1
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Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R. Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa. Microlife 2024; 5:uqae002. [PMID: 38444699 PMCID: PMC10914365 DOI: 10.1093/femsml/uqae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
The introduction of high-throughput sequencing has resulted in a surge of available bacteriophage genomes, unveiling their tremendous genomic diversity. However, our current understanding of the complex transcriptional mechanisms that dictate their gene expression during infection is limited to a handful of model phages. Here, we applied ONT-cappable-seq to reveal the transcriptional architecture of six different clades of virulent phages infecting Pseudomonas aeruginosa. This long-read microbial transcriptomics approach is tailored to globally map transcription start and termination sites, transcription units, and putative RNA-based regulators on dense phage genomes. Specifically, the full-length transcriptomes of LUZ19, LUZ24, 14-1, YuA, PAK_P3, and giant phage phiKZ during early, middle, and late infection were collectively charted. Beyond pinpointing traditional promoter and terminator elements and transcription units, these transcriptional profiles provide insights in transcriptional attenuation and splicing events and allow straightforward validation of Group I intron activity. In addition, ONT-cappable-seq data can guide genome-wide discovery of novel regulatory element candidates, including noncoding RNAs and riboswitches. This work substantially expands the number of annotated phage-encoded transcriptional elements identified to date, shedding light on the intricate and diverse gene expression regulation mechanisms in Pseudomonas phages, which can ultimately be sourced as tools for biotechnological applications in phage and bacterial engineering.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, 3001 Leuven, Belgium
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2
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Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M. Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches. Curr Opin Microbiol 2024; 77:102419. [PMID: 38271748 PMCID: PMC10884466 DOI: 10.1016/j.mib.2023.102419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]
Abstract
In the last decade, powerful high-throughput sequencing approaches have emerged to analyse microbial transcriptomes at a global scale. However, to date, applications of these approaches to microbial viruses such as phages remain scarce. Tailoring these techniques to virus-infected bacteria promises to obtain a detailed picture of the underexplored RNA biology and molecular processes during infection. In addition, transcriptome study of stress and perturbations induced by phages in their infected bacterial hosts is likely to reveal new fundamental mechanisms of bacterial metabolism and gene regulation. Here, we provide references and blueprints to implement emerging transcriptomic approaches towards addressing transcriptome architecture, RNA-RNA and RNA-protein interactions, RNA modifications, structures and heterogeneity of transcription profiles in infected cells that will provide guides for future directions in phage-centric therapeutic applications and microbial synthetic biology.
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Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Laura Wicke
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium; Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany
| | - Ana Brandão
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Diana P Pires
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), Medical Faculty, University of Würzburg, Würzburg, Germany; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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3
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Chaban A, Minakhin L, Goldobina E, Bae B, Hao Y, Borukhov S, Putzeys L, Boon M, Kabinger F, Lavigne R, Makarova KS, Koonin EV, Nair SK, Tagami S, Severinov K, Sokolova ML. Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail. Nat Commun 2024; 15:317. [PMID: 38182597 PMCID: PMC10770324 DOI: 10.1038/s41467-023-44630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Thermus thermophilus bacteriophage P23-45 encodes a giant 5,002-residue tail tape measure protein (TMP) that defines the length of its extraordinarily long tail. Here, we show that the N-terminal portion of P23-45 TMP is an unusual RNA polymerase (RNAP) homologous to cellular RNAPs. The TMP-fused virion RNAP transcribes pre-early phage genes, including a gene that encodes another, non-virion RNAP, that transcribes early and some middle phage genes. We report the crystal structures of both P23-45 RNAPs. The non-virion RNAP has a crab-claw-like architecture. By contrast, the virion RNAP adopts a unique flat structure without a clamp. Structure and sequence comparisons of the P23-45 RNAPs with other RNAPs suggest that, despite the extensive functional differences, the two P23-45 RNAPs originate from an ancient gene duplication in an ancestral phage. Our findings demonstrate striking adaptability of RNAPs that can be attained within a single virus species.
