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End date: 2022 × Start date: 2022 × DDC: 570 × Has files: Yes × Type: Text × WGL Institute: IPHT ×

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Now showing 1 - 10 of 24
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    Surface-Enhanced Raman Spectroscopy to Characterize Different Fractions of Extracellular Vesicles from Control and Prostate Cancer Patients
    (Basel : MDPI, 2021) Osei, Eric Boateng; Paniushkina, Liliia; Wilhelm, Konrad; Popp, Jürgen; Nazarenko, Irina; Krafft, Christoph
    Extracellular vesicles (EVs) are membrane-enclosed structures ranging in size from about 60 to 800 nm that are released by the cells into the extracellular space; they have attracted interest as easily available biomarkers for cancer diagnostics. In this study, EVs from plasma of control and prostate cancer patients were fractionated by differential centrifugation at 5000× g, 12,000× g and 120,000× g. The remaining supernatants were purified by ultrafiltration to produce EV-depleted free-circulating (fc) fractions. Spontaneous Raman and surface-enhanced Raman spectroscopy (SERS) at 785 nm excitation using silver nanoparticles (AgNPs) were employed as label-free techniques to collect fingerprint spectra and identify the fractions that best discriminate between control and cancer patients. SERS spectra from 10 µL droplets showed an enhanced Raman signature of EV-enriched fractions that were much more intense for cancer patients than controls. The Raman spectra of dehydrated pellets of EV-enriched fractions without AgNPs were dominated by spectral contributions of proteins and showed variations in S-S stretch, tryptophan and protein secondary structure bands between control and cancer fractions. We conclude that the AgNPs-mediated SERS effect strongly enhances Raman bands in EV-enriched fractions, and the fractions, EV12 and EV120 provide the best separation of cancer and control patients by Raman and SERS spectra.
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    Characterization and prediction of the mechanism of action of antibiotics through NMR metabolomics
    (London : BioMed Central, 2016) Hoerr, Verena; Duggan, Gavin E.; Zbytnuik, Lori; Poon, Karen K.H.; Große, Christina; Neugebauer, Ute; Methling, Karen; Löffler, Bettina; Vogel, Hans J.
    Background: The emergence of antibiotic resistant pathogenic bacteria has reduced our ability to combat infectious diseases. At the same time the numbers of new antibiotics reaching the market have decreased. This situation has created an urgent need to discover novel antibiotic scaffolds. Recently, the application of pattern recognition techniques to identify molecular fingerprints in ‘omics’ studies, has emerged as an important tool in biomedical research and laboratory medicine to identify pathogens, to monitor therapeutic treatments or to develop drugs with improved metabolic stability, toxicological profile and efficacy. Here, we hypothesize that a combination of metabolic intracellular fingerprints and extracellular footprints would provide a more comprehensive picture about the mechanism of action of novel antibiotics in drug discovery programs. Results: In an attempt to integrate the metabolomics approach as a classification tool in the drug discovery processes, we have used quantitative 1H NMR spectroscopy to study the metabolic response of Escherichia coli cultures to different antibiotics. Within the frame of our study the effects of five different and well-known antibiotic classes on the bacterial metabolome were investigated both by intracellular fingerprint and extracellular footprint analysis. The metabolic fingerprints and footprints of bacterial cultures were affected in a distinct manner and provided complementary information regarding intracellular and extracellular targets such as protein synthesis, DNA and cell wall. While cell cultures affected by antibiotics that act on intracellular targets showed class-specific fingerprints, the metabolic footprints differed significantly only when antibiotics that target the cell wall were applied. In addition, using a training set of E. coli fingerprints extracted after treatment with different antibiotic classes, the mode of action of streptomycin, tetracycline and carbenicillin could be correctly predicted. Conclusion: The metabolic profiles of E. coli treated with antibiotics with intracellular and extracellular targets could be separated in fingerprint and footprint analysis, respectively and provided complementary information. Based on the specific fingerprints obtained for different classes of antibiotics, the mode of action of several antibiotics could be predicted. The same classification approach should be applicable to studies of other pathogenic bacteria.
