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  1. AU="Karsten Niehaus"
  2. AU=Sakurada Tsutomu
  3. AU="Ravinovich"
  4. AU="Le Corroller, Thomas"
  5. AU=Wang Lihua
  6. AU="Balducci, Ivan"
  7. AU="Kamble, Nitish" AU="Kamble, Nitish"
  8. AU="Violetta Dziedziejko"
  9. AU="Pablo Cañón"
  10. AU="Boone, Darren"
  11. AU="Nadeem S. Sheikh"
  12. AU="Means, Gary"
  13. AU="Tania Kew"
  14. AU="Williams, Scott A"
  15. AU="Dvir, May"

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  1. Artikel ; Online: Corrigendum

    Jeanne Friedrichs / Rabea Schweiger / Svenja Geisler / Judith M. Neumann / Sullivan J. M. Sadzik / Karsten Niehaus / Caroline Müller

    Frontiers in Ecology and Evolution, Vol

    Development of a polyphagous leaf beetle on different host plant species and its detoxification of glucosinolates

    2023  Band 11

    Schlagwörter glucosinolate-myrosinase system ; metabolism ; polyphagous herbivore ; performance ; detoxification ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Sprache Englisch
    Erscheinungsdatum 2023-02-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Development of a polyphagous leaf beetle on different host plant species and its detoxification of glucosinolates

    Jeanne Friedrichs / Rabea Schweiger / Svenja Geisler / Judith M. Neumann / Sullivan J. M. Sadzik / Karsten Niehaus / Caroline Müller

    Frontiers in Ecology and Evolution, Vol

    2022  Band 10

    Abstract: Herbivores face a broad range of defences when feeding on plants. By mixing diets, polyphagous herbivores are assumed to benefit during their development by gaining a better nutritional balance and reducing the intake of toxic compounds from individual ... ...

    Abstract Herbivores face a broad range of defences when feeding on plants. By mixing diets, polyphagous herbivores are assumed to benefit during their development by gaining a better nutritional balance and reducing the intake of toxic compounds from individual plant species. Nevertheless, they also show strategies to metabolically cope with plant defences. In this study, we investigated the development of the polyphagous tansy leaf beetle, Galeruca tanaceti (Coleoptera: Chrysomelidae), on mono diets consisting of one plant species [cabbage (Brassica rapa), Brassicaceae; lettuce (Lactuca sativa), or tansy (Tanacetum vulgare), Asteraceae] vs. two mixed diets, both containing tansy. Leaves of the three species were analysed for contents of water, carbon and nitrogen, the specific leaf area (SLA) and trichome density. Furthermore, we studied the insect metabolism of two glucosinolates, characteristic defences of Brassicaceae. Individuals reared on cabbage mono diet developed fastest and showed the highest survival, while the development was slowest for individuals kept on tansy mono diet. Lettuce had the highest water content and SLA but the lowest C/N ratio and no trichomes. In contrast, tansy had the lowest water content and SLA but the highest C/N ratio and trichome density. Cabbage was intermediate in these traits. Analysis of insect samples with UHPLC-DAD-QTOF-MS/MS revealed that benzyl glucosinolate was metabolised to N-benzoylglycine, N-benzoylalanine and N-benzoylserine. MALDI-Orbitrap-MS imaging revealed the localisation of these metabolites in the larval hindgut region. 4-Hydroxybenzyl glucosinolate was metabolised to N-(4-hydroxybenzoyl)glycine. Our results highlight that G. tanaceti deals with toxic hydrolysis products of glucosinolates by conjugation with different amino acids, which may enable this species to develop well on cabbage. The high trichome density and/or specific plant chemistry may lower the accessibility and/or digestibility of tansy leaves, leading to a poorer beetle development on pure tansy ...
    Schlagwörter glucosinolate-myrosinase system ; metabolism ; polyphagous herbivore ; performance ; detoxification ; Evolution ; QH359-425 ; Ecology ; QH540-549.5
    Thema/Rubrik (Code) 580 ; 590
    Sprache Englisch
    Erscheinungsdatum 2022-08-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
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  3. Artikel: Using transposition to introduce eGFP fusions in Sinorhizobium meliloti: A tool to analyze protein localization patterns in bacteria

    Bednarz, Hanna / Karsten Niehaus

    Journal of biotechnology. 2017 Sept. 10, v. 257

    2017  

    Abstract: Conventional methods used for the in vivo analysis of subcellular protein localizations and their spatio-temporal dynamics in prokaryotes are based on either the engineering of N(amino)- or C(carboxy)-terminal fusions of fluorescent proteins with the ... ...

