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- ItemFast, Label-Free Tracking of Single Viruses and Weakly Scattering Nanoparticles in a Nanofluidic Optical Fiber(Washington, DC : Soc., 2015) Faez, Sanli; Lahini, Yoav; Weidlich, Stefan; Garmann, Rees F.; Wondraczek, Katrin; Zeisberger, Matthias; Schmidt, Markus A.; Orrit, Michel; Manoharan, Vinothan N.High-speed tracking of single particles is a gateway to understanding physical, chemical, and biological processes at the nanoscale. It is also a major experimental challenge, particularly for small, nanometer-scale particles. Although methods such as confocal or fluorescence microscopy offer both high spatial resolution and high signal-to-background ratios, the fluorescence emission lifetime limits the measurement speed, while photobleaching and thermal diffusion limit the duration of measurements. Here we present a tracking method based on elastic light scattering that enables long-duration measurements of nanoparticle dynamics at rates of thousands of frames per second. We contain the particles within a single-mode silica fiber having a subwavelength, nanofluidic channel and illuminate them using the fiber's strongly confined optical mode. The diffusing particles in this cylindrical geometry are continuously illuminated inside the collection focal plane. We show that the method can track unlabeled dielectric particles as small as 20 nm as well as individual cowpea chlorotic mottle virus (CCMV) virions-26 nm in size and 4.6 megadaltons in mass-at rates of over 3 kHz for durations of tens of seconds. Our setup is easily incorporated into common optical microscopes and extends their detection range to nanometer-scale particles and macromolecules. The ease-of-use and performance of this technique support its potential for widespread applications in medical diagnostics and micro total analysis systems.
- ItemRapid Colorimetric Detection of Pseudomonas aeruginosa in Clinical Isolates Using a Magnetic Nanoparticle Biosensor(Washington, DC : ACS Publications, 2019) Alhogail, Sahar; Suaifan, Ghadeer A.R.Y; Bikker, Floris J.; Kaman, Wendy E.; Weber, Karina; Cialla-May, Dana; Popp, Jürgen; Zourob, Mohammed M.A rapid, sensitive, and specific colorimetric biosensor based on the use of magnetic nanoparticles (MNPs) was designed for the detection of Pseudomonas aeruginosa in clinical samples. The biosensing platform was based on the measurement of P. aeruginosa proteolytic activity using a specific protease substrate. At the N-terminus, this substrate was covalently bound to MNPs and was linked to a gold sensor surface via cystine at the C-terminus of the substrates. The golden sensor appears black to naked eyes because of the coverage of the MNPs. However, upon proteolysis, the cleaved peptide–MNP moieties will be attracted by an external magnet, revealing the golden color of the sensor surface, which can be observed by the naked eye. In vitro, the biosensor was able to detect specifically and quantitatively the presence of P. aeruginosa with a detection limit of 102 cfu/mL in less than 1 min. The colorimetric biosensor was used to test its ability to detect in situ P. aeruginosa in clinical isolates from patients. This biochip is anticipated to be useful as a rapid point-of-care device for the diagnosis of P. aeruginosa-related infections.
- ItemSecondary Structure and Glycosylation of Mucus Glycoproteins by Raman Spectroscopies(Columbus, Ohio : American Chemical Society, 2016) Davies, Heather S.; Singh, Prabha; Deckert-Gaudig, Tanja; Deckert, Volker; Rousseau, Karine; Ridley, Caroline E.; Dowd, Sarah E.; Doig, Andrew J.; Pudney, Paul D. A.; Thornton, David J.; Blanch, Ewan W.The major structural components of protective mucus hydrogels on mucosal surfaces are the secreted polymeric gel-forming mucins. The very high molecular weight and extensive O-glycosylation of gel-forming mucins, which are key to their viscoelastic properties, create problems when studying mucins using conventional biochemical/structural techniques. Thus, key structural information, such as the secondary structure of the various mucin subdomains, and glycosylation patterns along individual molecules, remains to be elucidated. Here, we utilized Raman spectroscopy, Raman optical activity (ROA), circular dichroism (CD), and tip-enhanced Raman spectroscopy (TERS) to study the structure of the secreted polymeric gel-forming mucin MUC5B. ROA indicated that the protein backbone of MUC5B is dominated by unordered conformation, which was found to originate from the heavily glycosylated central mucin domain by isolation of MUC5B O-glycan-rich regions. In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D′-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. Using these findings, we employed TERS, which combines the chemical specificity of Raman spectroscopy with the spatial resolution of atomic force microscopy to study the secondary structure along 90 nm of an individual MUC5B molecule. Interestingly, the molecule was found to contain a large amount of α-helix/unordered structures and many signatures of glycosylation, pointing to a highly O-glycosylated region on the mucin.
