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  • 1.
    Decker, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Lindberg, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Eriksson, Jonas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kleczkowski, Leszek A.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    A luminescence-based assay of UDP-sugar producing pyrophosphorylases2014In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 6, no 1, p. 57-61Article in journal (Refereed)
    Abstract [en]

    A coupled luminescence assay was applied to monitor pyrophosphate (PPi) production by either purified barley UDP-glucose pyrophosphorylase (UGPase) or purified Leishmania UDP-sugar pyrophosphorylase (USPase). In the assay, the PPi produced by the pyrophosphorylases was converted to ATP by ATP-sulfurylase, and the ATP produced was linked to luminescent light formation through the action of firefly luciferase. The assay allowed for a quantitative measurement of UGPase and USPase activities, down to a pmol per min level. The activities were linear with time and proportional to the amount of the enzyme added, and were neither affected by Pi nor by DTT. For UGPase, K-m values with UTP and Glc-1-P were 0.14 and 0.26 mM, respectively, whereas for USPase the respective K-m values with UTP, Glc-1-P and Gal-1-P were 0.4, 2.9 and 3.9 mM. Possible applications of the luminescence-based assay for not only UDP-sugar producing pyrophosphorylases, but also other types of pyrophosphorylases are discussed.

  • 2.
    Do, Lan
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Xuan, Thong H.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lundstedt, Staffan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Modular pressurized liquid extraction for simultaneous extraction, clean-up and fractionation of PCDD/Fs in soil, sediment and sludge samples2013In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, no 5, p. 1231-1237Article in journal (Refereed)
    Abstract [en]

    Modular pressurized liquid extraction (M-PLE) procedures were developed for simultaneous extraction, clean-up and fractionation of polychlorinated dioxins and furans (PCDD/Fs) in soil, sediment and sludge samples. The procedures utilize two coupled extraction cells: an upstream cell filled with the sample and layers of silica and acid- and base-modified silica, and a downstream cell filled with activated carbon. The silica layers were added to remove polar or hydrolysable matrix components, and the carbon to perform planarity-based fractionation. Two solvent systems (dichloromethane–heptane, DCM–Hp and diethyl ether–heptane, DEE–Hp) and two activated carbon loads (1% and 3% carbon on Celite) were evaluated using certified reference materials (CRM-529 and WMS-01) and materials from previous inter-calibration studies. Using any of the four procedures, data statistically equivalent to the certified or reference values were obtained. The M-PLE procedure using DCM–Hp and 1% carbon sometimes extracted the reference materials more efficiently than the reference methods, while the DEE–Hp procedure extracted them equally efficient, offering an alternative with less environmental impact. The methods with 1% carbon on Celite produced sufficiently pure extracts for sample loads up to one gram, but for greater sample loads the higher carbon load (3% carbon on Celite) was required to avoid breakthrough of target analytes. The new streamlined procedures are fast, cost-efficient, involve relatively low environmental impact (in the case of DEE–Hp) and are well suited for high-throughput analysis of solid samples, e.g. in connection with environmental monitoring campaigns and major soil remediation efforts.

  • 3.
    Kumar, Keshav
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Discrete wavelet assisted correlation optimised warping of chromatograms: optimizing the computational time for correcting the drifts in peak positions2017In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 9, no 13, p. 2049-2058Article in journal (Refereed)
    Abstract [en]

    Correlation optimised warping (COW) has been the most favourite chromatographic peak alignment approach in recent years. After optimization of the two parameters, slack and segment length, COW works well in aligning the chromatograms. However, one of the serious disadvantages of COW is that it is computationally time consuming. Often several segment lengths and slack parameters need to be tested to find the optimum combination for achieving the alignment that makes the whole analysis take several hours. In the present work, it has been shown that with the application of wavelet analysis prior to alignment it is possible to provide the necessary computational economy to the COW algorithm.

  • 4.
    Kumar, Keshav
    et al.
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Cava, Felipe
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Chromatographic analysis of peptidoglycan samples with the aid of a chemometric technique: introducing a novel analytical procedure to classify bacterial cell wall collection2019In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 11, no 12, p. 1671-1679Article in journal (Refereed)
    Abstract [en]

    The technical development of liquid chromatography has provided the necessary sensitivity to characterise peptidoglycan samples. However, the analysis of large numbers of complex chromatographic data sets without the aid of a proper chemometric technique is a laborious task, carrying a high risk of losing important biochemical information. The present work describes the development of a simple analytical procedure using self-organising map (SOM) analysis to analyse the large number of complex chromatographic data sets from bacterial peptidoglycan samples. SOM analysis essentially maps the samples to a hexagonal sheet based on their compositional similarity, and thus provides an approach to classify the bacterial cell wall collection in an unsupervised manner. The utility of the proposed approach was successfully validated by analysing peptidoglycan samples belonging to the Alphaproteobacterium class. The classification results achieved with SOM analysis were found to correlate well with their relative similarity in peptidoglycan compositions. In summary, the SOM analysis-based analytical procedure is shown to be useful towards automatising the analyses of chromatographic data sets of peptidoglycan samples from bacterial collections.

  • 5.
    Kumar, Keshav
    et al.
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Cava, Felipe
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Integrating network analysis with chromatography: introducing a novel chemometry-chromatography based analytical procedure to classify the bacterial cell wall collection2018In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 10, no 10, p. 1172-1180Article in journal (Refereed)
    Abstract [en]

    The present work integrates network analysis with chromatography and proposes a novel analytical procedure to classify the bacterial cell wall collection. The network analysis model can capture the heterogeneity present in the datasets and hence can provide unsupervised classification. The proposed approach is successfully applied for classifying the peptidoglycan samples of certain bacterial collections belonging to the class of Alphaproteobacteria. The obtained classification results are found to correlate well with their relative similarity in the peptidoglycan compositions. In summary, the proposed network analysis approach can be helpful in automatizing the bacterial cell wall analysis. The proposed approach can be useful to accelerate the research related to understanding the morphology of bacterial cell walls, host-pathogen interaction and development of effective antibiotics.

  • 6.
    Ripszam, Matyas
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Grabic, Roman
    Haglund, Peter
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Elimination of interferences caused by simultaneous use of deuterated and carbon-13 standards in GC-MS analysis of polycyclic aromatic hydrocarbons (PAHs) in extracts from passive sampling devices2013In: Analytical Methods, ISSN 1759-9660, E-ISSN 1759-9679, Vol. 5, no 12, p. 2925-2928Article in journal (Refereed)
    Abstract [en]

    Two types of isotope-labelled reference compounds are typically used for the passive sampling of polycyclic aromatic hydrocarbons. One type is added before the exposure of the sampler and is called a performance reference compound (PRC). The other is the laboratory internal standard, which is spiked into the sample after extraction (dialysis) from the membrane and is used for quantification. Generally, PRCs are deuterium-labelled while internal standards are C-13-labelled. Interference originating from the internal standards occurs when the molecular ions of the PRCs gradually lose deuterium in the ion source to generate fragments that overlap with the molecular ions of the C-13-labelled internal standards. This can cause significant systematic errors in quantification. Gas chromatography-high resolution time-of-flight mass spectrometry (GC-HRTOF-MS) was used to investigate the degree of interference at varying virtual resolutions of the MS instrument, and it was shown that many of the spectral interferences can be avoided by using high MS resolutions (35 000 or better).

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