New Output: Unique chemical parameters and microbial activity lead to increased archaeological preservation

Orr, C.H., Williams, R., Halldórsdóttir, H.H. et al. Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK. Sci Rep 11, 15837 (2021).

Published: 04 August 2021

Abstract: Waterlogged burial conditions impact upon artefact preservation. One major determinant of preservation is presence and behaviour of microorganisms, however, unravelling the mechanisms, especially in waterlogged conditions is challenging. In this study, we analysed elemental composition, bacterial diversity and community structure from excavation trenches at the Roman Site of Vindolanda, Northumberland, UK, using pXRF and 16S rRNA gene amplicon sequencing. Excavation trenches provide information of different occupation periods. The results indicated that microbial communities were dominated by Firmicutes, Bacteroidetes and Proteobacteria at a phylum level. Samples which also had visible vivianite presence showed that there were marked increases in Methylophilus. Methylophilus might be associated with favourable preservation in these anaerobic conditions. More research is needed to clearly link the presence of Methylophilus with vivianite production. The study emphasises the need for further integration of chemical and microbiome approaches, especially in good preservation areas, to explore microbial and chemical degradation mechanisms.

Slogging for Skelton

Just this week, our new paper on “Mapping an archaeological site: Interpreting portable X-ray fluorescence (pXRF) soil analysis at Boroughgate, Skelton, UK” was published! And so, we thought it would be nice to share some of the work that went toward this with you all.

Boroughgate was a 12th Century medieval borough in Skelton, North Yorkshire UK, near the All Saint’s Old Church and Skelton Castle. It was placed in the perfect location to support trade and income for the castle via but unfortunately it was unsuccessful and abandoned around 1400 CE. The remnants of earthworks at the site and medieval documentation recording some of the tradespersons at Boroughgate gave some clues as to the history of the site. Tees Archaeology went through a series of surveys before excavating the site, inviting us out to complete some pXRF analysis and explore whether pXRF elemental analysis can enhance and support their interpretations of the site. This was also an excellent opportunity for us to show the value of our method development for pXRF soil analysis in archaeology! Admittedly, this also may have been a bit of an excuse to get out on such a glorious Summers day…

Better get the sun lotion on because it’s a scorcher at Boroughgate!

pXRF is often seen as a rapid point-and-shoot method  but for good quality data, we really need an appropriate methodology. The soil matrix can vary greatly over just short distances, and we need to make sure that all our soil is examined in the same way, otherwise our comparisons are inconsistent and not well validated. We extract soil samples, dry them in the lab (preferably oven dried), grind down and sieve the samples so they’re nice and homogenous, and prepare them into pXRF sample cups. This does of course mean that we end up with a fair bit of soil samples in the lab from just one small area of soil..!

Nice selection of sorts sorted for scanning back at the lab

Research into social organisation and the activities or use of space from archaeological excavations uncover hidden knowledge on past societal practices and the structuring of historic communities. This work explored whether we could map out the elemental distribution of soil to identify different activity areas. This is discussed in much more detail in the journal article but just briefly, the distribution of aluminium, phosphorus, potassium calcium and iron distinguished between the internal dwelling and external area of a longhouse. Aluminium, potassium and calcium also distinguished a likely clean or food preparation area against a refuse area. These areas also aligned closely with the locations of artefacts such as pottery fragments, daub, and domestic or charred waste, as well as structural remains such as building foundation pads, postholes and wall foundations.

Summary of the pXRF interpretation. More pictures and diagrams in the paper!

This was a well worthwhile investigation into mapping pXRF of soil which we’re very excited to continue further. Don’t hesitate to contact us if you’re interested in surveying your site with pXRF, we’d love to see how much more we can learn about past communities with pXRF! Now before you go, don’t forget to say hi to the ridiculously sweet kitten which I’ve dubbed Sandy the Archaeology Cat because of its love for sitting in soil buckets and climbing over your shoulders judging your use of the Harris Matrix:

Sandy is the sweetest!

And finally, thanks to David Errickson at Cranfield University, and Tees Archaeology for inviting us out to your site!


pXRF on pathology! Catching up with a student publication

Recently, we worked with Naomi Kilburn, a Master’s student at Durham University, whose dissertation project titled ‘Assessing pathological conditions in archaeological bone using portable X-ray fluorescence (pXRF)’ was published just this month! Fab, right? We took a moment from our calendar of Teams calls to have a Zoom call with Naomi and catch up on her work, experience, and the research.

