BioArch News

BioArCh make top five (or six)

2009-07-02T12:47:00.000-07:00

In the latest standings of the most downloaded articles in the Journal of Arhchaelogical Science - BioArCh publications make the top five - and also number six spot.

The articles are

No 4. Starch granules, dental calculus and new perspectives on ancient diet
Journal of Archaeological Science, Volume 36, Issue 2, February 2009, Pages 248-255

No 6. Probable human hair found in a fossil hyaena coprolite from Gladysvale cave, South Africa
Journal of Archaeological Science

Go on, download them and get them both in the top five!

Oliver on Radio York

2009-02-12T02:21:00.000-08:00

Oliver Craig has been interviewed by Radio York on his public lecture (see post below). The broadcast can be listened to here.

Understanding human history is archaeologists’ food and drink

2009-02-09T01:17:00.000-08:00

The desire to improve our health has made food and diet a modern obsession but discovering what our ancestors ate and how they prepared food can reveal remarkable details about the way they lived.

Archaeologists Dr Allan Hall and Dr Oliver Craig will offer an insight into this fascinating area in two public lectures at the University of York. The lectures are the first in a new series at the University entitled Are You What You Eat? The Science of Food.

Dr Hall will discuss how archaeologists approach the difficult task of finding evidence of what our ancestors ate, looking in particular at what has been discovered about the foods consumed in Roman, Viking and Medieval York.

The lecture by Dr Craig will examine how discarded plant and animal remains, the contents of preserved stomachs and even fossilised faeces can help answer fundamental questions such as ‘when did we start growing, raising and cooking foods?’, ‘how did eating together become such a common occurrence for us?’ and ‘how has our diet effected our health?’.

Dr Craig said: "‘You are what you eat’ is a well known truism, but what we are and what we eat have both undergone major transformations during the course of human evolution and more recent human history.

"Molecular analysis of fragments of bone, pottery and even soils are now starting to reveal surprisingly rich accounts of what was eaten thousands of years ago."

Lectures later in the Are You What You Eat? The Science of Food series will look at obesity, breastfeeding and eating and exercise in childhood.

The University of York’s public lectures are open to all and admission is free.

PhD Studentship: Amino acid geochronology

2009-02-02T15:33:00.000-08:00

Building a better egg timer?

The chronological time scale underpins our understanding of the past, but beyond the limit of radiocarbon dating (~50,000 years), archaeological and geological sites become more difficult to date. Amino acid geochronology has the potential to date the whole of the Quaternary (the last two million years), a crucial period for geological understanding with impacts on both climate change and human evolution. The combination of a closed-system approach (Penkman et al., 2008) with advances in chromatography provides an extremely powerful dating tool (e.g. Parfitt et al., 2005).

However, in order to fully exploit the extent of protein degradation for both geochronology and palaeothermometry, we need to better understand the breakdown mechanisms. This PhD project aims to use the recent advances and expertise at York in proteomics and racemization to gain an unprecedented insight into the kinetics of protein degradation in a natural closed system. The project is ideally placed to take advantage of state-of-the-art equipment (including dedicated RP-HPLCs in the NERC-recognised facility, a wide range of mass spectrometers, as well as bioinformatic resources) and expertise in the closely collaborating departments of Chemistry, Archaeology and Biology. The PhD student will be trained in a range of laboratory techniques, with a focus on chiral amino acid analysis and soft-ionization mass spectrometry, including use of the new instruments being acquired for the new Yorkshire Forward Centre of Excellence in Mass Spectrometry. This research is strongly inter-disciplinary, and the student will be fully supported by the project team in the archaeological, geological and geochemical background and interpretation, with additional training available through exciting opportunities to go out into the field for sample collection.

