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  1. Article: High-throughput assays to identify archaea-targeting nitrification inhibitors.

    Beeckman, Fabian / Drozdzecki, Andrzej / De Knijf, Alexa / Audenaert, Dominique / Beeckman, Tom / Motte, Hans

    Frontiers in plant science

    2024  Volume 14, Page(s) 1283047

    Abstract: Nitrification is a microbial process that converts ammonia ( ... ...

    Abstract Nitrification is a microbial process that converts ammonia (NH
    Language English
    Publishing date 2024-01-08
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1283047
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book: Plant chemical biology

    Audenaert, Dominique / Overvoorde, Paul

    2014  

    Abstract: The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to ... ...

    Author's details edited by Dominique Audenaert, Paul Overvoorde
    Abstract "The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to identify small molecules that can be used to identify the targets of currently used herbicides, as well as to develop new herbicides or plant growth regulators. The author introduces researchers and graduate students to the chemical biology toolbox required to perform successful chemical biology studies. The text also examines several chemical biology studies to show how they allowed novel insights into the field of plant physiology and plant cellular processes"--Provided by publisher.
    MeSH term(s) Plants/chemistry ; Plant Physiological Phenomena ; Biochemical Phenomena
    Language English
    Size xi, 299 pages :, illustrations
    Document type Book
    ISBN 9780470946695 ; 0470946695
    Database Catalogue of the US National Library of Medicine (NLM)

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  3. Book: Plant chemical biology

    Audenaert, Dominique / Overvoorde, Paul

    2014  

    Abstract: The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to ... ...

    Author's details ed. by Dominique Audenaert; Paul Overvoorde
    Abstract "The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to identify small molecules that can be used to identify the targets of currently used herbicides, as well as to develop new herbicides or plant growth regulators. The author introduces researchers and graduate students to the chemical biology toolbox required to perform successful chemical biology studies. The text also examines several chemical biology studies to show how they allowed novel insights into the field of plant physiology and plant cellular processes"--Provided by publisher
    MeSH term(s) Biochemical Phenomena ; Plant Physiological Phenomena ; Plants/chemistry
    Keywords Botanical chemistry
    Language English
    Size XI, 299 S., [4 Bl.], Ill., graph. Darst.
    Publisher Wiley
    Publishing place Hoboken, NJ
    Document type Book
    Note Literaturangaben
    ISBN 9780470946695 ; 0470946695
    Database Leibniz Institute of Plant Biochemistry

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  4. Book: Plant chemical biology

    Audenaert, Dominique / Overvoorde, Paul

    2014  

    Abstract: The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to ... ...

    Author's details ed. by Dominique Audenaert; Paul Overvoorde
    Abstract "The application of plant chemical biology is currently limited to specialized subfields of plant research. By examining how chemical biology can be applied to study plant biology, Plant Chemical Biology illustrates how chemical biology is a means to identify small molecules that can be used to identify the targets of currently used herbicides, as well as to develop new herbicides or plant growth regulators. The author introduces researchers and graduate students to the chemical biology toolbox required to perform successful chemical biology studies. The text also examines several chemical biology studies to show how they allowed novel insights into the field of plant physiology and plant cellular processes"--Provided by publisher
    MeSH term(s) Biochemical Phenomena ; Plant Physiological Phenomena ; Plants/chemistry
    Keywords Botanical chemistry
    Language English
    Size XI, 299 S., Ill., graph. Darst.
    Publisher Wiley
    Publishing place Hoboken, NJ
    Document type Book
    Note Literaturangaben
    ISBN 9780470946695 ; 0470946695
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  5. Article ; Online: Local structural preferences in shaping tau amyloid polymorphism.

    Louros, Nikolaos / Wilkinson, Martin / Tsaka, Grigoria / Ramakers, Meine / Morelli, Chiara / Garcia, Teresa / Gallardo, Rodrigo / D'Haeyer, Sam / Goossens, Vera / Audenaert, Dominique / Thal, Dietmar Rudolf / Mackenzie, Ian R / Rademakers, Rosa / Ranson, Neil A / Radford, Sheena E / Rousseau, Frederic / Schymkowitz, Joost

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1028

    Abstract: Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each ... ...

