Recent Developments in Ring-Opening Metathesis Polymerization (ROMP)

Properties and applications of newly developed homogeneous Ring-Opening Metathesis Polymerization catalysts as well as Photo-induced Ring-Opening Metathesis Polymerization catalysts are discussed. In contrast to well-defined, one-component metal-carbene catalysts, the aqueous ROMP with simple RuII salts is a chain reaction and not a living polymerization. One-component Photo-ROMP initiators were developed with good thermal latency and are either based on early-transition-metal alkyl complexes or on [Ru(arene)2]2+ complexes. Mechanistic aspects of the photochemically induced solvation of RuII complexes are presented

Genetic and Molecular Analyses of PEG10 Reveal New Aspects of Genomic Organization, Transcription and Translation

The paternally expressed gene PEG10 is a retrotransposon derived gene adapted through mammalian evolution located on human chromosome 7q21. PEG10 codes for at least two proteins, PEG10-RF1 and PEG10-RF1/2, by -1 frameshift translation. Overexpression or reinduced PEG10 expression was seen in malignancies, like hepatocellular carcinoma or B-cell acute and chronic lymphocytic leukemia. PEG10 was also shown to promote adipocyte differentiation. Experimental evidence suggests that the PEG10-RF1 protein is an inhibitor of apoptosis and mediates cell proliferation. Here we present new data on the genomic organization of PEG10 by identifying the major transcription start site, a new splice variant and report the cloning and analysis of 1.9 kb of the PEG10 promoter. Furthermore, we show for the first time that PEG10 translation is initiated at a non-AUG start codon upstream of the previously predicted AUG codon as well as at the AUG codon. The finding that PEG10 translation is initiated at different sides adds a new aspect to the already interesting feature of PEG10's −1 frameshift translation mechanism. It is now important to unravel the cellular functions of the PEG10 protein variants and how they are related to normal or pathological conditions. The generated promoter-reporter constructs can be used for future studies to investigate how PEG10 expression is regulated. In summary, our study provides new data on the genomic organization as well as expression and translation of PEG10, a prerequisite in order to study and understand the role of PEG10 in cancer, embryonic development and normal cell homeostasis

Efficient characterization of high-dimensional parameter spaces for systems biology

BACKGROUND: A biological system's robustness to mutations and its evolution are influenced by the structure of its viable space, the region of its space of biochemical parameters where it can exert its function. In systems with a large number of biochemical parameters, viable regions with potentially complex geometries fill a tiny fraction of the whole parameter space. This hampers explorations of the viable space based on "brute force" or Gaussian sampling. RESULTS: We here propose a novel algorithm to characterize viable spaces efficiently. The algorithm combines global and local explorations of a parameter space. The global exploration involves an out-of-equilibrium adaptive Metropolis Monte Carlo method aimed at identifying poorly connected viable regions. The local exploration then samples these regions in detail by a method we call multiple ellipsoid-based sampling. Our algorithm explores efficiently nonconvex and poorly connected viable regions of different test-problems. Most importantly, its computational effort scales linearly with the number of dimensions, in contrast to "brute force" sampling that shows an exponential dependence on the number of dimensions. We also apply this algorithm to a simplified model of a biochemical oscillator with positive and negative feedback loops. A detailed characterization of the model's viable space captures well known structural properties of circadian oscillators. Concretely, we find that model topologies with an essential negative feedback loop and a nonessential positive feedback loop provide the most robust fixed period oscillations. Moreover, the connectedness of the model's viable space suggests that biochemical oscillators with varying topologies can evolve from one another. CONCLUSIONS: Our algorithm permits an efficient analysis of high-dimensional, nonconvex, and poorly connected viable spaces characteristic of complex biological circuitry. It allows a systematic use of robustness as a tool for model discrimination

Synthesis of Polypyrrole-Coated Core/Shell Nanoparticles

The synthesis, physical characterization and scale-up of conductive, re-dispersible core/shell nanoparticles containing polypyrrole (PPy) in the shell are described. The compressed powders/films show a DC conductivity which is considerably higher than that of commercial standard products based on PEDOT/PSS ('AL 4083' from H.C. Starck). The particles have excellent film-forming properties since thin films (50–100 nm) made by spin-coating from aqueous dispersions of the particles have an AFM film roughness o