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Affiliation(s)
- Anastasiia Chaban
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany
| | - Leonid Minakhin
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, 19107, USA
| | - Ekaterina Goldobina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Brain Bae
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yue Hao
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sergei Borukhov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine at Stratford, Stratford, NJ, 08084-1489, USA
| | - Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Institute of Molecular Genetics National Kurchatov Center, Moscow, 123182, Russia.
| | - Maria L Sokolova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany.
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Putzeys L, Intizar D, Lavigne R, Boon M. Obtaining Detailed Phage Transcriptomes Using ONT-Cappable-Seq. Methods Mol Biol 2024; 2793:207-235. [PMID: 38526733 DOI: 10.1007/978-1-0716-3798-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Detailed transcription maps of bacteriophages are not usually explored, limiting our understanding of molecular phage biology and restricting their exploitation and engineering. The ONT-cappable-seq method described here brings phage transcriptomics to the accessible nanopore sequencing platform and provides an affordable and more detailed overview of transcriptional features compared to traditional RNA-seq experiments. With ONT-cappable-seq, primary transcripts are specifically capped, enriched, and prepared for long-read sequencing on the nanopore sequencing platform. This enables end-to-end sequencing of unprocessed transcripts covering both phage and host genome, thus providing insight on their operons. The subsequent analysis pipeline makes it possible to rapidly identify the most important transcriptional features such as transcription start and stop sites. The obtained data can thus provide a comprehensive overview of the transcription by your phage of interest.
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Affiliation(s)
- Leena Putzeys
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Danish Intizar
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
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5
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Lammens EM, Putzeys L, Boon M, Lavigne R. Sourcing Phage-Encoded Terminators Using ONT-cappable-seq for SynBio Applications in Pseudomonas. ACS Synth Biol 2023; 12:1415-1423. [PMID: 37092882 DOI: 10.1021/acssynbio.3c00101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Efficient transcriptional terminators are essential for the performance of genetic circuitry in microbial SynBio hosts. In recent years, several libraries of characterized strong terminators have become available for model organisms such as Escherichia coli. Conversely, terminator libraries for nonmodel species remain scarce, and individual terminators are often ported over from model systems, leading to unpredictable performance in their new hosts. In this work, we mined the genomes of Pseudomonas infecting phages LUZ7 and LUZ100 for transcriptional terminators utilizing the full-length RNA sequencing technique "ONT-cappable-seq" and validated these terminators in three Gram-negative hosts using a terminator trap assay. Based on these results, we present nine terminators for E. coli, Pseudomonas putida, and Pseudomonas aeruginosa, which outperform current reference terminators. Among these, terminator LUZ7 T50 displays potent bidirectional activity. These data further support that bacteriophages, as evolutionary-adapted natural predators of the targeted bacteria, provide a valuable source of microbial SynBio parts.
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Affiliation(s)
- Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Leena Putzeys
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
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6
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Lammens EM, Feyaerts N, Kerremans A, Boon M, Lavigne R. Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species. Int J Mol Sci 2023; 24:ijms24087175. [PMID: 37108338 PMCID: PMC10138996 DOI: 10.3390/ijms24087175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
The phage T7 RNA polymerase (RNAP) and lysozyme form the basis of the widely used pET expression system for recombinant expression in the biotechnology field and as a tool in microbial synthetic biology. Attempts to transfer this genetic circuitry from Escherichia coli to non-model bacterial organisms with high potential have been restricted by the cytotoxicity of the T7 RNAP in the receiving hosts. We here explore the diversity of T7-like RNAPs mined directly from Pseudomonas phages for implementation in Pseudomonas species, thus relying on the co-evolution and natural adaptation of the system towards its host. By screening and characterizing different viral transcription machinery using a vector-based system in P. putida., we identified a set of four non-toxic phage RNAPs from phages phi15, PPPL-1, Pf-10, and 67PfluR64PP, showing a broad activity range and orthogonality to each other and the T7 RNAP. In addition, we confirmed the transcription start sites of their predicted promoters and improved the stringency of the phage RNAP expression systems by introducing and optimizing phage lysozymes for RNAP inhibition. This set of viral RNAPs expands the adaption of T7-inspired circuitry towards Pseudomonas species and highlights the potential of mining tailored genetic parts and tools from phages for their non-model host.
