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Infections with multi-resistant Gram negative pathogens are a major threat to our health system. In order to serve the needs in antibiotics development we selected untapped bioresources and implemented high throughput approaches suitable for the discovery of strains producing antibiotics with anti-Gram negative activity.
Our approaches rely on the hypothesis that Termite associated bacteria are likely to produce potent antibiotics to defend their hosts against entomopathogenic microorganisms. Termite nests and guts harbor suitable, highly diverse microbiomes in which bacterial taxa are present known to potentially produce natural compounds. In
a first step the diversity of Coptotermes species nest microbiomes was assessed carefully by using 16S rDNA amplicon sequencing on the Illumina MiSeq platform and nest material was selected to retrieve viable cells by using Nycodenz density gradient centrifugation. In order to analyze the diversity of the culturable termite nest microbiome, bacterial cells were either distributed in 384-well plates
(approach 1) or encapsulated in small spheric agarose beads by an high throughput microfluidics technique (approach 2). Cultures obtained from approach 1 were scaled-up in 96-well Duetz-systems for characterization of diversity and for rapid supernatant screening using the bioluminescence-labeled E. coli pFU166. The generated
droplets of approach 2 simultaneously received a small population of GFP-tagged Gram negative screening cells and were sorted for low fluorescence using FACS. After elimination of redundancy we performed a fast scale-up of active strains.
Implementation of this pipeline allows us to prioritize antibiotics producing strains in a ultra-high throughput fashion and by cultivation of broad diversity in our approches.
The research project focuses on tackling the detection, measurement, and elimination of per- and polyfluoroalkyl substances (PFAS) from polluted groundwater, with a particular emphasis on addressing short (C4-C7) and ultrashort (C1-C3) chain PFAS. Given the widespread use of PFAS in various products, they are commonly found in groundwater near industrial and military sites in Germany and Israel. Moreover, recent regulations limiting the use of long chain PFAS have led industries to shift towards shorter chain alternatives. Hence, our efforts are geared towards refining detection, quantification, and removal methods for short and ultrashort chain PFAS. In terms of detection, ww are developing passive sampling devices capable of collecting and tracking the temporal distribution of PFAS species in groundwater. This will enable us to analyze contaminations in German and Israeli groundwater using cutting-edge analytical techniques. Additionally, contaminated groundwater will undergo a two-stage treatment process aimed at concentrating the relatively low PFAS concentrations using innovative membrane technologies such as closed-circuit reverse osmosis and mixed matrix composite nanofiltration membrane adsorbers. Subsequently, the streams containing higher PFAS concentrations will be treated through coagulation, with the remaining PFAS being adsorbed onto carbonaceous nanomaterials. The outcome of this research will include the creation of advanced tools for detecting, measuring, and eliminating PFAS from polluted groundwater, while also enhancing our understanding of the scope of these contaminations.
Virulence determines the impact a pathogen has on the fitness of its host, yet current understanding of the evolutionary origins and causes of virulence of many pathogens is surprisingly incomplete. Here, we explore the evolution of Marek’s disease virus (MDV), a herpesvirus commonly afflicting chickens and rarely other avian species. The history of MDV in the 20th century represents an important case study in the evolution of virulence. The severity of MDV infection in chickens has been rising steadily since the adoption of intensive farming techniques and vaccination programs in the 1950s and 1970s, respectively. It has remained uncertain, however, which of these factors is causally more responsible for the observed increase in virulence of circulating viruses. We conducted a phylogenomic study to understand the evolution of MDV in the context of dramatic changes to poultry farming and disease control. Our analysis reveals evidence of geographical structuring of MDV strains, with reconstructions supporting the emergence of virulent viruses independently in North America and Eurasia. Of note, the emergence of virulent viruses appears to coincide approximately with the introduction of comprehensive vaccination on both continents. The time-dated phylogeny also indicated that MDV has a mean evolutionary rate of ~1.6 × 10−5 substitutions per site per year. An examination of gene-linked mutations did not identify a strong association between mutational variation and virulence phenotypes, indicating that MDV may evolve readily and rapidly under strong selective pressures and that multiple genotypic pathways may underlie virulence adaptation in MDV.
Bioinformatics meets virology: The European virus bioinformatics center's second annual meeting
(2018)
The Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting.
