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  • 1.
    Baldassarre, Maurizio
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Pushing the detection limit of infrared spectroscopy for structural analysis of dilute protein samples.2014Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 139, nr 21, s. 5393-5399Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fourier-transform infrared spectroscopy is a powerful and versatile tool to investigate the structure and dynamics of proteins in solution. The intrinsically low extinction coefficient of the amide I mode, the main structure-related oscillator, together with the high infrared absorptivity of aqueous media, requires that proteins are studied at high concentrations (>10 mg L(-1)). This may represent a challenge in the study of aggregation-prone proteins and peptides, and questions the significance of structural data obtained for proteins physiologically existing at much lower concentrations. Here we describe the development of a simple experimental approach that increases the detection limit of protein structure analysis by infrared spectroscopy. Our approach relies on custom-made filters to isolate the amide I region (1700-1600 cm(-1)) from irrelevant spectral regions. The sensitivity of the instrument is then increased by background attenuation, an approach consisting in the use of a neutral density filter, such as a non-scattering metal grid, to attentuate the intensity of the background spectrum. When the filters and grid are combined, a 2.4-fold improvement in the noise level can be obtained. We have successfully tested this approach using a highly diluted solution of pyruvate kinase in deuterated medium (0.2% w/v), and found that it provides spectra of a quality comparable to those recorded with a 10-fold higher protein concentration.

  • 2.
    Baldassarre, Maurizio
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    The carbonate/bicarbonate system as a pH indicator for infrared spectroscopy2014Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 139, nr 9, s. 2167-2176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Caged compounds capable of inducing large pH-jumps upon UV illumination have represented a breakthrough in time-resolved infrared spectroscopy of acidification-triggered phenomena, but their use is hampered by the inability to control the initial pH as well as to measure the final pH in mu L volumes. We have developed an experimental approach that accurately measures the initial and final pH values in pH-jump experiments. Our approach exploits the concomitant presence of two or more inorganic ions, such as carbonate and bicarbonate, that are added to the sample at a known concentration. The difference spectrum obtained in the infrared measurement is fitted to isolate the bands arising from the appearance or disappearance of either protonation state, and is then compared to a synthetic library of difference spectra generated using both qualitative (band position and width, extinction coefficient, pK) and quantitative (concentration, pathlength) parameters of the reporter ions. We have tested this approach in UV-photolysis experiments of 1-(2-nitrophenyl)ethyl sulfate in the presence of different concentrations of Na2CO3 and successfully used the infrared absorption of the carbonate and the bicarbonate ions to determine the initial and final pH values before and after the pH-jump, respectively.

  • 3.
    Baldassarre, Maurizio
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Bennett, Matthew
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Simultaneous acquisition of infrared, fluorescence and light scattering spectra of proteins: direct evidence for pre-fibrillar species in amyloid fibril formation2016Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 141, nr 3, s. 963-973Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Different spectroscopic approaches are often used to probe specific aspects of amyloid fibril formation but are usually performed separately and under different conditions. This makes it problematic to relate different aspects of the aggregation process when these are monitored by different methods. We report on a multispectral approach for simultaneous acquisition of infrared, fluorescence and light scattering spectra of proteins undergoing aggregation. We have applied our approach to study beta-lactoglobulin, a milk protein known to form amyloid fibrils under well-established conditions. Our real-time multispectral measurements show that unfolding of this protein is followed by formation of early aggregates consisting of intermolecular beta-sheets with a typical infrared absorption at similar to 1619 cm(-1) in (H2O)-H-2. These aggregates, which lead to an increase in the light scattering signal, do not bind the amyloid-specific fluorophore ThT and therefore consist of oligomers or protofibrils. Fibril growth is then observed as a sigmoidal increase in ThT fluorescence. After similar to 25 h, a plateau is observed in the intensities of ThT emission and of the band at 1619 cm(-1), indicating that no new fibrils are forming. However, a second phase in the light scattering signal taking place after similar to 25 h suggests that the fibrils are assembling into larger structures, known as mature fibrils. This is associated with an upshift of the main beta-sheet band in the infrared spectrum. TEM analyses confirmed the existence of thick fibrils comprising 3-5 filaments.

