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Start date: 2000 × DDC: 540 × WGL Institute: ISAS ×

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Now showing 1 - 10 of 16
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    High spatial and temporal resolution cell manipulation techniques in microchannels
    (Cambridge : Royal Society of Chemistry, 2016) Novo, Pedro; Dell’Aica, Margherita; Janasek, Dirk; Zahedi, René P.
    The advent of microfluidics has enabled thorough control of cell manipulation experiments in so called lab on chips. Lab on chips foster the integration of actuation and detection systems, and require minute sample and reagent amounts. Typically employed microfluidic structures have similar dimensions as cells, enabling precise spatial and temporal control of individual cells and their local environments. Several strategies for high spatio-temporal control of cells in microfluidics have been reported in recent years, namely methods relying on careful design of the microfluidic structures (e.g. pinched flow), by integration of actuators (e.g. electrodes or magnets for dielectro-, acousto- and magneto-phoresis), or integrations thereof. This review presents the recent developments of cell experiments in microfluidics divided into two parts: an introduction to spatial control of cells in microchannels followed by special emphasis in the high temporal control of cell-stimulus reaction and quenching. In the end, the present state of the art is discussed in line with future perspectives and challenges for translating these devices into routine applications.
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    Quantification of Dolichyl Phosphates Using Phosphate Methylation and Reverse-Phase Liquid Chromatography-High Resolution Mass Spectrometry
    (Columbus, Ohio : American Chemical Society, 2023) Kale, Dipali; Kikul, Frauke; Phapale, Prasad; Beedgen, Lars; Thiel, Christian; Brügger, Britta
    Dolichyl monophosphates (DolPs) are essential lipids in glycosylation pathways that are highly conserved across almost all domains of life. The availability of DolP is critical for all glycosylation processes, as these lipids serve as membrane-anchored building blocks used by various types of glycosyltransferases to generate complex post-translational modifications of proteins and lipids. The analysis of DolP species by reverse-phase liquid chromatography-mass spectrometry (RPLC-MS) remains a challenge due to their very low abundance and wide range of lipophilicities. Until now, a method for the simultaneous qualitative and quantitative assessment of DolP species from biological membranes has been lacking. Here, we describe a novel approach based on simple sample preparation, rapid and efficient trimethylsilyl diazomethane-dependent phosphate methylation, and RPLC-MS analysis for quantification of DolP species with different isoprene chain lengths. We used this workflow to selectively quantify DolP species from lipid extracts derived of Saccharomyces cerevisiae, HeLa, and human skin fibroblasts from steroid 5-α-reductase 3- congenital disorders of glycosylation (SRD5A3-CDG) patients and healthy controls. Integration of this workflow with global lipidomics analyses will be a powerful tool to expand our understanding of the role of DolPs in pathophysiological alterations of metabolic pathways downstream of HMG-CoA reductase, associated with CDGs, hypercholesterolemia, neurodegeneration, and cancer.
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    Synthetic glycopeptides and glycoproteins with applications in biological research
    (Frankfurt am Main : Beilstein-Institut, 2012) Westerlind, Ulrika
    Over the past few years, synthetic methods for the preparation of complex glycopeptides have been drastically improved. The need for homogenous glycopeptides and glycoproteins with defined chemical structures to study diverse biological phenomena further enhances the development of methodologies. Selected recent advances in synthesis and applications, in which glycopeptides or glycoproteins serve as tools for biological studies, are reviewed. The importance of specific antibodies directed to the glycan part, as well as the peptide backbone has been realized during the development of synthetic glycopeptide-based anti-tumor vaccines. The fine-tuning of native chemical ligation (NCL), expressed protein ligation (EPL), and chemoenzymatic glycosylation techniques have all together enabled the synthesis of functional glycoproteins. The synthesis of structurally defined, complex glycopeptides or glyco-clusters presented on natural peptide backbones, or mimics thereof, offer further possibilities to study protein-binding events.
