Raman and cathodoluminescence spectroscopic investigations on Permian fossil wood from Chemnitz--a contribution to the study of the permineralisation process

Samples of different three-dimensionally preserved fossil plants (Medullosa sp., Dadoxylon sp., Calamodendron striatum, Psaronius sp.) from the Lower Permian petrified forest of Chemnitz were examined with regard to their chemical composition and structural order. Raman spectroscopy and cathodoluminescence microscopy are shown to be powerful tools for such investigations. Silicified wood from Chemnitz-Hilbersdorf generally shows yellow cathodoluminescence (CL) of the cell walls and only weak yellow-brownish CL of the cell lumina. By time-resolved cathodoluminescence spectroscopy, a secondary mineralisation of hydrothermal origin was recognized. The latter is shown by short-lived blue CL at the cell walls extinguishing the yellow signal. Therefore, after the primary silicification step a secondary mineralisation step initiated by hydrothermal processes, seems to have taken place at probably slightly higher temperatures. The resulting silica matrix consists of phanerocrystalline and microcrystalline alpha-quartz as well as microcrystalline moganite, both partially associated with iron oxides. Dadoxylon sp. is a prominent example for parallel permineralisation by alpha-quartz and fluorspar, which is outstanding for the Chemnitz Petrified Forest. CL on this samples shows parallel silicification and fluoritisation, followed by infiltration of iron oxides. Permineralised samples show very low percentage of original organic remains. The seed fern Medullosa, for example, shows dispersed carbon, which is mainly restricted to the centres of the typical star-shaped vascular bundles. Raman spectroscopy revealed that these carbonaceous particles are of an anthracite structure. For experimental confirmation coal samples of different rank, especially anthracite from different geological times and localities, were studied by means of Raman spectroscopy. The remaining pith of the vascular bundles is white-coloured and consists of alpha-quartz and moganite, whereas surrounding tracheides exhibit white and reddish coloured parts. The reddish parts, mainly found in the rays, additionally contain alpha-Fe2O3 and Fe3O4 among the SiO2 polymorphs of alpha-quartz and moganite. Sometimes iron oxides could have dominated permineralisation processes as the peak intensities of distinct parts of the samples suggest.     

Direct identification of all oncogenic mutants in KRAS exon 1 by cycling temperature capillary electrophoresis

Over the past few decades, advances in genetics and molecular biology have revolutionized our understanding of cancer initiation and progression. Molecular progression models outlining genetic events have been developed for many solid tumors, including colon cancer. Previous reports in the literature have shown a relationship between different KRAS mutations and prognosis and response to medical treatment in colon cancer patients. Furthermore, the presence of a mutated KRAS has been correlated with different clinicopathological variables including age and gender of patients and tumor location. To our knowledge, few institutions screen for KRAS mutations on regular basis in colon cancer patients despite such evidence that knowledge of KRAS exon 1 status is informative. Here, we report on a mutation analysis method adapted to a 96-capillary electrophoresis instrument that allows identification of all 12 oncogenic mutations in KRAS exon 1 under denaturing conditions. To determine the optimal parameters, a series of DNA constructs generated by site-directed mutagenesis was analyzed and the migration times of all mutant peaks were measured. A classification tree was then made based on the differences in migration time between the mutants and an internal standard. A randomized series of 500 samples constructed with mutagenesis as well as 60 blind samples from sporadic colon carcinomas was analyzed to test the method. No wild-type samples were scored as mutants and all mutants were correctly identified. Post polymerase chain reaction (PCR) analysis time of 96 samples was performed within 40 min.     

Enhancing the effectiveness of virtual screening by fusing nearest neighbor lists: a comparison of similarity coefficients

This paper evaluates the effectiveness of various similarity coefficients for 2D similarity searching when multiple bioactive target structures are available. Similarity searches using several different activity classes within the MDL Drug Data Report and the Dictionary of Natural Products databases are performed using BCI 2D fingerprints. Using data fusion techniques to combine the resulting nearest neighbor lists we obtain group recall results which, in many cases, are a considerable improvement on standard average recall values obtained for individual structures. It is shown that the degree of improvement can be related to the structural diversity of the activity class that is searched for, the best results being found for the most diverse groups. The group recall of active compounds using subsets of the class is also investigated: for highly self-similar activity classes, the group recall improvement saturates well before the full activity class size is reached. A rough correlation is found between the relative improvement using the group recall and the square of the number of unique compounds available in all of the merged lists. The Tanimoto coefficient is found unambiguously to be the best coefficient to use for the recovery of active compounds using multiple targets. Furthermore, when using the Tanimoto coefficient, the "MAX" fusion rule is found to be more effective than the "SUM" rule for the combination of similarity searches from multiple targets. The use of group recall can lead to improved enrichment in database searches and virtual screening.     

Application of flow-injection analysis in the on-line monitoring of sugars,lactic acid,protein and biomass during lactic acid fermentations

A laboratory system for the on-line monitoring of important lactic acid fermentation variables is described. The system contains flow-injection analysers for glucose, lactose, galactose, lactate and protein and a continuous-flow analyser for the biomass concentration. The sugar and lactate analysers are based on enzymatic reactions involving oxidases followed by chemiluminescence detection of the hydrogen peroxide formed. The protein analyser is based on the biuret reaction. The system has been used to monitor many fermentation experiments, and some results are presented as examples.     

