Dr Jamie Bojko at the National Horizons Centre (Teesside University), and colleagues at the Centre for Environment, Fisheries and Aquaculture Sciences (Cefas) and the University of Florida, have found and described a new DNA virus. The Nudiviridae are a family of large double-stranded DNA viruses that infect the cells of the gut in invertebrates, including insects and crustaceans. The phylogenetic range of the family has recently been enhanced via the description of viruses infecting penaeid shrimp, crangonid shrimp, homarid lobsters and portunid crabs. Here we extend this by presenting the genome of another nudivirus infecting the amphipod Dikerogammarus haemobaphes. The virus, which infects cells of the host hepatopancreas, has a circular genome of 119,754 bp in length, and encodes a predicted 106 open reading frames. This novel virus encodes all the conserved nudiviral genes (sharing 57 gene homologues with other crustacean-infecting nudiviruses) but appears to lack the p6.9 gene. Phylogenetic analysis revealed that this virus branches before the other crustacean-infecting nudiviruses and shares low levels of gene/protein similarity to the Gammanudivirus genus. Comparison of gene synteny from known crustacean-infecting nudiviruses reveals conservation between Homarus gammarus nudivirus and Penaeus monodon nudivirus; however, three genomic rearrangements in this novel amphipod virus appear to break the gene synteny between this and the ones infecting lobsters and penaeid shrimp. We explore the evolutionary history and systematics of this novel virus, suggesting that it be included in the novel Epsilonnudivirus genus (Nudiviridae). https://www.nature.com/articles/s41598-020-71776-3
Research grant to study viruses in mosses
Dr Jamie Bojko, undergraduate student Adam Ozkan and Dr Ambroise Baker were successful in securing a research grant from the British Bryological Society to carry out preliminary research into the viruses of bryophytes (small plants also known as mosses and liverworts) in the UK.
This research aims to conduct preliminary screening of three bryophyte species, and their microbiomes, to search for the presence of DNA viruses as well as endogenous viral insertions, reflecting their evolutionary history with viruses. This pioneering work will open new horizons to comprehend yet unsubscribed bryophyte-virus relationships, which underpin the ecosystem services provided by bryophytes.
New output : A new holistic framework for inter-basin water transfer schemes
Sinha P, Rollason E, Bracken LJ, Wainwright J, Reaney SM. 2020. A new framework for integrated, holistic, and transparent evaluation of inter-basin water transfer schemes. Science of the Total Environment.
Water shortages are forecast to affect 50% of the world’s population by 2030, impacting developing nations most acutely. To increase water security there has been a significant increase in Inter-basin Water Transfer (IBWT) schemes, engineering mega-projects that redistribute water from one basin to another. However, the implementation of these schemes is often contested, and evaluation of their complex impacts inadequate, or hidden from full public scrutiny. There is an urgent need to develop more integrated, holistic, and transparent ways of evaluating the multiple interlinking impacts of IBWT schemes of this scale. In this paper, we address this gap by outlining an experimental methodology to evaluate IBWT schemes using a multidisciplinary and transparent methodology which utilises publicly available data. We illustrate the method using a case study from the Inter-Linking Rivers Project in Northern India, comparing the results of the experimental approach against the official analysis of the proposed scheme produced by the State Government of Jharkhand. The results demonstrate that the proposed experimental method allows more detailed evaluation of spatial and temporal variability in water availability and demand, as well as holistic evaluation of the functioning of the proposed scheme under different future scenarios. Based on these results we propose a flexible framework for future evaluation of proposed water transfer schemes which embeds the principles of integrated assessment, transparency, and sound science which can be adapted to other IBWT projects across the world
Infectious disease in wildlife
Our very own Jamie Bojko was in the limelight again with this Teesside University press release that was relayed in the local press (Teesside biologist explores infectious diseases
Northern Echo, p.45 and online, 12/06/2020). Originally published online by Teesside University’s Media Centre
“Dr Jamie Bojko, a Biology Lecturer in the University’s School of Health & Life Sciences, says that understanding disease diversity and emergence in wildlife systems is vital to determine how emerging diseases arise and how they might evolve.
Together with colleagues at the University of Florida (UF) and Fish and Wildlife Commission (FWC), the research team have recently identified a new genetic lineage of parasite, known as a microsporidian, from crustacean hosts.
Jamie said: ‘This parasite infects the muscle of four crayfish species local to Florida and eats away their tissues, leaving a husk of parasitic spores.
‘The parasite uses a straw-like tube to inject a gooey-centre into a crayfish muscle cell. This then develops into multiple clone parasites, which form spores to survive in the environment and move on to infect new hosts, completing the cycle.’
Dr Jamie Bojko is working with Dr Donald Behringer, Dr Lindsey Reisinger and PhD student Cheyenne Stratton, all from the University of Florida, along with Paul Moler, from the FWC. The Research team recently published a paper in the Journal of Invertebrate Pathology which highlights the findings of this brand new lineage of parasite, which is reducing the health of crayfish populations.
The group are now looking to examine what effect this disease has on crayfish and how any changes might result in alterations to the local ecology. To do this, the researchers are examining how the disease might change its host’s behaviour, how it might be contracted, and what risk it poses to other invertebrates.
The team have now received further funding from the Wisconsin Department of Natural Resources, to explore this parasite group, in addition to further parasites, to determine whether this disease is able to infect other hosts.
