Protein-based biomarkers

Stress/heat shock proteins (see Gagne and Blaise, Chapter 7 of this volume). These constitute a set of protein families of different molecular weights that generally have been referred to as heat shock proteins (HSPs), classified into 

Metallothionein, metal-binding proteins and phytochelatins (see Gagne and Blaise, Chapter 7 of this volume). Metallothioneins are low molecular weight, cysteine-rich proteins with a high affinity for transition metals. After they were first discovered in the kidney cortex of the horse they have been detected in a variety of animal species. It is widely accepted that metallothioneins are multifunctional proteins primarily involved in the homeostasis of essential trace metals, zinc-mediated gene regulation, and in the protection of cells against oxidative 

In a detailed analysis of earthworm metallothioneins, Stiirzenbaum et al. (1998c) identified two complementary DNAs (cDNAs) encoding metallothio-nein-like proteins. Both isoforms were induced by copper and cadmium and also a number of mine site soils. This work for both snails and earthworms confirms that metallothioneins are inducible by metal exposure and are thus useful biomarkers of exposure. 

In plants, two kinds of metal-binding peptides or proteins are synthesized. Plant metallothioneins are inducible cysteine-rich entities very like those found in animals. Differential expression (induction) of metallothionein genes can be due to both variation of external heavy metal concentrations and the influence of various environmental factors. The principle role of plant metallothioneins seems to be in homeostasis rather than in metal detoxification. Plants are also known to have so-called phytochelatins, which are non-protein thiols specifically induced upon exposure to heavy metals. A close positive relationship between the concentrations of cadmium and phytochelatins in the plant shoot material has been observed and linked to the degree of growth inhibition (Keltjens and Van Beu-sichem, 1998). These observations make the use of phytochelatins promising for the assessment of heavy metal effect on plants. 

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The development of an automated selection process, the intrinsic properties of aptamers combined with their conversion into signaling elements, and the ease of conjugating oligonucleotides on different surfaces make them appropriate for their use in microarray formats. Interest in aptamer chips was outlined long ago (Brody and Gold, 2000). They could be used for the identification and quantification of multiple proteins or biomarkers. There are still few reports on the development of microarray-based aptamer assays. Detection of the analyte... 

Blood which contains most of the proteins and biomarkers is one of the most crucial body fluids for the disease diagnostics. Immunoassay is one of the most useful biological detection approaches and medical diagnostic methods due to its high sensitivity and specificity. A whole blood immunoassay test can measure the level or concentration of some substances in blood based on the unique affinity of an antibody. 

The US National Institutes of Health defines biomarkers as molecules that can be objectively measured and evaluated as indicators of normal or disease processes and pharmacologic responses to therapeutic intervention [12]. A broader definition of biomarkers for cancer consist of any measurable or observable factors in a patient that indicate normal or disease-related biological processes or responses to therapy [13, 14]. These can include physical symptoms, mutated DNAs and RNAs, secreted proteins, cell death or proliferation, and semm concentrations of small molecules such as glucose or cholesterol. In this chapter, we focus on emerging nanoscience-based electrochemical methods to detect levels of proteins as biomarkers that can be used for detection and monitoring cancer [2, 6, 15]. 

In order to evaluate the proteomic profile of whole cells and to correctly identify proteins based solely on the intact mass, advanced instrumentation offering high mass accuracy is necessary. The application of Fourier transform mass spectrometry (FTMS) to intact cell analysis allowed for unambiguous identification of biomarker proteins due to the high resolution and mass... 

S. Xue, J. Qiao, F. Pu, M. Cameron and J. J. Yang, Design of a Novel Class of Protein-Based Magnetic Resonance Imaging Contrast Agents for the Molecular Imaging of Cancer Biomarkers, Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol., 2013, 5, 163. 

BACTERIAL PROTEIN BIOMARKER DISCOVERY A FOCUSED APPROACH TO DEVELOPING MOLECULAR-BASED IDENTIFICATION SYSTEMS... 

Additionally it has been our experience that mass spectrometry as a routine detection/identification technique for bacteria is not well received by microbiologists and clinicians who prefer less expensive, less complicated approaches to bacterial typing and identification, such as methods based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). For that reason we have adapted our MS approach to serve as a means of biomarker discovery that feeds candidate proteins or leads into development as PCR targets or other immunoassay techniques. 

It is therefore not surprising that the interest in PyMS as a typing tool diminished at the turn of the twenty-first century and hence why taxonomists have turned to MS-based methods that use soft ionization methods such as electrospray ionization (ESI-MS) and matrix-assisted laser desorption ionization (MALDI MS). These methods generate information-rich spectra of metabolites and proteins, and because the molecular ion is seen, the potential for biomarker discovery is being realized. The analyses of ESI-MS and MALDI-MS data will still need chemometric methods, and it is hoped that researchers in these areas can look back and learn from the many PyMS studies where machine learning was absolutely necessary to turn the complex pyrolysis MS data into knowledge of bacterial identities. 

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