Synthesis of β3‐Homophenylalanine‐Derived Amino Acids and Peptides by Suzuki Coupling in Solution and on Solid Support

β‐Peptides and, to a certain extent, also mixed α,β‐peptides, are resistant to degradation by a variety of proteolytic enzymes that rapidly degrade natural α‐peptides. This is one of many characteristics that make β‐peptides an attractive class of compounds for drug‐discovery studies. On the other hand, modern organometallic reactions such as the Suzuki–Miyaura cross‐coupling have become standard tools in industry laboratories to derivatize side chains of α‐peptidic compounds to build up libraries of unnatural peptides. Combining both features, we prepared (4‐bromo)‐β³‐homophenylalanine derivatives 3 – 5 and 12 as precursors for Suzuki–Miyaura couplings. From these bromo compounds, we synthesized biaryl‐substituted β‐homoamino acids 6 , and analogs 13 and 15 of the anti‐AIDS drug Saquinavir.     

Density fluctuations in amorphous and semicrystalline polymers

Summary The small-angle scattering of amorphous and semicrystalline polymers contains an intensity component due to density fluctuations within the crystalline and amorphous domains.For amorphous polymers, the density fluctuations aboveT _g correspond to the theoretical value for a fluid system in thermodynamic equilibrium. BelowT _g , a temperature dependence proportional to T is observed over a range of about 50°. At lower temperatures, a linear relationship with a smaller slope has been found which extrapolates to a non-zero value at 0 °K. This value corresponds to the frozen-in disorder, the slope at low temperatures is related to thermal vibrations and can be evaluated in terms of photon-phonon scattering.Semicrystalline polymers show a temperature dependence of the density fluctuation similar to that of the amorphous polymers. At constant temperature the density fluctuations vary linearly with crystallinity.Natural rubber shows an increase of the density fluctuations with increasing cross-linking densities from which information on the density changes in the vicinity of a cross-link and on the statistics of the distribution of cross-linking can be obtained.

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Zusammenfassung Die Kleinwinkelstreuung amorpher und teilkristalliner Polymere besitzt eine Intensitätskomponente, die von Dichtefluktuationen innerhalb der kristallinen und amorphen Bezirke herrührt. Für amorphe Polymere entspricht die Dichtefluktuation oberhalb vonT _g dem theoretischen Wert für ein fluides System im thermodynamischen Gleichgewicht. UnterhalbT _g wird eine Temperaturabhängigkeit proportional zuT über einen Bereich von etwa 50° beobachtet. Bei tieferen Temperaturen wird eine lineare Beziehung mit einer geringeren Steigung gefunden, welche zu einem endlichen Wert bei 0 °K extrapoliert werden kann. Dieser Wert bezieht sich auf die eingefrorene Fehlordnung, die Steigung bei tiefen Temperaturen ist auf thermische Schwingungen zurückzuführen und kann als Photon-Phonon-Streuung ausgewertet werden.Teilkristalline Polymere zeigen eine Temperaturabhängigkeit der Dichtefluktuation, die der von amorphen Polymeren ähnlich ist. Bei konstanter Temperatur ändert sich die Dichtefluktuation linear mit der Kristallinität.Naturkautschuk zeigt eine mit der Vernetzungsdichte ansteigende Dichtefluktuation, aus der man Information über die Dichteänderung in der Umgebung eines Netzpunktes und die Statistik der Netzpunktverteilung erhalten kann.

     

A novel method for the filterless preconcentration of iron

A novel method of analysis of iron by filterless preconcentration is presented. This is the first example of efficient preconcentration of a refractory transition metal where coprecipitation and columns were omitted. The method applies a manifold of flow injection analysis (FIA) to iron species that are preconcentrated on the inner walls of a tubular reactor. It was found that the adsorption of iron species to the walls was particularly pronounced in reactors of nylon material and enrichment factors of 30-35 could be attained, as dependent on the length of the reactor and on the time of preconcentration. In the preconcentration step of the FIA accessory, the optimum efficacy was obtained when the acidity of the samples was adjusted by HCl to pH = 2.5 whereas the ammonia preconcentration buffer should be kept alkaline at pH = 9.8. After being preconcentrated on the tubular reactor, the iron species were eluted by hydrochloric acid and analysed by flame atomic absorption spectrometry (FAAS). An unprecedented low limit of detection (LOD, 3sigma) of 1.8 microg L(-1) was thus obtained for the analysis of iron by FAAS, and the calibration line was linear up to 100 microg L(-1). A high sampling frequency of 40 per hour was obtained and the protocol allowed analysis of small amounts of iron in drinking water, in digested samples and in saline water. The major influence of interferences originated from ligands that are known to complex strongly to iron species. The method thus developed was uncomplicated in operation and it exhibited an excellent long-term stability and a high selectivity. Further, it was environmentally safe owing to production of non-toxic waste disposals. Equally high enrichment factors (EF) were obtained for Fe(ii) and Fe(iii), which is explained by the very low solubility product of both species.