Linking chemical and microbial diversity in marine sponges: possible role for poribacteria as producers of methyl-branched fatty acids

Many marine sponges contain massive numbers of largely uncultivated, phylogenetically diverse bacteria that seem to be important contributors to the chemistry of these animals. Insights into the diversity, origin, distribution, and function of their metabolic gene communities are crucial to dissect the chemical ecology and biotechnological potential of sponge symbionts. This study reveals a sharp dichotomy between high and low microbial abundance sponges with respect to polyketide synthase (PKS) gene content, the presence of methyl-branched fatty acids, and the presence of members of the symbiotic candidate phylum "Poribacteria". For the symbiont-rich sponge Cacospongia mycofijiensis, a source of the tubulin-inhibiting fijianolides (=laulimalides), near-exhaustive large-scale sequencing of PKS gene-derived PCR amplicons was conducted. Although these amplicons exhibit high diversity at the sequence level, almost all of them belong to a single, architecturally unique group of PKSs present in "Poribacteria" and are proposed to synthesize methyl-branched fatty acids. Three components of this PKS were studied in vitro, providing initial insight into its biochemistry.     

The First Anionic Thia‐Fries Rearrangements at Ferrocene: Ready Access to Trifluoromethylsulfonyl‐Substituted Hydroxyferrocenes and an Extremely High Interannular Stereoinduction between Cyclopentadienyl Ligands

Attempts originally directed towards the generation of ferrocyne (1,2‐dehydroferrocene, 4 ) and ferrocenediyne (1,2,1′,2′‐tetradehydroferrocene, 5 ) by triflate elimination from the respective ferrocenyl triflates led to the discovery of the first anionic thia‐Fries rearrangements at a five‐membered ring. These reactions take place with remarkable efficiency under very mild reaction conditions and yield the respective trifluoromethylsulfonyl‐substituted ferrocenols. Most remarkably, the reaction starting from 1,1′‐ferrocenediyl ditriflate ( 9 ) adopts an extremely high interannular stereoinduction in that exclusively the meso rearrangement product, meso‐2,2′‐bis(trifluoromethylsulfonyl)‐1,1′‐ferrocenediol ( 16 ), is formed, the corresponding racemic product 17 is not observed. It is shown that the second anionic thia‐Fries rearrangement proceeds at a much larger rate than the first one. The stereochemistry and the high rate of this reaction are explained on the basis of electronic as well as steric considerations. The redox behavior of some of the unprecedented ferrocene derivatives has been characterized by cyclovoltammetry.     

Fragment‐Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition

Fragment‐based drug discovery has gained a foothold in today's lead identification processes. We present the application of in silico fragment‐based screening for the discovery of novel lead compounds for the metalloendoproteinase thermolysin. We have chosen thermolysin to validate our screening approach as it is a well‐studied enzyme and serves as a model system for other proteases. A protein‐targeted virtual library was designed and screening was carried out using the program AutoDock. Two fragment hits could be identified. For one of them, the crystal structure in complex with thermolysin is presented. This compound was selected for structure‐based optimization of binding affinity and improvement of ligand efficiency, while concomitantly keeping the fragment‐like properties of the initial hit. Redesigning the zinc coordination group revealed a novel class of fragments possessing K_i values as low as 128 μM , thus they provide a good starting point for further hit evolution in a tailored lead design.     

Convergence behavior of non-equidistant sampling series

The convergence of sampling series with non-equidistant sampling points cannot be guaranteed for the Paley–Wiener space if the class of sampling patterns is not restricted. In this paper we consider sampling patterns that are made of the zeros of sine-type functions and analyze the local and global convergence behavior of the sampling series. It is shown that oversampling is necessary for global uniform convergence. If no oversampling is used there exists for every sampling pattern a signal such that the peak value of the approximation error grows arbitrarily large. Furthermore, we use the findings to derive results about the mean-square convergence behavior of the sampling series for bandlimited wide-sense stationary stochastic processes. Finally, a procedure is given to construct functions of sine type and possible sampling patterns.     