References:
Parfitt, S.A., Barendregt, R.W., Breda, M., Candy, I., Collins, M.J., Coope, G.R., Durbidge, P., Field, M.H., Lee, J.R., Lister, A.M., Mutch, R., Penkman, K.E.H., Preece, R.C., Rose, J., Stringer, C.B., Symmons, R., Whittaker, J.E., Wymer, J.J & Stuart, A.J. 2005. The earliest humans in Northern Europe: artefacts from the Cromer Forest-bed Formation at Pakefield, Suffolk, UK. Nature 438, 1008-1012

Penkman, K.E.H., Kaufman, D. S., Maddy, D. & Collins, M.J. 2008. Closed-system behaviour of the intra-crystalline fraction of amino acids in mollusc shells. Quaternary Geochronology 3, 2-25

for further details contact: Dr Kirsty Penkman

NERC CASE PhD Studentship: Forensic proteomics

2009-02-02T15:23:00.000-08:00

Flying Feathers: Bird Keratin Proteomics

Proteins that persist for long periods of time in the environment are of growing concern, but these same proteins provide useful scientific tools in feed regulation enforcement. Existing collaboration between the DEFRA Central Science Laboratory, (CSL) and BioArCh, University of York is providing valuable methods to identify the species of animal protein in high temperature processed animal feed. The methods, based on identifying amino acid sequences of collagen , will ultimately be used throughout Europe to enable a lifting of the animal feed ban which has been in place since the spread of BSE ('mad cow' disease). Currently virtually all animal protein not for human consumption is incinerated. Declining risks associated with BSE are leading to the suggestion that other 'low risk' animal protein, particularly chicken feathers, could be dumped to land (after light thermal treatment or composting). Keratin dumping has a number of attractions, it is a cheaper option than incineration, has lower CO2 emissions, and can improve land quality by providing a source of nitrogen. However, there is a desperate need to investigate the impact of dumping robust, extracellular animal proteins on trophic webs and particularly on overwintering of animal pests. These studies require methods to identify the species of feather (keratin) after passage through the intestines of rodents and other larger mammals.

The studentship (between the Food and Environment groups at the DEFRA Central Science Laboratories, CSL and BioArCh, University of York) will be supported by both regulators (Scott Reaney, the Veterinary Laboratories Agency) and the Rendering Industry (Steve Woodgate, Beacon Research, Technical Director, European Fat Processors and Renderers Association, seconded from PDM).

In the UK since the rise of BSE and increased awareness of other transmissible spongiform encephalopathies over 1,500MT of feathers are being disposed every week. Keratin in waste feathers is resistant to biodegradation, unless keratinolytic fungi (or bacteria) are present. If composted feather is used to improve land, a method to assess the integrity of keratins after processing is required.

The project will expose the student to an integrated range of techniques, specifically a combination of state-of-the-art (and older generation) mass spectrometry, bioinformatics and experimental diagenesis. We will use a range of proteases (found in digestive systems) to release a characteristic mixture of peptides (peptide fingerprint). Non-substrate specific proteases are inhibited unless prior reduction of keratin's intermolecular disulfide bonds has been carried out. During biodegradation, this is accomplished by intracellular disulfide reductases. Crude assessments of 'bioavailability' will be made on processed keratin by comparing the release of peptides in samples before and after chemical reduction. Following digestion, mass spectrometry will be used to measure the 'peptide mass fingerprint', both to (i) identify the origin of the feather keratin in unknown samples and (ii) in association with chiral amino acid analysis, to assess the extent of keratin deterioration. This approach should be suitable to assess both thermally treated and composted feather keratin.

An ability to assess the origin and diagenetic state of the keratin will have widespread application, notably to (i) the validation of treatment and origin claims for imported feathers, (ii) the integrity of feathers following processing (iii) the identity of feathers in archaeological sites, sediments and even aircraft engines. For example in the latter case, total costs of aircraft bird strikes are estimated at over $1Bn per annum. The identity of the bird (and thence its size and flocking behaviour) is important in understanding and engineering against engine failure, but of the 79,972 aircraft bird strike reports between 1990 and 2007, only 26% of the birds were identified to species.