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    PEGylation of Guanidinium and Indole Bearing Poly(methacrylamide)s - Biocompatible Terpolymers for pDNA Delivery
    (Weinheim : Wiley-VCH, 2021) Cokca, Ceren; Hack, Franz J.; Costabel, Daniel; Herwig, Kira; Hülsmann, Juliana; Then, Patrick; Heintzmann, Rainer; Fischer, Dagmar; Peneva, Kalina
    This study describes the first example for shielding of a high performing terpolymer that consists of N-(2-hydroxypropyl)methacrylamide (HPMA), N-(3-guanidinopropyl)methacrylamide (GPMA), and N-(2-indolethyl)methacrylamide monomers (IEMA) by block copolymerization of a polyethylene glycol derivative – poly(nona(ethylene glycol)methyl ether methacrylate) (P(MEO9MA)) via reversible addition–fragmentation chain transfer (RAFT) polymerization. The molecular weight of P(MEO9MA) is varied from 3 to 40 kg mol–1 while the comonomer content of HPMA, GPMA, and IEMA is kept comparable. The influence of P(MEO9MA) block with various molecular weights is investigated over cytotoxicity, plasmid DNA (pDNA) binding, and transfection efficiency of the resulting polyplexes. Overall, the increase in molecular weight of P(MEO9MA) block demonstrates excellent biocompatibility with higher cell viability in L-929 cells and an efficient binding to pDNA at N/P ratio of 2. The significant transfection efficiency in CHO-K1 cells at N/P ratio 20 is obtained for block copolymers with molecular weight of P(MEO9MA) up to 10 kg mol–1. Moreover, a fluorescently labeled analogue of P(MEO9MA), bearing perylene monoimide methacrylamide (PMIM), is introduced as a comonomer in RAFT polymerization. Polyplexes consisting of labeled block copolymer with 20 kg mol–1 of P(MEO9MA) and pDNA are incubated in Hela cells and investigated through structured illumination microscopy (SIM).
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    Long-Term Sinonasal Carriage of Staphylococcus aureus and Anti-Staphylococcal Humoral Immune Response in Patients with Chronic Rhinosinusitis
    (Basel : MDPI, 2021) Thunberg, Ulrica; Hugosson, Svante; Ehricht, Ralf; Monecke, Stefan; Müller, Elke; Cao, Yang; Stegger, Marc; Söderquist, Bo
    We investigated Staphylococcus aureus diversity, genetic factors, and humoral immune responses against antigens via genome analysis of S. aureus isolates from chronic rhinosinusitis (CRS) patients in a long-term follow-up. Of the 42 patients who provided S. aureus isolates and serum for a previous study, 34 could be included for follow-up after a decade. Clinical examinations were performed and bacterial samples were collected from the maxillary sinus and nares. S. aureus isolates were characterized by whole-genome sequencing, and specific anti-staphylococcal IgG in serum was determined using protein arrays. S. aureus was detected in the nares and/or maxillary sinus at both initial inclusion and follow-up in 15 of the 34 respondents (44%). Three of these (20%) had S. aureus isolates from the same genetic lineage as at inclusion. A low number of single-nucleotide polymorphisms (SNPs) were identified when comparing isolates from nares and maxillary sinus collected at the same time point. The overall change of antibody responses to staphylococcal antigens over time showed great variability, and no correlation was found between the presence of genes encoding antigens and the corresponding anti-staphylococcal IgG in serum; thus our findings did not support a role, in CRS, of the specific S. aureus antigens investigated.
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    The Pheno- and Genotypic Characterization of Porcine Escherichia coli Isolates
    (Basel : MDPI, 2021) Bernreiter-Hofer, Tanja; Schwarz, Lukas; Müller, Elke; Cabal-Rosel, Adriana; Korus, Maciej; Misic, Dusan; Frankenfeld, Katrin; Abraham, Kerstin; Grünzweil, Olivia; Weiss, Astrid; Feßler, Andrea T.; Allerberger, Franz; Schwarz, Stefan; Szostak, Michael P.; Ruppitsch, Werner; Ladinig, Andrea; Spergser, Joachim; Braun, Sascha D.; Monecke, Stefan; Ehricht, Ralf; Loncaric, Igor
    Escherichia (E.) coli is the main causative pathogen of neonatal and post-weaning diarrhea and edema disease in swine production. There is a significant health concern due to an increasing number of human infections associated with food and/or environmental-borne pathogenic and multidrug-resistant E. coli worldwide. Monitoring the presence of pathogenic and antimicrobial-resistant E. coli isolates is essential for sustainable disease management in livestock and human medicine. A total of 102 E. coli isolates of diseased pigs were characterized by antimicrobial and biocide susceptibility testing. Antimicrobial resistance genes, including mobile colistin resistance genes, were analyzed by PCR and DNA sequencing. The quinolone resistance-determining regions of gyrA and parC in ciprofloxacin-resistant isolates were analyzed. Clonal relatedness was investigated by two-locus sequence typing (CH clonotyping). Phylotyping was performed by the Clermont multiplex PCR method. Virulence determinants were analyzed by customized DNA-based microarray technology developed in this study for fast and economic molecular multiplex typing. Thirty-five isolates were selected for whole-genome sequence-based analysis. Most isolates were resistant to ampicillin and tetracycline. Twenty-one isolates displayed an ESBL phenotype and one isolate an AmpC β-lactamase-producing phenotype. Three isolates had elevated colistin minimal inhibitory concentrations