  • 4.
    Isetun, Sindra
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Nilsson, Ulrika
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Dynamic field sampling of airborne organophosphate triesters using solid-phase microextraction under equilibrium and non-equilibrium conditions2005Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 30, s. 94-98Artikel i tidskrift (Refereegranskat)
    Abstract [en]

     

    A simple setup for dynamic air sampling using a solid-phase microextraction (SPME) device

    designed for use in the field was evaluated for organophosphate triester vapour under both

    equilibrium and non-equilibrium conditions. The effects of varying the applied airflows in the

    sampling device were evaluated in order to optimise the system with respect to the Reynolds

    number and magnitude of the boundary layer that developed near the surface. Further, the

    storage stability of the analytes was studied for both capped and uncapped 100-

     

     

    m

    m PDMS fibres.

    Organophosphate triesters are utilized on large scales as flame-retardants and/or plasticizers, for

    instance in upholstered furniture. In indoor working environments these compounds have become

    common components in the surrounding air. Measurements were performed in a recently

    furnished working environment and the concentration of tris(2-choropropyl) phosphate was

    found to be 7

     

     

    mg m23

    .

  • 5.
    Li, Chenge
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Kumar, Saroj
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Montigny, Cedric
    le Mairebcd, Marc
    Barth, Andreas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Quality assessment of recombinant proteins by infrared spectroscopy. Characterisation of a protein aggregation related band of the Ca2+-ATPase2014Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 139, nr 17, s. 4231-4240Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Infrared spectroscopy was used to characterise recombinant sarcoplasmic reticulum Ca2+-ATPase (SERCA1a). In the amide I region, its spectrum differed from that of Ca2+-ATPase prepared from rabbit fast twitch muscle below 1650 cm(-1). A band at 1642 cm(-1) is reduced in the spectrum of the recombinant protein and a band at 1631 cm(-1) is more prominent. By comparison of amide 1 band areas with the known secondary structure content of the protein, we assigned the 1642 cm(-1) band to beta-sheet structure. Further investigation revealed that the 1642 cm(-1) band decreased and the 1631 cm-1 band increased upon storage at room temperature and upon repeated washing of a protein film with water. Also protein aggregates obtained after solubilisation of the rabbit muscle enzyme showed a prominent band at 1631 cm(-1), whereas the spectrum of solubilised ATPase resembled that of the membrane bound protein. The spectral position of the 1631 cm(-1) band is similar to that of a band observed for inclusion bodies of other proteins. The findings show that the absence of the 1642 cm(-1) band and the presence of a prominent band at 1631 cm(-1) indicate protein aggregation and can be used as a quality marker for the optimisation of recombinant protein production. We conclude that recombinant production of SERCA1a, storage at room temperature, repeated washing and aggregation after solubilisation all modify existing beta-sheets in the cytosolic domains so that they become similar to those found in inclusion bodies of other proteins.

