H^infinity well-posedness for degenerate p-evolution operators

Untersucht wird das Cauchy Problem für degenerierte $p$-Evolutionsgleichungen. Dabei kann für Gleichungen höherer Ordnung in $D_t$, die nur von der Zeit abhängen, gezeigt werden, dass das Problem H^\\infinity korrekt ist. Dafür werden gewisse Bedingungen an die Koeffizienten und deren erste Ableitungen gestellt. H^\\infinity korrekt bedeutet dabei, dass die Anfangsdaten $u_0\\in H^s$, $u_1$ in einem dazugehörigen Sobolevraum und die Lösung bezüglich $x$ in $H^{s-s_0}$ liegen. Eine Notwendigkeit für die Bedingungen kann allerdings nicht gezeigt werden. Auch ist offen, ob der Regularitätsverlust wirklich eintritt. Später wird der Beweis erweitert um das Ergebniss für Koeffizienten zu zeigen, die in gewisser Weise auch vom Ort abhängen können. Im zweiten Teil der Dissertation geht es um Korrektheit für degenerierte $p$-Evolutionsgleichungen mit zeitabhängigen Koeffizienten und zweiter Ordnung in $D_t$. Gefordert werden Bedingungen an die Koeffizienten und die ersten beiden Ableitungen bezüglich der Zeit. Damit wird gezeigt, dass diese in Skalen von Sobolevräumen korrekt gestellt sind. Abschließend wird die Schärfe der Bedingungen und das tatsächliche Auftreten des Regularitätsverlustes in der Lösung bewiesen

Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS

Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D [1H,1H]-NOESY spectra during denovoprotein structure determination by NMR, which have been implemented in the new software ATNOS (automated NOESY peak picking). The input for ATNOS consists of the amino acid sequence of the protein, chemical shift lists from the sequence-specific resonance assignment, and one or several 2D or 3D NOESY spectra. In the present implementation, ATNOS performs multiple cycles of NOE peak identification in concert with automated NOE assignment with the software CANDID and protein structure calculation with the program DYANA. In the second and subsequent cycles, the intermediate protein structures are used as an additional guide for the interpretation of the NOESY spectra. By incorporating the analysis of the raw NMR data into the process of automated denovoprotein NMR structure determination, ATNOS enables direct feedback between the protein structure, the NOE assignments and the experimental NOESY spectra. The main elements of the algorithms for NOESY spectral analysis are techniques for local baseline correction and evaluation of local noise level amplitudes, automated determination of spectrum-specific threshold parameters, the use of symmetry relations, and the inclusion of the chemical shift information and the intermediate protein structures in the process of distinguishing between NOE peaks and artifacts. The ATNOS procedure has been validated with experimental NMR data sets of three proteins, for which high-quality NMR structures had previously been obtained by interactive interpretation of the NOESY spectra. The ATNOS-based structures coincide closely with those obtained with interactive peak picking. Overall, we present the algorithms used in this paper as a further important step towards objective and efficient de novoprotein structure determination by NM

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustnes

Different pathways of the formation of highly oxidized multifunctional organic compounds (HOMs) from the gas-phase ozonolysis of β-caryophyllene

