40 research outputs found
Aliasing effects for random fields over spheres of arbitrary dimension
No full textIn this paper, aliasing effects are investigated for random fields defined on the d-dimensional
sphere Sd, and reconstructed from discrete samples. First, we introduce the concept of an aliasing function
on Sd. The aliasing function allows to identify explicitly the aliases of a given harmonic coefficient in
the Fourier decomposition. Then, we exploit this tool to establish the aliases of the harmonic coefficients approximated by means of the quadrature procedure named spherical uniform sampling. Subsequently, we
study the consequences of the aliasing errors in the approximation of the angular power spectrum of an isotropic random field, the harmonic decomposition of its covariance function. Finally, we show that band-
limited random fields are aliases-free, under the assumption of a sufficiently large amount of nodes in the quadrature rule
Signal molecules and regulatory components in the Rhizobium-legume symbiosis.
No full textPriefer UB, Patschkowski T, Schlüter A. Signal molecules and regulatory components in the Rhizobium-legume symbiosis. Endocytobiosis and Cell Research. 1998;12(3):201-202
Light-Induced Conformational Changes in the Plant Cryptochrome Photolyase Homology Region Resolved by Selective Isotope Labeling and Infrared Spectroscopy
No full textSommer C, Dietz MS, Patschkowski T, Mathes T, Kottke T. Light-Induced Conformational Changes in the Plant Cryptochrome Photolyase Homology Region Resolved by Selective Isotope Labeling and Infrared Spectroscopy. Photochemistry and Photobiology. 2017;93(3):881-887
Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris
No full textBuß M, Geerds C, Patschkowski T, Niehaus K, Niemann H. Perfect merohedral twinning combined with noncrystallographic symmetry potentially causes the failure of molecular replacement with low-homology search models for the flavin-dependent halogenase HalX from Xanthomonas campestris. Acta Crystallographica Section F Structural Biology Communications. 2018;74(6):345-350
THE RHIZOBIUM-LEGUMINOSARUM FNRN PROTEIN IS FUNCTIONALLY SIMILAR TO ESCHERICHIA-COLI FNR AND PROMOTES HETEROLOGOUS OXYGEN-DEPENDENT ACTIVATION OF TRANSCRIPTION
No full textSchlüter A, Patschkowski T, UNDEN G, PRIEFER UB. THE RHIZOBIUM-LEGUMINOSARUM FNRN PROTEIN IS FUNCTIONALLY SIMILAR TO ESCHERICHIA-COLI FNR AND PROMOTES HETEROLOGOUS OXYGEN-DEPENDENT ACTIVATION OF TRANSCRIPTION. MOLECULAR MICROBIOLOGY. 1992;6(22):3395-3404.An open reading frame from Rhizobium leguminosarum bv. viciae strain VF39, previously identified and found to be similar to Escherichia coli fnr and Rhizobium meliloti fixK (orf240, thereafter called fnrN), was further analysed. Analysis of the expression of an fnrN-lacZ transcriptional fusion revealed that fnrN is preferentially expressed under oxygen limitation. Using R. meliloti fixN-lacZ fusions it was shown that the fnrN gene product only mediates transcriptional activation under microaerobiosis, indicating that the FnrN protein responds, directly or indirectly, to oxygen. Plasmids which expressed fnrN under the control of an E. coli promoter were able to complement an E. coli fnr mutant with respect to anaerobic growth on nitrate but not fumarate, and to promote anaerobic but not aerobic activation of the Fnr-dependent E. coli genes narGHJI, nirB and fdnGHI coding for nitrate reductase, NADH-dependent nitrite reductase and formate dehydrogenase-N, respectively. Fumarate and DMSO reductase activities were not induced by FnrN. The E. coli fnr gene substituted for fnrN in oxygen-regulated transcription of nirB- and fixN-lacZ fusions in R. leguminosarum. The results indicate that Fnr and FnrN are functionally very similar and share a common mode of oxygen-dependent transcriptional activation. From hybridizaton studies, it appeared that fnrN-like genes are present in a number of different R. leguminosarum strains
Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (< 250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry
No full textGiampa M, Lissel M, Patschkowski T, et al. Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (< 250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry. Chemical Communications. 2016;52(63):9801-9804.A novel vacuum stable proton sponge, 4-maleicanhydridoproton sponge (MAPS), was prepared and applied as the matrix in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) of an aggressive brain tumor tissue (glioblastoma multiforme). Ionic maps of lactate, 2-hydroxyglutarate and chloride anions (m/z 89, 147, 35, respectively) were obtained using a routine MALDI ToF mass spectrometer
Flavin-Dependent Halogenases from Xanthomonas campestris pv. campestris B100 Prefer Bromination over Chlorination
