New Research: The observer effect in biological X-ray fluorescence microscopy

The observer effect. At what point does the act of measuring a specimen make the measurements invalid?

X-ray fluorescence microscopy is an interesting  and powerful technique. Trace elements can be imaged in astonishing detail from intact specimens. But every measured fluorescent X-ray photon had its origins in an electron forcibly removed from its resting place. Technically the very first photon we measure is a result of specimen damage, but how X-rays does it take before we observe the damage?

“Our dehydrated samples received a combined radiation dose of ~106 Gy with no apparent morphological changes in Compton scattering …” (Hare et al., Metallomics (8) 2016).

But what do radiation-induced morphological changes look like? And how can we be sure? We wanted to find out.

DamageFig1The experiment is simple. Keep on measuring a sample (a – left) until it breaks (b – left). At some point we see an obvious change in the bulk specimen and it is broken (c – left). Totally broken. Before the total annihilation of the specimen there are more subtle changes.

DamageFig2Comparing three different chemical-free specimen preparations, we find that cryofixation (b – right) provides the most protection. Although the sample is damaged, nothing can move and the specimen appears unchanged up to a radiation dose approaching 108 Gy. Upon thawing however the extent of the damage is revealed with the specimen being destroyed (below). Lyophilized (freeze dried) specimens (a – right) showed the next level of radiation protection. However, we observe that different elements display damage before others. Potassium begins to show signs of damage at 107 Gy, with other elements following the trend with the ultrastructure destruction (c – above) at 3 x 107 Gy.


In contrast, anesthetized specimens (c – above) show a different profile , with iron exhibiting signs of damage as early as 106 Gy before the bulk sample is destroyed (left). This result confirms previous assertions we’ve made, it’s nice when results agree.


What does all this mean? Firstly, we were correct in our previous assessment, and our quote above was correct (phew), we can safely irradiate a lyophilized c. elegans with ~106 Gy with no changes in morphological or elemental distribution at ~1um length scales. Secondly, we’ve set limits for X-ray fluorescence microscopy of c. elegans at ~1um length scales for a variety of preparations. Experiments can now be planned so they don’t exceed certain limits depending of what elements are of interest. This is a huge bonus, no longer are we flying dark and crossing our fingers. No longer do we have to mage vague statements about not seeing morphological changes. We can have confidence that what we observe is what we believe we observe. The observer effect is not in play within these limits.

Head over to Analytical Chemistry to see the article with all the gory details, and don’t forget to check out the supplementary material for extra information and some detail rich movies where you can see what the changes look like.

Posted in Freshly forged: New research from our lab

Interview from the March for Science

Hey folks, it’s been a while. I promise there’s quite a bit to update you all with, and will try to do so in the coming weeks.

In the meantime, I was proud to be a marshal at the Melbourne March for Science on April 22, and Adam Ford from Science, Technology & The Future did this little interview with me.

Posted in Irons in the fire: News from our lab

Vote in the Centenary Institute’s Lawrence Creative Prize

Hey guys, long time no post. Trust me, there’s more coming soon when I can find the time to talk about some of the recent metal-centric work coming from our lab.

In the meantime, I’ve entered the Centenary Institute’s Lawrence Creative Prize for 2016 on my current research obsession: early life iron overload and Parkinson’s disease. Here’s a video we shot:

You can vote over here, all you need to do is create an account, or log in via Facebook or your Google account. Be sure to check out the other submissions too, you can vote more than once.

Posted in Irons in the fire: News from our lab

New Research: Can lead and manganese in blood identify Alzheimer’s disease?

Unfortunately not.

Lead has been in the news a lot recently; you’d have to be hiding under a rock to not know about the current environmental tragedy happening in Flint, Michigan, where toxic levels of lead have been found in the municipal water supply.

Although lead as many practical uses, it’s probably just as famous as being extremely poisonous. Similarly, manganese, which unlike lead actually has an essential role in normal physiology, is also toxic when present at high levels. In an upcoming special issue on the neurotoxicity of lead, manganese and mercury in Ferrumblogger’s favourite journal Metallomics (you can access the article for free here), we’ve just published findings from the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing, one of the world’s largest group of Alzheimer’s disease patients, looking at whether lead and manganese in blood can be used to predict the disease.

Read more ›

Posted in Irons in the fire: News from our lab

New Research: Changing metal levels in traumatic brain injury

It’s been a while since we’ve been active here, but as annual money-begging season has drawn to a close, it’s time to update everyone on the slew of new papers coming from our lab. Over the next few weeks, there’ll be a bunch more posts on the exciting developments happening in the ferrumblogger world.

To start, we’re going to look at a new paper, written by Florey PhD student Stuart Portbury, who’s been looking at how the brain responds to traumatic brain injury, or TBI. TBI is a hot topic right now, from the dangers of multiple concussions experienced by American NFL players (and the controversy regarding the recent pull-out by the NFL for a multi-million dollar project to study it’s effects in living patients) to people who like to get into locked cages and punch each other in the head (hey, consenting adults and all that…). And perhaps the biggest elephant in the room are the effects of traumatic brain injuries in the multiple sites of conflict currently tak17143ing place around the world.