Enzymatic on-chip enhancement for high resolution genotyping DNA microarrays

Antibiotic resistance among pathogenic microorganisms is emerging as a major human healthcare concern. While there are a variety of resistance mechanisms, many can be related to single nucleotide polymorphisms and for which DNA microarrays have been widely deployed in bacterial genotyping. However, genotyping by means of allele-specific hybridization can suffer from the drawback that oligonucleotide probes with different nucleotide composition have varying thermodynamic parameters. This results in unpredictable hybridization behavior of mismatch probes. Consequently, the degree of discrimination between perfect match and mismatch probes is insufficient in some cases. We report here an on-chip enzymatic procedure to improve this discrimination in which false-positive hybrids are selectively digested. We find that the application of CEL1 Surveyor nuclease, a mismatch-specific endonuclease, significantly enhances the discrimination fidelity, as demonstrated here on a microarray for the identification of variants of carbapenem resistant Klebsiella pneumoniae carbapenemases and monitored by end point detection of fluorescence intensity. Further fundamental investigations applying total internal reflection fluorescence detection for kinetic real-time measurements confirmed the enzymatic enhancement for SNP discrimination.     

SVD-based MIMO Precoding and Equalization Schemes for Realistic Channel Knowledge: Design Criteria and Performance Evaluation

Multiple-input multiple-output (MIMO) based communication systems with precoding, bit-loading and equalization procedures are considered in this paper. Applications of precoding schemes, which are based on Singular Value Decomposition (SVD) of the channel matrix H assume almost always ideal channel knowledge at the transmitter and/or receiver site. This paper investigates an SVD based MIMO approach considering non ideal radio channel estimation results. In any case the MIMO channel matrix H is decomposed into Eigenmodes. In case of an ideal radio channel knowledge the SVD based precoding procedure, which is applied at the transmitter site, is going to consider all possible Eigenmodes which results in a perfect separation of all signals at the receive antenna output and into a minimum bit-error-rate (BER). It will be shown in this paper that in case of non ideal channel knowledge and a limited accuracy in the channel matrix H estimation a reduced number of Eigenmodes in the precoding process will become an optimum and will lead into an increased BER performance.

