High-resolution biomarker discovery: Moving from large-scale proteome profiling to quantitative validation of lead candidates

Diverse proteomic techniques based on protein MS have been introduced to systematically characterize protein perturbations associated with disease. Progress in clinical proteomics is essential for personalized medicine, wherein treatments will be tailored to individual needs based on patient stratification using noninvasive disease monitoring procedures to reveal the most appropriate therapeutic targets. However, breakthroughs await the successful development and application of a robust proteomic pipeline capable of identifying and rigorously assessing the relevance of multiple candidate proteins as informative diagnostic and prognostic indicators or suitable drug targets involved in a pathological process. While steady progress has been made toward more comprehensive proteome profiling, the emphasis must now shift from in depth screening of reference samples to stringent quantitative validation of selected lead candidates in a broader clinical context. Here, we present an overview of the emerging proteomic strategies for high-throughput protein detection focused primarily on targeted MS/MS as the basis for biomarker verification in large clinical cohorts. We discuss the conceptual promise and practical pitfalls of these methods in terms of achieving higher dynamic range, higher throughput, and more reliable quantification, highlighting research avenues that merit additional inquiry.     

Development and applications of surface-activated chemical ionization

This review regards the recently developed ionization source named surface-activated chemical ionization (SACI) that employs an interaction with a surface placed at low voltage for the activation of the ionization of sample molecules to increase the sensitivity in the analysis of various compounds of biological and clinical interest. These results are due to the strong chemical noise decrease and the increase of ionization efficiency. This ionization source has been employed for the analysis of various compounds of different molecular mass and polarity (addicted and pharmaceutical drugs, amino acids, steroids, peptides, and proteins). The SACI development theoretical mechanism, benefits, disadvantages, applications, and future developments are reported and discussed.     

Modulation of the mitochondrial cyclosporin A-sensitive permeability transition pore. I. Evidence for two separate Me2+ binding sites with opposing effects on the pore open probability

This paper reports an investigation on the regulation of the mitochondrial cyclosporin A-sensitive permeability transition pore (MTP). Energized, coupled rat liver mitochondria incubated in sucrose medium in the presence of phosphate maintain a high proton electrochemical gradient (delta microH) and a low permeability to solutes. Addition of a small (10-20 microM) Ca2+ pulse leads to a transient membrane depolarization. After Ca2+ accumulation, a high delta microH is recovered, and mitochondria remain coupled indefinitely. Yet, addition of fully uncoupling concentrations of carbonyl cyanide-p-trifluoromethoxyphenyl hydrazone (FCCP) brings about MTP opening within seconds. This finding confirms that MTP opening is the consequence rather than the cause of membrane depolarization, and allowed us to study the operation of the MTP in a synchronized population of mitochondria, since pore opening can be triggered by the addition of uncoupler under a series of experimental conditions. We find that three regulatory sites can be defined: (i) an internal Me2+ binding site: when this site is occupied by Ca2+, the pore "open" probability increases, while other Me2+ ions (Sr2+, Mn2+) have an inhibitory effect; (ii) an external Me2+ binding site: when this site is occupied by Me2+ ions, including Ca2+, the pore open probability decreases; (iii) an independent cyclosporin A binding site: when this site is occupied by cyclosporin A the pore open probability decreases. We show that at variance from the case of cyclosporin A, MTP inhibition by the phospholipase A2 inhibitors nupercaine and trifluoperazine is Ca(2+)-competitive and is presumably related to interference by these drugs with Ca2+ binding to the internal regulatory site.     

Variation in the local motion statistics of real-life optic flow scenes

Optic flow motion patterns can be a rich source of information about our own movement and about the structure of the environment we are moving in. We investigate the information available to the brain under real operating conditions by analyzing video sequences generated by physically moving a camera through various typical human environments. We consider to what extent the motion signal maps generated by a biologically plausible, two-dimensional array of correlation-based motion detectors (2DMD) not only depend on egomotion, but also reflect the spatial setup of such environments. We analyzed the local motion outputs by extracting the relative amounts of detected directions and comparing the spatial distribution of the motion signals to that of idealized optic flow. Using a simple template matching estimation technique, we are able to extract the focus of expansion and find relatively small errors that are distributed in characteristic patterns in different scenes. This shows that all types of scenes provide suitable motion information for extracting ego motion despite the substantial levels of noise affecting the motion signal distributions, attributed to the sparse nature of optic flow and the presence of camera jitter. However, there are large differences in the shape of the direction distributions between different types of scenes; in particular, man-made office scenes are heavily dominated by directions in the cardinal axes, which is much less apparent in outdoor forest scenes. Further examination of motion magnitudes at different scales and the location of motion information in a scene revealed different patterns across different scene categories. This suggests that self-motion patterns are not only relevant for deducing heading direction and speed but also provide a rich information source for scene structure and could be important for the rapid formation of the gist of a scene under normal human locomotion.     

A symbolic summation approach to Feynman integral calculus

Given a Feynman parameter integral, depending on a single discrete variable N$N$ and a real parameter ε$\epsilon$, we discuss a new algorithmic framework to compute the first coefficients of its Laurent series expansion in ε$\epsilon$. In a first step, the integrals are expressed by hypergeometric multi-sums by means of symbolic transformations. Given this sum format, we develop new summation tools to extract the first coefficients of its series expansion whenever they are expressible in terms of indefinite nested product–sum expressions. In particular, we enhance the known multi-sum algorithms to derive recurrences for sums with complicated boundary conditions, and we present new algorithms to find formal Laurent series solutions of a given recurrence relation.     

Reduced order optimization for model predictive control using principal control moves

In order to reduce the computational complexity of model predictive control (MPC) a proper input signal parametrization is proposed in this paper which significantly reduces the number of decision variables. This parametrization can be based on either measured data from closed-loop operation or simulation data. The snapshots of representative time domain data for all manipulated variables are projected on an orthonormal basis by a Karhunen-Loeve transformation. These significant features (termed principal control moves, PCM) can be reduced utilizing an analytic criterion for performance degradation. Furthermore, a stability analysis of the proposed method is given. Considerations on the identification of the PCM are made and another criterion is given for a sufficient selection of PCM. It is shown by an example of an industrial drying process that a strong reduction in the order of the optimization is possible while retaining a high performance level.     

Form-Profiling of Optics Using the Geometry Measuring Machine and the M-48 CMM at NIST

We are developing an instrument, the Geometry Measuring Machine (GEMM), to measure the profile errors of aspheric and free form optical surfaces, with measurement uncertainties near 1 nm. Using GEMM, an optical profile is reconstructed from local curvatures of a surface, which are measured at points on the optic’s surface. We will describe a prototype version of GEMM, its repeatability with time, a measurements registry practice, and the calibration practice needed to make nanometer resolution comparisons with other instruments. Over three months, the repeatability of GEMM is 3 nm rms, and is based on the constancy of the measured profile of an elliptical mirror with a radius of curvature of about 83 m. As a demonstration of GEMM’s capabilities for curvature measurement, profiles of that same mirror were measured with GEMM and the NIST Moore M-48 coordinate measuring machine. Although the methods are far different, two reconstructed profiles differ by 22 nm peak-to-valley, or 6 nm rms. This comparability clearly demonstrates that with appropriate calibration, our prototype of the GEMM can measure complex-shaped optics.