and carried the mcr-1 gene. Thirty-seven isolates displayed a multi-drug resistance phenotype. The most predominant β-lactamase gene classes were blaTEM-1 (56%) and blaCTX-M-1 (13.71%). Mutations in QRDR were observed in 14 ciprofloxacin-resistant isolates. CH clonotyping divided all isolates into 51 CH clonotypes. The majority of isolates belonged to phylogroup A. Sixty-four isolates could be assigned to defined pathotypes wherefrom UPEC was predominant. WGS revealed that the most predominant sequence type was ST100, followed by ST10. ST131 was detected twice in our analysis. This study highlights the importance of monitoring antimicrobial resistance and virulence properties of porcine E. coli isolates. This can be achieved by applying reliable, fast, economic and easy to perform technologies such as DNA-based microarray typing. The presence of high-risk pathogenic multi-drug resistant zoonotic clones, as well as those that are resistant to critically important antibiotics for humans, can pose a risk to public health. Improved protocols may be developed in swine farms for preventing infections, as well as the maintenance and distribution of the causative isolates.
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    Raman Stable Isotope Probing of Bacteria in Visible and Deep UV-Ranges
    (Basel : MDPI, 2021) Azemtsop Matanfack, Georgette; Pistiki, Aikaterini; Rösch, Petra; Popp, Jürgen
    Raman stable isotope probing (Raman-SIP) is an excellent technique that can be used to access the overall metabolism of microorganisms. Recent studies have mainly used an excitation wavelength in the visible range to characterize isotopically labeled bacteria. In this work, we used UV resonance Raman spectroscopy (UVRR) to evaluate the spectral red-shifts caused by the uptake of isotopes (13C, 15N, 2H(D) and 18O) in E. coli cells. Moreover, we present a new approach based on the extraction of labeled DNA in combination with UVRR to identify metabolically active cells. The proof-of-principle study on E. coli revealed heterogeneities in the Raman features of both the bacterial cells and the extracted DNA after labeling with 13C, 15N, and D. The wavelength of choice for studying 18O- and deuterium-labeled cells is 532 nm is, while 13C-labeled cells can be investigated with visible and deep UV wavelengths. However, 15N-labeled cells are best studied at the excitation wavelength of 244 nm since nucleic acids are in resonance at this wavelength. These results highlight the potential of the presented approach to identify active bacterial cells. This work can serve as a basis for the development of new techniques for the rapid and efficient detection of active bacteria cells without the need for a cultivation step.
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    Grasshopper herbivory immediately affects element cycling but not export rates in an N‐limited grassland system
    (Ithaca, NY : ESA, 2021) Potthast, Karin; Meyer, Stefanie; Tischer, Alexander; Gleixner, Gerd; Sieburg, Anne; Frosch, Torsten; Michalzik, Beate
    As a cause of ecosystem disturbances, phytophagous insects are known to directly influence the element and organic matter (OM) cycling in ecosystems by their defoliation and excretion activity. This study focuses on the interplay between short-term, insect herbivory, plant responses to feeding activity, rhizosphere processes, and belowground nutrient availability under nutrient-poor soil conditions. To test the effects of insect herbivory on OM and nutrient cycling in an N-limited pasture system, mesocosm laboratory experiments were conducted using Dactylis glomerata as common grass species and Chorthippus dorsatus, a widespread grasshopper species, to induce strong defoliating herbivory. 13CO2 pulse labeling was used together with labeled 15N feces to trace the fate of C in soil respiration at the beginning of herbivory, and of C and N in above- and belowground plant biomass, grasshopper, feces, bulk soil, soil microbial biomass, throughfall solutions, and soil solutions. Within five days, herbivory caused a reduction in aboveground grass biomass by about 34%. A linear mixed-effects model revealed that herbivory significantly increased total dissolved C and N amounts in throughfall solutions by a factor of 4–10 (P < 0.05) compared with the control. In total, 27.6% of the initially applied feces 15N were translocated from the aboveground to the belowground system. A significant enrichment of 15N in roots led to the assumption that feces-derived 15N was rapidly taken up to compensate for the frass-related foliar N losses in light of N shortage. Soil microorganisms incorporated newly available 13C; however, the total amount of soil microbial biomass remained unaffected, while the exploitative grass species rapidly sequestered resources to facilitate its regrowth after herbivory attack. Heavy herbivory by insects infesting D. glomerata-dominated, N-deficient grasslands remarkably impacted belowground nutrient cycling by an instant amplification of available nutrients, which led to an intensified nutrient competition between plants and soil microorganisms. Consequently, these competitive plant–soil microbe interactions accelerated N cycling and effectively retained herbivory-mediated C and N surplus release resulting in diminished N losses from the system. The study highlighted the overarching role of plant adaptations to in situ soil fertility in short-term ecosystem disturbances.
