Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Characterisation and analysis of micro-contaminants in industrial polymers

Analysis of very small particles can present problems. This paper describes the application of temperature programmed solid insertion probe mass spectrometry (TP-SIP-MS), scanning electron microscopy and SEM X-ray microanalysis to the identification of foreign particles present in an industrial product. The relative advantages and limitations of the techniques are discussed. It is shown that TP-SIP-MS is a powerful tool for such work and complements the use of more conventional microanalytical methods.     

Calculating similarities between biological activities in the MDL Drug Data Report database

There are a number of licensed databases that assign biological activities to druglike compounds. The MDL Drug Data Report (MDDR), compiled from the patent literature, is a popular example. It contains several hundred distinct activities, some of which are therapeutic areas (e.g., Antihypertensive) and some of which are related to specific enzymes or receptors (e.g., ACE inhibitor). There are several data mining applications where it would be useful to calculate a similarity between any two activities. Two distinct activity labels can have a significant similarity for a number of reasons: two activities can be nearly synonymous (e.g., CCK B antagonist vs Gastrin antagonist), one activity may be a subset of another (e.g., Dopamine (D2) agonist vs Dopamine agonist), or an activity can be the mechanism by which another activity works (e.g., ACE inhibitor vs Antihypertensive), etc. In an ideal world, similarities for two activities could be calculated simply by comparing the compounds they have in common, but in hand-curated databases such as the MDDR the assignment of activities to compounds are inevitably inconsistent and incomplete. We propose a number of methods of calculating activity-activity similarities that hopefully compensate for errors in hand-curation. Two of these, TIMI and trend vector, show promise. Soft clustering of the activities using a union of similarity methods shows a reasonable association of therapeutic areas with their mechanisms.     

The Effect of Temperature on GPC for the Separation of PCBs from Transformer Oil and Subsequent Analysis by GC-MSD

Abstract

The analysis of PCBs often involves lengthy and expensive cleanup procedures to remove interferences associated with environmental sample matrices. Gel permeation chromatography (GPC) has proven to be a useful tool in removing many of these interferences from environmental samples, especially from difficult matrices such as oils, lipids and sediments. This paper describes the effect of temperature upon the GPC column in separating PCBs from transformer oil and its implication on GC-MS analysis.     

Controlling speckle using lenses and free space

The correlation properties of speckle fields are studied for general paraxial systems. The previous studies on lateral and longitudinal speckle size for the case of free-space propagation (Fresnel transform) are generalized to the case of the linear canonical transform. These results have implications for the control of speckle size, through appropriate design of optical systems, with particular relevance for speckle interferometry.