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!

TUBA

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.

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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!

TUBA

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!

TUBA Blog

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!

TUBA

Geographies of Comfort

A volume edited by McNally, Price and Crang.

Bringing together conceptual and empirical research from leading thinkers, this book critically examines ‘comfort’ in everyday life in an era of continually occurring social, political and environmental changes.

Comfort and discomfort have assumed a central position in a range of works examining the relations between place and emotion, the senses, affect and materiality. This book argues that the emergence of this theme reflects how questions of comfort intersect humanistic, cultural-political and materialist registers of understanding the world. It highlights how geographies of comfort becomes a timely concern for Human Geography after its cultural, emotional and affective aspects. More specifically, comfort has become a vital theme for work on mobilities, home, environment and environmentalism, sociability in public space and the body. ‘Comfort’ is recognized as more than just a sensory experience through which we understand the world; its presence, absence and pursuit actively make and un-make the world. In light of this recognition, this book engages deeply with ‘comfort’ as both an analytic approach and an object of analysis.

This book offers international and interdisciplinary perspectives that deploys the lens of comfort to make sense of the textures of everyday life in a variety of geographical contexts. It will appeal to those working in human geography, anthropology, feminist theory, cultural studies and sociology.

New Paper: Dung fungal spores for the study of past megaherbivores

Van Asperen, E.N., Perrotti, A., Baker, A. (2020) Coprophilous fungal spores: NPPs for the study of past megaherbivores.

Published online on Dec. 2020 /Jan. 2021

This publication, lead by my colleague Eline van Asperen, will be an invaluable resources to scholars researching past populations of megharbivores or other aspects of palaeoeology using non-pollen palynomorphs, whether be it for the MSc dissertation, PhD, postdoc or at any point of their career. It is supplemented by an open-access key to the identification of dung fungal spores, which supersedes that previously provided on this blog (but some may find useful to still have access to both!):

https://doi.org/10.6084/m9.figshare.c.5240664

Abstract:

Spores from coprophilous fungi are some of the most widely used non-pollen palynomorphs. Over the last decades, these spores have become increasingly important as a proxy to study the Pleistocene and Holocene megafauna. Although the number of types used in palaeoecology is relatively small, there is a wide range of coprophilous fungal taxa whose utility in palaeoenvironmental reconstruction remains under-researched. However, environmental and taphonomic factors influencing preservation and recovery of these spores are still poorly understood. Furthermore, our understanding of whether and how spores are transported across the landscape is limited.

Dung fungal spore presence appears to correlate well with megaherbivore presence. However, depending on the site, some limitations can remain to quantitative reconstructions of megaherbivore abundance from dung fungal spore records. The presence of dung fungal spores is often more significant than their absence and variation in in abundance with time should be interpreted with caution. Correlation with other proxies may provide a promising way forward.

The majority of studies using dung fungal spores as an indicator for large herbivore abundance are of records of Late Pleistocene and Holocene age, with a focus on Late Quaternary megafaunal extinction. However, more research could potentially extend records further back in time.

Next fortnightly meetings

The dates for our next Earth, Ecology and Environment Research Collective fortnightly meeting can be found below.

Agendas/program to follow. let us know if you would like to come and speak to us or if you would like to join!

Scheduled Earth, Ecology and Environment fortnightly meetings: Wednesdays 1-2pm

  • Jan 6th
  • Jan 20th
  • Feb 3rd
  • Feb 17th
  • March 3rd
  • March 17th
  • March 31st
  • April 14th
  • April 28th
  • May 12th
  • May 26th
  • June 9th
  • June 23rd

Lisa Baldini providing expert climate opinion

Teesside Lecturer in Environmental Science, Dr Lisa Baldini was recently asked to comment on a new study in Nature highlighting the increased risk of landfalling North Atlantic hurricanes tracking further inland under climate change. Here is the article for more details:  https://insideclimatenews.org/news/13112020/hurricanes-climate-change-extreme-weather-climate-science.

Geography and Geology undergraduate taster sessions

Are you a teacher in geography, geology, or environmental science?

The University is hosting Environmental Science, Geography and Geology taster sessions. Your students can hear about these degrees, along with seeing evidence of global issues of our time. We would love you to join us!


The online taster session is aimed at year 12, 13 or Access students:-

Join Peter Beveridge, the course leader for Earth Sciences at Teesside University to learn about the exciting subject areas of Environmental Science, Geography and Geology. Peter will explain how a degree in these subjects can lead to rewarding careers with real impact on society.

Peter will also show you evidence of great global issues of our time – climate change, fresh water supply and energy generation!

Booking is essential by the student.

The session will be delivered using Microsoft Teams Live, a link will be sent the day before the event.

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!

TUBA

Student Researcher Work: Developing an inexpensive and safe methodology to extract microplastics from river sediments using LST Heavy Liquid

Joseph Mwamba conducted a research project with the Earth, Ecology and Environment research collective, while studying for his undergraduate degree at Teesside University and shares his conclusion:

“Plastic forms part of land and marine litter around the world. Plastics are manufactured in their hundreds of millions of metric tons globally and are often abandoned after use in the environment where they can remain for a long time. These form 2 types of pollutants: macro and micro litter.

Macro litter is big (> 5mm) while micro litter is small (<5mm).

Plastic macro litter, macroplastics, have been observed to injure or kill marine animals and birds by process of entanglement or suffocation from ingestion. Over time, macro litter fragments into micro litter due to the influence of UV radiation, hydrolytic properties of seawater/ water and oxidative properties of the atmosphere etc.

Plastic micro litter, microplastics, have been shown to be ingested by birds, fish and other marine organisms and there is concern about the implications of this. The full impact of microplastic pollution is yet to be understood and more research is needed.

Currently, efforts are being made to understand the impact of microplastic pollution. Identifying and isolating microplastics are the initial steps of the process. Microplastics sampled from sediment are extracted primarily by density separation or floatation. Microplastics in biota are extracted by chemical digestion.

Microplastics from seawater are extracted by filtering with nets. Once microplastics are extracted, there are identified visually under dissecting microscope with the help of fluorescence microscopy. Other identification methods include Infrared spectroscopy, Raman spectroscopy and Pyrolysis – GC/MS.

In this Student Researchers project, I wrote a mini literature review on various methods of extracting microplastics from sediments. By reviewing the extraction efficiencies and methodology of different methods, we found that methods that improve on classic density separation by using denser extraction liquids and more extraction techniques i.e. elutriation followed by density separation or the Munich Plastic Sediment Separator (MPSS), were the most successful at extraction of microplastics (small/ S-MPP: < 1 mm and large/ L-MPP: 1 – 5 mm) from sediment.

This informed our choice and method construction to improve the classic density by using the technique with LST Heavy Liquid to extract microplastics from sediment. We also found out in the review that although techniques for the extraction of microplastics were > 90% efficient now, in every other new method reported to the field, data was recorded differently and this posed a problem in the comparability of data from and studies couldn’t fully inform each other of microplastic studies around the globe. We kept this in mind when designing our method.

We then designed a method to extract microplastics from sediment using LST Heavy Liquid. Here we presented a less toxic and recyclable alternative extraction fluid to zinc chloride (1.6 – 1.7 kg/L) which is currently one of the best extraction solutions. LST Heavy Liquid’s density is much higher and allows for extractions of more microplastics than before.

Our method for extraction analysis is counting under a dissection microscope and this allows for data comparison as this is a popular analysis. This blog post makes public our work and allows those who read it to understand important issues of data comparison and work to make sure the problem is solved in future. We also through this work hope to inspire further innovation that will allow extractions to get better as has been the trend thus far.”