Synthese und Charakterisierung neuartiger Photosäuren auf Basis von Pyren und Diazapyren - Protonentransfer in konzentrierter Schwefelsäure

Photoacids show a strong increase in their acidity while transitioning to the excited state, which allows them to release protons on demand by a short laser pulse. This is the most convenient tool for studying proton transfer reactions and can be used for both, intramolecular and intermolecular applications. Although used several times intramolecularly, intermolecular reactions of photoacids have been limited to the release of a single proton. Part one of this work is about the development of intermolecular double photoacids based on dihydroxpyrenes, which due to their structure could even be suitable for a light-driven, formal release of molecular hydrogen. In excited-state proton transfer (ESPT), the acidity of the excited state is the main parameter to specify to which molecules a proton can be transferred. Even with the strongest known photoacids, only protic or strongly basic molecules can act as acceptors. In the second part of the thesis, a novel aminopyrene photoacid is synthesized and characterized, which not only exceeds the acid strength of all known photoacids, but also that of concentrated sulfuric acid. Its outstanding high chemical stability and fluorescent properties enables time-resolved studies of proton transfer reactions in mineral acids and organic solvents with low basicity.Beim Übergang in den angeregten Zustand zeigen Photosäuren einen starken Anstieg ihrer Azidität, was ihnen die Freisetzung von Protonen auf Abruf durch einen kurzen Laserpuls ermöglicht. Dieses praktische Werkzeug zur Untersuchung von Protonentransferreaktionen kann sowohl auf intramolekularer als auch auf intermolekularer Ebene angewendet werden. Obwohl intramolekular bereits mehrfach verwendet, beschränken sich intermolekulare Reaktionen von Photosäuren bisher auf die Abgabe eines einzelnen Protons. Der erste Teil dieser Arbeit beschäftigt sich daher mit der Entwicklung von intermolekularen Doppelphotosäuren auf Basis von Dihydroxpyrenen, die aufgrund ihrer Struktur möglicherweise sogar für eine lichtgetriebene, formale Freisetzung von molekularem Wasserstoff geeignet wären. Zudem gibt die Säurestärke des angeregten Zustands maßgeblich vor, auf welche Moleküle ein Proton übertragen werden kann. Selbst mit den bisher stärksten Photosäuren können nur protische oder stark basische Verbindungen als Akzeptor fungieren. Im zweiten Teil der Arbeit wird eine neuartige Aminopyrenphotosäure synthetisiert und charakterisiert, die nicht nur die Säurestärken all ihrer Vorgänger, sondern selbst die der konzentrierten Schwefelsäure übertrifft. Die außergewöhnlich hohe chemische Stabilität und fluoreszierenden Eigenschaften des Derivats ermöglichen sogar zeitaufgelöste Studien von Protonentransferreaktionen in Mineralsäuren und organischen Lösungsmitteln mit geringer Basizität.DFG - Deutsche Forschungsgesellschaf

FABIO - The Construction of the Food and Agriculture Biomass Input-Output Model

Primary crops are linked to final consumption by networks of processes and actors that convert and distribute food and non-food goods. Achieving a sustainable metabolism of this bio-economy is an overarching challenge which manifests itself in a number of the UN Sustainable Development Goals. Modelling the physical dimensions of biomass conversion and distribution networks is essential to understanding the characteristics, drivers and dynamics of our societies' biomass metabolism. In this paper, we present the Food and Agriculture Biomass Input-Output model (FABIO), a set of multi-regional supply, use and input-output tables in physical units, that document the complex flows of agricultural and food products in the global economy. The model assembles FAOSTAT statistics reporting crop production, trade, and utilisation in physical units, supplemented by data on technical and metabolic conversion efficiencies, into a consistent, balanced, input-output framework. FABIO covers 191 countries and 130 agriculture, food and forestry products from 1986 to 2013. The physical supply-use tables offered by FABIO provide a comprehensive, transparent and flexible structure for organising data representing flows of materials within metabolic networks. They allow tracing biomass flows and embodied environmental pressures along global supply chains at an unprecedented level of product and country detail and can help to answer a range of questions regarding environment, agriculture, and trade.Series: Ecological Economic Paper

Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses

Krahn T, Wibberg D, Maus I, et al. Complete Genome Sequence ofAcinetobacter baumanniiCIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses. Genome Announcements. 2015;3(4):e00850-15

Complete genome sequence of the clinical strain Acinetobacter baumannii R2090 Carrying the chromosomally encoded Metallo-β-Lactamase Gene blaNDM-1

Acinetobacter baumannii is an emerging human pathogen causing nosocomial and community-acquired infections. Here, we present the complete genome sequence of the clinical A. baumannii strain R2090 carrying the metallo-β-lactamase gene blaNDM-1 in its chromosome within the transposon Tn125

Inverse Protein Folding Using Deep Bayesian Optimization

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

Background: In recent years biogas plants in Germany have been supposed to be involved in amplification and dissemination of pathogenic bacteria causing severe infections in humans and animals. In particular, biogas plants are discussed to contribute to the spreading of Escherichia coli infections in humans or chronic botulism in cattle caused by Clostridium botulinum. Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches. Results: All datasets featured a low abundance of reads that were taxonomically assigned to the genus Escherichia or further selected genera comprising pathogenic species. Higher numbers of reads were taxonomically assigned to the genus Clostridium. However, only very few sequences were predicted to originate from pathogenic clostridial species. Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. Likewise, known virulence determinants could hardly be detected. Only a marginal number of reads showed similarity to sequences described in the Microbial Virulence Database MvirDB such as those encoding protein toxins, virulence proteins or antibiotic resistance determinants. Conclusions: Findings of this first study of metagenomic sequence reads of biogas producing microbial communities suggest that the risk of dissemination of pathogenic bacteria by application of digestates from biogas fermentations as fertilizers is low, because obtained results do not indicate the presence of putative pathogenic microorganisms in the samples analyzed

Complete Genome Sequence of the MethanogenMethanoculleus bourgensisBA1 Isolated from a Biogas Reactor

Maus I, Wibberg D, Winkler A, Pühler A, Schnürer A, Schlüter A. Complete Genome Sequence of the MethanogenMethanoculleus bourgensisBA1 Isolated from a Biogas Reactor. Genome Announcements. 2016;4(3): e00568-16.Methanoculleus bourgensis BA1, a hydrogenotrophic methanogen, was isolated from a laboratory-scale biogas reactor operating under an elevated ammonium concentration. Here, the complete genome sequence of M. bourgensis BA1 is reported. The availability of the BA1 genome sequence enables detailed comparative analyses involving other Methanoculleus spp. representing important members of microbial biogas communities

Complete genome sequence of the methanogen Methanoculleus bourgensis BA1 isolated from a biogas reactor

Methanoculleus bourgensis BA1, a hydrogenotrophic methanogen, was isolated from a laboratory-scale biogas reactor operating under an elevated ammonium concentration. Here, the complete genome sequence of M. bourgensis BA1 is reported. The availability of the BA1 genome sequence enables detailed comparative analyses involving other Methanoculleus spp. representing important members of microbial biogas communities

The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9T, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, Lachnospiraceae species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative Lachnospiraceae strain, Anaeropeptidivorans aminofermentans M3/9T was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9T possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9T was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9T and closely related Anaerotignum type strains, genome sequence comparisons were performed. M3/9T harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9T in other environments, large-scale fragment recruitments with the M3/9T genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.Peer Reviewe