  • 6. Moein, Mohammad Mahdi
    et al.
    Javanbakht, Mehran
    Karimi, Mohammad
    Akbari-Adergani, Behrouz
    Abdel-Rehim, Mohamed
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    A new strategy for surface modification of polysulfone membrane by in situ imprinted sol-gel method for the selective separation and screening of L-Tyrosine as a lung cancer biomarker2015Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 140, nr 6, s. 1939-1946Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work, a novel method based on in situ molecularly imprinted sol-gel for the surface modification of a polysulfone membrane (PSM) was developed. A modified molecularly imprinted sol-gel polysulfone membrane (MSM) was placed in a homemade plastic tube and coupled on-line with LC/MS/MS for the selective extraction and screening of L-Tyrosine (Tyr) as a tentative lung cancer biomarker in human plasma samples. The existence of molecularly imprinted sol-gel layers on both sides of a PSM was examined using scanning electron microscopy (SEM). To evaluate the role of precursor in the extraction performance, repeatability, and selectivity of developed method, three precursors, 3-(propylmethacrylate) trimethoxysilane (P1), 3-(triethoxysilyl)-propylamine (P2), tetraethyl orthosilicate (P3), individually and together were used for treatment of PSM. Our investigation showed that a single precursor's route is more repeatable, straightforward, precise, accurate, and selective for the extraction of Tyr in plasma samples. Moreover, to achieve the best conditions and extraction efficiency, the effect of influential parameters, including the conditioning, washing, and elution of solvents, sample flow rate, loading time, desorption time, loading sample volume, salt effect, pH, and adsorption capacity for the most efficiently prepared membranes were truly investigated. The non-molecularly imprinted sol-gel polysulfone membrane (NSM) was prepared as a blank via the same process but in the absence of the Tyr. The LOD (S/N = 3/1) was 0.1 nmol L-1 and the LOQ (S/N = 10/1) was 0.34 nmol L-1 for Tyr in the plasma samples. The linearity for the Tyr was in the range of 0.34-2000 nmol L-1 in the plasma samples. The coefficients of determination values were >= 0.998 for all runs. The extraction recovery was between 80%-85% for Tyr in the plasma samples. In addition, MSM could be used for up to 50 extractions without a significant change in recovery percentage.

  • 7.
    Quaranta, Alessandro
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Spasova, Maya
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Passarini, Elena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Karlsson, Isabella
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Ndreu, Lorena
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    Thorsén, Gunnar
    Ilag, Leopold L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för miljövetenskap och analytisk kemi.
    N-Glycosylation profiling of intact target proteins by high-resolution mass spectrometry (MS) and glycan analysis using ion mobility-MS/MS2020Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 145, nr 5, s. 1737-1748Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glycosylation influences the structure and functionality of glycoproteins, and is regulated by genetic and environmental factors. The types and abundance of glycans on glycoproteins can vary due to diseases such as cancer, inflammation, autoimmune and neurodegenerative disorders. Due to the crucial role glycans play in modulating protein function, glycosylation analysis could lead to the discovery of novel biomarkers and is of prime importance in controlling the quality of glycoprotein biopharmaceuticals. Here, we present a method for the identification and quantification of glycoforms directly on intact proteins, after immunoaffinity purification from biological fluids. The method was validated and applied to serum transferrin and the biopharmaceutical trastuzumab. The accuracy of the method, expressed as the relative error (RE), ranged from 2.1 (at high concentrations) to 7.9% (at low concentrations), and intra- and inter-day precision, expressed as relative standard deviation (RSD), was 3.2 and 8.2%, respectively. The sensitivity and linearity of the method were suitable for serum analysis and the LOQ was calculated to be 3.1 and 4.4 mu g mL(-1) for transferrin (TFN) and trastuzumab (TRA), respectively. Its application to transferrin from five healthy human serum samples yielded concentrations between 1.61 and 3.17 mg mL(-1), which are in agreement with blood reference levels. In parallel, the structure of the identified glycans was determined by ion mobility spectrometry coupled with tandem mass spectrometry. No chromatographic separation was required and sample preparation was performed in a semi-automatic manner, facilitating the handling of up to 12 samples at a time. This method should be useful for clinical laboratories and for the quality control of large batches of biopharmaceuticals.

  • 8. Shibata, Aya
    et al.
    Nakano, Yukiko
    Ito, Mika
    Araki, Mika
    Zhang, Jie
    Yoshida, Yasuhiko
    Shuto, Satoshi
    Mannervik, Bengt
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för neurokemi. Uppsala University, Sweden.
    Mogenstern, Ralf
    Ito, Yoshihiro
    Abe, Hiroshi
    Fluorogenic probes using 4-substituted-2-nitrobenzenesulfonyl derivatives as caging groups for the analysis of human glutathione transferase catalyzed reactions2013Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 138, nr 24, s. 7326-7330Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have synthesized a series of 4-substituted-2-nitrobenzene-sulfonyl compounds for caged fluorogenic probes and conducted a Hammett plot analysis using the steady-state kinetic parameters. The results revealed that the glutathione transferase (GST) alpha catalyzed reaction was dependent on the sigma value in the same way as the non-enzymatic reaction, whereas the dependence of the sigma value of the GST mu and pi was not as pronounced as that of GST alpha.