For further information please contact Professor Matthew Collins

For other funding sources, please visit Overview of PhD Scholarships & Studentships for further information.

Congratulations, Dr. Luisa!

2009-01-12T02:47:00.000-08:00

We received word from Luisa that she has successfully completed her viva and is from January 8th on, a PhD at Second University of Napels. In her presentation she covered her experience in York, the results of her practical work, protein-ageing as a common ground between her own scientific interests and BioArCh, and how the Marie Curie-Palaeo studentship helped her with her project. Due to the presence of two external professors in immunology, she got many questions about the immunological relevance of her work and a question about methods to hydrolyse Aβ-amyloid. She received praise about the multi-technological and thematic approach she applied in her work towards her PhD. Matthew, Kirsty, Enrico and Beatrice were acknowledged for their contributions and help.

Congratulations, Luisa!

Fishing for fish fragments

2009-01-11T05:44:00.000-08:00

Matthew and colleagues in Archaeology and Chemistry have been funded by the AHRC to see if they can identify tiny fragments of fish from archaeological sites.

Many fish remains survive on as fragments, so small that they lack the characteristic morphology required to identify them to species. Zoo-MS offers an alternative approach to the problem. Zoo is for Zooarchaeology, or more accurately the part of Zooarchaeology that deals with species identification. MS stands for Mass Spectrometry. Using peptide fingerprints they hope to identify fish from medieval sites and track the arrival of carp into Britain.

For more information see www.Zoo-MS.com.

Image is of the John Deere - Electronic Fishing Pole

Kirsty to improve upon the egg-timer

2009-01-11T05:37:00.000-08:00

Kirsty has been funded by NERC to develop an improved egg-timer, but one which runs for slightly more than three minutes; more like three hundred thousand years....

She and her team drawn from Archaeology and Chemistry at York, the University of Bradford, the University of Aberystwyth and Arizona State University plan to explore the reaction pathways in ostrich eggshell fragments, the ultimate “egg-timer”. By using a combination of model systems and shell fragments they will explore how eggshell proteins decay. The then hope to put together a model of the decay pathway and apply this model to estimate the age of eggshell fragments found in a rich archaeological sequence at Pinnacle Point, South Africa.

Christmas Party

2008-12-15T00:59:00.000-08:00

There are images of the Christmas party circulating...

ancient DNA? now we are cooking...

2008-12-15T00:45:00.000-08:00

BioArCh team members have discovered that cooking may not be as bad as thought for old DNA. Claudio Ottoni of the University of Rome, lead a study which investigated early Medieval cattle bones from York discovered that the more cooked the bones were the better was the DNA preservation. See report in New Scientist or the full article in Naturwissenschaften (DOI: 10.1007/s00114-008-0478-5).

Someone on campus finally shown to have brain

2008-12-11T23:14:00.000-08:00

Someone on the new campus has finally been found with a brain... and BioArCh scientists are planning to analyse it. A team from the York Archaeological Trust unearthed the brain in an Iron Age skull. Ancient brain, scientists in white coats, old building, dark winter nights..... For full details see the BBC website.

YPS Prize Presentations

2008-12-10T07:34:00.000-08:00

David Harker and Ben Elliot have both been awarded Charles Wellbeloved prizes by the Yorkshire Philosophical Society for their outstanding undergraduate dissertations of 2008. Both David and Ben gave short presentations in which they outlined their work.

David's work titled Making thermal age accessible using web based applications, introduced a novel approach for predicting the preservation of biomolecules. Algorithms based on thermal models, obtained from published databases, were used to predict the preservation of DNA in particular. The predicted thermal age was found to closely correlate to published values from real samples. This web-based application is helpful in deciding whether specimens are suitable for further research. The DNA Recovery Rate Calculator (DRRC) can be accessed here.