Naomi Kilburn, the newly published researcher!

Hi Naomi! So first off, tell us about yourself – what’s your research passion?

My passion is for palaeopathology – I love looking at human skeletons to see what they can tell us about health, diseases, and life in the past.

Oh wow, fascinating! What area of palaepathology do you enjoy the most?

There are so many fascinating areas to explore, but… at the top are studying infant and childhood health and looking for ways to expand how we learn about health in the past.

What pathway did you take to get into palaeopathology?

I recently completed my master’s at Durham University and I’m currently working on securing some PhD funding so that I can keep asking (and maybe sometimes even answering) exciting questions about people and their bones.

So your paper, Assessing Pathological Conditions in Archaeological Bone using pXRF… how did that get started?

Well, this project came about through talking with Becky Gowland, my advisor at Durham, about possible dissertation projects.

Becky suggested portable X-ray fluorescence (generally called pXRF, as otherwise it’s quite a mouthful) as a way to combine studying children with a new palaeopathological technique.

My major research question was thus formed: Can pXRF be used to distinguish between different diseases in archaeological bone?

Mmm yes I can see how that idea was formed! Were you ready and raring to go or did you have a couple more hurdles to jump?

Ah yes, so, with the project idea settled, I then needed to figure out how to access a pXRF. Luckily, Becky knows many people and put me in contact with Tim Thompson at Teesside University.

After getting the go-ahead from Tim, I carefully packed some femora into boxes and headed to Teesside.

pXRF set up and ready to go.. safety first!

Excellent! How did you find coming to Teesside for a few days?

Rhys and Helga rolled out the welcome mat, showed me around the campus and gave me a crash course in using pXRF. And bingo, I was all set!.. until some unexpected hiccups…

Oh no! What happened?

The pXRF stopped working properly and had to be repaired, which muddles up all the project timelines. Disaster! (Okay, so it wasn’t that much of a disaster). But, with Helga’s supreme organisation and flexibility of everyone using the pXRF, things were quickly back on track better than ever!

Glad to hear it was sorted out! So… what did the pXRF do?

With pXRF, I could zap the bones with X-Rays and find out what kinds of elements are in the bones (and how much of them there is!).

What did this tell you?

I found that the real time-consuming part of pXRF was playing with all the numbers and figuring out what they might mean. My summer was spent making scatterplots and doing statistical tests to try and tease out patterns in the data that could be related to scurvy, or rickets, or any of the other diseases I was looking at.

Data, data, data! What did you find out?

The patterns remained elusive (science!), but the search was fun! I looked at elemental ratios potentially related to cribra orbitalia, neoplastic disease, rickets, scurvy, syphilis, and pathological new bone formation. Unfortunately, elemental ratios were more closely related to post-burial processes, but examining larger sample sizes of each pathology could shed light on new information.

I see! Did you find out anything else?

Actually, I found out how useful the pXRF is! This work couldn’t have been done without pXRF because it allows rapid and non-destructive analysis (can’t go chopping up and grinding down archaeological collections willy-nilly!).

Awesome, go Team pXRF!


It’s absolutely fantastic to see students get their work get published, it’s such a great boon for PhD application process. I’m sure you’ll join us in wishing Naomi all the best in her bright academic future, we look forward to seeing what comes next!


Telling the Beavers

You may have seen recently some talk about the reintroduction of certain animals into the UK. There are a few animals you might never have realised were native to the UK, such as lynx and bears, the white-tailed eagle, and the ridiculously cute pine marten (seriously, look at them!). Well, we’ve just started work on a project alongside our Ecology and Environmental friends at Teesside for the Forestry Commission investigating a new beaver enclosure!

You must answer the riddle to pass the beaver’s dam (image: BBC)

A beaver’s paradise

Within just a year, what started as a small stream passing through the private woodlands has now become home to two beavers, their four new-born kits (yeah, I wish they were called babe-eavers too) and this massive pond teeming with new aquatic life! And to think, you used to be able to stroll through here without needing overalls and a raft just a year ago…

Fancy a quick dip? This guacamole pond is much deeper than it looks!