The gas-phase mechanism of the formation of highly oxidized multifunctional organic compounds (HOMs) from the ozonolysis of β-caryophyllene was investigated in a free-jet flow system at atmospheric pressure and a temperature of 295 ± 2 K. Reaction products, mainly highly oxidized RO2 radicals containing up to 14 oxygen atoms, were detected using chemical ionization – atmospheric pressure interface – time-of-flight mass spectrometry with nitrate and acetate ionization. These highly oxidized RO2 radicals react with NO, NO2, HO2 and other RO2 radicals under atmospheric conditions forming the first-generation HOM closed-shell products. Mechanistic information on the formation of the highly oxidized RO2 radicals is based on results obtained with isotopically labelled ozone (18O3) in the ozonolysis reaction and from hydrogen/deuterium (H/D) exchange experiments of acidic H atoms in the products. The experimental findings indicate that HOM formation in this reaction system is considerably influenced by the presence of a double bond in the RO2 radicals primarily formed from the β-caryophyllene ozonolysis. Three different reaction types for HOM formation can be proposed, allowing for an explanation of the detected main products: (i) the simple autoxidation, corresponding to the repetitive reaction sequence of intramolecular H-abstraction of a RO2 radical, RO2  →  QOOH, and subsequent O2 addition, next forming a peroxy radical, QOOH + O2  →  R′O2; (ii) an extended autoxidation mechanism additionally involving the internal reaction of a RO2 radical with a double bond forming most likely an endoperoxide and (iii) an extended autoxidation mechanism including CO2 elimination. The individual reaction steps of the reaction types (ii) and (iii) are uncertain at the moment. From the product analysis it can be followed that the simple autoxidation mechanism accounts only for about one-third of the formed HOMs. Time-dependent measurements showed that the HOM formation proceeds at a timescale of 3 s or less under the concentration regime applied here. The new reaction pathways represent an extension of the mechanistic understanding of HOM formation via autoxidation in the atmosphere, as recently discovered from laboratory investigations on monoterpene ozonolysis

Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY

ASCAN is a new algorithm for automatic sequence-specific NMR assignment of amino acid side-chains in proteins, which uses as input the primary structure of the protein, chemical shift lists of 1HN, 15N, 13Cα, 13Cβ and possibly 1Hα from the previous polypeptide backbone assignment, and one or several 3D 13C- or 15N-resolved [1H,1H]-NOESY spectra. ASCAN has also been laid out for the use of TOCSY-type data sets as supplementary input. The program assigns new resonances based on comparison of the NMR signals expected from the chemical structure with the experimentally observed NOESY peak patterns. The core parts of the algorithm are a procedure for generating expected peak positions, which is based on variable combinations of assigned and unassigned resonances that arise for the different amino acid types during the assignment procedure, and a corresponding set of acceptance criteria for assignments based on the NMR experiments used. Expected patterns of NOESY cross peaks involving unassigned resonances are generated using the list of previously assigned resonances, and tentative chemical shift values for the unassigned signals taken from the BMRB statistics for globular proteins. Use of this approach with the 101-amino acid residue protein FimD(25-125) resulted in 84% of the hydrogen atoms and their covalently bound heavy atoms being assigned with a correctness rate of 90%. Use of these side-chain assignments as input for automated NOE assignment and structure calculation with the ATNOS/CANDID/DYANA program suite yielded structure bundles of comparable quality, in terms of precision and accuracy of the atomic coordinates, as those of a reference structure determined with interactive assignment procedures. A rationale for the high quality of the ASCAN-based structure determination results from an analysis of the distribution of the assigned side chains, which revealed near-complete assignments in the core of the protein, with most of the incompletely assigned residues located at or near the protein surfac

Automated Protein NMR Structure Determination in Crude Cell-Extract

A fully automated, NOE-based NMR structure determination of a uniformly 13C,15N-labeled protein was achieved in crude cell-extract, without purification of the overexpressed protein. Essentially complete sequence-specific assignments were obtained using triple resonance experiments, based on the high intensity of the resonances from the overexpressed protein relative to those of the background. For the collection of NOE distance constraints, efficient discrimination between NOE cross peaks from the target protein and background signals was achieved using the programs ATNOS and CANDID. In the iterative ATNOS/CANDID procedure, the identification of the desired protein NOEs is initially guided by the self-consistency of the protein NOE-network. Although the intensities of the signals in this network vary over a wide range, and are in many instances comparable to or smaller than those of the background, the first cycle of calculations resulted in the correct global polypeptide fold, and the structure was then refined in six subsequent cycles using the intermediate NMR structures for additional guidance. The experience gained with this work demonstrates that the ATNOS/CANDID procedure for automatic protein structure determination is highly robust and reliable in the presence of intense background signals, and might thus also represent a platform for future protein structure determinations in physiological fluid

The J-UNIO protocol for automated protein structure determination by NMR in solution

The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6-10days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP_926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluate

Direct Probing of Criegee Intermediates from Gas-Phase Ozonolysis Using Chemical Ionization Mass Spectrometry