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    Alignment of retention time obtained from multicapillary column gas chromatography used for VOC analysis with ion mobility spectrometry
    (Heidelberg : Springer, 2010) Perl, Thorsten; Bödeker, Bertram; Jünger, Melanie; Nolte, Jürgen; Vautz, Wolfgang
    Multicapillary column (MCC) ion mobility spectrometers (IMS) are increasingly in demand for medical diagnosis, biological applications and process control. In a MCC-IMS, volatile compounds are differentiated by specific retention time and ion mobility when rapid preseparation techniques are applied, e.g. for the analysis of complex and humid samples. Therefore, high accuracy in the determination of both parameters is required for reliable identification of the signals. The retention time in the MCC is the subject of the present investigation because, for such columns, small deviations in temperature and flow velocity may cause significant changes in retention time. Therefore, a universal correction procedure would be a helpful tool to increase the accuracy of the data obtained from a gas-chromatographic preseparation. Although the effect of the carrier gas flow velocity and temperature on retention time is not linear, it could be demonstrated that a linear alignment can compensate for the changes in retention time due to common minor deviations of both the carrier gas flow velocity and the column temperature around the MCC-IMS standard operation conditions. Therefore, an effective linear alignment procedure for the correction of those deviations has been developed from the analyses of defined gas mixtures under various experimental conditions. This procedure was then applied to data sets generated from real breath analyses obtained in clinical studies using different instruments at different measuring sites for validation. The variation in the retention time of known signals, especially for compounds with higher retention times, was significantly improved. The alignment of the retention time—an indispensable procedure to achieve a more precise identification of analytes—using the proposed method reduces the random error caused by small accidental deviations in column temperature and flow velocity significantly.
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    Fast IR laser mapping ellipsometry for the study of functional organic thin films
    (Cambridge : Royal Society of Chemistry, 2015) Furchner, Andreas; Sun, Guoguang; Ketelsen, Helge; Rappich, Jörg; Hinrichs, Karsten
    Fast infrared mapping with sub-millimeter lateral resolution as well as time-resolved infrared studies of kinetic processes of functional organic thin films require a new generation of infrared ellipsometers. We present a novel laboratory-based infrared (IR) laser mapping ellipsometer, in which a laser is coupled to a variable-angle rotating analyzer ellipsometer. Compared to conventional Fourier-transform infrared (FT-IR) ellipsometers, the IR laser ellipsometer provides ten- to hundredfold shorter measurement times down to 80 ms per measured spot, as well as about tenfold increased lateral resolution of 120 μm, thus enabling mapping of small sample areas with thin-film sensitivity. The ellipsometer, equipped with a HeNe laser emitting at about 2949 cm−1, was applied for the optical characterization of inhomogeneous poly(3-hexylthiophene) [P3HT] and poly(N-isopropylacrylamide) [PNIPAAm] organic thin films used for opto-electronics and bioapplications. With the constant development of tunable IR laser sources, laser-based infrared ellipsometry is a promising technique for fast in-depth mapping characterization of thin films and blends.
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    IR-MALDI Mass Spectrometry Imaging with Plasma Post-Ionization of Nonpolar Metabolites
    (Columbus, Ohio : American Chemical Society, 2022) Schneemann, Julian; Schäfer, Karl-Christian; Spengler, Bernhard; Heiles, Sven
    Ambient mass spectrometry imaging (MSI) methods come with the advantage of visualizing biomolecules from tissues with no or minimal sample preparation and operation under atmospheric-pressure conditions. Similar to all other MSI methodologies, however, ambient MSI modalities suffer from a pronounced bias toward either polar or nonpolar analytes due to the underlying desorption and ionization mechanisms of the ion source. In this study, we present the design, construction, testing, and application of an in-capillary dielectric barrier discharge (DBD) module for post-ionization of neutrals desorbed by an ambient infrared matrix-assisted laser desorption/ionization (IR-MALDI) MSI source. We demonstrate that the DBD device enhances signal intensities of nonpolar compounds by up to 104 compared to IR-MALDI without affecting transmission of IR-MALDI ions. This allows performing MSI experiments of mouse tissue and Danaus plexippus caterpillar tissue sections, visualizing the distribution of sterols, fatty acids, monoglycerides, and diglycerides that are not detected in IR-MALDI MSI experiments. The pronounced signal enhancement due to IR-MALDI-DBD compared to IR-MALDI MSI enables mapping of nonpolar analytes with pixel resolutions down to 20 μm in mouse brain tissue and to discern the spatial distribution of sterol lipids characteristic for histological regions of D. plexippus.