    Abstract Conventional methods used for the in vivo analysis of subcellular protein localizations and their spatio-temporal dynamics in prokaryotes are based on either the engineering of N(amino)- or C(carboxy)-terminal fusions of fluorescent proteins with the protein of interest, or involved probing internal sites for tag integration. In addition, the use of inducible or constitutive promoters for the expression of fluorescent fusion proteins can lead to overexpression and result in localization artifacts. Here, we describe a method for the synthesis of fluorescent fusion proteins using transposable elements, which can randomly integrate in the internal sections of the protein coding sequence to produce full-length fluorescent fusion proteins expressed at endogenous levels. The established method was used for investigating subcellular localization of proteins in the soil bacterium and plant symbiont Sinorhizobium meliloti. Two constructs for transposition-based insertion of the enhanced green fluorescent protein (eGFP), as well as for in vivo excision of the selection marker for the production of full-length proteins were engineered. Conjugation with pHB14 plasmid and induction of the transposition in S. meliloti produced approx. 3.22×104 transconjugant colonies harboring the fluorescent marker with the transposition efficiency of 0.8%. Sixteen randomly targeted proteins of diverse functions, fused to the eGFP were identified and analyzed in living cells by epifluorescence microscopy, demonstrating the suitability of the novel tool for massive, random production of fluorescent proteins and for following of these proteins with different localizations inside the prokaryotic cell.
    Schlagwörter Ensifer meliloti ; fluorescence ; fluorescence microscopy ; green fluorescent protein ; plasmids ; prokaryotic cells ; promoter regions ; soil bacteria ; symbionts ; transposition (genetics) ; transposons
    Sprache Englisch
    Erscheinungsverlauf 2017-0910
    Umfang p. 139-149.
    Erscheinungsort Elsevier B.V.
    Dokumenttyp Artikel
    ZDB-ID 843647-2
    ISSN 1873-4863 ; 0168-1656 ; 1389-0352
    ISSN (online) 1873-4863
    ISSN 0168-1656 ; 1389-0352
    DOI 10.1016/j.jbiotec.2016.12.013
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  4. Artikel ; Online: Fast visual exploration of mass spectrometry images with interactive dynamic spectral similarity pseudocoloring

    Karsten Wüllems / Annika Zurowietz / Martin Zurowietz / Roland Schneider / Hanna Bednarz / Karsten Niehaus / Tim W. Nattkemper

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Band 15

    Abstract: Abstract Mass Spectrometry Imaging (MSI) is an established and still evolving technique for the spatial analysis of molecular co-location in biological samples. Nowadays, MSI is expanding into new domains such as clinical pathology. In order to increase ... ...

    Abstract Abstract Mass Spectrometry Imaging (MSI) is an established and still evolving technique for the spatial analysis of molecular co-location in biological samples. Nowadays, MSI is expanding into new domains such as clinical pathology. In order to increase the value of MSI data, software for visual analysis is required that is intuitive and technique independent. Here, we present QUIMBI (QUIck exploration tool for Multivariate BioImages) a new tool for the visual analysis of MSI data. QUIMBI is an interactive visual exploration tool that provides the user with a convenient and straightforward visual exploration of morphological and spectral features of MSI data. To improve the overall quality of MSI data by reducing non-tissue specific signals and to ensure optimal compatibility with QUIMBI, the tool is combined with the new pre-processing tool ProViM (Processing for Visualization and multivariate analysis of MSI Data), presented in this work. The features of the proposed visual analysis approach for MSI data analysis are demonstrated with two use cases. The results show that the use of ProViM and QUIMBI not only provides a new fast and intuitive visual analysis, but also allows the detection of new co-location patterns in MSI data that are difficult to find with other methods.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 004
    Sprache Englisch
    Erscheinungsdatum 2021-02-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Detection and visualization of communities in mass spectrometry imaging data

    Karsten Wüllems / Jan Kölling / Hanna Bednarz / Karsten Niehaus / Volkmar H. Hans / Tim W. Nattkemper

    BMC Bioinformatics, Vol 20, Iss 1, Pp 1-

    2019  Band 12

    Abstract: Abstract Background The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community detection for the ... ...

