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First comparison of array-derived rotational ground motions with direct ring laser measurements
(2006)
Recently, ring laser technology has provided the first consistent observations of rotational ground motions around a vertical axis induced by earthquakes. "Consistent," in this context, implies that the observed waveforms and amplitudes are compatible with collocated recordings of translational ground motions. In particular, transverse accelerations should be in phase with rotation rate and their ratio proportional to local horizontal phase velocity assuming plane-wave propagation. The ring laser installed at the Fundamental station Wettzell in the Bavarian Forest, Southeast Germany, is recording the rotation rate around a vertical axis, theoretically a linear combination of the space derivatives of the horizontal components of motion. This suggests that, in principle, rotation can be derived from seismic-array experiments by "finite differencing." This has been attempted previously in several studies; however, the accuracy of these observations could never be tested in the absence of direct measurements. We installed a double cross-shaped array of nine stations from December 2003 to March 2004 around the ring laser instrument and observed several large earthquakes on both the ring laser and the seismic array. Here we present for the first time a comparison of array-derived rotations with direct measurements of rotations for ground motions induced by the M 6.3 Al Hoceima, Morocco, earthquake of 24 February 2004. With complete 3D synthetic seismograms calculated for this event we show that even low levels of noise may considerably influence the accuracy of the array-derived rotations when the minimum number of required stations (three) is used. Nevertheless, when using all nine stations, the overall fit between direct and array-derived measurements is surprisingly good (maximum correlation coefficient of 0.94).
Molecule-detective
(2006)
Biosensors are analytical devices incorporating biological material (receptor) intimately associated with or integrated within a physicochernical transducer. Advantages are the high selectivity for analyte detection. Examples given comprise the very successful commercial blood glucose biosensors made for the self-control by the diabetic patients. Other biosensors are part of an analytic system, including the sensor chips Of surface plasmon resonance or interferometry based devices, piezoelectric or reflectometric sensors capable of direct measurement of mass changes, and thermometric and other reagentless sensors. The development of nanotubes-based devices allows for significant enhancment of the signal-to-noise ratio of the biosensors. A milestone on the way towards miniaturization and parallelization of biosensors is the recently developed and prize-winning electronic DNA chip
We describe eight new microsatellite loci for the critically endangered fire-bellied toad, Bombina bombina. Seven of them are polymorphic with two to seven alleles per locus, an expected heterozygosity between 0.41 and 0.8, and an observed heterozygosity between 0.27 and 0.7. The yield of new loci was relatively low, presumably due to mildly repetitive sequence motifs in microsatellite flanking regions. As typical for anurans, cross-species amplification was limited (here, to congeners Bombina orientalis and Bombina variegata). Combining these new loci with those already available provides a reasonable number of loci for population studies and pedigree analysis in Bombina
Ionic liquids based on imidazolium, pyridinium, and alkylammonium salts were investigated as solvents in free radical polymerization of the model monomer n-butyl methacrylate. The properties of the ionic liquids were systematically varied by changing the length of the alkyl substituents on the cations, and by employing different anions such as tetrafluoroborate, hexafluorophosphate, tosylate, triflate, alkyl sulfates and dimethyl phosphate. Results were compared to analogous polymerizations in toluene and in bulk. The solvents have no detectable influence on polymer tacticity. However, the molar masses obtained and the degree of polymerization, respectively, are very sensitive to the choice of the solvent. The degrees of polymerization are significantly higher when polymerizations were carried out in ionic liquids compared to polymerization in toluene, and can even exceed the values obtained by bulk polymerization. Imidazolium salts unsubstituted at C-2 result in an increase in the degree of polymerization of the poly(butyl methacrylate) with increasing viscosity of these ionic liquids. Methyl substitution at C-2 of the imidazolium ion results in an increase in the viscosity of the ionic liquid and in a viscosity independent degree of polymerization of the poly(butyl methacrylate). Ionic liquids based on imidazolium salts seem preferable over pyridinium and alkylammonium salts because of the higher degree of polymerization of the poly(butyl methacrylate)s obtained in the imidazolium salts. The glass transition temperatures and thermal stabilities are higher for poly(butyl methacrylate)s synthesized in the ionic liquids compared to the polymer made in toluene
Free radical homo- and copolymerization of the highly polar 3-(N-[2-methacryloyloxyethyl]-N,N-dimethylammonio) propane sulfonate with the nonpolar n-butylmethacrylate was investigated in the ionic liquids 1-butyl-3-methyl imidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium hexafluoro phosphate, and compared to analogous polymerizations in standard solvents. Higher molar masses are obtained for the zwitterionic homopolymer when the polymerization is carried out in an ionic liquid compared to the classical reaction in water. Although homopolymerization of the sulfobetain monomer as well as of n-butylmethacrylate results in phase separation during the polymerization process, copolymerization of a stoichiometric ratio of the two monomers in the ionic liquids produced transparent gels indicating that no macrophase separation occurs. The use of ionic liquids as reaction medium improved the copolymerization behavior of the two methacrylates significantly. Whereas only minor amounts of n-butyl methacrylate were incorporated in the copolymer when synthesized in acetonitrile, the content of the non-polar monomer units in the zwitterionic copolymer approached increasingly its content in the polymerization mixture when ionic liquids were employed as solvents