  • 9.
    Spacil, Zdenek
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Eriksson, Johan
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Jonasson, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Rasmussen, Ulla
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Ilag, Leopold L.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Bergman, Birgitta
    Stockholms universitet, Naturvetenskapliga fakulteten, Botaniska institutionen.
    Analytical protocol for identification of BMAA and DAB in biologicalsamples2010Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 135, s. 127-132Artikel i tidskrift (Refereegranskat)
    Abstract [en]

     

    b

    -N-methylamino-L-alanine (BMAA) is a non-protein amino acid, thought to be inflicting neurodegenerative diseases related to ALS/PDC in human beings. Due to conflicting data concerning the presence of BMAA in various biological matrixes, we present a robust and sensitive method for high confidence identification of BMAA after derivatization by 6-aminoquinolyl-N

    -hydroxysuccinimidyl carbamate (AQC). The efficient sample pretreatment in combination with LC-MS/MS SRM enables chromatographic separation of BMAA from the isomer 2,3-diaminobutyric acid (DAB). The method is applicable for selective BMAA/DAB detection in various biological samples ranging from a prokaryotic cyanobacterium to eukaryotic fish.

  • 10. Venzac, B.
    et al.
    Diakite, M. L.
    Herthnek, David
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).
    Cisse, I.
    Bockelmann, U.
    Descroix, S.
    Malaquin, L.
    Viovy, J. -L.
    On-chip conductometric detection of short DNA sequences via electro-hydrodynamic aggregation2018Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 143, nr 1, s. 190-199Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fluorescence measurement is the main technology for post-amplification DNA detection in automated systems. Direct electrical reading of DNA concentration in solution could be an interesting alternative to go toward more miniaturized or less expensive devices, in particular in the pathogen detection field. Here we present the detection of short bacterial biomarkers with a direct impedancemetric measurement, within solutions of amplified and elongated DNA sequences in a microchannel. This technology relies on the electrohydrodynamic instability occurring in solutions of long charged macromolecules in a strong electric field. This instability specifically induces the aggregation of long DNAs and triggers conductivity variations that can be monitored by on-contact conductometry. An innovative isothermal amplification and elongation strategy was developed, combining SDA and HRCA reactions, in order to yield long DNAs suitable to be detected by the above principle, from a dilute initial DNA target. In contrast with previous label-free detection methods, this new strategy is very robust to matrix effects, thanks to the unique molecular weight dependence of the instability, coupled with this specific DNA amplification strategy. We demonstrate the detection of a 1 pM gene sequence specific to Staphylococcus aureus, in a portable system.

  • 11.
    Wiberg, Kent
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Hagman, Anders
    Jacobsson, Sven P.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för analytisk kemi.
    Burén, Peter
    Determination of the content and identity of lidocaine soluions with UV-visible spectroscopy and multivariate calibration2001Ingår i: The Analyst, ISSN 0003-2654, E-ISSN 1364-5528, Vol. 126, nr 7, s. 1142-1148Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A method is proposed for the determination of the content and identity of the active compound in pharmaceutical solutions by means of ultraviolet-visible (UV–Vis) spectroscopy, orthogonal signal correction (OSC) and multivariate calibration with soft independent modelling of class analogy (SIMCA) classification and partial least squares (PLS) regression. The content was determined with PLS regression and the identity with PLS regression and SIMCA classification. The method was tested on the local anaesthetic compound lidocaine. For the validation, external test sets of both manufactured sample solutions and samples from a stability study were used. For comparison with this new method, liquid chromatography was used as a reference method. The results show that in respect of accuracy, precision and repeatability, the new method is comparable to the reference method. The main advantage over liquid chromatography is the much shorter time of analysis and the simpler analytical procedure. An estimate of the analysis time saved with the proposed method compared with using liquid chromatography, together with practical considerations, is given.

1 - 11 av 11
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