Why do we give a dam?

Beavers have a pretty well-known habit of building dams. Did you know that a major reason for this is winter survival? The deep water behind the dam doesn’t freeze the whole depth, allowing the beavers to anchor a food source at the bottom of the water and survive the winter. When building the dams, the beavers scurry around the environment selecting the juiciest of trees and have a little nibble. Okay, more like a feast. As they munch on the bark, the trees eventually give way and topple over. Sometimes these are left in place for a while, sometimes they’re broken down and moved elsewhere, generally somewhere that would be a good place to fill up with water. These branches accumulate, slowing down the movement of water and creating a sort of reservoir. Eventually, this forms a series of dams that can reach several meters high, filling up with water. This water is amazing for the ecosystem, providing a good quality environment for many sensitive plants and animals whilst also potentially improving flood control. When we visited this week, there were frogs everywhere, you had to play leapfrog around them! Frogs are fantastic for the environment, so we certainly want lots and lots of lil’ froggos bopping around.

Time for Change, Time for TUBA!

Hold up, conservation… beavers… ok ok, so why were TUBA there? Part of TUBAs research involves recording and visualising the environment, and exploring ways to show this information to the public and improve learning without disrupting the beavers. Whilst it’s early days and we’re limited on what we can show and tell you right now (I mean, we did only just complete our first recording session), we’re so looking forward to show some awesome applications of digital technology to the environment and sustainability.

Sneaking in some filming – perfect for a 10-hour loop of the dam’s tranquillity for YouTube study channels!

That’s all for now, but keep an eye open for some more updates on this project in the coming months, whether through the blog or our new Twitter page @TUBArch. Until next time!


An Update on TUBA

It’s been some rather tubalent times and as we haven’t been posting much about our activities and exciting outings for a while (I’m sure you can guess why), we thought it would be good to give an update on the TUBA team and what’s happening with the TUBA blog over the coming months!


We’ll still be posting our longer updates and stories here every month or so. We especially plan to give some of the juicy behind-the-scenes details to our new research papers and conference visits. The fact is, behind every fantastic high-flying paper, there are several months of unsuccessful experiments and cute animals. But, we want to keep the TUBA blog as the fun and friendly blog that you’ve all come to know and unconditionally love for its occasional posts. We will instead be posting more regularly on our new Twitter page which you should definitely give a follow, no doubt about it!

TUBA Twitter

That’s right, we’re now on Twitter, at @TUBArch! We’ll all be posting smaller bits and fun stuff more regularly through Twitter.

Our full blog updates will still be linked on our Twitter and our Facebook page TU.BioArch so don’t worry if you can’t get the email updates via the blog site.

Project Updates

We have a couple projects in the pipeline which we’re very excited to bring to you. And so, we’ll soon start a “Project Update” series of posts where we will occasionally share some updates on the behind-the-scenes work. We’re sure you’ll find these interesting, even if just to confirm that the long-term projects are, in fact, still alive and in progress!

Guest Posts

We’re also looking into starting a series of occasional guest posts by other students and researchers at Teesside University and beyond that we work with. These may showcase a wide range of subjects, such as biomedicine, forensic science, digital technology, all sorts! We hope you’ll join us in reading their fascinating stories, and get in touch if you’d like to join in!


What wood would be good for 3D?

Last week, we visited Vindolanda for a bit of a tester session of how effective 3D imaging strategies may be on some of their wooden collection. Yes – we actually  visited… in PERSON! Our first socially distanced visit and with the glorious company of two other researchers at Teesside University, Rebecca Strong and Matthew Crowther:

Rebecca, Matthew and Rhys forming a love of 3D triangle

Vindolanda has a lot of wood in fantastic preservation. 3D imaging can normally capture wood beautifully, but we were interested to see whether we could capture the difficult things, such as little bits of graffiti carved into tools, woodworker’s stamps in the intricately designed combs, and the combination of wood, cob nails and vivianite in shoes. By and large, it was pretty successful! We’re still processing the scans, which will unfortunately take a while longer due to COVID-related access issues, but hopefully we can share them all with you soon. But for now, how about one of the shoes!

