Protein arrays in functional genome research

AFM-fishing technology for protein detection in solutions

The review considers the possibility of using atomic force microscopy (AFM) as a basic method for protein detection in solutions with low protein concentrations. The demand for new bioanalytical approaches is determined by the problem of insufficient sensitivity of systems used in routine practice for protein detection. Special attention is paid to demonstration of the use in bioanalysis of a combination of AFM and fishing methods as an approach of concentrating biomolecules from a large volume of the analyzed solution on a small surface area.

Vitreous proteomics and diabetic retinopathy

Diabetic retinopathy is the major cause of acquired blindness in working-age adults. Studies of the vitreous proteome have provided insights into the etiology of diabetic retinopathy and suggested potential molecular targets for treatments. Further characterization of the protein changes associated with the progression of this disease may suggest additional therapeutic approaches as well as reveal novel factors that may be useful in predicting risk and functional outcomes of interventional therapies. This article provides an overview of the various techniques used for proteomic analysis of the vitreous and details results from various studies evaluating vitreous of diabetic patients using the proteomic approach.

Fluorescent sensor array in a microfluidic chip

Miniaturization and automation are highly important issues for the development of high-throughput processes. The area of micro total analysis systems (muTAS) is growing rapidly and the design of new schemes which are suitable for miniaturized analytical devices is of great importance. In this paper we report the immobilization of self-assembled monolayers (SAMs) with metal ion sensing properties, on the walls of glass microchannels. The parallel combinatorial synthesis of sensing SAMs in individually addressable microchannels towards the generation of optical sensor arrays and sensing chips has been developed. [figure: see text] The advantages of microfluidic devices, surface chemistry, parallel synthesis, and combinatorial approaches have been merged to integrate a fluorescent chemical sensor array in a microfluidic chip. Specifically, five different fluorescent self-assembled monolayers have been created on the internal walls of glass microchannels confined in a microfluidic chip.

Layered expression scanning: multiplex molecular analysis of diverse life science platforms

With the advent of the genomic era, there is an increasing use of high-throughput techniques to generate transcriptome- and proteome-based profiles of biological specimens. Each of these methodologies offers a unique window into the inner workings of cell and tissue samples. Often, these studies generate large data sets and provide investigators with a substantial number of candidate dysregulated genes and pathways. Follow-up studies are then undertaken to independently validate the original findings and to extend the study to additional samples or more quantitative measurements. Although there are several methods available for these validation efforts, they are often tedious and laborious to perform; thus, additional tools that enable this task are needed. One such approach is layered expression scanning (LES), a new technique developed via a cooperative research and development agreement (CRADA) between the National Cancer Institute and 20/20 GeneSystems, Inc. The technique is based on the movement of biomolecules from a two-dimensional life science platform (histological tissue section, electrophoresis gel, multi-well plate, etc.) through a set of analysis membranes while maintaining the original distribution pattern of the molecules. Each membrane measures one analyte and the data are then mapped back to the original specimen, permitting each component of the life science platform to be studied in detail. LES can be configured in several different ways depending on the goals of the study. In this review, we summarize the use of the LES technique for a variety of biological applications.

Antibodies against heat shock proteins in environmental stresses and diseases: friend or foe?

Heat shock proteins (Hsps) can be found in two forms, intracellular and extracellular. The intracellular Hsps are induced as a result of stress and have been found to be cytoprotective in many instances due to their chaperone functions in protein folding and in protein degradation. The origin and role of extracellular Hsps is less clear. Although they were suspected originally to be released from damaged cells (necrosis), their presence in most normal individuals rather suggests that they have regulatory functions in circulation. As immunodominant molecules, Hsps can stimulate the immune system, leading to the production of autoantibodies recognizing epitopes shared by microbial and human Hsps. Thus, extracellular Hsps can influence the inflammatory response as evidenced by the production of inflammatory cytokines. Antibodies to Hsps have been found under normal conditions but seem to be increased in certain stresses and diseases. Such antibodies could regulate the inflammatory response positively or negatively. Here, we review the literature on the findings of antibodies to Hsps in situations of environmental or occupational stress and in a number of diseases and discuss their possible significance for the diagnosis, prognosis, or pathogenesis of these diseases.

Proteomics technology in systems biology

It has now become apparent that a full understanding of a biological process (e.g. a disease state) is only possible if all biomolecular interactions are taken into account. Systems biology works towards understanding the intricacies of cellular life through the collaborative efforts of biologists, chemists, mathematicians and computer scientists and recently, a number of laboratories around the world have embarked upon such research agendas. The fields of genomics and proteomics are foundational in systems biology studies and a great deal of research is currently being conducted in each worldwide. Moreover, many technological advances (particularly in mass spectrometry) have led to a dramatic rise in the number of proteomic studies over the past two decades. This short review summarizes a selection of technological innovations in proteomics that contribute to systems biology studies.