    Abstract Tauopathies encompass a group of neurodegenerative disorders characterised by diverse tau amyloid fibril structures. The persistence of polymorphism across tauopathies suggests that distinct pathological conditions dictate the adopted polymorph for each disease. However, the extent to which intrinsic structural tendencies of tau amyloid cores contribute to fibril polymorphism remains uncertain. Using a combination of experimental approaches, we here identify a new amyloidogenic motif, PAM4 (Polymorphic Amyloid Motif of Repeat 4), as a significant contributor to tau polymorphism. Calculation of per-residue contributions to the stability of the fibril cores of different pathologic tau structures suggests that PAM4 plays a central role in preserving structural integrity across amyloid polymorphs. Consistent with this, cryo-EM structural analysis of fibrils formed from a synthetic PAM4 peptide shows that the sequence adopts alternative structures that closely correspond to distinct disease-associated tau strains. Furthermore, in-cell experiments revealed that PAM4 deletion hampers the cellular seeding efficiency of tau aggregates extracted from Alzheimer's disease, corticobasal degeneration, and progressive supranuclear palsy patients, underscoring PAM4's pivotal role in these tauopathies. Together, our results highlight the importance of the intrinsic structural propensity of amyloid core segments to determine the structure of tau in cells, and in propagating amyloid structures in disease.
    MeSH term(s) Humans ; Alzheimer Disease/genetics ; Amyloid/chemistry ; Amyloidogenic Proteins ; Supranuclear Palsy, Progressive/pathology ; tau Proteins/genetics ; tau Proteins/chemistry ; Tauopathies/genetics ; Tauopathies/pathology
    Chemical Substances Amyloid ; Amyloidogenic Proteins ; tau Proteins ; MAPT protein, human
    Language English
    Publishing date 2024-02-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45429-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The Screening for Novel Inhibitors of Auxin-Induced Ca

    De Vriese, Kjell / Nguyen, Long / Stael, Simon / Audenaert, Dominique / Beeckman, Tom / Vanneste, Steffen

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2213, Page(s) 89–98

    Abstract: ... ...

    Abstract Ca
    MeSH term(s) Calcium/metabolism ; Calcium Signaling ; Cell Line ; Genetic Testing/methods ; Indoleacetic Acids/metabolism ; Reproducibility of Results ; Nicotiana/cytology ; Transformation, Genetic
    Chemical Substances Indoleacetic Acids ; Calcium (SY7Q814VUP)
    Language English
    Publishing date 2020-12-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0954-5_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Drug discovery-based approach identifies new nitrification inhibitors.

    Beeckman, Fabian / Drozdzecki, Andrzej / De Knijf, Alexa / Corrochano-Monsalve, Mario / Bodé, Samuel / Blom, Pieter / Goeminne, Geert / González-Murua, Carmen / Lücker, Sebastian / Boeckx, Pascal / Stevens, Christian V / Audenaert, Dominique / Beeckman, Tom / Motte, Hans

    Journal of environmental management

    2023  Volume 346, Page(s) 118996

    Abstract: Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with ...

    Abstract Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.
    Language English
    Publishing date 2023-09-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 184882-3
    ISSN 1095-8630 ; 0301-4797
    ISSN (online) 1095-8630
    ISSN 0301-4797
    DOI 10.1016/j.jenvman.2023.118996
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    In stock of ZB MED Bonn / Germany

    Z 7556: Show issues

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  8. Article ; Online: Systematic optimization of Cas12a base editors in wheat and maize using the ITER platform.

    Gaillochet, Christophe / Peña Fernández, Alexandra / Goossens, Vera / D'Halluin, Katelijn / Drozdzecki, Andrzej / Shafie, Myriam / Van Duyse, Julie / Van Isterdael, Gert / Gonzalez, Camila / Vermeersch, Mattias / De Saeger, Jonas / Develtere, Ward / Audenaert, Dominique / De Vleesschauwer, David / Meulewaeter, Frank / Jacobs, Thomas B

    Genome biology

    2023  Volume 24, Issue 1, Page(s) 6

    Abstract: Background: Testing an ever-increasing number of CRISPR components is challenging when developing new genome engineering tools. Plant biotechnology has few high-throughput options to perform iterative design-build-test-learn cycles of gene-editing ... ...