Now, the combs. We can say with pretty high confidence that these did not scan well. This was expected really, due to how intricate the geometry was and the stamp of interest being flush with the surface and visually unclear in the original object. But, we could maybe work a bit of photographic manipulation and extract some of the details to make a 3D relief of the comb instead, similar to some work we have done with the writing tablets. This certainly can’t be used for geometric analysis, and the colourful woody textures are lost, but it does offer a different approach to viewing the small and sometimes indiscernible evidence of individuals working away at Roman Vindolanda!

Pretty funky, right!? These visits are really important when planning a new 3D strategy within archaeological projects and museum displays because whilst we can offer some suggestions from afar, actually having a go scanning and engaging in detailed discussion really lays out what can, can’t, and could be done with the specific objects and their display! So, keep and eye open for some more of our wooden models, and who knows, maybe there will be some exciting developments soon..!

Anyway, happy to say that Vindolanda is even more picturesque than before 2020. If you’re sick of walking around the same old park for the past 8 months, commenting on the same old tree and the same old weather today, how about visiting the fabulous site and museum? As a bonus, they still serve great cakes in the café!

Vindolanda really is very pretty this time of year!

Now, at the start of the year, back when many people probably hadn’t heard of the place Wuhan before, we were gearing up for a couple research talks across Europe and planning our best-selling, No.1 hit blog posts to accompany them. Unfortunately, these were cancelled, as you can probably guess why. One of these, the Roman Finds Group, postponed the meeting to this weekend, to which we had the absolutely pleasure of being invited to showcase our 3D modelling work in a session dedicated to digital engagement at Vindolanda. Better yet, the normally modest audience bolstered to over 250 delegates across the two days! It was so good to see unanimous agreement on the importance of 3D in public engagement, exploring new and inclusive applications beyond focusing purely on a research viewpoint. There were even people that had held our 3D printed cranium many moons ago and still remember it fondly with every passing day! (Okay I may have embellished a little there). Maybe I’m bigging it up too much, but this was the first time I ever received a “hear hear” so I’m rolling with it.

Getting all prepared to present! All this time working from home and it’s STILL a really weird experience presenting to the PC/wall.

If you’re interested in viewing some of the talks for yourself, keep an eye out on the Roman Finds Group because they should be available online soon! In the meantime, check out the new Vindolanda game Vindolanda: The Missing Dead, available on the Google Play Store now ready for your next visit. It looks super! The entire meeting was fantastic, great work being shown from across Roman Scotland, North England and Vindolanda, but of course y’all know we love our 3D – I mean… it’s in the title of this post!

Until next time!


Cracking On During Lockdown

Hello, been a while! So, we were originally planning to give you an exciting blog post around now, all about lots of different research going on at Vindolanda, and other conferences that each of us were attending during Spring. Unfortunately, as we all know, plans have changed just a little tiddle bit. But of course, there are still plenty of things going on at TUBA!

Digital Models

The fantastic thing about digital modelling in archaeology is that people can view artefacts without needing to directly handle them and risk damage. This is not just within the museum environment, but from your home too! Have you seen our new 3D models? We’ve got a few!

Come on down and do the locomotion! This is a laser scan of the Locomotion No. 1 at the Head of Steam Museum, Darlington. This has also been 3D printed for the museum!

Explore part of Teesside University campus! This involved terrestrial laser scanning and a ton of compression to make small enough for online hosting.

If you’re interested in 3D imaging for your own research and museum collections, feel free to take a look at our reference collection of different colours and materials, and get in contact if you’d like more information or scanning done!

PhD, or not to be?

Although that-which-must-not-be-named has thrown a right spanner into all our work plans, we’re adjusting our plans accordingly and doing our best working from home. Luckily (?), we all had plenty of writing up to focus on whilst we can’t access the labs. Although, admittedly, working from the kitchen table on those precious IKEA dining chairs comes with a bit more backache than from our lovely office space at the NHC and Middlesbrough campus. And yet – style over substance, they say!

Even under those conditions, we have seen some major milestones, and what kind of update would this be without at least mentioning PhD progressions? Better yet, it’s all good news. Helga has passed her 3rd annual review and is flying into her final write-up! Aboli has also passed her 2nd annual review, and is raring to go with degradation experiments. Finally, Rhys has submitted his thesis (!!) and is nervously excitedly looking forward toward his viva in the coming weeks. Fortunately, TUBA can still virtually get together each to make sure we are all in good spirits which, admittedly, always ends up as teasing Helga about what stage her unborn baby is on the vegetable scale [edit from Helga: currently a cauliflower or acorn squash depending on your sources].

