The peroxisome is a key organelle of low abundance that fulfils various functions essential for human cell metabolism. Severe genetic diseases in humans are caused by defects in peroxisome biogenesis or deficiencies in the function of single peroxisomal proteins. To improve our knowledge of this important cellular structure, we studied for the first time human liver peroxisomes by quantitative proteomics. Peroxisomes were isolated by differential and Nycodenz density gradient centrifugation. A label-free quantitative study of 314 proteins across the density gradient was accomplished using high resolution mass spectrometry. By pairing statistical data evaluation, cDNA cloning and in vivo colocalization studies, we report the association of five new proteins with human liver peroxisomes. Among these, isochorismatase domain containing 1 protein points to the existence of a new metabolic pathway and hydroxysteroid dehydrogenase like 2 protein is likely involved in the transport or β-oxidation of fatty acids in human peroxisomes. The detection of alcohol dehydrogenase 1A suggests the presence of an alternative alcohol-oxidizing system in hepatic peroxisomes. In addition, lactate dehydrogenase A and malate dehydrogenase 1 partially associate with human liver peroxisomes and enzyme activity profiles support the idea that NAD+ becomes regenerated during fatty acid β-oxidation by alternative shuttling processes in human peroxisomes involving lactate dehydrogenase and/or malate dehydrogenase. Taken together, our data represent a valuable resource for future studies of peroxisome biochemistry that will advance research of human peroxisomes in health and disease.

The paper summarizes the results of several industrial surveys on issues related to the development of systems using Commercial-Off-The-Shelf and Open Source Software components. The results demonstrate the following. (1) There is a discrepancy between academic theory and industrial practices regarding the use of components. One reason is that researchers have empirically evaluated only a few theoretical methods; hence, industrial practitioners currently have no reason to adopt them. Another reason might be that researchers have specified the contexts of application of only a small number of theories in sufficient detail to avoid misleading users. (2) Academic researchers often hold false assumptions about industry. For example, research on requirement negotiations often assumes that a client will be interested in, and be capable of, discussing the technical details of a project. However, in practice this is usually not true. In addition, the quality of a component in the final system is often attributed solely to component quality before integration, ignoring quality improvements by integrators during component integration.

The paper presents a controlled experiment, focusing on the impact of applying quality design principles such as the ones provided by P. Coad and E. Yourdon (1991) on the maintainability of object oriented designs. Results, which repeat the findings of a previous study, strongly suggest that such design principles have a beneficial effect on the maintainability of object oriented designs. It is argued that object oriented designs are sensitive to poor design practices because the cognitive complexity introduced becomes increasingly unmanageable. However, as our ability to generalize these results is limited, they should be considered as preliminary, i.e., it is very likely that they can only be generalized to programmers with little object oriented training and programming experience. Such programmers can, however, be commonly found on maintenance projects. As well as additional research, external replications of this study are required to confirm the results and achieve confidence in these findings

Component-based software engineering (CBSE) with Commercial-Off-The-Shelf (COTS) or Open Source Software (OSS) components are more and more frequently being used in industrial software development. We therefore need to issue experience-based guidelines for the evaluation, selection and integration of such components. We have performed a survey on industrial COTS/OSS development in three countries - Norway, Italy and Germany. Concrete survey results, e.g. on risk management policies and process tailoring, are not being described here, but in other papers. This is a method paper, reporting on the challenges, approaches and experiences gained by conducting the main survey. The main contributions are as follows: At best we can achieve a stratifled-random sample of ICT companies, followed by a convenience sample of relevant projects. This is probably the first software engineering survey using census type data, and has revealed that the entire sampling and contact process ca n be unexpectedly expensive. It is also hard to avoid national variations in the total process, possibly leading to uncontrollable method biases

An advanced method has been developed for the analysis of proteolytic digests of complex protein mixtures by reversed phase high-performance liquid chromatography coupled to mass spectrometry. The occurrence of memory effects was prevented by a parallel set of two precolumns employed for simultaneous separation and washing procedures. The system was tested extensively, and tryptic digests of three single proteins were analyzed. In addition, different solvent systems were evaluated for effective washing of the employed precolumns. Using the analytical strategy presented, a reliable identification of proteins in complex mixtures was obtained and not hampered by the occurrence of memory effects.