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    Azapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells
    (Cambridge : RSC, 2023) Vanhoutte, Roeland; Barniol-Xicota, Marta; Chiu, Winston; Vangeel, Laura; Jochmans, Dirk; De Jonghe, Steven; Zidane, Hadeer; Barr, Haim M.; London, Nir; Neyts, Johan; Verhelst, Steven H. L.
    The COVID-19 pandemic has revealed the vulnerability of the modern, global society. With expected waves of future infections by SARS-CoV-2, treatment options for infected individuals will be crucial in order to decrease mortality and hospitalizations. The SARS-CoV-2 main protease is a validated drug target, for which the first inhibitor has been approved for use in patients. To facilitate future work on this drug target, we designed a solid-phase synthesis route towards azapeptide activity-based probes that are capped with a cysteine-reactive electrophile for covalent modification of the active site of Mpro. This design led to the most potent ABP for Mpro and one of the most potent inhibitors reported thus far. We demonstrate that this ABP can be used to visualize Mpro activity and target engagement by drugs in infected cells.
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    Why phosphoproteomics is still a challenge
    (Cambridge : Royal Society of Chemistry, 2015) Solari, Fiorella A.; Dell'Aica, Margherita; Sickmann, Albert; Zahedi, René P.
    Despite continuous improvements phosphoproteomics still faces challenges that are often neglected, e.g. partially poor recovery of phosphopeptide enrichment, assessment of phosphorylation stoichiometry, label-free quantification, poor behavior during chromatography, and general limitations of peptide-centric proteomics. Here we critically discuss current limitations that need consideration in both qualitative and quantitative studies.
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    The influence of Sb doping on the local structure and disorder in thermoelectric ZnO:Sb thin films
    (Lausanne : Elsevier, 2023) Ribeiro, Joana M.; Rodrigues, Frederico J.; Correia, Filipe C.; Pudza, Inga; Kuzmin, Alexei; Kalinko, Aleksandr; Welter, Edmund; Barradas, Nuno P.; Alves, Eduardo; LaGrow, Alec P.; Bondarchuk, Oleksandr; Welle, Alexander; Telfah, Ahmad; Tavares, Carlos J.
    Thermoelectric transparent ZnO:Sb thin films were deposited by magnetron sputtering, with Sb content varying between 2 and 14 at%. As evidenced by X-ray diffraction analysis, the films crystallize in the ZnO wurtzite structure for lower levels of Sb-doping, developing a degree of amorphization for higher levels of Sb-doping. Temperature-dependent (10–300 K) X-ray absorption spectroscopy studies of the produced thin films were performed at the Zn and Sb K-edges to shed light on the influence of Sb doping on the local atomic structure and disorder in the ZnO:Sb thin films. The analysis of the Zn K-edge EXAFS spectra by the reverse Monte Carlo method allowed to extract detailed and accurate structural information in terms of the radial and bond angle distribution functions. The obtained results suggest that the introduction of antimony to the ZnO matrix promotes static disorder, which leads to partial amorphization with very small crystallites (∼3 nm) for large (12–14 at%) Sb content. Rutherford backscattering spectrometry (RBS) experiments enabled the determination of the in-depth atomic composition profiles of the films. The film composition at the surfaces determined by X-ray photoelectron spectroscopy (XPS) matches that of the bulk determined by RBS, except for higher Sb-doping in ZnO films, where the concentration of oxygen determined by XPS is smaller near the surface, possibly due to the formation of oxygen vacancies that lead to an increase in electrical conductivity. Traces of Sb–Sb metal bonds were found by XPS for the sample with the highest level of Sb-doping. Time-of-flight secondary ion mass spectrometry obtained an Sb/Zn ratio that follows that of the film bulk determined by RBS, although Sb is not always homogeneous, with samples with smaller Sb content (2 and 4 at% of Sb) showing a larger Sb content closer to the film/substrate interface. From the optical transmittance and reflectance curves, it was determined that the films with the lower amount of Sb doping have larger optical band-gaps, in the range of 2.9–3.2 eV, while the partially amorphous films with higher Sb content have smaller band-gaps in the range of 1.6–2.1 eV. Albeit the short-range crystalline order (∼3 nm), the film with 12 at% of Sb has the highest absolute Seebeck coefficient (∼56 μV/K) and a corresponding thermoelectric power factor of ∼0.2 μW·K−2·m−1.