Whilst Teams has been fantastic at enabling distance communications, control over the camera layout leaves a lot to be desired… sorry Helga!!


We’ve got a couple papers well in the peer-review process, covering our work with pXRF for leather and soil analysis, archaeological mapping, 3D imaging, and burial degradation. These will get their own behind-the-scenes blog post when they come out, so look out for those hopefully coming soon!


Finally, the National Horizons Centre will be reopening within the next 1-2 months, with enough social distancing measures in place to avoid needing an eyesight test. And oh boy, are we excited to get stuck in with using brand new, top-range equipment in a whole load of experiments we have planned! If you’re struggling to get some analysis done or can’t access your labs more than once a fortnight due to social distancing in the coming months, get in touch and see what we might be able to do together!

The NHC waiting in anticipation to welcome us again

Until next time, when we shall have some brand-spanking, tip-top, exciting new things to share with you!


National Horizons Centre: The grand opening of a world-class bioscience research centre

It’s here!! We’ve had the absolute, utmost pleasure of officially opening the NHC to researchers from across the Tees Valley, the UK and the world. After several years of intense planning, building and procurement,  it almost feels like a dream that the NHC is now open. And what better way to unveil the building than with a day of celebration, inspirational speeches and demos of labwork our researchers and PhDs are already undertaking at the NHC? The day was a fantastic success, with over 100 partners, leaders and stakeholders visiting the NHC for the whole day, and some very inspirational talks about our innovations of research and university life.

Photos courtesy of the NHC twitter page. Give them a follow at @TU_NHC!

So, what kind of equipment and techniques can we use at the NHC? LOTS! The four main areas of research focus include bioanalyticla science, bioinformatics, bioimaging and bioprocessing. Within these, we have a range of microscopic and histological techniques; bacterial, DNA and metabolomic analyses;  Raman spectroscopy; MALDI and DESI; a mass spectrometry suite; several bioreactors; and 3D imaging and radiography (a complete list can be found here). All of these are brand new, top-of-the-range models, setup in a fantastic workflow around the building, with high security. Gone are the days  of worry about someone contaminating or binning your samples! These facilities place the NHC right at the forefront of the ambitious bioscience industry, critical to the future of the UK. But hey, rather than listen to me reel off our amazing facilities, why not our video featured by the Royal Society of Biology show you!

We’ve already had numerous key institutions being involved with our work, including Fujifilm, THYME, NHS, Hart Biologicals, Absolute Biologicals, and each of the local councils… maybe we can add your fantastic work to this list! Get in touch and let’s see where we can take the future of biosciences!


Digitising Vindolanda Workshop

Last week, TUBA had the fantastic opportunity to place our research directly in the public’s hands and show them just what happens behind the scenes at Vindolanda Museum. As you may well already know, I’m a tad passionate about breaking down barriers in museum, unlocking the display cabinets and allowing people to make their own discoveries. And so, we showed all the hard work we’ve put in to 3D scanning and printing – perfect for allowing these discoveries!

What a display! 10/10 if I do say so myself.

After a few too many weeks of preparing 3D scans and printing models (sorry to those suffering PTSD after my printer harassment!), we finally produced quite the little display of heads shoved onto pikes. C’mon, admit it, you’re just as impressed as we are!

all photos were taken with express permission, but please get in contact if you want them removed.

The whole aim of this workshop was to really gauge “what’s the point, the impact?”. Visitors progressed through three zones. First, they swiped through the iPads, formulating some ideas as to what really happened to the range of heads. After, they handled the printed models, allowing them to contextualise much of this digitised information. This was key – it’s really, really, difficult explaining the dips in the human head caused by forcing onto the pike without feeling them, otherwise you beg the question “which dip? Ketchup, guac, garlic mayo?”.

Finally, visitors finished with a miniature archery range, really shooting home with how amazing Roman archers were (or rather, how abysmally terrible we are now). Sometimes visitors had pretty great aim with the little dinky bows:

And other times… it looked like the museum was under attack!