    Abstract Abstract Background The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community detection for the analysis of m/z-images to group molecules with correlative spatial distribution into communities so they hint at functional networks or pathway activity. To detect communities, we investigate a spectral approach by optimizing the modularity measure. We present an analysis pipeline and an online interactive visualization tool to facilitate explorative analysis of the results. The approach is illustrated with synthetical benchmark data and two real world data sets (barley seed and glioblastoma section). Results For the barley sample data set, our approach is able to reproduce the findings of a previous work that identified groups of molecules with distributions that correlate with anatomical structures of the barley seed. The analysis of glioblastoma section data revealed that some molecular compositions are locally focused, indicating the existence of a meaningful separation in at least two areas. This result is in line with the prior histological knowledge. In addition to confirming prior findings, the resulting graph structures revealed new subcommunities of m/z-images (i.e. metabolites) with more detailed distribution patterns. Another result of our work is the development of an interactive webtool called GRINE (Analysis of GRaph mapped Image Data NEtworks). Conclusions The proposed method was successfully applied to identify molecular communities of laterally co-localized molecules. For both application examples, the detected communities showed inherent substructures that could easily be investigated with the proposed visualization tool. This shows the potential of this approach as a complementary addition to pixel clustering methods.
    Schlagwörter MALDI imaging ; Networks ; Clustering ; Community detection ; Visualization ; Graphs ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 004
    Sprache Englisch
    Erscheinungsdatum 2019-06-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel: A robust protocol for the isolation of cellular proteins from Xanthomonas campestris to analyze the methionine effect in 2D‐gel experiments

    Schulte, Fabian / Markus Hardt / Karsten Niehaus

    Electrophoresis. 2017 Oct., v. 38, no. 20

    2017  

    Abstract: Two‐dimensional PAGE (2D‐PAGE) is a key technique for the separation of complex protein samples to survey the protein inventory of prokaryotic microorganisms. Although the preparation of proteins is a critical step in 2D gel experiments, its effect ... ...

    Abstract Two‐dimensional PAGE (2D‐PAGE) is a key technique for the separation of complex protein samples to survey the protein inventory of prokaryotic microorganisms. Although the preparation of proteins is a critical step in 2D gel experiments, its effect on the outcome of proteome data is often underestimated. In this work, we show that the choice of protein isolation method can have a profound impact on the quality of 2D gels of protein extracts from prokaryotes. Based on Xanthomonas campestris, a commercially relevant producer of the thickening agent xanthan, we validated a phenol extraction protocol for the purification of bacterial proteins that provides excellent 2D gel separation. As a proof of concept, this method was used to study the effect of methionine—a medium compound that reduces the xanthan output of industrial fermentations—on the cellular proteome of Xanthomonas. The detection of nine regulated proteins associated with sulfur metabolism (Cgl, CysI, CysJ, CysK, MetH1, MetY) and sugar nucleotide biosynthesis (Pgi, Ugd, XanA) proved the efficiency of phenol extraction for the screening of statistically significant abundance changes in 2D gel spots and MALDI‐TOF‐MS based identification in bacteria. Since this method is very robust, it may be useful for the study of other prokaryotes that are relevant in industrial biotechnology.
    Schlagwörter Xanthomonas campestris ; bacteria ; bacterial proteins ; biosynthesis ; biotechnology ; gels ; inventories ; isolation techniques ; matrix-assisted laser desorption-ionization mass spectrometry ; methionine ; phenol ; polyacrylamide gel electrophoresis ; prokaryotic cells ; proteome ; screening ; sugars ; sulfur ; surveys ; two-dimensional gel electrophoresis ; xanthan gum
    Sprache Englisch
    Erscheinungsverlauf 2017-10
    Umfang p. 2603-2609.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 619001-7
    ISSN 1522-2683 ; 0173-0835
    ISSN (online) 1522-2683
    ISSN 0173-0835
    DOI 10.1002/elps.201700064
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  7. Artikel: An integrated approach to study novel properties of a MALDI matrix (4-maleicanhydridoproton sponge) for MS imaging analyses

    Corinti, Davide / Maria Elisa Crestoni / Simonetta Fornarini / Maren Pieper / Karsten Niehaus / Marco Giampà

    Analytical and bioanalytical chemistry. 2019 Feb., v. 411, no. 4

    2019  

    Abstract: The chemical properties accounting for the operation of a valuable matrix used in matrix-assisted laser desorption ionization (MALDI) to perform mass spectrometry imaging (MSI), namely 3-(4,5-bis(dimethylamino)napthalen-1-yl)furan-2,5-dione (4- ... ...

