Monday, 2 February 2009

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.


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