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Affiliation(s)
- Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Nathalie Feyaerts
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
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7
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Chou C, Kim H, Huntley C, Boon M, Liu S, Capasso R. Predictors of Voltage Amplitude in Patients who Respond to Hypoglossal Nerve Stimulation for Obstructive Sleep Apnea. Sleep Med 2022. [DOI: 10.1016/j.sleep.2022.05.726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Ramalho A, Cuyx S, Boon M, Proesmans M, Dupont L, Van Hoorenbeeck K, De Wachter E, Van Biervliet S, De Boeck K, Vermeulen F. 692 Importance of cystic fibrosis transmembrane conductance regulator messenger ribonucleic acid testing to uncover other variants in cystic fibrosis genotype that affect cystic fibrosis transmembrane conductance regulator expression. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)01382-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Vreys M, Gosselink R, Kinoo D, Van Steen K, Vanhaerents C, Proesmans M, Boon M, Vermeulen F. P232 Feasibility and added value of the computer game “Sparky©” when learning spirometry in preschool children with cystic fibrosis. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Cuyx S, Ramalho A, Proesmans M, Boon M, Ensinck M, Carlon M, Dupont L, De Boeck K, Vermeulen F. P025 Assessment of CFTR modulator combinations in rectal organoids from F508del homozygous patients with cystic fibrosis. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Putzeys L, Boon M, Lammens EM, Kuznedelov K, Severinov K, Lavigne R. Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages. Comput Struct Biotechnol J 2022; 20:2624-2638. [PMID: 35685363 PMCID: PMC9163698 DOI: 10.1016/j.csbj.2022.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Leena Putzeys
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
- Corresponding author.
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Lammens EM, Boon M, Grimon D, Briers Y, Lavigne R. SEVAtile: a standardised DNA assembly method optimised for Pseudomonas. Microb Biotechnol 2021; 15:370-386. [PMID: 34651450 PMCID: PMC8719830 DOI: 10.1111/1751-7915.13922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/29/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022] Open
Abstract
To meet the needs of synthetic biologists, DNA assembly methods have transformed from simple 'cut-and-paste' procedures to highly advanced, standardised assembly techniques. Implementing these standardised DNA assembly methods in biotechnological research conducted in non-model hosts, including Pseudomonas putida and Pseudomonas aeruginosa, could greatly benefit reproducibility and predictability of experimental results. SEVAtile is a Type IIs-based assembly approach, which enables the rapid and standardised assembly of genetic parts - or tiles - to create genetic circuits in the established SEVA-vector backbone. Contrary to existing DNA assembly methods, SEVAtile is an easy and straightforward method, which is compatible with any vector, both SEVA- and non-SEVA. To prove the efficiency of the SEVAtile method, a three-vector system was successfully generated to independently co-express three different proteins in P. putida and P. aeruginosa. More specifically, one of the vectors, pBGDes, enables genomic integration of assembled circuits in the Tn7 landing site, while self-replicatory vectors pSTDesX and pSTDesR enable inducible expression from the XylS/Pm and RhaRS/PrhaB expression systems, respectively. Together, we hope these vector systems will support research in both the microbial SynBio and Pseudomonas field.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
| | - Dennis Grimon
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, Gent, 9000, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 Box 2462, Leuven, 3001, Belgium
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De Smet J, Wagemans J, Boon M, Ceyssens PJ, Voet M, Noben JP, Andreeva J, Ghilarov D, Severinov K, Lavigne R. The bacteriophage LUZ24 "Igy" peptide inhibits the Pseudomonas DNA gyrase. Cell Rep 2021; 36:109567. [PMID: 34433028 DOI: 10.1016/j.celrep.2021.109567] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/20/2021] [Accepted: 07/29/2021] [Indexed: 01/01/2023] Open
Abstract