    Abstract The chemical properties accounting for the operation of a valuable matrix used in matrix-assisted laser desorption ionization (MALDI) to perform mass spectrometry imaging (MSI), namely 3-(4,5-bis(dimethylamino)napthalen-1-yl)furan-2,5-dione (4-maleicanhydridoproton sponge, MAPS), have been elucidated also by comparison with the parent molecule 1,8-bis(dimethylamino) naphthalene (so-called proton sponge, PS). Both compounds present the bis(dimethylamino) groups, apt to efficiently trap a proton imparting positive charge. Only MAPS, though, owns the maleicanhydrido function acting as electrophile and yielding covalently bound adducts with a variety of analytes. In this way, MAPS performs as “carrier” for the analyte (A) of interest, at the same time minimizing the presence of useless, background ions. The covalent character of the adducts, [MAPS+H + A]⁺, is testified by their collision-induced dissociation pattern, quite distinct from the one displayed by [PS + H]⁺, while PS does not form any [PS + H + A]⁺, thus confirming the key role of the maleicanhydrido functionality of MAPS. Vibrational spectroscopy of [MAPS+H + A]⁺ adducts (A = H₂O, NH₃) provided further structural evidence. The presence of a mobile proton on A was found to be a requisite for adduct formation by electrospray ionization of acetonitrile solutions, pointing to a possible role of MAPS in discriminating competing analytes based on molecular features. The performance of MAPS has been verified in MALDI-MSI of Atropa belladonna berries, exploiting MAPS binding to atropine. Graphical abstract ᅟ
    Schlagwörter Atropa belladonna ; Lewis acids ; acetonitrile ; ammonia ; atropine ; chemical bonding ; chemical species ; desorption ; dissociation ; image analysis ; ionization ; ions ; mass spectrometry ; naphthalene ; physicochemical properties ; small fruits
    Sprache Englisch
    Erscheinungsverlauf 2019-02
    Umfang p. 953-964.
    Erscheinungsort Springer Berlin Heidelberg
    Dokumenttyp Artikel
    ISSN 1618-2642
    DOI 10.1007/s00216-018-1531-7
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  8. Artikel ; Online: Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging.

    Karin Gorzolka / Jan Kölling / Tim W Nattkemper / Karsten Niehaus

    PLoS ONE, Vol 11, Iss 3, p e

    2016  Band 0150208

    Abstract: MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific ... ...

    Abstract MALDI mass spectrometry imaging was performed to localize metabolites during the first seven days of the barley germination. Up to 100 mass signals were detected of which 85 signals were identified as 48 different metabolites with highly tissue-specific localizations. Oligosaccharides were observed in the endosperm and in parts of the developed embryo. Lipids in the endosperm co-localized in dependency on their fatty acid compositions with changes in the distributions of diacyl phosphatidylcholines during germination. 26 potentially antifungal hordatines were detected in the embryo with tissue-specific localizations of their glycosylated, hydroxylated, and O-methylated derivates. In order to reveal spatio-temporal patterns in local metabolite compositions, multiple MSI data sets from a time series were analyzed in one batch. This requires a new preprocessing strategy to achieve comparability between data sets as well as a new strategy for unsupervised clustering. The resulting spatial segmentation for each time point sample is visualized in an interactive cluster map and enables simultaneous interactive exploration of all time points. Using this new analysis approach and visualization tool germination-dependent developments of metabolite patterns with single MS position accuracy were discovered. This is the first study that presents metabolite profiling of a cereals' germination process over time by MALDI MSI with the identification of a large number of peaks of agronomically and industrially important compounds such as oligosaccharides, lipids and antifungal agents. Their detailed localization as well as the MS cluster analyses for on-tissue metabolite profile mapping revealed important information for the understanding of the germination process, which is of high scientific interest.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 500
    Sprache Englisch
    Erscheinungsdatum 2016-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel: Micro‐organisms growing on rapeseed during storage affect the profile of volatile compounds of virgin rapeseed oil

    Wagner, Claudia / Anja Bonte / Ludger Brühl / Karsten Niehaus / Hanna Bednarz / Bertrand Matthäus

    Journal of the science of food and agriculture. 2018 Apr., v. 98, no. 6

    2018  

    Abstract: BACKGROUND: Micro‐organisms populate on rapeseed after harvest during storage depending on the growing conditions. The composition of the bacterial colonization is unknown, although its contribution to the profile of volatile aroma‐active compounds ... ...