    Abstract Background: Testing an ever-increasing number of CRISPR components is challenging when developing new genome engineering tools. Plant biotechnology has few high-throughput options to perform iterative design-build-test-learn cycles of gene-editing reagents. To bridge this gap, we develop ITER (Iterative Testing of Editing Reagents) based on 96-well arrayed protoplast transfections and high-content imaging.
    Results: We validate ITER in wheat and maize protoplasts using Cas9 cytosine and adenine base editors (ABEs), allowing one optimization cycle - from design to results - within 3 weeks. Given that previous LbCas12a-ABEs have low or no activity in plants, we use ITER to develop an optimized LbCas12a-ABE. We show that sequential improvement of five components - NLS, crRNA, LbCas12a, adenine deaminase, and linker - leads to a remarkable increase in activity from almost undetectable levels to 40% on an extrachromosomal GFP reporter. We confirm the activity of LbCas12a-ABE at endogenous targets in protoplasts and obtain base-edited plants in up to 55% of stable wheat transformants and the edits are transmitted to T1 progeny. We leverage these improvements to develop a highly mutagenic LbCas12a nuclease and a LbCas12a-CBE demonstrating that the optimizations can be broadly applied to the Cas12a toolbox.
    Conclusion: Our data show that ITER is a sensitive, versatile, and high-throughput platform that can be harnessed to accelerate the development of genome editing technologies in plants. We use ITER to create an efficient Cas12a-ABE by iteratively testing a large panel of vector components. ITER will likely be useful to create and optimize genome editing reagents in a wide range of plant species.
    MeSH term(s) CRISPR-Cas Systems ; Zea mays/genetics ; Triticum/genetics ; Gene Editing/methods ; Mutagenesis
    Language English
    Publishing date 2023-01-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-022-02836-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Mapping the sequence specificity of heterotypic amyloid interactions enables the identification of aggregation modifiers.

    Louros, Nikolaos / Ramakers, Meine / Michiels, Emiel / Konstantoulea, Katerina / Morelli, Chiara / Garcia, Teresa / Moonen, Nele / D'Haeyer, Sam / Goossens, Vera / Thal, Dietmar Rudolf / Audenaert, Dominique / Rousseau, Frederic / Schymkowitz, Joost

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1351

    Abstract: Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural ... ...

    Abstract Heterotypic amyloid interactions between related protein sequences have been observed in functional and disease amyloids. While sequence homology seems to favour heterotypic amyloid interactions, we have no systematic understanding of the structural rules determining such interactions nor whether they inhibit or facilitate amyloid assembly. Using structure-based thermodynamic calculations and extensive experimental validation, we performed a comprehensive exploration of the defining role of sequence promiscuity in amyloid interactions. Using tau as a model system we demonstrate that proteins with local sequence homology to tau amyloid nucleating regions can modify fibril nucleation, morphology, assembly and spreading of aggregates in cultured cells. Depending on the type of mutation such interactions inhibit or promote aggregation in a manner that can be predicted from structure. We find that these heterotypic amyloid interactions can result in the subcellular mis-localisation of these proteins. Moreover, equilibrium studies indicate that the critical concentration of aggregation is altered by heterotypic interactions. Our findings suggest a structural mechanism by which the proteomic background can modulate the aggregation propensity of amyloidogenic proteins and we discuss how such sequence-specific proteostatic perturbations could contribute to the selective cellular susceptibility of amyloid disease progression.
    MeSH term(s) Amino Acid Sequence ; Amyloid/metabolism ; Amyloidogenic Proteins/metabolism ; Amyloidosis ; Humans ; Proteomics
    Chemical Substances Amyloid ; Amyloidogenic Proteins
    Language English
    Publishing date 2022-03-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-28955-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: How tech-savvy employees make the difference in core facilities: Recognizing core facility expertise with dedicated career tracks: Recognizing core facility expertise with dedicated career tracks.

    Lippens, Saskia / Audenaert, Dominique / Botzki, Alexander / Derveaux, Stefaan / Ghesquière, Bart / Goeminne, Geert / Hassanzadeh, Reza / Haustraete, Jurgen / Impens, Francis / Lamote, Jochen / Munck, Sebastian / Vandamme, Niels / Van Isterdael, Gert / Lein, Marijke / Van Minnebruggen, Geert

    EMBO reports

    2022  Volume 23, Issue 6, Page(s) e55094

    Abstract: Core facilities have a different mission than academic research labs. Accordingly, they require different career paths and structures. ...

    Abstract Core facilities have a different mission than academic research labs. Accordingly, they require different career paths and structures.
    Language English
    Publishing date 2022-06-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202255094
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    In stock of ZB MED Cologne/Königswinter

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