The bacterial DNA gyrase complex (GyrA/GyrB) plays a crucial role during DNA replication and serves as a target for multiple antibiotics, including the fluoroquinolones. Despite it being a valuable antibiotics target, resistance emergence by pathogens including Pseudomonas aeruginosa are proving problematic. Here, we describe Igy, a peptide inhibitor of gyrase, encoded by Pseudomonas bacteriophage LUZ24 and other members of the Bruynoghevirus genus. Igy (5.6 kDa) inhibits in vitro gyrase activity and interacts with the P. aeruginosa GyrB subunit, possibly by DNA mimicry, as indicated by a de novo model of the peptide and mutagenesis. In vivo, overproduction of Igy blocks DNA replication and leads to cell death also in fluoroquinolone-resistant bacterial isolates. These data highlight the potential of discovering phage-inspired leads for antibiotics development, supported by co-evolution, as Igy may serve as a scaffold for small molecule mimicry to target the DNA gyrase complex, without cross-resistance to existing molecules.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Julia Andreeva
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Dmitry Ghilarov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Konstantin Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Leuven, Belgium.
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14
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Vanstapel A, Weynand B, De Zutter A, Dubbeldam A, De Sadeleer L, Kaes J, Verbeken E, Ceulemans L, Geudens V, Goos T, Gyselinck I, Van Raemdonck D, Neyrinck A, Dupont L, Boon M, Boone M, Vanaudenaerde B, Vos R, Verleden G, Verleden S. Phenotypical Characterization of Airway Morphology in Post-Infectious vs Post-Lung Transplantation Bronchiolitis Obliterans. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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15
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Goudschaal K, Beeksma F, Boon M, Bijveld M, Visser J, Hinnen K, van Kesteren Z. Accuracy of an MR-only workflow for prostate radiotherapy using semi-automatically burned-in fiducial markers. Radiat Oncol 2021; 16:37. [PMID: 33608008 PMCID: PMC7893889 DOI: 10.1186/s13014-021-01768-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/11/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The benefit of MR-only workflow compared to current CT-based workflow for prostate radiotherapy is reduction of systematic errors in the radiotherapy chain by 2-3 mm. Nowadays, MRI is used for target delineation while CT is needed for position verification. In MR-only workflows, MRI based synthetic CT (sCT) replaces CT. Intraprostatic fiducial markers (FMs) are used as a surrogate for the position of the prostate improving targeting. However, FMs are not visible on sCT. Therefore, a semi-automatic method for burning-in FMs on sCT was developed. Accuracy of MR-only workflow using semi-automatically burned-in FMs was assessed and compared to CT/MR workflow. METHODS Thirty-one prostate cancer patients receiving radiotherapy, underwent an additional MR sequence (mDIXON) to create an sCT for MR-only workflow simulation. Three sources of accuracy in the CT/MR- and MR-only workflow were investigated. To compare image registrations for target delineation, the inter-observer error (IOE) of FM-based CT-to-MR image registrations and soft-tissue-based MR-to-MR image registrations were determined on twenty patients. Secondly, the inter-observer variation of the resulting FM positions was determined on twenty patients. Thirdly, on 26 patients CBCTs were retrospectively registered on sCT with burned-in FMs and compared to CT-CBCT registrations. RESULTS Image registration for target delineation shows a three times smaller IOE for MR-only workflow compared to CT/MR workflow. All observers agreed in correctly identifying all FMs for 18 out of 20 patients (90%). The IOE in CC direction of the center of mass (COM) position of the markers was within the CT slice thickness (2.5 mm), the IOE in AP and RL direction were below 1.0 mm and 1.5 mm, respectively. Registrations for IGRT position verification in MR-only workflow compared to CT/MR workflow were equivalent in RL-, CC- and AP-direction, except for a significant difference for random error in rotation. CONCLUSIONS MR-only workflow using sCT with burned-in FMs is an improvement compared to the current CT/MR workflow, with a three times smaller inter observer error in CT-MR registration and comparable CBCT registration results between CT and sCT reference scans. Trial registry Medical Research Involving Human Subjects Act (WMO) does apply to this study and was approved by the Medical Ethics review Committee of the Academic Medical Center. Registration number: NL65414.018.18. Date of registration: 21-08-2018.