Criegee intermediates (CIs), mainly formed from gas-phase ozonolysis of alkenes, are considered as atmospheric oxidants besides OH and NO3 radicals as well as ozone. Direct CI measurement techniques are inevitably needed for reliable assessment of CIs' role in atmospheric processes. We found that CIs from ozonolysis reactions can be directly probed by means of chemical ionization mass spectrometry with a detection limit of about 10(4)-10(5) molecules cm(-3). Results from quantum chemical calculations support the experimental findings. The simplest CI, CH2OO, is detectable as an adduct with protonated ethers, preferably with protonated tetrahydrofuran. Kinetic measurements yielded k(CH2OO + SO2) = (3.3 +/- 0.9) X 10(-11) and k(CH2OO + acetic acid) = (1.25 +/- 0.30) x 10(-10) cm(3) molecule(-1) s(-1) at 295 +/- 2 K, in very good agreement with recent measurements using diiodomethane photolysis for CH2OO generation. CIs from the ozonolysis of cydohexene, acting as surrogate for cyclic terpenes, are followed as protonated species (CI)H+ using protonated amines as reagent ions. Kinetic investigations indicate a different reactivity of cydohexene-derived CIs compared with that of simple CIs, such as CH2OO. It is supposed that the aldehyde group significantly influences the CI reactivity of the cydohexene-derived CIs. The direct CI detection method presented here should allow study of the formation and reactivity of a wide range of different CIs formed from atmospheric ozonolysis reactions.Peer reviewe

Population ecology and life-history tactics of shallow, sand-bottom crustaceans at Kaikoura

Quantitative random sampling of a shallow, sand bottom exposed to unpredictable storm wave action at Kaikoura, New Zealand, between Oct. 1978 and Oct. 1980 provided detailed information on the population biologies of five crustaceans, the large myodocopid ostracod Cyaloleberis zealandiaa, and the gammaridean amphipods Hippomedon whero, Patuki roperi, Metaphoxus littoralis and Paraphoxus australis. Data for each species included seasonal changes in population density and structure, cohort composition, age at maturity, longevity, frequency and occurrence of breeding, egg size, duration of embryonic development, brood size and mortality, number of instars and broods per life-time and population sex ratios. The biology of myodocopid ostracods is reviewed and discussed with respect to Cyaloleberis and the question of instar size variations in ostracods generally is explored. Results for the amphipods are discussed in relation to current knowledge of amphipod biology. Utilization of the sand habitat was examined by comparing species population densities and compositions in ripples and in troughs at different times. Species sediment-depth distributions in ripples and in troughs were investigated in two successive months by sectioning cores into five layers. In some species juveniles, males and females inhabited different depths and other species were more abundant in either ripples or troughs. Sediment depths inhabited are discussed with respect to species burrowing rates, food, and an optimal sediment depth where niche overlap, and presumably competition also, is greatest. Recolonization of defaunated sand by each species was monitored over 1, 4, 8, 16 and 26 days initially and over 1 and 26 - 39 days during each of five subsequent months. Initial results showed remarkably fast recolonization by some species and changes in species population densities as recolonization proceeded. Within species the relative recolonization rates of juveniles, males and females may differ along with the sizes of recolonizing and control species subgroups. However, the experiments in subsequent months revealed that the pattern of species recolonization may change with time in response to no obvious factors. Results of the preceeding chapters are brought together in a final discussion of crustacean life-history tactics. Sediment depths inhabited provided a ranking of species habitat stabilities and mortality risks, both greatest at the sand surface. Population parameters, including net reproductive rates and innate capacities for increase, confirmed the ranking, but comparisons with species combinations of life-history traits strongly disagree with the predictions of two theories, r- and K-selection and bet-hedging. The failure of these theories is principally due to the existence of phylogenetic constraints, the lack of viable genetic alternatives for a trait. A new theory is required that encompasses phylogenetic constraints and recognizes the possibility of several equally successful combinations of traits in a given situation. Such a theory based on established ideas of costs of reproduction and of larger offspring from larger eggs being ecologically fitter must incorporate recent ideas on growth rates, body size and size-specific mortality