Berücksichtigung der Fließgeschwindigkeit bei Hochwasser‐Schadensmodellen

Die Quantifizierung der Schadenspotentiale infolge Hochwasser setzt realistische Zusammenhänge zwischen Einwirkungs‐ und Verlustkenngrößen voraus. Da sich herkömmliche Schadensfunktionen auf den Zusammenhag zwischen Fluthöhe und den versicherungsseitig nachvollziehbaren Kosten für eine bestimmte Nutzungsklasse (wie. z. B. private Wohngebäude) beschränken, fehlt zum einen die notwendige Differenzierung nach den für die Widerstandsseite relevanten Merkmalen, zum anderen bleiben weitere Einwirkungsgrößen wie die Fließgeschwindigkeit unberücksichtigt. Auf der Grundlage einer einheitlichen Datenerhebung wurde ein System entwickelt, mit dem die strukturelle Schädigung eines Bauwerks oder eines betroffenen Bauwerksbestands für konkrete Hochwasserszenarien bestimmt werden kann. Dieses Instrumentarium wird erweitert, so dass der Zusammenhang zwischen den Einwirkungskenngrößen Überflutungshöhe und Fließgeschwindigkeit und dem strukturellen Schaden hergestellt werden kann. Die Studie stützt sich auf dabei zwei Datensätze, die nach dem Hochwasser 2002 erhoben wurden: – Datensatz 1 bezieht sich auf eine schriftliche Befragung, welche zwischen 2002 und 2004 in Sachsen durchgeführt wurde. – Datensatz 2 stellt dabei das Ergebnis einer Auswertung von Schadensgutachten im Auftrag der Landestalsperrenverwaltung Sachsen dar. Im Ergebnis kann ein neuartiger Typ von Verletzbarkeitsfunktionen bereitgestellt werden, der den Zusammenhang zwischen Überflutungshöhe, Fließgeschwindigkeit und den Schadensgraden D_i in Abhängigkeit von der konkreten Bauwerksverletzbarkeit beschreibt. Mit Hilfe ebenfalls neu entwickelter Schadensfunktionen werden die so berechneten Schadensgrade in konkrete Verlustaussagen überführt. Wie an drei Testgebieten im Freistaat Sachsen nachgewiesen werden kann, gelingt es mit diesen Funktionen, die gemeldeten Verluste infolge des Hochwassers 2002 in guter Übereinstimmung nachzuvollziehen. Im Weiteren werden erste Untersuchungen zum Einfluss der städtebaulichen Einbindung und der Anströmrichtung auf die strukturellen Schäden vorgestellt. Consideration of flow velocity in flood damage models. Reliable prognoses of building damage caused by flood impact require realistic relationships between action and damage or loss describing parameters. Due to the fact that commonly applied damage functions are related to the different usage classes (i.e. private housing), the required differentiation according to the parameters on the resistance side is still missing and further impact parameters like flow velocity remain unconsidered. On the basis of the August 2002 Saxony flood data base, a method to determine the structural damage for any given flood scenario was developed. This method is improved to consider the correlation between inundation level and flow velocity and structural damage. The study is based on two different datasets collected after the flood 2002 in Saxony: – Dataset 1 is related to the outcome of a questionnaire survey performed by the authors between 2002 and 2004. – Dataset 2 is the outcome of an evaluation of damage expertises by order of the “Landestalsperrenverwaltung Sachsen”. A set of new Specific Vulnerability Functions (SVF) for calculation of damage grades is derived considering the inundation level and the flow velocity depending on the vulnerability of the predominant building types. Based on new developed Specific Damage Functions (SDF) the calculated damage grades are transferred into loss estimates. The developed tools are applied to the reinterpretation of the August 2002 flood damage. Results of the approach are presented for three different study areas in the free state of Saxony. In all cases a remarkable good agreement between the predicted and the reported loss can be stated. First investigations with respect to the location of buildings, the direction of inflow and the structural damage are represented.     

A dose-controlled system for air-liquid interface cell exposure and application to zinc oxide nanoparticles

Background  

Engineered nanoparticles are becoming increasingly ubiquitous and their toxicological effects on human health, as well as on the ecosystem, have become a concern. Since initial contact with nanoparticles occurs at the epithelium in the lungs (or skin, or eyes), in vitro cell studies with nanoparticles require dose-controlled systems for delivery of nanoparticles to epithelial cells cultured at the air-liquid interface.     

Early colonization of stone by freshwater lichens of restored habitats: A case study in northern Italy

This study evaluated the effectiveness and life-strategies of freshwater lichens in colonizing newly constructed stone structures in low-elevation streams in a small nature reserve in northern Italy. Species richness, size of thalli, morphological and ontogenetic traits of the species were related to the age of restored habitats. Lichen colonization was surprisingly rapid, indicating the high potential of these organisms in colonizing restored habitats. However, the species pool found in the restored habitats was different than that found in natural sites in the same study area. The age of newly constructed habitats influenced both species richness and thallus size of the two most frequent Verrucaria species. Verrucaria aquatilis was a rapid colonizer invading the substrate by several small-sized and thin thalli which soon supported a large number of small perithecia whose development began in the earlier phase of thallus formation. V. elaeomelaena, on the contrary, developed according to a different strategy, establishing a thick thallus on which relatively large perithecia were formed much later than in V. aquatilis. As these taxa are important photoautotrophic components of freshwater ecosystems more ecological knowledge is needed to evaluate the effectiveness of different measures of river restoration on lichen communities. The main practical implication of our study is related to the value of small stone structures, such as riffles and ramps, for enhancing the establishment of pioneer freshwater lichens to rapidly colonize newly available substrata.