This White Paper sets out a Life Sciences Grand Challenge for Proteomics Technologies to enhance our understanding of complex biological systems, link genomes with phenotypes, and bring broad benefits to the biosciences and the US economy. The paper is based on a workshop hosted by the National Institute of Standards and Technology (NIST) in Gaithersburg, MD, 14–15 February 2011, with participants from many federal R&D agencies and research communities, under the aegis of the US National Science and Technology Council (NSTC). Opportunities are identified for a coordinated R&D effort to achieve major technology-based goals and address societal challenges in health, agriculture, nutrition, energy, environment, national security, and economic development.

A substantial number of aPL-positive patients have a concurrent diagnosis of MS or MSL, frequently presenting with elevated IgM aCL, optic neuritis, and transverse myelitis. The anti-phospholipid syndrome (APS) should be strongly considered as an alternative diagnosis to MS in these patients.

The adequacy of the recently developed bonded hard-sphere (BHS) theory in describing the critical behavior of the homologous series of the alkanes and perfluoroalkanes is examined in this work. A simple united atom model, formed from chains of tangent hard spheres, reproduces the major experimental trends and provides good quantitative agreement for systems with two or more carbon atoms. This simple model cannot, however, reproduce the anomalous behavior of the critical pressure of the alkane series: the values of the critical pressure and temperature for methane are smaller than expected. A more sophisticated distributed-site model, which takes explicit account of the backbone and substituent atoms, reproduces this anomalous behavior. The BHS theory has also been used to predict the upper critical solution temperatures of alkane + perfiuoroalkane mixtures. For most systems, the segment-segment parameters are fitted to the butane + perfluorobutane system, although in the case of mixtures containing methane, methane + perfluoromethane parameters must be used. Excellent qualitative agreement with experimental data is seen. This indicates the strength of the BHS approach as a type of group contribution method.

The bonded hard-sphere (BRS) approach originally developed for diatomic and triatomic molecules is generalized to hard-sphere polyatomic models which are formed by bonding together their constituent hard spheres. The thermodynamic properties of the polyatomic tluid are obtained from the known properties of a corresponding multicomponent mixture of different sized hard spheres with bonding sites. In the limit of complete bonding, hard-sphere polyatomic molecules are formed. As well as the general expressions for polyatomic molecules and their mixtures, the equation of state of hard-sphere chain molecules, which are simple models of homologous series such as the alkanes, perfluoroaIkanes, etc., is pre-sented. More specifically, the chain molecules are formed from two different types of hard spheres 1 and 2. Spheres of type I make up the backbone of the chain and, in this case, would represent the carbon atoms; spheres of type 2 represent the substituents, i.e., the hydrogen or fluorine atoms. Although the BRS theory is only strictly valid for molecules of tangent spheres, the theory can also be applied to fused hard-sphere (FRS) molecules with overlapping spheres. The latter are more realistic models of actual molecules. In the spirit of the semiempirical scaled particle theories (SPT), the properties of the FRS molecule can be related to those of an equivalent BRS molecule of tangent spheres with the same parameter of nonsphericity, a. When dealing with large polyatomic molecules, a does not need to be calculated numerically as is the case with the usual SPT approach. As an approximation one may use the analytical values of a for the diatomic segments making up the molecule. This simple approach turns out to be quite successful. The BRS equation of state has been compared with "exact" computer simulation data for homonuclear and heteronuclear FRS systems of diatomics, linear and nonlinear triatomics, and tetrahedral pentatomics, as well as mixtures of FRS molecules. Good agreement is found for all of these systems. In general, the BRS approach is more rigorous and easier to extend to larger polyatomic molecules and their mixtures than SPT. 4604

In an effort to improve affinity biomarker validation in fixed patient tissue specimens, we have developed a novel quantum dotbased bioimaging system that utilizes chicken IgY antibody for high sensitivity and specificity relative quantitation of cancer proteins. Monospecific, polyclonal IgYs were generated against human HER2 and telomerase, and analytically validated for specificity by western blot and immunohistochemistry on tumor and normal cells and for relative affinity by layered peptide array (LPA). IgYs bound desired targets in cell lines and fixed tissues and showed greater affinity than commercial mammalian antibodies for both HER2 and telomerase proteins. In tissue microarray experiments, HER2 quantitation with IgY antibody and quantum dot imaging correlated well with chromogenic in situ hybridization (CISH), whereas telomerase quantitation suggested a trend toward correlation with prostate cancer Gleason Grade and differentiation. Although patient numbers were small, these findings demonstrate the feasibility of relative quantitation of cancer biomarkers with IgY and quantum dot fluorophores, and show promise for rigorous clinical validation in large patient cohorts. ' 2008 Wiley-Liss, Inc.Key words: IgY antibody; cancer biomarker; HER2; telomerase; quantum dots Few new early cancer biomarkers have surfaced in recent years. 1 Among novel proteomic biomarkers for early cancer detection, some have proven controversial. 2,3 Analytical and clinical validation of cancer biomarkers has suffered from bias in the design, conduct and interpretation of such research, 4 incompletely validated imaging, 5 and lack of affinity standards 6 and antibodies that did not, in fact, detect correct targets. 7 Here, we describe a novel approach to cell-based bioimaging with relative quantitation for biomarker validation. We report characterization of two new IgY antibodies for quantitation of model cancer biomarker systems, HER2 and telomerase, 8 and explore analytical improvements, including low cross-reactivity IgY-isotype chicken polyclonal antibodies raised against recombinant polypeptides; digital quantification of antibody signals with streptavidin-conjugated semiconductor nanocrystals to obviate photobleaching of organic fluorescent dyes; complete z-plane fluorescence image capture using 3D-deconvolution microscopy; high-throughput, automated, robotic slide processing; and quantitative, massively parallel, high-throughput analysis of peptide antigen-antibody interactions by layered peptide array (LPA) technology. 9