Ben's presentation, Is there evidence for barbed point manufacturing at Star Carr?, revisited the material from this Mesolithic site, and focussed on the manufacture of barbed points made from antlers. He carried out experimental work to mimic the production process using authentic tools. The debitage produced was compared to the remains found at the site to try to determine whether Star Carr was indeed a production site for these barbed points.

Well done and congratulations to both!

Good Luck, Luisa!

2008-12-10T07:07:00.000-08:00

Luisa returned home 3rd of December after finishing her six month Palaeo Fellowship at S-Block. She was investigating racemization and protein aging on Aβ-amyloid, which is responsible for Alzheimer's disease.
As we will miss her at the Christmas party, Luisa invited everyone for a drink at the Mason Arms. She will return to us in mid-January after her viva.

Luisa, good luck with the final hurdle and have a happy holiday!

Congratulations to Oliver & Cecile!

2008-12-04T13:41:00.000-08:00

Congratulations to Oliver and Cecile on the birth of baby Luce Marie Craig!

Double Fellowship success

2008-12-04T13:20:00.000-08:00

A double celebration, Both Enrico Cappellini and Caroline Solazzo have scored highly in the Marie Curie Fellowship competition. Enrico plans to travel to Copenhagen to work with Eske Willerslev and Tom Gilbert integrating proteomic and genomic approaches to study ancient seeds. Caroline will travel to New Zealand to work and study with AgResearch New Zealand's largest Crown Research Institute. The team at the Lincoln Research Centre are arguably the world experts in wool proteomics. Both will maintain links with BioArCh, and the newly formed Centre of Excellence in Mass Spectrometry.

BioArCh endorses Web 2.0 (again)

2008-12-04T13:14:00.000-08:00

Another plug for BioArCh's use of Wiki sites appears in an article by Michelle Perry in Information World Review this week on the role that social applications will have on the future of research. Matthew, do you have shares in Google?

Caroline awarded Newton Fellowship

2008-11-08T03:40:00.000-08:00

Caroline Solazzo has been awarded a Newton International Fellowship to investigate the archaeology of the wool trade. The intention of the scheme will select the very best early stage post-doctoral researchers from all over the world, and offer support for two years at UK research institutions. Caroline is currently working at the Smithsonian Institute and will be joining BioArCh has a Newton Fellow in the new year.

Visit from the VU

2008-10-31T03:11:00.000-07:00

BioArCh hosted a visit from the Institute for Geo- and Bioarchaeology to celebrate five years since its foundation in 2003. IGBA is a multidisciplinary research group applying analytical methods from the Earth and Life Sciences to archeological problems. Together with members of the Department of Archaeology the two groups hosted an afternoon seminar followed by a meal and drinks. The next day IGBA members visited archaeological sites in York.

BioArCh Wiki features in Computing magazine

2008-10-31T03:07:00.001-07:00

BioArCh's use of Wiki based tools has lead to us featuring in, of all places, Computing magazine.

Read the article here

Karen takes up a new post as ICREA Research Professor

2008-10-18T01:16:00.000-07:00

Karen has just taken up her post as a new ICREA Research Professorship in the Departament de Prehistòria at the Universitat Autònoma de Barcelona this month.

Karen will be setting up her starch research at UAB, but will remain working with BioArCh

Her new address is

Karen Hardy
ICREA Research Professor, Profesora de Investigación ICREA
Departament de Prehistòria
Facultat de Filosofia i Lletres.
Campus UAB
08193 Bellaterra.
Barcelona
Spain
Telf.: 00 34 93 581 4333
mob. 00 44 7809 766 164
Fax. : 00 34 93 581 1140

ISBA3 in Science

2008-10-17T14:50:00.000-07:00

Hannah Koon's work was one of the highlights of report in this weeks Science (17 October 2008), in a report by John Travis on the 3rd International Symposium on Biomolecular Archaeology conference which was hosted by BioArCh this year in York. If you want to know more please see below.