- ItemDetection of Protein Glycosylation Using Tip-Enhanced Raman Scattering(Columbus, Ohio : American Chemical Society, 2016) Cowcher, David P.; Deckert-Gaudig, Tanja; Brewster, Victoria L.; Ashton, Lorna; Deckert, Volker; Goodacre, RoystonThe correct glycosylation of biopharmaceutical glycoproteins and their formulations is essential for them to have the desired therapeutic effect on the patient. It has recently been shown that Raman spectroscopy can be used to quantify the proportion of glycosylated protein from mixtures of native and glycosylated forms of bovine pancreatic ribonuclease (RNase). Here we show the first steps toward not only the detection of glycosylation status but the characterization of glycans themselves from just a few protein molecules at a time using tip-enhanced Raman scattering (TERS). While this technique generates complex data that are very dependent on the protein orientation, with the careful development of combined data preprocessing, univariate and multivariate analysis techniques, we have shown that we can distinguish between the native and glycosylated forms of RNase. Many glycoproteins contain populations of subtly different glycoforms; therefore, with stricter orientation control, we believe this has the potential to lead to further glycan characterization using TERS, which would have use in biopharmaceutical synthesis and formulation research.
- ItemTowards on-site testing of Phytophthora species(Cambridge : RSC Publ., 2014) Schwenkbier, Lydia; Pollok, Sibyll; König, Stephan; Urban, Matthias; Werres, Sabine; Cialla-May, Dana; Weber, Karina; Popp, JürgenRapid detection and accurate identification of plant pathogens in the field is an ongoing challenge. In this study, we report for the first time on the development of a helicase-dependent isothermal amplification (HDA) in combination with on-chip hybridization for the detection of selected Phytophthora species. The HDA approach allows efficient amplification of the yeast GTP-binding protein (Ypt1) target gene region at one constant temperature in a miniaturized heating device. The assay's specificity was determined by on-chip DNA hybridization and subsequent silver nanoparticle deposition. The silver deposits serve as stable endpoint signals that enable the visual as well as the electrical readout. Our promising results point to the direction of a near future on-site application of the combined techniques for a reliable detection of Phytophthora species.
- ItemActivity and electron donor preference of two denitrifying bacterial strains identified by Raman gas spectroscopy(Berlin [u.a.] : Springer, 2022) Blohm, Annika; Kumar, Swatantar; Knebl, Andreas; Herrmann, Martina; Küsel, Kirsten; Popp, Jürgen; Frosch, TorstenHuman activities have greatly increased the input of reactive nitrogen species into the environment and disturbed the balance of the global N cycle. This imbalance may be offset by bacterial denitrification, an important process in maintaining the ecological balance of nitrogen. However, our understanding of the activity of mixotrophic denitrifying bacteria is not complete, as most research has focused on heterotrophic denitrification. The aim of this study was to investigate substrate preferences for two mixotrophic denitrifying bacterial strains, Acidovorax delafieldii and Hydrogenophaga taeniospiralis, under heterotrophic, autotrophic or mixotrophic conditions. This complex analysis was achieved by simultaneous identification and quantification of H2, O2, CO2, 14N2, 15N2 and 15N2O in course of the denitrification process with help of cavity-enhanced Raman spectroscopic (CERS) multi-gas analysis. To disentangle electron donor preferences for both bacterial strains, microcosm-based incubation experiments under varying substrate conditions were conducted. We found that Acidovorax delafieldii preferentially performed heterotrophic denitrification in the mixotrophic sub-experiments, while Hydrogenophaga taeniospiralis preferred autotrophic denitrification in the mixotrophic incubation. These observations were supported by stoichiometric calculations. The results demonstrate the prowess of advanced Raman multi-gas analysis to study substrate use and electron donor preferences in denitrification, based on the comprehensive quantification of complex microbial gas exchange processes. © 2021, The Author(s).
- ItemIsolation of bacteria from artificial bronchoalveolar lavage fluid using density gradient centrifugation and their accessibility by Raman spectroscopy(Berlin [u.a.] : Springer, 2021) Wichmann, Christina; Rösch, Petra; Popp, JürgenRaman spectroscopy is an analytical method to identify medical samples of bacteria. Because Raman spectroscopy detects the biochemical properties of a cell, there are many factors that can influence and modify the Raman spectra of bacteria. One possible influence is a proper method for isolation of the bacteria. Medical samples in particular never occur in purified form, so a Raman-compatible isolation method is needed which does not affect the bacteria and thus the resulting spectra. In this study, we present a Raman-compatible method for isolation of bacteria from bronchoalveolar lavage (BAL) fluid using density gradient centrifugation. In addition to measuring the bacteria from a patient sample, the yield and the spectral influence of the isolation on the bacteria were investigated. Bacteria isolated from BAL fluid show additional peaks in comparison to pure culture bacteria, which can be attributed to components in the BAL sample. The isolation gradient itself has no effect on the spectra, and with a yield of 63% and 78%, the method is suitable for isolation of low concentrations of bacteria from a complex matrix. Graphical abstract.
