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Experiments have been performed to explore the potential of the low emittance 855 MeV electron beam of the Mainz Microtron MAMI for imaging with coherent X-rays. Transition radiation from a micro-focused electron beam traversing a foil stack served as X-ray source with good transverse coherence. Refraction contrast radiographs of low absorbing materials, in particular polymer strings with diameters between 30 and 450 µm, were taken with a polychromatic transition radiation X-ray source with a spectral distribution in the energy range between 8 and about 40 keV. The electron beam spot size had standard deviation σh=(8.6 ± 0.1) µm in the horizontal and σv=(7.5 ± 0.1) µm in the vertical direction. X-ray films were used as detectors. The source-to-detector distance amounted to 11.4 m. The objects were placed in a distance of up to 6 m from the X-ray film. Holograms of strings were taken with a beam spot size σv=(0.50 ± 0.05) µm in vertical direction, and a monochromatic X-ray beam of 6 keV energy. A good longitudinal coherence has been obtained by the (111) reflection of a flat silicon single crystal in Bragg geometry. It has been demonstrated that a direct exposure CCD chip with a pixel size of 13 × 13 µm2 provides a highly effcient on-line detector. Contrast images can easily be generated with a complete elimination of all parasitic background. The on-line capability allows a minimization of the beam spot size by observing the smallest visible interference fringe spacings or the number of visible fringes. It has been demonstrated that X-ray films are also very useful detectors. The main advantage in comparison with the direct exposure CCD chip is the resolution. For the Structurix D3 (Agfa) X-ray film the standard deviation of the resolution was measured to be σf=(1.2 ± 0.4) µm, which is about a factor of 6 better than for the direct exposure CCD chip. With the small effective X-ray spot size in vertical direction of σv=(1.2±0.3) µm and a geometrical magnification of up to 7.4 high-quality holograms of tiny transparent strings were taken in which the holographic information is contained in up to 18 interference fringes. [ABSTRACT FROM AUTHOR]

In the present paper we explain the basic ideas of Robust Perron Cluster Analysis (PCCA+) and exemplify the different application areas of this new and powerful method. Recently, Deuflhard and Weber [5] proposed PCCA+ as a new cluster algorithm in conformation dynamics for computational drug design. This method was originally designed for the identification of almost invariant subsets of states in a Markov chain. As an advantage, PCCA+ provides an indicator for the number of clusters. It turned out that PCCA+ can also be applied to other problems in life science. We are going to show how it serves for the clustering of gene expression data stemming from breast cancer research [20]. We also demonstrate that PCCA+ can be used for the clustering of HIV protease inhibitors corresponding to their activity. In theoretical chemistry, PCCA+ is applied to the analysis of metastable ensembles in monomolecular kinetics, which is a tool for RNA folding [21]. [ABSTRACT FROM AUTHOR]

The analysis of the effects of expression of one viral protein on the host cell separately from the effect of other viral proteins is often limited by the efficiency of the transfection method. Lymphoid cells are effectively transfected by electroporation (1-4). However, the transfection efficiency varies usually between 5 and 20% of the living cells, depending on the cell line used. In the case of primary lymphoid cells, the transfection efficiency is below 5% (5-7). Thus the analysis of the influence of viral genes on the expression of cellular proteins is often impossible because of the predominance of untransfected cells. In addition, some viral genes could result in cytostasis, such as latent membrance protein 1 (LMP1; 8). The establishment of cell lines, where the viral gene is expressed constitutively or in an inducible fashion, is one way to try to address the problem, but is associated with a selection process (8,9). This selection process prevents the analysis of early effects of expressed viral genes and could also lead to secondary cell culture effects not associated with the viral gene. Often, inducible gene expression systems are difficult to modulate and can be leaky. To overcome these problems, it is useful to analyze transiently transfected cells and enrich them to obtain pure cell populations without a selection process. A number of methods exist, with magnetic- or fluorescence-activated cell sorting (MACS/FACS) being the most common approaches used (10). FACS and MACS are powerful and sophisticated methods for efficient purification of cells expressing a specific immunological marker molecule. Since the introduction of the green fluorescence protein (GFP) the purification of cells by FACS is no longer limited to immunological-stained proteins, which thus opens new applications for this approach. [ABSTRACT FROM AUTHOR]