No full textIsmail M, Frese M, Patschkowski T, Ortseifen V, Niehaus K, Sewald N. Flavin-Dependent Halogenases from Xanthomonas campestris pv. campestris B100 Prefer Bromination over Chlorination. ADVANCED SYNTHESIS & CATALYSIS. 2019;361(11):2475-2486.Flavin-dependent halogenases selectively introduce halogen substituents into (hetero-)aromatic substrates and require only molecular oxygen and halide salts for this regioselective oxidative CH-functionalization. Genomic analysis of Xanthomonas campestris pv. campestris B100 identified three novel putative members of this enzyme class. They were shown to introduce halogen substituents into, e. g., substituted indoles, while preferring bromide over chloride
Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT)
No full textWatt SA, Patschkowski T, Kalinowski J, Niehaus K. Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT). Journal of Biotechnology. 2003;106(2-3):287-300.The chemically-coded affinity tag (CCAT) method combines standard electrophoresis protocols with MALDI-TOF-MS analysis to identify and quantify protein abundances in complex samples in one step. This method is designed to fit into the workflow of SDS-PAGE or two-dimensional electrophoresis (2-DE) only requiring basic proteome laboratory equipment. Prior to electrophoresis two protein samples are separately labelled with a heavy or a light version of the CCAT reagent via reduced cysteines in the proteins. Equal amounts are then combined and electrophoretically separated. Proteins can then be excised from the gel to obtain their peptide mass fingerprint by mass spectrometry. This fingerprint enabled not only identification, but also quantification by comparing relative peak intensities of CCAT-labelled peptides. In this article, we display how the CCAT method can be used to analyse two protein samples in one gel and that the peak intensities of labelled peptides reflect the abundance of a protein in it. (C) 2003 Published by Elsevier B.V
Analysis of the secretome of the soybean symbiont Bradyrhizobium japonicum
No full textHempel J, Zehner S, Goettfert M, Patschkowski T. Analysis of the secretome of the soybean symbiont Bradyrhizobium japonicum. JOURNAL OF BIOTECHNOLOGY. 2009;140(1-2):51-58.Proteins from the supernatant of Bradyrhizobium japonicum were separated by two-dimensional gel electrophoresis and stained with Coomassie. This revealed more than 100 protein spots. Sixty-eight proteins were identified by mass spectrometry. Thirty-five are predicted to contain an N-terminal signal peptide characteristic for proteins transported by the general secretory pathway. Most of these appear to be substrate-binding proteins of the ABC transported family. Ten proteins were categorized as unclassified conserved or hypothetical. None of the proteins has similarity to proteins transported by a type I secretion system or to autotransporters. Three of the proteins might be located in the outer membrane. The addition of genistein led to changes in the spot pattern of three flagellar proteins and resulted in the identification of the nodulation outer protein Pgl. Moreover, the application of shot-gun mass spectrometry resulted in the first-time identification of NopB. NopH and NopT, which were present only after genistein induction. Replacing genistein with daidzein or coumestrol reduced the amount of the type III-secreted protein GunA2. (C) Elsevier B.V. All rights reserved
Identification of the bacterial superoxide dismutase (SodM) as plant-inducible elicitor of an oxidative burst reaction in tobacco cell suspension cultures
No full textWatt SA, Tellstroem V, Patschkowski T, Niehaus K. Identification of the bacterial superoxide dismutase (SodM) as plant-inducible elicitor of an oxidative burst reaction in tobacco cell suspension cultures. In: Journal of Biotechnology. Journal of Biotechnology. Vol 126. Elsevier; 2006: 78-86.Three of the most abundant proteins (OmpW, MopB and SodM) of the extracellular proteome of Xanthomonas campestris pv. campestris were analysed in a luminol-based oxidative burst assay to identify novel pathogen-associated molecular patterns (PAMP). Tobacco cell suspension cultures were used as a model system to monitor elicitor induced plant defence reaction. The candidate proteins were isolated from two-dimensional gels prior to application to the oxidative burst assay. The superoxide dismutase (SodM) was the only isolated protein that could elicit a notable hydrogen peroxide (H2O2) production in tobacco cell cultures indicating the initiation of plant defence. An alignment of the SodM sequences from X. campestris pv. campestris and Escherichia coli revealed 55.7% identity and 29% of the sequence were substitutions for amino acids with similar physicochemical properties. By using a commercially available purified E coli derived SodM preparation, it was possible to show that the amino acid sequence of this protein is responsible for the elicitation of an oxidative burst reaction in the tobacco cell culture model. This suggests that the bacterial superoxide dismutase is a novel pathogen-associated molecular pattern. The minimal elicitor active sequence, however, is still elusive. (c) 2006 Elsevier B.V. All rights reserved