The spin probes TEMPO, TEMPOL, and CAT-1 were used to investigate microviscosity and micropolarity of imidazolium based ionic liquids bearing either tetrafluoroborate or hexafluorophosphate as anions and a variation of the substitution at the imidazolium ion. The average rotational correlation times (r) obtained by complete simulation of the X-band ESR spectra of TEMPO, TEMPOL, and CAT-1 increase with increasing viscosity of the ionic liquid although no Stokes Einstein behavior is observed. This is caused by microviscosity effects of the ionic liquids shown by application of the Gierer-Wirtz theory. Interestingly, the jump of the probe molecule into the free volume of the ionic liquids is a nonactivated process. The hyperfine coupling constants (A(iso) (N-14)) of TEMPO and TEMPOL dissolved in the ionic liquids do not depend on the structure of the ionic liquids. The A(iso) (N-14) values show a micropolarity of the ionic liquids that is comparable with methylenchloride in case of TEMPO and with dimethylsulfoxide in case of TEMPOL. Micropolarity monitored by CAT-1 strongly depends on structural variation of the ionic liquid. CAT-1 dissolved in imidazolium salts substituted with shorter alkyl chains at the nitrogen atom exhibits a micropolarity comparable with dimethylsulfoxide. A significant lower micropolarity is found for imidazolium. salts bearing a longer alkyl substituent at the nitrogen atom or a methyl substituent at C-2. Copyright (c) 2006 John Wiley & Sons, Ltd
The averaged dynamics of various two-phase systems in a high-frequency vibration field is studied theoretically. The continuum approach is applied to describe such systems as solid particle suspensions, emulsions, bubbly fluids, when the volume concentration of the disperse phase is small and gravity is insignificant. The dynamics of the disperse system is considered by means of the method of averaging, when the fast pulsation and slow averaged motion can be treated separately. Two averaged models for both nondeformable and deformable particles, when the compressibility of the disperse phase becomes important, are obtained. A criterion when the compressibility of bubbles cannot be neglected is figured out. For both cases the developed models are applied to study the averaged dynamics of the disperse media in an infinite plane layer under the action of transversal vibration. (C) 2006 American Institute of Physics
In side pumped laser head geometries good extraction of energy has to be weighted against diffraction effects of the amplified beam. Beam clipping at the aperture of laser rods can be avoided by using an undoped cladding around the doped core. The wings of e. g. Gaussian beams can be accommodated in the cladding. Phase distortion by the refractive index step of the rod can be compensated by a phase conjugating mirror in double pass configuration. In our proof of principle experiment the brightness of the beam from core doped amplifier rods was shown to be doubled compared to a conventional rod of the same outer diameter. (c) 2006 Optical Society of America
The spin probes 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), 4-hydroxy-2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPOL), and 2,2,6,6-tetramethyl-4-trimethylammoniumpiperidine-1-oxyllodide (CAT-1) are examined in a number of ionic liquids based on substituted imidazolium cations and tetrafluoroborate and hexafluorophosphate anions, respectively. The reorientation correlation times tau(R) of the spin probes in these systems have been determined by complete spectra simulation and, for rapid reortientation, by analysis of the intensities of the hyperfine lines of the electron spin resonance (ESR) spectra. A comparison of the results with those from the model system glycerol/water and selected organic solvents is made. Additions of diamagnetic and paramagnetic ions allow the conclusion that salt effects and spin exchange are present, and that both are superimposed by motional effects. Specific interactions in the ionic liquids, as well as between the spin-probe molecules and the constituents of the ionic liquids are reflected in the spectra of the spin probes, depending on their molecular structure
Profiling of plant secondary metabolites is still a very difficult task. Liquid chromatography (LC) or capillary electrophoresis hyphenated with different kinds of detectors are methods of choice for analysis of polar, thermo labile compounds with high molecular masses. We demonstrate the applicability of LC combined with UV diode array or/and mass spectrometric detectors for the unambiguous identification and quantification of flavonoid conjugates isolated from Arahidopsis thaliana leaves of different genotypes and grown in different environmental conditions. During LC/UV/MS/MS analyses we were able to identify tetra-, tri, and di-glycosides of kaempferol, quercetin and isorhamnetin. Based on our results we can conclude that due to the co-elution of different chemical compounds in reversed phase H PLC systems the application of UV detectors does not allow to precisely profile all flavonoid conjugates existing in A. thaliana genotypes. Using MS detection it was possible to unambiguously recognize the glycosylation patterns of the aglycones. However, from the mass spectra we could not conclude neither the anomeric form of the C-1 carbon atoms of sugar moieties in glycosidic bonds between sugars or sugar and aglycone nor the position of the second carbon involved in disaccharides. The applicability of collision induced dissociation techniques (CID MS/MS) for structural analyses of the studied group of plant secondary metabolites with two types of analyzers (triple quadrupole or ion trap) was demonstrated.
