Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures

Efficiently identifying and quantifying disease- or treatment-related changes in the abundance of proteins is an important area of research for the pharmaceutical industry. Here we describe an automated, label-free method for finding differences in complex mixtures using complete LC-MS data sets, rather than subsets of extracted peaks or features. The method selectively finds statistically significant differences in the intensity of both high-abundance and low-abundance ions, accounting for the variability of measured intensities and the fact that true differences will persist in time. The method was used to compare two complex peptide mixtures with known peptide differences. This controlled experiment allowed us to assess the validity of each difference found and so to analyze the method's sensitivity and specificity. The method detects both presence versus absence and a 2-fold change in peptide concentration near the limit of detection of the instrument used, where chromatographic peaks may not be sufficiently well defined to be detected in individual samples. The method is more sensitive and gives fewer false positives than subtractive methods that ignore signal variability. Differential mass spectrometry combined with targeted MS/MS analysis of only identified differences may save both computation time and human effort compared to shotgun proteomics approaches.     

In Planta Response of Arabidopsis to Photothermal Impact Mediated by Gold Nanoparticles

Biological responses to photothermal effects of gold nanoparticles (GNPs) have been demonstrated and employed for various applications in diverse systems except for one important class – plants. Here, the uptake of GNPs through Arabidopsis thaliana roots and translocation to leaves are reported. Successful plasmonic nanobubble generation and acoustic signal detection in planta is demonstrated. Furthermore, Arabidopsis leaves harboring GNPs and exposed to continuous laser or noncoherent light show elevated temperatures across the leaf surface and induced expression of heat‐shock regulated genes. Overall, these results demonstrate that Arabidopsis can readily take up GNPs through the roots and translocate the particles to leaf tissues. Once within leaves, GNPs can act as photothermal agents for on‐demand remote activation of localized biological processes in plants.     

Some Characteristics of Free Cell Population in the Airways of Rats after Intratracheal Instillation of Copper-Containing Nano-Scale Particles

We used stable water suspensions of copper oxide particles with mean diameter 20 nm and of particles containing copper oxide and element copper with mean diameter 340 nm to assess the pulmonary phagocytosis response of rats to a single intratracheal instillation of these suspensions using optical, transmission electron, and semi-contact atomic force microscopy and biochemical indices measured in the bronchoalveolar lavage fluid. Although both nano and submicron ultrafine particles were adversely bioactive, the former were found to be more toxic for lungs as compared with the latter while evoking more pronounced defense recruitment of alveolar macrophages and especially of neutrophil leukocytes and more active phagocytosis. Based on our results and literature data, we consider both copper solubilization and direct contact with cellular organelles (mainly, mitochondria) of persistent particles internalized by phagocytes as probable mechanisms of their cytotoxicity.     

西九文化区

正OMA发展西九文化区,必须面对一项挑战:将一个盛载政府极大抱负,以及持分者多元利益的超大型多用途项目,转化成一个既有趣又严肃、既有规划又允许即兴、既中国化又国际化的文化区。这个文化区规模庞大,但不失亲密融洽的感觉;富地标性,但十分谦和;容易理解,却能带来惊喜。为避免造成过分冲击,OMA采纳了一种每个香港市民都熟悉的建筑类型作为方案的发展     

The effect of red pigment on the amyloidization of yeast proteins

The intensity of amyloid-bound thioflavine T fluorescence was studied in crude lysates of yeast strains carrying mutations in the ADE1 or ADE2 genes and accumulating the red pigment (a result of polymerization of aminoimidazoleribotide), and in white isogenic strains--either adenine prototrophs or carrying mutations at the first stages of purine biosynthesis. We found that the red pigment leads to a drop of amyloid content. This result, along with the data on separation of protein polymers of white and red strains in PAGE, suggests that the red pigment inhibits amyloid fibril formation. The differences in transmission of the thioflavine T fluorescence pattern by cytoduction and in blot-hybridization of pellet proteins of red and white [PSI(+) ] strains with Sup35p antibodies confirmed this conclusion. Purified red pigment treatment also led to a decrease of fluorescence intensity of thioflavine T bound to insulin fibrils and to yeast pellet protein aggregates from [PSI(+) ] strains. This suggests red pigment interaction with amyloid fibrils. Comparison of pellet proteins from red and white isogenic strains separated by 2D-electrophoresis followed by MALDI analysis has allowed us to identify 48 pigment-dependent proteins. These proteins mostly belong to functional classes of chaperones and proteins involved in glucose metabolism, closely corresponding to prion-dependent proteins that we characterized previously. Also present were some proteins involved in stress response and proteolysis. We suppose that the red pigment acts by blocking certain sites on amyloid fibrils that, in some cases, can lead in vivo to interfere with their contacts with chaperones and the generation of prion seeds.     

