Dieter Naumann

Bio: Dieter Naumann is an academic researcher from Robert Koch Institute. The author has contributed to research in topics: Infrared spectroscopy & Protein secondary structure. The author has an hindex of 55, co-authored 173 publications receiving 11138 citations. Previous affiliations of Dieter Naumann include University of Cologne.

Microbiological characterizations by FT-IR spectroscopy

Abstract: Infrared signals of microorganisms are highly specific fingerprint-like patterns that can be used for probing the identity of microorganisms. The simplicity and versatility of Fourier-transform infrared spectroscopy (FT-IR) makes it a versatile technique for rapid differentiation, classification, identification and large-scale screening at the subspecies level.

Classification and identification of bacteria by Fourier-transform infrared spectroscopy

Abstract: Summary: This study describes a computer-based technique for classifying and identifying bacterial samples using Fourier-transform infrared spectroscopy (FT-IR) patterns. Classification schemes were tested for selected series of bacterial strains and species from a variety of different genera. Dissimilarities between bacterial IR spectra were calculated using modified correlation coefficients. Dissimilarity matrices were used for cluster analysis, which yielded dendrograms broadly equated with conventional taxonomic classification schemes. Analyses were performed with selected strains of the taxa Staphylococcus, Streptococcus, Clostridium, Legionella and Escherichia coli in particular, and with a database containing 139 bacterial reference spectra. The latter covered a wide range of Gram-negative and Gram-positive bacteria. Unknown specimens could be identified when included in an established cluster analysis. Thirty-six clinical isolates of Staphylococcus aureus and 24 of Streptococcus faecalis were tested and all were assigned to the correct species cluster. It is concluded that: (1) FT-IR patterns can be used to type bacteria; (2) FT-IR provides data which can be treated such that classifications are similar and/or complementary to conventional classification schemes; and (3) FT-IR can be used as an easy and safe method for the rapid identification of clinical isolates.

Ft-infrared and ft-raman spectroscopy in biomedical research

Abstract: ANN artificial neural network A/T absorbance/transmission ATR attenuated total reflectance DTGS deuterated triglycine sulfate FT Fourier transform FT-IR Fourier transform-infrared IR infrared LPS l...

Infrared Spectroscopy in Microbiology

Abstract: Infrared (IR) spectra of intact microbial cells are highly specific fingerprint-like signatures which are used to differentiate, classify, and identify diverse microbial species and strains. Microbial IR spectra are also useful to (1) detect in situ intracellular compounds or structures such as inclusion bodies, storage materials, and endospores, (2) monitor and quantify metabolically released CO2 in response to various different substrates, and (3) characterize growth-dependent phenomena and cell–drug interactions. The characteristic information, useful for microbial characterizations, is generally distributed over the entire IR region of the electromagnetic spectrum, i.e. over the near-infrared (NIR), mid-infrared (MIR), and far-infrared (FIR). The spectral traits can be systematically extracted from the typically broad and complex spectral contours applying resolution enhancement techniques, difference spectroscopy, and pattern recognition methods such as factor-analysis and cluster-analysis, and artificial neural networks (ANNs). Additional applications arise by means of a light microscope coupled to the IR spectrometer. IR spectra of microcolonies containing less than 103 cells are obtained from colony replica by a stamping technique that transfers microcolonies growing on culture plates to a special IR-sample holder. Using a computer-controlled x,y-stage together with mapping and video techniques, the fundamental tasks of microbiological analysis, namely detection, enumeration, and differentiation of microorganisms, are perspectively integrated in one single apparatus.

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

Abstract: Gram-negative bacteria characteristically are surrounded by an additional membrane layer, the outer membrane. Although outer membrane components often play important roles in the interaction of symbiotic or pathogenic bacteria with their host organisms, the major role of this membrane must usually be to serve as a permeability barrier to prevent the entry of noxious compounds and at the same time to allow the influx of nutrient molecules. This review summarizes the development in the field since our previous review (H. Nikaido and M. Vaara, Microbiol. Rev. 49:1-32, 1985) was published. With the discovery of protein channels, structural knowledge enables us to understand in molecular detail how porins, specific channels, TonB-linked receptors, and other proteins function. We are now beginning to see how the export of large proteins occurs across the outer membrane. With our knowledge of the lipopolysaccharide-phospholipid asymmetric bilayer of the outer membrane, we are finally beginning to understand how this bilayer can retard the entry of lipophilic compounds, owing to our increasing knowledge about the chemistry of lipopolysaccharide from diverse organisms and the way in which lipopolysaccharide structure is modified by environmental conditions.

Mechanisms of Antimicrobial Peptide Action and Resistance

Abstract: Antimicrobial peptides have been isolated and characterized from tissues and organisms representing virtually every kingdom and phylum, ranging from prokaryotes to humans. Yet, recurrent structural and functional themes in mechanisms of action and resistance are observed among peptides of widely diverse source and composition. Biochemical distinctions among the peptides themselves, target versus host cells, and the microenvironments in which these counterparts convene, likely provide for varying degrees of selective toxicity among diverse antimicrobial peptide types. Moreover, many antimicrobial peptides employ sophisticated and dynamic mechanisms of action to effect rapid and potent activities consistent with their likely roles in antimicrobial host defense. In balance, successful microbial pathogens have evolved multifaceted and effective countermeasures to avoid exposure to and subvert mechanisms of antimicrobial peptides. A clearer recognition of these opposing themes will significantly advance our understanding of how antimicrobial peptides function in defense against infection. Furthermore, this understanding may provide new models and strategies for developing novel antimicrobial agents, that may also augment immunity, restore potency or amplify the mechanisms of conventional antibiotics, and minimize antimicrobial resistance mechanisms among pathogens. From these perspectives, the intention of this review is to illustrate the contemporary structural and functional themes among mechanisms of antimicrobial peptide action and resistance.

Synthesis and Applications of RuCl2(CHR‘)(PR3)2: The Influence of the Alkylidene Moiety on Metathesis Activity

Abstract: The reactions of RuCl2(PPh3)3 with a number of diazoalkanes were surveyed, and alkylidene transfer to give RuCl2(CHR)(PPh3)2 (R = Me (1), Et (2)) and RuCl2(CH-p-C6H4X)(PPh3)2 (X = H (3), NMe2 (4), OMe (5), Me (6), F (7), Cl (8), NO2 (9)) was observed for alkyl diazoalkanes RCHN2 and various para-substituted aryl diazoalkanes p-C6H4XCHN2. Kinetic studies on the living ring-opening metathesis polymerization (ROMP) of norbornene using complexes 3−9 as catalysts have shown that initiation is in all cases faster than propagation (ki/kp = 9 for 3) and that the electronic effect of X on the metathesis activity of 3−9 is relatively small. Phosphine exchange in 3−9 with tricyclohexylphosphine leads to RuCl2(CH-p-C6H4X)(PCy3)2 10−16, which are efficient catalysts for ROMP of cyclooctene (PDI = 1.51−1.63) and 1,5-cyclooctadiene (PDI = 1.56−1.67). The crystal structure of RuCl2(CH-p-C6H4Cl)(PCy3)2 (15) indicated a distorted square-pyramidal geometry, in which the two phosphines are trans to each other, and the alkyli...

Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability

Abstract: Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of >80°C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.