Background: The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group. Results: In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12: 1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes. Conclusion: We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files.
To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.
Rezensiertes Werk:
Frank, Robert: Phrase Structure Composition and Syntactic Dependencies. - Cambridge, MA : MIT Press, 2002. - xiv + 326 S.
Context: Placental and circulatory soluble fms-like tyrosine kinase 1 (sFlt1) has proven to be elevated in pregnant women with preeclampsia, a disease characterized by hypertension, proteinuria, and endothelial dysfunction. Recent studies also demonstrated an autoantibody against the angiotensin II type 1 (AT1) receptor (AT1-AA) in that disease. Objective: Both factors are discussed as key players in the etiology of preeclampsia. However, it has not yet been clarified whether these two circulating factors correlate and whether synergy determines the severity of pathology. Design: AT1-AA was retrospectively determined by a bioassay and sFlt1 by an ELISA. Patients: Serum from second-trimester pregnancies with normal or abnormal uterine perfusion and in women at term with or without pregnancy pathology was analyzed. Results: Most of the preeclamptic patients were characterized by high sFlt1 levels and the presence of AT1-AA, although the agonistic effects of the antibody did not correlate with the sFlt1 concentrations (P = 0.85). Although AT1- AA was also detected in second-trimester pregnancies evidencing abnormal uterine perfusion without later pathology, sFlt1 was not significantly elevated in these pregnancies, compared with those with normal uterine perfusion. However, whereas women with abnormal perfusion and later pregnancy pathology did not differ in AT1-AA, compared with those with normal outcome, sFlt1 was significantly increased. Again, the two factors did not correlate (P = 0.15). Conclusions: We conclude that AT1-AA bioactivity and sFlt1 concentrations do not correlate, are not mutually dependent, and are thus probably involved in distinct pathogenetic mechanisms. Both factors in combination may not be causative for the early impaired trophoblast invasion and pathological uterine perfusion
The terrestrial biosphere impacts considerably on the global carbon cycle. In particular, ecosystems contribute to set off anthropogenic induced fossil fuel emissions and hence decelerate the rise of the atmospheric CO₂ concentration. However, the future net sink strength of an ecosystem will heavily depend on the response of the individual processes to a changing climate. Understanding the makeup of these processes and their interaction with the environment is, therefore, of major importance to develop long-term climate mitigation strategies. Mathematical models are used to predict the fate of carbon in the soil-plant-atmosphere system under changing environmental conditions. However, the underlying processes giving rise to the net carbon balance of an ecosystem are complex and not entirely understood at the canopy level. Therefore, carbon exchange models are characterised by considerable uncertainty rendering the model-based prediction into the future prone to error. Observations of the carbon exchange at the canopy scale can help learning about the dominant processes and hence contribute to reduce the uncertainty associated with model-based predictions. For this reason, a global network of measurement sites has been established that provides long-term observations of the CO₂ exchange between a canopy and the atmosphere along with micrometeorological conditions. These time series, however, suffer from observation uncertainty that, if not characterised, limits their use in ecosystem studies. The general objective of this work is to develop a modelling methodology that synthesises physical process understanding with the information content in canopy scale data as an attempt to overcome the limitations in both carbon exchange models and observations. Similar hybrid modelling approaches have been successfully applied for signal extraction out of noisy time series in environmental engineering. Here, simple process descriptions are used to identify relationships between the carbon exchange and environmental drivers from noisy data. The functional form of these relationships are not prescribed a priori but rather determined directly from the data, ensuring the model complexity to be commensurate with the observations. Therefore, this data-led analysis results in the identification of the processes dominating carbon exchange at the ecosystem scale as reflected in the data. The description of these processes may then lead to robust carbon exchange models that contribute to a faithful prediction of the ecosystem carbon balance. This work presents a number of studies that make use of the developed data-led modelling approach for the analysis and interpretation of net canopy CO₂ flux observations. Given the limited knowledge about the underlying real system, the evaluation of the derived models with