on trying to build some rules for it.

There are some good resources available to researchers that highlight the dangers of phototoxicity and provide advice on how to limit it. Methods in Cell Biology Vol 114 has an excellent chapter by Magidson and Khodjakov, Circumventing Photodamage in Live-Cell Microscopy, that should be mandatory reading for all researchers using fluorescence microscopy for biological research. Also, Nikon’s MicroscopyU has a literature list with several dozen references and recommended reading on phototoxicity. It could use some updating but is still useful.

Despite the amount of microscopy literature that discusses phototoxicity, discussion of the phenomenon in research articles published in Nature Journals is conspicuously absent. This is highlighted by a simple full-text search we performed on the HTML versions of research articles published in Nature, Nature Cell Biology, Nature Immunology, Nature Methods and Nature Neuroscience. The articles retrieved were limited to original research articles.

The table below lists the number of occurrences of each of the listed words in the period from January 1, 2005 to November 3, 2013 in each of the indicated journals. The percentages represent the number fraction of articles containing ‘phototoxicity’ relative to the numbers of articles containing each of the microscopy- or fluorescence-related terms. Note that this is NOT a measure of co-occurrence, only a measure of how common the term ‘phototoxicity’ is relative to the other terms.

phototoxicity fluorescence fluorescent microscopy microscope
# # % # % # % # %
Nature 8 2120 0.4% 1925 0.4% 1995 0.4% 1918 0.4%
Nature Cell Biology 8 815 1.0% 728 1.1% 866 0.9% 822 1.0%
Nature Immunology 6 552 1.1% 574 1.0% 408 1.5% 326 1.8%
Nature Methods 27 565 4.8% 494 5.5% 441 6.1% 407 6.6%
Nature Neuroscience 18 639 2.8% 727 2.5% 587 3.1% 736 2.4%

The same analysis was repeated with the term ‘photodamage’ to determine if there was a substantial difference in the usage of these two similar terms.

photodamage fluorescence fluorescent microscopy microscope
# # % # % # % # %
Nature 18 2120 0.8% 1925 0.9% 1995 0.9% 1918 0.9%
Nature Cell Biology 6 815 0.7% 728 0.8% 866 0.7% 822 0.7%
Nature Immunology 2 552 0.4% 574 0.3% 408 0.5% 326 0.6%
Nature Methods 29 565 5.1% 494 5.9% 441 6.6% 407 7.1%
Nature Neuroscience 12 639 1.9% 727 1.7% 587 2.0% 736 1.6%

These results carry the potentially large caveat that the analysis did not include the text of the supplementary information, but the rarity with which phototoxicity or photodamage is discussed (0.4% to 7% relative to microscopy terms) suggests that researchers don’t appreciate how important it is to pay attention to artifacts that result from light irradiation. Luckily, there are exceptions to this state of affairs.

An excellent example of testing for phototoxicity and the subtle effects it can induce can be found in a manuscript from Jeff Magee’s lab at Janelia Farm Research Campus published last year in Nature. Quoting from the manuscript, “Particular care was taken to limit photodamage during imaging and uncaging. This included the use of a passive 8× pulse splitter in the uncaging path in most experiments to reduce photodamage drastically [Ji, N. et al. Nat. Methods (2008)]. Basal fluorescence of both channels was continuously monitored as an immediate indicator of damage to cellular structures. Subtle signs of damage included decreases in or loss of phasic Ca2+ signals in spine heads in response to either uncaging or current injection, small but persistent depolarization following uncaging, and changes in the kinetics of voltage responses to uncaging or current injection. Experiments were terminated if neurons exhibited any of these phenomena.”

It is easy to see how these changes in Ca2+ responses could easily have been interpreted as real biological effects caused by the uncaged glutamate, rather than the uncaging light itself.

It is unrealistic to expect that any mandates or oversight would be able to prevent or detect such consequences of phototoxicity in research studies. It is essential that investigators themselves be vigilant and implement appropriate controls to detect these effects. Na Ji, also at Janelia Farm Research Campus says, “It is not enough to only look for instant and dramatic signs of phototoxicity. Sometimes the effects may be more subtle and even unperceivable during the imaging period, but may become obvious when the same sample is imaged the next day. Care has to be taken in data collection and interpretation, especially when the biological process under investigation itself is a subtle one.”

Finally, the application is just as important as the imaging method being used. For example, light-sheet microscopy is excellent at reducing irradiation levels in volumetric imaging. But some applications of super-resolution microscopy, even on living samples, might be less susceptible to artifacts caused by phototoxicity than are sensitive long-term imaging applications of living samples by light-sheet microscopy. Nobody’s microscope earns them a free pass on the dangers of photodamage arising from phototoxicity. Everyone needs to be vigilant.

Update: A reader helpfully pointed out that the danger of phototoxicity and photodamage also applies to optogenetics, where light (often in the blue region of the spectrum) is used to control protein activity.

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