J. Barr

The Human Urinary Proteome Fingerprint Database UPdb

The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Here, we report the establishment of a human urinary proteomic fingerprint database using urine from 200 individuals analysed by SELDI-TOF (surface enhanced laser desorption ionisation-time of flight) mass spectrometry (MS) on several chip surfaces (SEND, HP50, NP20, Q10, CM10, and IMAC30). The database currently lists 2490 unique peaks/ion species from 1172 nonredundant SELDI analyses in the mass range of 1500 to 150000. All unprocessed mass spectrometric scans are available as “.xml” data files. Additionally, 1384 peaks were included from external studies using CE (capillary electrophoresis)-MS, MALDI (matrix assisted laser desorption/ionisation), and CE-MALDI hybrids. We propose to use this platform as a global resource to share and exchange primary data derived from MS analyses in urinary research.

N‐acetyl aspartate estimation: a potential method for determining neuronal loss in the transmissible spongiform encephalopathies

Neurodegenerative pathology is typical of the transmissible spongiform encephalopathies (TSEs), and is thought to underlie clinical disease. Some morphometric studies have shown early focal neurone loss, but the full extent of TSE induced neuronal loss in the central nervous system is not known, and can only be accurately estimated using intensive morphometric techniques. We have used a murine scrapie model in which we determined the levels of N‐acetyl aspartate (NAA), a putative neuronal marker, by both high‐performance liquid chromatography and high resolution, proton magnetic resonance spectroscopy in samples taken sequentially from the hippocampus. This scrapie model develops severe neuronal loss in the hippocampus, and the NAA levels showed a significant positive correlation with our previous morphometric estimates of neurone number. NAA measurement may therefore provide a practical alternative to intensive morphometric techniques in the investigation of neurodegeneration in the TSEs.

Microdissection: A method developed to investigate mechanisms involved in transmissible spongiform encephalopathy pathogenesis

BackgroundThe transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative diseases affecting both human and animals. The neuroanatomical changes which occur in the central nervous system (CNS) of TSE infected animals include vacuolation, gliosis, neuronal loss and the deposition of a disease specific protein, PrPSc. Experimental murine models of scrapie, a TSE of sheep, have revealed that pathology may be confined to specific brain areas with targeting of particular neuronal subsets depending on route of injection and scrapie isolate.To assess the biochemical changes which are taking place in these targeted areas it was necessary to develop a reliable sampling procedure (microdissection) which could be used for a variety of tests such as western blotting and magnetic resonance spectroscopy.MethodsThe method described is for the microdissection of murine brains. To assess the usefulness of this dissection technique for producing similar sample types for analysis by various down-stream biochemical techniques, the areas dissected were analysed for PrPSc by western blotting and compared to immunocytochemical (ICC) techniques.ResultsResults show that the method generates samples yielding a consistent protein content which can be analysed for PrPSc. The areas in which PrPSc is found by western blotting compares well with localisation visualised by immunocytochemistry.ConclusionThe microdisssection method described can be used to generate samples suitable for a range of biochemical techniques. Using these samples a range of assays can be carried out which will help to elucidate the molecular and cellular mechanisms underlying TSE pathogenesis. The method would also be useful for any study requiring the investigation of discrete areas within the murine brain.

Differential protein expression profiling in BSE disease

Bovine spongiform encephalopathy (BSE) is a fatal neurodegenerative disease affecting cattle. Current tests for the detection of BSE are based solely on the only definitive marker of the disease, an abnormal conformer (PrPd), of the host encoded prion protein (PrPc). Recent evidence that other transmissible spongiform encephalopathy diseases can be present in the absence of PrPd, coupled with the need to establish pre-mortem diagnostic assays have led to a search for alternative diagnostic approaches. In this study we apply differential protein expression profiling for the prediction of BSE disease in post-mortem bovine brain tissue. The protein profiles of groups of 27 BSE diseased cattle were compared with 28 control animals. Analysis using statistical learning (and linear discriminant analysis) techniques established protein markers of disease with good predictive power (sensitivity 85% and specificity 71%). Further work will be required to test the predictive markers in a wider range of diseases, particularly other neurological conditions.