synthetic canopy exchange data is introduced as a standard procedure prior to any real data employment. The derived data-led models prove successful in several different applications. First, the data-based nature of the presented methods makes them particularly useful for replacing missing data in the observed time series. The resulting interpolated CO₂ flux observation series can then be analysed with dynamic modelling techniques, or integrated to coarser temporal resolution series for further use e.g., in model evaluation exercises. However, the noise component in these observations interferes with deterministic flux integration in particular when long time periods are considered. Therefore, a method to characterise the uncertainties in the flux observations that uses a semi-parametric stochastic model is introduced in a second study. As a result, an (uncertain) estimate of the annual net carbon exchange of the observed ecosystem can be inferred directly from a statistically consistent integration of the noisy data. For the forest measurement sites analysed, the relative uncertainty for the annual sum did not exceed 11 percent highlighting the value of the data. Based on the same models, a disaggregation of the net CO₂ flux into carbon assimilation and respiration is presented in a third study that allows for the estimation of annual ecosystem carbon uptake and release. These two components can then be further analysed for their separate response to environmental conditions. Finally, a fourth study demonstrates how the results from data-led analyses can be turned into a simple parametric model that is able to predict the carbon exchange of forest ecosystems. Given the global network of measurements available the derived model can now be tested for generality and transferability to other biomes. In summary, this work particularly highlights the potential of the presented data-led methodologies to identify and describe dominant carbon exchange processes at the canopy level contributing to a better understanding of ecosystem functioning.
Electrospray ionization was employed to study the mass spectrometric behavior of the maleonitrile tetrathiacrown ethers mn12S(4) (1) and mn13S(4) (2) and maleonitrile pentathiacrown ether mn15S(5) (3) and of their complexes with various metal salts (MX2, M=Pd, Pt, Ni, Co, Fe; X=Cl, CrCl3, Ni(BF4)(2), TIPF6 or Cd(NO3)(2)) and Cu(SO3CF3)(2). Both singly charged, [MXL](+) and [MXL2]+, and doubly charged complexes, [MLn](2+) (n = 2-5), were observed. The formation of the different complexes consisting of the transition metal ion, the counterion and the various crown ethers and their subsequent dissociation was also studied by collision-induced dissociation measurements which were also used to evaluate the relative stabilities of the complexes. It was found that the collisional voltages for the dissociation of the complexes were generally greater in the [MXL](+) complexes than in the corresponding [MXL2]+ complexes. Copyright (c) 2006 John Wiley & Sons, Ltd
A time-staggered semi-Lagrangian discretization of the rotating shallow-water equations is proposed and analysed. Application of regularization to the geopotential field used in the momentum equations leads to an unconditionally stable scheme. The analysis, together with a fully nonlinear example application, suggests that this approach is a promising, efficient, and accurate alternative to traditional schemes.
The ancestral galectin from the sponge Geodia cydonium (GCG) is classified on a structural basis to the prototype subfamily, whereas its carbohydrate-binding specificity is related to that of the mammalian chimera-type galectin-3. This dual coordination reveals GCG as a potential precursor of the later evolved galectin subfamilies, which is reflected in the primary structure of the protein. This study provides evidence that GCG is the LECT1 gene product, while neither a previously described LECT2 gene nor a functional LECT2 gene product was found in the specimen under investigation. The electrophoretically separated protein isomers with apparent molecular masses of 13, 15, and 16 kDa correspond to variants of the LECT1 protein-exhibiting peptide sequence polymorphisms that concern critical positions of the carbohydrate recognition domain (13 kDa: Leu51, Asn55, His130, Gly137; 15 kDa: Ser51, Asn55, Asn130, Gly137; 16 kDa: Ser51, Tyr55, Asn130, Glu137). Four residues, highly conserved in the galectin family, are substituted. None of the residues claimed to be involved in interactions with GalNAc alpha 1-3 moieties at an extended binding subsite of galectin-3 was identified in the corresponding positions of GCG. Apparently, the substitutions do not confer distinct binding characteristics to the GCG variants as evidenced by binding studies with a recombinantly expressed 15-kDa isoform. The natural isoforms as well as the recombinant 15-kDa isoform oligomerize by the formation of non-covalent heteromeric or homomeric complexes. A phosphorylation of the galectin was confirmed neither by mass spectrometry nor by alkaline phosphatase treatment combined with isoelectric focusing