    Abstract BACKGROUND: Micro‐organisms populate on rapeseed after harvest during storage depending on the growing conditions. The composition of the bacterial colonization is unknown, although its contribution to the profile of volatile aroma‐active compounds determines the sensory quality of virgin cold‐pressed rapeseed oil. RESULTS: From four rapeseed samples, 46 bacterial strains were isolated. By DNA‐sequencing, the identification of four bacteria species and 17 bacteria genera was possible. In total, 22 strains were selected, based on their typical off‐flavors resembling those of virgin sensory bad cold‐pressed rapeseed oils. The cultivation of these strains on rapeseed meal agar and examination of volatile compounds by solid phase microextraction–gas chromatography–mass spectrometry allowed the identification of 29 different compounds, mainly degradation products of fatty acids such as alkanes, alkenes, aldehydes, ketones and alcohols and, in addition, sulfur‐containing compounds, including one terpene and three pyrazines. From these compounds, 19 are described as aroma‐active in the literature. CONCLUSION: Micro‐organisms populating on rapeseed during storage may strongly influence the sensory quality of virgin rapeseed oil as a result of the development of volatile aroma‐active metabolic products. It can be assumed that occurrence of off‐flavor of virgin rapeseed oils on the market are the result of metabolic degradation products produced by micro‐organisms populating on rapeseed during storage. © 2017 Society of Chemical Industry
    Schlagwörter agar ; alcohols ; aldehydes ; alkanes ; alkenes ; bacteria ; bacterial colonization ; fatty acids ; ketones ; markets ; mass spectrometry ; off flavors ; pyrazines ; rapeseed ; rapeseed meal ; rapeseed oil ; volatile compounds
    Sprache Englisch
    Erscheinungsverlauf 2018-04
    Umfang p. 2147-2155.
    Erscheinungsort John Wiley & Sons, Ltd
    Dokumenttyp Artikel
    Anmerkung JOURNAL ARTICLE
    ZDB-ID 184116-6
    ISSN 1097-0010 ; 0022-5142
    ISSN (online) 1097-0010
    ISSN 0022-5142
    DOI 10.1002/jsfa.8699
    Datenquelle NAL Katalog (AGRICOLA)

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    Z 1003: Hefte anzeigen

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  10. Artikel ; Online: Experimental Measurements and Mathematical Modeling of Cytosolic Ca2+ Signatures upon Elicitation by Penta-N-acetylchitopentaose Oligosaccharides in Nicotiana tabacum Cell Cultures

    Kalina Mrozek / Karsten Niehaus / Petra Lutter

    Plants, Vol 2, Iss 4, Pp 750-

    2013  Band 768

    Abstract: Plants have developed sophisticated recognition systems for different kinds of pathogens. Pathogen-associated molecular patterns (PAMPs) can induce various defense mechanisms, e.g., the production of reactive oxygen species (ROS) as an early event. Plant ...

    Abstract Plants have developed sophisticated recognition systems for different kinds of pathogens. Pathogen-associated molecular patterns (PAMPs) can induce various defense mechanisms, e.g., the production of reactive oxygen species (ROS) as an early event. Plant defense reactions are initiated by a signal transduction cascade involving the release of calcium ions (Ca2+) from both external and internal stores to the plant cytoplasm. This work focuses on the analysis of cytosolic Ca2+ signatures, experimentally and theoretically. Cytosolic Ca2+ signals were measured in Nicotiana tabacum plant cell cultures after elicitation with penta-N-acetylchitopentaose oligosaccharides (Ch5). In order to allow a mathematical simulation of the elicitor-triggered Ca2+ release, the Li and Rinzel model was adapted to the situation in plants. The main features of the Ca2+ response, like the specific shape of the Ca2+ transient and the dose-response relationship, could be reproduced very well. Repeated elicitation of the same cell culture revealed a refractory behavior with respect to the Ca2+ transients for this condition. Detailed analysis of the obtained data resulted in further modifications of the mathematical model, allowing a predictive simulation of Ch5-induced Ca2+ transients. The promising results may contribute to a deeper understanding of the underlying mechanisms governing plant defense.
    Schlagwörter plant defense ; calcium ; modeling ; Plant culture ; SB1-1110 ; Agriculture ; S ; DOAJ:Plant Sciences ; DOAJ:Agriculture and Food Sciences
    Thema/Rubrik (Code) 580
    Sprache Englisch
    Erscheinungsdatum 2013-11-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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