ARCHAEOLOGY: Old Bones Reveal New Signs of Scurvy John Travis
Science 17 October 2008: 368-369.
Summary: At the Third International Symposium on Biomolecular Archaeology, researchers described a new way to detect more subtle signs of scurvy in ancient bones. Full Text »

Beatrice wins again and again

2008-10-13T00:24:00.000-07:00

Beatrice's oral presentation at BOGS08 (British Organic Geochemistry Society), Newcastle, July 2008 was awarded the first prize as best student talk, whilst her poster was awarded third prize at ISBA3.

Kirsty Wins Award

2008-01-03T05:05:00.000-08:00

Dr Kirsty Penkman has been awarded the Lewis Penny medal by the Quaternary Research Association, for her "significant contribution to the Quaternary Stratigraphy of the British Isles and its maritime environment". She will be presented with the medal at the QRA annual meeting, at the Royal Geographical Society in January. Dr Penkman's research, into the application of protein breakdown as a dating tool in fossils, has been recognised because the developments have made it a routinely-applicable and reliable method for dating the Quaternary (the last two million years; a time period crucial for our understanding of climate change and human evolution).

Karen & Allan, Nicky & Hannah on the radio

2007-11-12T04:50:00.000-08:00

Staff from the department have been off filling the air waves... again. Nicky Milner and Hannah Koon have been helping to explain to listners what has been happening at the critically important Mesolithic site of Star Carr on Radio 4's Making History. Meanhwile Karen Hardy and Alan Hall have been helping Fergus the Forager (Fergus Drennan) explore the wilder side of food in Britian on Shared Earth

Listen to Fergus here and here

Toney Blakeney visits BioArch

2007-07-14T14:22:00.000-07:00

Toney Blakeny (University of Sydney/ Cereal Solutions) thought he was on a flying visity to BioArch when he arrive last week, but he is still here and we are not letting him go. Tony and expert in starch biochemistry has been visiting BioArch where he has been collaborating with Karen Hardy on the preservation of starch in archaeological artefacts. Problem is, he is simply too useful to have around, and we are not sure that we will let him go - sorry Rosemary.

Wellcome Trust Bioarchaeology Fellows present their work

2007-07-14T14:09:00.000-07:00

The three Wellcome Trust Bioarchaeology Fellows, Kirsty Penkman, Hannah Koon and Stephen Buckley present their research to Dr Mark Walport - Director of the Wellcome Trust when her presented the the York Biology Open Lecture on Wednesday 23rd May.

Rebecca has a new job.

2007-07-14T14:03:00.000-07:00

Congratulations to Rebecca (at back), who has been awarded a lectureship in Dental Morphology at the University of Liverpool. It will great to have Rebecca up north again after her sojourns in Bristol and Exeter and we hope to see her back in BioArch soon.

Enrico on Canadian Radio, Matthew on the BBC

2007-07-14T13:45:00.001-07:00

BioArch hit the media heights when the paper "Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland" was published in Science. Matthew appeared on BBC News 24, while Enrico featured on Radio Canada. OK so you wern't watching, BBC News 24, but never mind, Matthews dad has the video of his appearance, so you can count the number of times he said "amazing!" No one has tracked down Enrico's radio performance, but there is audio of Matthew talking to BBC Radio Scotland on the departmental website (so there is no excuse to miss it).

Below is a selection of the news stories - the actual article is here.