What causes the long-lasting effects of concussions are still a matter of much contention, so it’s important for us to know what’s going on at the chemical level in precisely controlled conditions to better understand both how the brain responds, and what can be done to prevent it. Click through to read about thr work from Stuart and his supervisor, Associate Professor Paul Adlard, who runs the Synaptic Neurobiology Laboratory at the Florey. (Picture used from the US National Library of Medicine).

Read more ›

Posted in Freshly forged: New research from our lab

Feature on early life iron at

Laura Sanders, who writes the blog Growth Curve at ScienceNews has just written a great piece talking about my early life iron exposure work, with comments from several experts in the field. Thanks Laura! Head on over here to have a read.

Posted in Metal filings: Odds and ends from around the web

Do we need another “-omics”?

If you are reading this blog it seems likely that you’ll have at least a passing familiarity with some (perhaps even many) kinds of “-omics”. Increasingly for every conceivable “-ome” there is a corresponding “-omics” aimed at the “collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms” (well said Wikipedia!). Indeed a quick google reveals a long list of “-omes” each the target of study for an associated group of dedicated “-omics” researchers. The ease with which one can find commentary espousing the power of “-omics” to revolutionise < insert field of study here > coupled with the rapid spread of these neologisms through the scientific literature might even tempt the more cynical among us to utter those most scientifically contemptuous terms “buzz word” or “fishing trip” when discussing the latest results from some or another “-omic” study.

Full disclosure: I have occupied precisely this position. However, I write now as a (surprised) convert. This change evolved stealthily and I recognised my new position only recently; I had occasion to be evangelising about the importance of bioinorganic chemistry to fundamental biology (as is my want) and realised I am completely comfortable with the terms “metallome” and “metallomics”. On reflection this struck me as hypocritical, how suspicious that the “-omics” I hold in high esteem – metallomics – happens to be the very one pertaining to my area of study? …

Obviously my personal relegation of “-omics” to the “buzz-word” bin stemmed from ignorance. By necessity every scientist carves out a small portion of nature to chip away at while we look for insight and the great number of “-omics” simply reflects the diversity of worthy biochemical mysteries that remain to be solved. While each “-omics” has its star, be they genes, proteins, mRNA or metals, I am hearted to realize that the spread of “-omics” reflects researchers seeking greater context for their investigations. While establishing that A+B ⇄ C remains the cornerstone of the fruitful reductionist approache to biochemistry the benefit of “-omics” is that this interaction can be seen in a more complete way. I think Hiroki Haraguchi from Nagoya University, in his 2004 JAAS article, does a great job of contextualising metallomics by making the point that genomics, proteomics, metabolomics, metallomics etc. must all develop together.

I for one am excited to be following my line of metal biology focused enquiry as part of our collective effort to understand how the physical processes occurring inside the bags of chemicals we call cells ultimately gives rise to such interesting biology.

Posted in Irons in the fire: News from our lab

Fiona Larner: Looking at cancer from a different angle

Dr Fiona Larner from the University of Oxford’s Department of Earth Sciences might not sound like she’s in the right place to be studying cancer, but Fiona’s work is a testament to how understanding the role of metals in disease takes more than just your run-of-the-mill biologist (sorry, biologists)

Read more ›

Posted in Iron men (and women): Researcher profiles

As the year comes to a close…

…I’ve finally got around to updating our publications for 2015. You can find them here, and a lot of them are open access, so you can take a look for free. More will be added over the coming days.

Posted in Irons in the fire: News from our lab

Tonight’s main event: Testicles versus the brain for selenium bragging rights

The good folks over at Science News asked me to comment recently on a new paper in the Journal of Neuroscience discussing the competition between the brain and testes for selenium in mice, with ballgame firmly in favour of the, ahem, underdog when selenium levels are scarce.

My epic contribution to this story can be summed up in this excerpt:

The results are some of the first to show competition between two organs for trace nutrients, says analytical neurochemist Dominic Hare of the University of Technology Sydney and the Florey Institute of Neuroscience and Mental Health in Melbourne. In addition to uncovering this brain-testes scuffle, the study “highlights that selenium in the brain is something we can’t continue to ignore,” he says.

In this paper, the authors examined what happens to selenoprotein hierarchy when mice were castrated, showing that the neurological effects of a selenium deficient diet early in life can be prevented by removing the competing organs. Though this isn’t exactly a workable solution for places like northern China, where selenium deficiency is endemic, it does shine some more light into a burgeoning field of bioelement research – just how important is selenium for normal brain function?

I’d say the ball is in your court, but I think all signs point to very much so.

Posted in Metal filings: Odds and ends from around the web