Copolyesters with an alternating sequence of terephthalic acid and aliphatic dicarboxylic acids were prepared with three different methods. First, dicarboxylic acid dichlorides were reacted with bis(2-hydroxyethyl)terephthalate (BHET) in refluxing 1,2-dichlorobenzene. Second, the same monomers were polycondensed at 0-20 °C in the presence of pyridine. Third, dicarboxylic acid dichlorides and silylated BHET were polycondensed in bulk. Only this third method gave satisfactory molecular weights. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry revealed that the copolyesters prepared by the pyridine and silyl methods might have contained considerable fractions of cyclic oligoesters and polyesters despite the absence of transesterification and backbiting processes. The alternating sequences and thermal properties were characterized with 1H NMR spectroscopy and differential scanning calorimetry measurements, respectively. In agreement with the alternating sequence, all copolyesters proved to be crystalline, but the crystallization was extremely slow [slower than that of poly(ethylene terephthalate)]. A second series of alternating copolyesters was prepared by the polycondensation of silylated bis(4-hydroxybut- yl)terephthalate with various aliphatic dicarboxylic acid dichlorides. The resulting copolyesters showed significantly higher rates of crystallization, and the melting temperatures were higher than those of the BHET-based copolyesters. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3371-3382, 2001
A novel family of air-stable dendrimers with a N-Si-C framework has been prepared up to the fourth generation. The divergent synthesis starts with the hydrosilylation of the trisilazane N(SiMe2vinyl)3 [0-G(vinyl)] by HSiMe2Cl, which gives the three-directional core molecule N(SiMe2CH2CH2SiMe2Cl)3 [0-G(Cl)]. A 1-to-2 branching achieved by reacting the core molecule [0-G(Cl)] with 3 equiv of KN(SiMe2vinyl)2 affords the first generation dendrimer [1-G(vinyl)]. By repeating the above two steps, the second [2-G(vinyl)], third [3-G(vinyl)], and fourth generation [4-G(vinyl)] can be obtained. The compounds have been characterized by 1H, 13C, and 29Si NMR spectroscopy, by elemental analysis, and up to the third generation by MALDI-TOF mass spectrometry. Gel permeation chromatography was used to prove the fourth generation [4-G(vinyl)].
Technetium- and Rhenium-Labelled Fatty Acids as Model Compounds for Myocardial Metabolism Imaging
(2002)
In an attempt to develop new technetium-based radiopharmaceuticals for the non-invasive diagnosis of oxidative myocardial metabolism, rhenium model compounds according to the 3+1' mixed ligand approach as well as the organometallic tricarbonyl-design were synthesized. The geometrical impact of different chelates on the integrity of the fatty acid head structure was determined by single crystal X-ray analyses. To evaluate the diagnostic potential of the analogous Technetium-99m compounds, fatty acid complexes of the 3+1' mixed ligand type were prepared on n.c.a.-level and studied in the isolated constant-flow-perfused guinea pig heart model; compared to established [123I]Iodine-labelled fatty acid radiotracers, the tested Technetium-99m derivatives showed a specific, however significantly lower myocardial extraction rate.
In an attempt to develop new technetium-based radiopharmaceuticals for the noninvasive diagnosis of myocardial metabolism, we have synthesized three examples of novel metal-containing fatty acid derivatives according to the 3+1 mixed-ligand and the Schiff base/tricarbonyl design. The chelates contain the metal core in the oxidation states +5 and +1, respectively, and are attached to the end-position of a fatty acid chain. The complex formation was accomplished by ligand-exchange reactions with three different rhenium precursors, whereas the inactive rhenium metal was utilized as a surrogate of the technetium radionuclide. The molecular structures of the fatty acid complexes 7, 10 and 14 were determined by single-crystal X-ray diffraction analyses and impressively show a general problem in technetium tracer research, namely the significant structural alterations of bioactive molecules by coordination even to small metal chelates.
The role of 1,1-diphenylethylene (DPE) in radical emulsion polymerization of methyl methacrylate is investigated. The presence of DPE causes a strong decrease in both the rate of polymerization and the molecular weight. According to the results of structure analysis by means of MALDI-TOF mass spectrometry, UVvis spectroscopy, and 1HNMR spectroscopy, DPE is incorporated in the copolymer chain exclusively as a reactive recombinant ?,p-dimer, underlining the peculiar role of DPE in radical polymerizations.
A new method for the physical characterization of rock matrices for use in site investigations of nuclear waste repositories has been developed. The method can provide information needed in the assessment of the performance of the geosphere working as a natural barrier retarding the migration of radionuclides by diffusion into the rock matrix. Most conventional methods for the physical characterization of rocks give only bulk information. The combination of mercury porosimetry and computer tomography can give 3-D data on mineral-specific porosity distributions with additional pore size information. Additionally, limits for mineral-specific internal surface areas can be estimated, which is essential for the assessment of water-rock interaction and reactive interaction with radionuclides (sorption). Results of measurements on granitic rock (granodiorite) from the Baltic shield are discussed and integrated with results by complementary methods.