Jamie says that exploring different ecologies for new diseases is hugely important to understand both presence and risk, not only to local species but, additionally, how diseases can change the environment.
Jamie added: ‘There are not many people in the world who research aquatic wildlife disease so to be involved in something like this from the beginning – looking at how a brand-new disease evolves underwater – is incredibly exciting.
‘It is great for me as a biologist, but also great for Teesside University to be working with partners in Florida on such an important piece of research.’
One of the key elements of the new research will be trying to find out if any of the parasites they have discovered are a risk to local species.
‘Many of the crayfish we are working with are invasive species, and can often introduce new parasites to different locations. These parasites may be able to infect native species and cause a wildlife epidemic,’ said Jamie.
‘If we can understand how these new parasites transmit and what else they can infect, we can then start to learn more about the disease and how it might spread and evolve.
‘This brand-new parasite, which we have named Cambaraspora floridanus (after the hosts and location), has little known about it and there is a lot to do. As with any new disease, it is vitally important to understand how it fits into the ecosystem and whether it might cause any irreversible changes to the ecology and crayfish population.
‘We have explored the pathology caused by the parasite and now want to determine whether it has a wider impact on the ecosystem. If it is able to infect multiple species of crayfish then it may be able to infect other invertebrates and maybe even fish, resulting in an impact on the wider freshwater community.’ “
“Seeing Red” contribution to Athena Swan stories
The Ecology and Environment Research Collective contributed to Athena Swan stories on Teesside University’s website with a piece called “Seeing Red”. We described efforts to make field work in the natural environment more inclusive to our community of researchers and students.
The article is reproduce here:
“Field trips are an essential practical and experiential part of teaching, learning and researching the natural environment for degrees and research programmes across biology and geography.
“However, there are many barriers to bringing people into the field and some of these barriers can be particularly discriminatory towards women. To address these barriers and facilitate access to field experiences for women, a team in the School of Health and Life Sciences has been developing measures aimed at greater inclusivity, some of which are specific to women. A key part of this strategy is the development of workflow authorisation for field trips which features a checklist of inclusivity measures.
“When planning taught sessions in the natural environment we try as much as possible to keep the similar time slot as used for classroom teaching and attempt to blend as much as possible a mixture of short field trips and residential trips. This enables learners with caring responsibilities to participate in field trips.
“Increasingly, a high proportion of learners express difficulties of a psychological nature, such as anxiety, prior to taking part to group activities in an un-familiar environment. We have seen this from our experience but it has also been evidenced in national studies which shows that young women are three times more likely to suffer some form of mental health than young men. To help those who are anxious about group activity in an un-familiar environment, we have integrated field preparation sessions into the programme and are currently developing a Minecraft tool to give students an opportunity to familiarise themselves with field work techniques before stepping outdoors. To enable students to build up field skills gradually we start field work in a familiar destination such as the university campus.
“From our experience, we found that some of the anxiety surrounding field trips came about as a result of concerns in relation to availability of toilet/hygiene facilities during field trips. In response to this, staff in the School of Health and Life Sciences have adopted an innovative approach to this. Our new student field guides now identify and signpost, in advance, all opportunities for toilet / hygiene facilities during visits. Typically we plan at least two stops (with plenty of time) into each trip. In addition, the guides highlight the ‘period pack’ carried along with all field equipment, making sure that students who have periods during a field trip are able to access toiletries if required, hopefully reducing anxiety.
Period and Menstrual Hygiene Equality Guide
Toilet stops in the field: An educational primer and recommended best practices for field-based teaching“
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].
Papers
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!
NHC
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!
Until next time, when we shall have some brand-spanking, tip-top, exciting new things to share with you!
TUBA
New Output: Zinc release from seaweed (Fucus serratus) as soil amendment
D. A. Oluwadare, H. E. Carney, M. H. Sarker, C. J. Ennis, 2020. Kinetics of water-extractable zinc release from seaweed (Fucus serratus) as soil amendment. Journal of Plant Nutrition and Soil Science. 183, 136–143. DOI: 10.1002/jpln.201900398
First published: 07 February 2020
Abstract:
Soil fertilization with trace-metal rich organic fertilizers such as Fucus serratus seaweed may be an effective way to combat micronutrient deficiency. In this study the kinetics of zinc release from Fucus serratus seaweed was investigated in a packed soil column leaching experiment over 1,776 h. The release of zinc from control (soil only) and treatment (soil + seaweed; equivalent zinc application rate of 1.42 kg ha−1) columns, measured by ICP-MS, demonstrated two distinct release stages. The cumulative zinc release data for each phase were fitted to five kinetic models: zero order, first order, Elovich, power function and parabolic diffusion. In the first stage (0–400 hours) the release of zinc from both control and treatment was best described by a parabolic rate law, indicating release of zinc from a soluble soil reservoir. In the second stage (400–1,776 h) zinc release followed a zero order rate law indicative of slow release from an essentially insoluble reservoir. The modelled difference between the amount of zinc released from treatment and control columns in stage 1 (230 ± 11 µg) represented the total amount of zinc added via seaweed. The parabolic rate constant for seaweed zinc release was 12.09 µg g−1 h−0.5. In summary, the addition of F. serratus to soil is a viable source of labile zinc and a low cost agronomic option for mitigating zinc deficiency in soils.
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!
TUBA
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!
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!
TUBA
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..?!).
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).
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.
‘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!
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!
TUBA