Controlling Through‐Space and Through‐Bond Exchange Pathways in Bis‐Cobaltocenes for Molecular Spintronics

Pinching molecules via chemical strain suggests intuitive consequences, such as compression at the pinched site and clothespin‐like opening of other parts of the structure. If this opening affects two spin centers, it should result in reduced communication between them. We show that for naphthalene‐bridged biscobaltocenes with competing through‐space and through‐bond pathways, the consequences of pinching are far less intuitive: despite the known dominance of through‐space interactions, the bridge plays a much larger role for exchange spin coupling than previously assumed. Based on a combination of chemical synthesis, structural, magnetic, and redox characterization, and a newly developed theoretical pathway analysis, we can suggest a comprehensive explanation for this non‐intuitive behavior. These results are of interest for molecular spintronics, as naphthalene‐linked cobaltocenes can form wires on surfaces for potential spin‐only information transfer.     

Parameter estimation based synchronization for an epidemic model with application to tuberculosis in Cameroon

We propose a method based on synchronization to identify the parameters and to estimate the underlying variables for an epidemic model from real data. We suggest an adaptive synchronization method based on observer approach with an effective guidance parameter to update rule design only from real data. In order, to validate the identifiability and estimation results, numerical simulations of a tuberculosis (TB) model using real data of the region of Center in Cameroon are performed to estimate the parameters and variables. This study shows that some tools of synchronization of nonlinear systems can help to deal with the parameter and state estimation problem in the field of epidemiology. We exploit the close link between mathematical modelling, structural identifiability analysis, synchronization, and parameter estimation to obtain biological insights into the system modelled.     

Two-dimensional simulation of the single-sided air-coupled ultrasonic pitch-catch technique for non-destructive testing

Non-contact air-coupled ultrasonic inspection of materials using single-sided access offers interesting possibilities for the development of in-line non-destructive testing (NDT) systems. This contribution reports observations and simulations obtained from a single-sided air-coupled pitch-catch configuration. The pitch-catch technique involves a set-up in which transmitter and receiver are located at the same side of the test object. Sound waves, reflected once or multiple times from the back-wall of the object or refracted by a discontinuity, are recorded and analyzed for visualization. The feasibility of the technique is demonstrated, experimentally, in the case of artificial defects in aluminium samples. Depending on the configuration one or more ultrasonic images of the defect can be observed, their number and relative position containing information about the location of the defect. The experiments are simulated using two distinctive methods. The first simulation is based on a ray tracing (shadow) approach, the second method uses a spectral solution implemented within Comsol. Both simulation methods allow simple prediction of the response images in experimental conditions with supplementary levels of complexity, which will assist the development and optimization of online inspection techniques.     

Phosphopeptide fragmentation and analysis by mass spectrometry

Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision‐induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss‐dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS³ and multistage activation (MSA), have been designed to generate more sequence‐informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron‐driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large‐scale phosphoproteomics studies. Copyright © 2009 John Wiley & Sons, Ltd.     

Nondestructive characterization of nanoscale layered samples

Multilayered samples consisting of Al, Co and Ni nanolayers were produced by MBE and characterized nondestructively by means of SRXRF, μ-XRF, WDXRF, RBS, XRR, and destructively with SIMS. The main aims were to identify the elements, to determine their purity and their sequence, and also to examine the roughness, density, homogeneity and thickness of each layer. Most of these important properties could be determined by XRF methods, e.g., on commercial devices. For the thickness, it was found that all of the results obtained via XRR, RBS, SIMS and various XRF methods (SRXRF, μ-XRF, WDXRF) agreed with each other within the limits of uncertainty, and a constant deviation from the presets used in the MBE production method was observed. Some serious preliminary discrepancies in the results from the XRF methods were examined, but all deviations could be explained by introducing various corrections into the evaluation methods and/or redetermining some fundamental parameters.     

Protein expression dynamics during replicative senescence of endothelial cells studied by 2-D difference in-gel electrophoresis

Endothelial senescence contributes to endothelium dysfunctionality and is thereby linked to vascular aging. A dynamic proteomic study on human umbilical vein endothelial cells, isolated from three umbilical cords, was performed. The cells were cultured towards replicative senescence and whole cell lysates were subjected to 2-D difference gel electrophoresis (DIGE). Despite the biological variability of the three independent isolations, a set of proteins was found that showed senescence-dependent expression patterns in all isolations. We focused on those proteins that showed significant changes, with a paired analysis of variance (RM-ANOVA) p-value of < or =0.05. Thirty-five proteins were identified with LC-Fourier transform MS, and functional annotation revealed that endothelial replicative senescence is accompanied by increased cellular stress, protein biosynthesis and reduction in DNA repair and maintenance. Nuclear integrity becomes affected and cytoskeletal structure is also changed. Such important changes in the cell infrastructure might accelerate endothelium dysfunctionality. This study provides biological information that will initiate studies to further unravel endothelial senescence and gain more knowledge about the consequences of this process in the in vivo situation.     

Tandem mass spectrometry of intact GroEL-substrate complexes reveals substrate-specific conformational changes in the trans ring

It has been suggested that the bacterial GroEL chaperonin accommodates only one substrate at any given time, due to conformational changes to both the cis and trans ring that are induced upon substrate binding. Using electrospray ionization mass spectrometry, we show that indeed GroEL binds only one molecule of the model substrate Rubisco. In contrast, the capsid protein of bacteriophage T4, a natural GroEL substrate, can occupy both rings simultaneously. As these substrates are of similar size, the data indicate that each substrate induces distinct conformational changes in the GroEL chaperonin. The distinctive binding behavior of Rubisco and the capsid protein was further investigated using tandem mass spectrometry on the intact 800-914 kDa GroEL-substrate complexes. Our data suggest that even in the gas phase the substrates remain bound inside the GroEL cavity. The analysis revealed further that binding of Rubisco to the GroEL oligomer stabilizes the chaperonin complex significantly, whereas binding of one capsid protein did not have the same effect. However, addition of a second capsid protein molecule to GroEL resulted in a similar stabilizing effect to that obtained after the binding of a single Rubisco. On the basis of the stoichiometry of the GroEL chaperonin-substrate complex and the dissociation behavior of the two different substrates, we hypothesize that the binding of a single capsid polypeptide does not induce significant conformational changes in the GroEL trans ring, and hence the unoccupied GroEL ring remains accessible for a second capsid molecule.