Thursday, 2 July 2009

BioArCh make top five (or six)

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!

Thursday, 12 February 2009

Oliver on Radio York

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

Monday, 9 February 2009

Understanding human history is archaeologists’ food and drink

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.

Monday, 2 February 2009

PhD Studentship: Amino acid geochronology

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.

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

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.


Monday, 12 January 2009

Congratulations, Dr. Luisa!

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!

Sunday, 11 January 2009

Fishing for fish fragments

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
Image is of the John Deere - Electronic Fishing Pole

Kirsty to improve upon the egg-timer

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.