Kinetic characterization of the deproteinization of trabecular and cortical bovine femur bones

The present study proposes an interpretation of the mechanism of bone deproteinization. Cortical and trabecular bovine femur bones were deproteinized using 6% NaOCl (37, 50, 60 °C). The kinetic parameters (rate constant and activation energy) were calculated, and the surface area of each type of bone was considered. A statistical analysis of the rate constants shows that cortical bone deproteinizes at a lower rate than trabecular. The activation energy is higher for trabecular than cortical bone, and no significant differences are found in the protein concentration values for both bones. Therefore, although trabecular bone deproteinizes at a higher rate than cortical, trabecular bone requires more energy for the deproteinization reaction to take place. Considering that both types of bones are constituted by mineral, protein, and water; the present work shows that the individual inner matrix architecture of trabecular and cortical bones, along with characteristics such as the mineral concentration and its bonding with collagen fibers, may be the responsible factors that control protein depletion.     

Photocatalytic hydrogen evolution from aqueous solutions of organophosphorous compounds

Photocatalytic hydrogen production from water solutions of dimethyl methylphosphonate (DMMP), trimethyl phosphate (TMP), triethyl phosphate (TEP), and radiation protective amine WR 2721, that imitate nerve chemical warfare agents was studied for the first time. Platinized titianium dioxide Degussa P25 was used as catalyst. No significant hydrogen evolution was detected without organic electron donors – sacrificial agents.     

Robust Parameter Estimation in Dynamic Systems

In this paper we present a practical method for robust parameter estimation in dynamic systems. In our study we follow the very successful approach for solving optimization problems in dynamic systems, namely the boundary value problem (BVP) approach. The suggested method combines multiple shooting for parameterizing dynamics, a flexible realization of the BVP principle, with a fast Gauss-Newton algorithm for solving the resulting constrained l ₁ problem. We give an overview of the theoretical background as well as the details of a numerical implementation. We discuss why the Gauss-Newton algorithm, which is known to perform well mainly on well-conditioned problems, is appropriate for parameter estimation problems, while quasi-Newton methods have only limited use for parameter estimation. The method is implemented on the basis of the direct multiple shooting method as implemented in PARFIT, thus inheriting all basic properties of PARFIT such as numerical stability, reliability and efficiency. The new code has been successfully applied to real-life parameter estimation problems in enzyme and chemical kinetics.     

Design and Management of Building＇s Resources

The developed modem control systems and buildings management resource systems would be effective if they are based on previously established optimal conditions during the building design. This is one of the key issues for a responsible architecture. The focus of this paper is on sustainable design methods and techniques for saving resources and their management throughout the building lifecycle. The main subject of the present article is the characteristics of these methods and their fundamental role in sustainable resource management during the building operation. The results which are based on conducted case studies of European and international practice in the construction of sustainable buildings are implemented here. Key features of a comprehensive approach for design and construction are outlined via comparative analysis, as well as various systems for the evaluation of sustainability for already constructed buildings. The mostly used criteria and indicators for sustainability are systematized, including those related to resource consumption. By analyzing a specific example, the role of sustainable design methods is justified as an important prerequisite for effective management of building resources in the process building maintenance. According to the conducted studies, during the longest life cycle period of a building, by implementation of control systems and resource management of building, the costs are successfully optimized. Specific directions that prove the effectiveness of such systems are systematized in the paper. Innovative approaches, complex methods and measures for design and management of buildings resources are presented as results of this study.     

Super‐Resolution Nonlinear Photothermal Microscopy

Super‐resolution fluorescence microscopy enables imaging of fluorescent structures beyond the diffraction limit. However, this technique cannot be applied to weakly fluorescent cellular components or labels. As an alternative, photothermal microscopy based on nonradiative transformation of absorbed energy into heat has demonstrated imaging of nonfluorescent structures including single molecules and ~1‐nm gold nanoparticles. However, previously photothermal imaging has been performed with a diffraction‐limited resolution only. Herein, super‐resolution, far‐field photothermal microscopy based on nonlinear signal dependence on the laser energy is introduced. Among various nonlinear phenomena, including absorption saturation, multiphoton absorption, and signal temperature dependence, signal amplification by laser‐induced nanobubbles around overheated nano‐objects is explored. A Gaussian laser beam profile is used to demonstrate the image spatial sharpening for calibrated 260‐nm metal strips, resolving of a plasmonic nanoassembly, visualization of 10‐nm gold nanoparticles in graphene, and hemoglobin nanoclusters in live erythrocytes with resolution down to 50 nm. These nonlinear phenomena can be used for 3D imaging with improved lateral and axial resolution in most photothermal methods, including photoacoustic microscopy.