- ItemIt Takes Three to Tango - the length of the oligothiophene determines the nature of the long-lived excited state and the resulting photocytotoxicity of a Ru(II) photodrug(Weinheim : Wiley-VCH, 2021) Chettri, Avinash; Roque, John A.; Schneider, Kilian R.A.; Cole, Houston D.; Cameron, Colin G.; McFarland, Sherri A.; Dietzek, BenjaminTLD1433 is the first Ru(II) complex to be tested as a photodynamic therapy agent in a clinical trial. In this contribution we study TLD1433 in the context of structurally-related Ru(II)-imidozo[4,5-f][1,10]phenanthroline (ip) complexes appended with thiophene rings to decipher the unique photophysical properties which are associated with increasing oligothiophene chain length. Substitution of the ip ligand with ter- or quaterthiophene changes the nature of the long-lived triplet state from metal-to-ligand charge-transfer to 3ππ* character. The addition of the third thiophene thus presents a critical juncture which not only determines the photophysics of the complex but most importantly its capacity for 1O2 generation and hence the potential of the complex to be used as a photocytotoxic agent.
- ItemUnderstanding Nonlinear Pulse Propagation in Liquid Strand-Based Photonic Bandgap Fibers(Basel : MDPI, 2021) Qi, Xue; Schaarschmidt, Kay; Li, Guangrui; Junaid, Saher; Scheibinger, Ramona; Lühder, Tilman; Schmidt, Markus A.Ultrafast supercontinuum generation crucially depends on the dispersive properties of the underlying waveguide. This strong dependency allows for tailoring nonlinear frequency conversion and is particularly relevant in the context of waveguides that include geometry-induced resonances. Here, we experimentally uncovered the impact of the relative spectral distance between the pump and the bandgap edge on the supercontinuum generation and in particular on the dispersive wave formation on the example of a liquid strand-based photonic bandgap fiber. In contrast to its air-hole-based counterpart, a bandgap fiber shows a dispersion landscape that varies greatly with wavelength. Particularly due to the strong dispersion variation close to the bandgap edges, nanometer adjustments of the pump wavelength result in a dramatic change of the dispersive wave generation (wavelength and threshold). Phase-matching considerations confirm these observations, additionally revealing the relevance of third order dispersion for interband energy transfer. The present study provides additional insights into the nonlinear frequency conversion of resonance-enhanced waveguide systems which will be relevant for both understanding nonlinear processes as well as for tailoring the spectral output of nonlinear fiber sources.
- ItemCharacterizing photocatalysts for water splitting: from atoms to bulk and from slow to ultrafast processes(London : Royal Society of Chemistry (RSC), 2021) Kranz, Christine; Wächtler, MariaResearch on light-driven catalysis has gained tremendous importance due to the ever-increasing power consumption and the threatening situation of global warming related to burning fossil fuels. Significant efforts have been dedicated to artificial photosynthesis mimicking nature to split H2O into H2 and O2 by solar energy. Novel semiconductor und molecular photocatalysts focusing on one-step excitation processes via single component photocatalysts or via two-step excitation processes mimicking the Z-scheme of natural photosynthesis are currently developed. Analytical and physicochemical methods, which provide information at different time and length scales, are used to gain fundamental understanding of all processes leading to catalytic activity, i.e., light absorption, charge separation, transfer of charges to the reaction centres and catalytic turnover, but also understanding degradation processes of the photocatalytic active material. Especially, molecular photocatalysts still suffer from limited long-Term stability due to the formation of reactive intermediates, which may lead to degradation. Although there is an overwhelming number of research articles and reviews focussing on various materials for photocatalytic water splitting, to date only few reviews have been published providing a comprehensive overview on methods for characterizing such materials. This review will highlight spectroscopic, spectroelectrochemical, and electrochemical approaches in respect to their potential in studying processes in semiconductor and (supra)molecular photocatalysts. Special emphasis will be on spectroscopic methods to investigate light-induced processes in intermediates of sequential electron transfer chains. Further, microscopic characterization methods, which are predominantly used for semiconducting and hybrid photocatalytic materials will be reviewed as surface area, structure, facets, defects, and bulk properties such as crystallinity and crystal size are key parameters for charge separation, transfer processes and suppression of charge recombination. Recent developments in scanning probe microscopy will also be highlighted as such techniques are highly suited for studying photocatalytic active material. © The Royal Society of Chemistry.