Greenland ice yields hope on climate
Boston Globe, United States - 6 Jul 2007

Greenland reveals its true colours
Globe and Mail, Canada - 6 Jul 2007

DNA reveals Greenland's lush past
BBC News, UK - 6 Jul 2007

Greenland really was green, world's oldest DNA reveals
Sydney Morning Herald, Australia - 6 Jul 2007

Long back, Greenland was really green
Times of India, India - 6 Jul 2007

Greenland once had thriving forests, say scientists
Canada.com, Canada - 6 Jul 2007

DNA shows Greenland was once green
Aljazeera.net, Qatar - 6 Jul 2007

Greenland greener than thought during last Ice Age

Kirsty Keynotes for the Worlds Malacologists

2007-07-14T13:39:00.000-07:00

Kirsty has been invited to be keynote speaker at theWorld Congress of Malacology - Antwerp, Belgium 15 - 20 July 2007. Not bad for an archaeologists, come chemist, come Quaternary Scientist.... Hang on a minute Kirsty, exactly what are you? Ah! the next story gives the answer - an Analytical Chemist.

Kirsty has a new job

2007-07-14T13:36:00.000-07:00

We say "Goodbye", then we say "Hello" to Kirsty, who will be leaving BioArch to take up a full time position as a lecturer in Analytical Chemistry this October in the Department of Chemistry, University of York.

Fortunately she will only be a short walk across the campus, and it gives us an excuse to play we even more equipment....

Caroline is Magnum Cum Laude

2007-07-14T13:34:00.000-07:00

Congratulations to Caroline, (seen here between Ines and Beatrice) who was awarded her PhD in Archaeological Proteomics at the University of Lille. Caroline was awarded her PhD with maximum honours - and although we at BioArch can claim no credit for it, we are very pleased that her PhD defence went so well!

Congratulations to Hannah

2007-04-02T13:50:00.000-07:00

Congratulations to Hannah Koon on the award of her PhD. Here she is with a strange man in a mismatched suit and gown.

Renee van de Locht visits Bioarch

2007-03-19T04:24:00.000-07:00

Renee van de Locht is a Master student Landscape Archaeology in the Institute for Geo-and BioArchaeology (IGBA), at the Vrije Universiteit in Amsterdam.

She is currently working on Starch analysis with Karen Hardy. This research will be her Master thesis project. The samples Renee and Karen are working on are from central Turkey; particularly, from the sites of Çatal Huyuk and Kaman Kalehuyuk.

Palaeofellows produce a Palaeoposter

2007-03-17T04:54:00.000-07:00

Palaeo PhD fellows and some short term fellows built a poster for the Dept of Archaeology - it seemed a good opportunity to explain the patchwork-like Palaeo projects to the archaeologists...

María Inés Zylber visits BioArch

2007-03-17T04:09:00.000-07:00

María Inés Zylber is a Ph.D. candidate at the Department of Parasitology, Hadassah Medical School, Hebrew University of Jerusalem (Supervisor: Prof. Charles Greenblatt)

Thesis title: “Mummy remains: morphological, microbiological and biochemical approaches to their molecular taphonomy”.

The objectives of her study are:

Extend the knowledge of changes in "ancient biomolecules" as caused by post-mortem transformation processes in human tissue.

Apply an interdisciplinary approach to the study of the stability of biomolecules in different ancient tissues, based on the visualized structures.

She is working on two collections: Nubian mummies (A.D. 550 – 1450) and Hungarian mummies (1731 – 1838).

At BioArch she is doing shotgun proteomics in order to study the level of degradation of mummy tissues by assesing the state of preservation of collagen type I in both populations of study. The techniques for this approach are protein extraction from soft and mineralised tissues with posterior characterization by nanoLC-MS/MS and TEM.

Contact details:
Lic. María Inés Zylber
Department of Parasitology
Hebrew University - Hadassah Medical School
P.O.Box 12272, Ein Karem
Jerusalem 91120, ISRAEL
Telephone: 972-(0)2-6757468
Mobile: 972-(0)52-3611774
Fax: 972-(0)2-6757425
Website: http://kuvin.huji.ac.il

Simona Varvara visits BioArch

2007-03-04T05:55:00.000-08:00

Simona Varvara is visiting BioArch for three weeks.
She is here to learn amino acid racemisation technique to use in her brand new lab in Alba Iulia (Romania). Hope to see her soon again!