Before visitors continued their exploration through the museum, they voted on what they enjoyed the most. Digital models? Printed models? Or, the original museum display? Clearly we evoked some excitement here because some visitors bragged to other people that they absolutely must come to our exhibit!

Yes, I know what (some) of you are thinking. What are the results?! Now now, let’s not get too ahead of ourselves here, there’s a while before we can release those. But for now, here are some juicy quotes, which also make up for the lack of visitor photos because we were SO BUSY:

“I’m just stopping on a whistle stop tour, what’s all this?” – 30 minutes later – “my mind is BLOWN”

Jessie James, aged 32

“Can we eat it? [the plastic cow target]… aw, well can I shoot my brother instead?”

Hannibella, aged 6

“Aw jeez Rhys, aw jeez, I dunno, doesn’t this seem a little barbaric of the Romans? I dunno, aw jeez”

Morty, aged 14

So, was this a success? Yes! Did anything break? Not at all! Will we continue to push 3D imaging and printing forward? Absolutely! Wink wink nudge nudge to anyone fancying our 3D work for yourselves..!

Looks like we’ve had the best way to close off a summer of research!


All aboard! Next stop: digital land!

Over here at TUBA, it’s been full focus on 3D work, Vindolanda, steam trains and puns (prepare yourself for a dad joke overload!)

Come on baby, scan the Locomotion

You may not know, but Darlington has rich history of railway travel. In fact, the very first public train journey was made here, from Darlington to Stockton, back in 1825. This journey was made by the rather inventively named locomotive, Locomotion No. 1. Though to be honest, it probably should have been called the slowcomotion thanks to the top speed of 12 miles an hour (and, bizarrely, a lack of brakes..?!).

Locomotion No. 1
Just imagine, people were scared for their lives on this cutesy 12 mph fella!

And so, we were invited alongside some of the fantastic forensic science researchers at Teesside University to take some 3D scans of the Locomotion. And what a beauty, if not a bit of a daunting task! We might have gotten a little too excited when agreeing to this one, but hey, that’s all part of research, right..? Crawling underneath the Locomotion through decades worth of cobwebs was not quite so expected (I’m pretty sure I saw Frodo trapped down there somewhere).

Rhys: “For the love of all things trains, DONT. START. MOVING.”

Whilst myself, Amber Collings and Tim Thompson were powering through taking Faro laser scans all around the Locomotion, Awatif Shamata and Rebecca Strong were going full steam ahead scanning smaller objects with the HP structured light scanner, including a penny lick. Yeah, you don’t want a penny lick. Originally used for serving a bit of ice cream at the cost of a penny, they ended up being banned because the lack of proper cleanliness resulted in widespread disease. But hey, these ended up being replaced for ice cream cones, so I guess the cholera and tuberculosis were worth it…

Well, looks like all the training with the Faro paid off! Once this model is tidied up and processed more, we should have a great platform for everyone to view and handle this marvelous train from their own home.

3D point clouds are pretty gorgeous! Shame they’re worse at sticking to time than trains are.


‘Google Maps-ing’ the Nation Horizons Centre

And now, for something totally unrelated to archaeology, we did some scanning at our new research building the NHC with a Matterport scanner. Think of this like a Google maps camera car, but for inside buildings. We went all over the building taking rapid scans to produce a neat floorplan and panoramic walk-through of the building, a la Google Maps style. Once the model goes public soon, you can all have a nosey of the building on your phones and iPads and plan out where you’re going to (comfortably) slave away in the labs!

The obligatory Faro/Matterport/NHC posing photo


Vindolanda Target Practice Weaponry

Last but certainly not least, some of the target practice weapons we scanned at Vindolanda (admittedly a while ago…) have now been perfected and put on display on Sketchfab along the crania! Follow these links to view a lancehead, an arrowhead and a ballista bolt. What better way to end a post about 3D than reminding ourselves of death and war? Ahem, ahem.

Speaking of, if you want to learn more about target practice, 3D imaging, and what we can do for museums, please do come along to our workshop at Vindolanda over August bank holiday weekend! Absolutely family friendly and, dare we say, thought-provokingly life changing (too much?), we hope this event will be the figurative cherry on the top of the literal ice cream you have sat out at Vindolanda.

Looking forward to seeing you at our workshop!