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    Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry
    (Oxford : Oxford University Press, 2015) Oetjen, Janina; Veselkov, Kirill; Watrous, Jeramie; McKenzie, James S.; Becker, Michael; Hauberg-Lotte, Lena; Kobarg, Jan Hendrik; Strittmatter, Nicole; Mróz, Anna K.; Hoffmann, Franziska; Trede, Dennis; Palmer, Andrew; Schiffler, Stefan; Steinhorst, Klaus; Aichler, Michaela; Goldin, Robert; Guntinas-Lichius, Orlando; von Eggeling, Ferdinand; Thiele, Herbert; Maedler, Kathrin; Walch, Axel; Maass, Peter; Dorrestein, Pieter C.; Takats, Zoltan; Alexandrov, Theodore
    Background: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. Findings: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. Conclusions: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.
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    Link to glow - iEDDA conjugation of a Ruthenium(II) tetrazine complex leading to dihydropyrazine and pyrazine complexes with improved 1O2 formation ability
    (Amsterdam : Elsevier, 2022) Müller, Carolin; Wintergerst, Pascal; Nair, Shruthi Santhosh; Meitinger, Nicolas; Rau, Sven; Dietzek-Ivanšić, Benjamin
    The synthesis and photophysical properties of the Ru-polypyridyl type complex [(tbbpy)2Ru(bptz)]2+ (Ru-bptz, tbbpy: 4,4’-di-tert-butyl-2,2’-bipyridine, bptz: 2,6-dipyrido-1,2,4,5-tetrazine), and the complexes [(tbbpy)2Ru(L)]2+ formed by inverse electron demand Diels Alder reaction (iEDDA) of Ru-bptz with with alkenes and alkynes, where L is 3,6-dipyrido-2,5-dihydropyridazine (bpdhpn) or 3,6-dipyrido-pyridazine (bppn) are described. A combination of steady-state and time-resolved spectroscopy complemented by the computation of state-specific absorption properties by means of time-dependent density functional theory reveals that the intense visible absorption band stems from Ru → tbbpy and Ru → L metal-to-ligand charge-transfer (MLCT) excitations. The studies show that lowest-lying L-centered MLCT states (3MLCTL) show comparably low emission quantum yields (3–9%) and lifetimes (90–150 ns). This correlates with the singlet oxygen generation ability, following the trend: Ru-bppn > Ru-bpdhpn > Ru-bptz.
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    Different storage conditions influence biocompatibility and physicochemical properties of iron oxide nanoparticles
    (Basel : Molecular Diversity Preservation International (MDPI), 2015) Zaloga, Jan; Janko, Christina; Agarwal, Rohit; Nowak, Johannes; Müller, Robert; Boccaccini, Aldo R.; Lee, Geoffrey; Odenbach, Stefan; Lyer, Stefan; Alexiou, Christoph
    Superparamagnetic iron oxide nanoparticles (SPIONs) have attracted increasing attention in many biomedical fields. In magnetic drug targeting SPIONs are injected into a tumour supplying artery and accumulated inside the tumour with a magnet. The effectiveness of this therapy is thus dependent on magnetic properties, stability and biocompatibility of the particles. A good knowledge of the effect of storage conditions on those parameters is of utmost importance for the translation of the therapy concept into the clinic and for reproducibility in preclinical studies. Here, core shell SPIONs with a hybrid coating consisting of lauric acid and albumin were stored at different temperatures from 4 to 45 °C over twelve weeks and periodically tested for their physicochemical properties over time. Surprisingly, even at the highest storage temperature we did not observe denaturation of the protein or colloidal instability. However, the saturation magnetisation decreased by maximally 28.8% with clear correlation to time and storage temperature. Furthermore, the biocompatibility was clearly affected, as cellular uptake of the SPIONs into human T-lymphoma cells was crucially dependent on the storage conditions. Taken together, the results show that the particle properties undergo significant changes over time depending on the way they are stored.