Atomic Force Microscopy Imaging of Living Cells

Over the last two decades, Atomic Force Microscopy (AFM) has emerged as the tool of choice to image living organisms in a near-physiological environment. Whereas fluorescence microscopy techniques allow labeling and tracking of components inside cells and the observation of dynamic processes, AFM is mainly a surface technique that can be operated on a wide range of substrates including biological samples. AFM enables extraction of topographical, mechanical and chemical information from these sample

A Web-based Platform for E-Learning and Blended Learning in Modelling and Simulation

The Mathematics Modelling and Tools (MMT) e-learning system is a platform used for supporting lectures and tutoring at the Vienna University and Technology. Additionally to traditional e-learning properties like up- and download of lecture notes, videos and slides the MMT system provides the surface for a virtual modelling and simulation laboratory. Very powerful calculation software like MATLAB, Java or Octave, running in behind, allows experimenting with targeted modelling and simulation examples prepared and developed by experts. These are first of all used to support the presentation directly at the lecture and can afterwards be accessed by students given a password at home. As especially MATLAB also allows development of suitable examples dealing with mathematics, so far about ten percent of all examples treat this specific topic and are used in math lectures. It showed that especially the live experience fiddling on pre-implemented examples poses a big improvement for lectures

Synthesis and NMR Spectroscopic Characterization of Organometallics in the Laboratory of Wolfgang von Philipsborn: Reminiscences of Former Graduate Students

On the occasion of his 80th birthday, former graduate students from the group of Prof. Wolfgang von Philipsborn from the Institute of Organic Chemistry, University of Zurich, describe from a personal perspective the scientific achievements of his group in the field of nuclear magnetic resonance, mainly applied to transition metals and in the field of organometallic chemistry. Interest in metal chemical shifts is driven by the need to understand reactivity of organometallic compounds in catalysis. Progress in the field is very much related to the technical development of NMR instruments. The range of experiments spans from simple 1D experiments with direct metal detection to 2D NMR experiments, in which metal frequencies are encoded via their attached protons or phosphorous ligands. Other examples come from the structural biology of metal-containing proteins or form the measurement of scalar couplings to quadrupolar nuclei via lineshape analysis. A particular emphasis is presented on how collaborations from various groups at the campus have been fruitful to the scientific progress in the von Philipsborn group. The article also contains a number of personal anecdotes that document life of the graduate students in his group at that time

A Web-based Platform for E-Learning and Blended Learning in Modelling and Simulation

The Mathematics Modelling and Tools (MMT) e-learning system is a platform used for supporting lectures and tutoring at the Vienna University and Technology. Additionally to traditional e-learning properties like up- and download of lecture notes, videos and slides the MMT system provides the surface for a virtual modelling and simulation laboratory. Very powerful calculation software like MATLAB, Java or Octave, running in behind, allows experimenting with targeted modelling and simulation examples prepared and developed by experts. These are first of all used to support the presentation directly at the lecture and can afterwards be accessed by students given a password at home. As especially MATLAB also allows development of suitable examples dealing with mathematics, so far about ten percent of all examples treat this specific topic and are used in math lectures. It showed that especially the live experience fiddling on pre-implemented examples poses a big improvement for lectures

Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments

BACKGROUND: The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10–100 μg of RNA. However, due to their small size, most biopsies do not yield this amount. Several different approaches for RNA amplification in vitro have been described and applied for microarray studies. In most of these, systematic analyses of the potential bias introduced by the enzymatic modifications are lacking. RESULTS: We examined the sources of error introduced by the T7 RNA polymerase based RNA amplification method through hybridisation studies on microarrays and performed statistical analysis of the parameters that need to be evaluated prior to routine laboratory use. The results demonstrate that amplification of the RNA has no systematic influence on the outcome of the microarray experiment. Although variations in differential expression between amplified and total RNA hybridisations can be observed, RNA amplification is reproducible, and there is no evidence that it introduces a large systematic bias. CONCLUSIONS: Our results underline the utility of the T7 based RNA amplification for use in microarray experiments provided that all samples under study are equally treated