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Affiliation(s)
- Karin Goudschaal
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - F. Beeksma
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - M. Boon
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - M. Bijveld
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - J. Visser
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - K. Hinnen
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
| | - Z. van Kesteren
- Department of Radiation Oncology, University of Amsterdam, Amsterdam UMC, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands
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16
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Modder M, Kuipers E, Held N, Het Panhuis WI, Ruppert P, Kersten S, Kooijman S, Guisas B, Houtkooper R, Rensen P, Boon M. A single day of high fat diet feeding induces lipid accumulation and insulin resistance in brown adipose tissue in mice. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Ying Z, Van Eenige R, Janssen L, Berbée J, Boon M, Kooijman S, Rensen P. Brown adipose tissue activation with mirabegron enhances fat oxidation in APOE*3-leiden.CETP mice and humans. Atherosclerosis 2020. [DOI: 10.1016/j.atherosclerosis.2020.10.304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Beeksma F, Visser J, Boon M, Goudschaal K, Bijveld M, Hinnen K, Van Kesteren Z. PH-0482: Inter-observer variation of burned-in fiducial marker positions for MR-only prostate radiotherapy. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00504-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Goudschaal K, Visser J, Beeksma F, Boon M, Bijveld M, Hinnen K, Van Kesteren Z. OC-0350: Registration accuracy of pseudoCT with burned-in markers with CBCT for MR-only prostate radiotherapy. Radiother Oncol 2020. [DOI: 10.1016/s0167-8140(21)00374-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Ramalho AS, Cuyx S, Boon M, Dupont L, Proesmans M, Sarouk I, Cordero C, Vermeulen F, De Boeck K. WS11.1 Response to CFTR modulators in organoids from patients with cystic fibrosis as a tool to select candidates to treatment. J Cyst Fibros 2020. [DOI: 10.1016/s1569-1993(20)30222-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Boon M, Holtappels D, Lood C, van Noort V, Lavigne R. Host Range Expansion of Pseudomonas Virus LUZ7 Is Driven by a Conserved Tail Fiber Mutation. Phage (New Rochelle) 2020; 1:87-90. [PMID: 36147895 PMCID: PMC9041470 DOI: 10.1089/phage.2020.0006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background: When subjected to phage infection, bacteria can rapidly become resistant by changes in the phage receptors at the bacterial surface. Phages thus require adaptive mechanisms to circumvent this type of resistance. Methods: LUZ7 phage with an altered host range were isolated and analysed for mutations and their effect. Results: We find that Pseudomonas virus LUZ7 has an unusually high number of mutants (0.01-0.1% of the population) that drive host range expansion. Interestingly, all tested mutants have a single D737Y mutation in the tail fiber. This mutation allows the phage to adsorb to P. aeruginosa strains that are not natively recognized by the wild-type phage. Conclusion: The high number and specificity of mutants suggests the presence of an uncharacterized mechanism that drives these mutations. This mechanism enables the phage to better evade host resistance at the surface level and expand its host range in general, a feature that could be valuable in phage therapeutic settings or for phage engineering.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Dominique Holtappels
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Cédric Lood
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Vera van Noort
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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22
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Huntley C, Doghramji K, Tschopp K, Tschopp S, Jardin PB, Heiser C, Schwab R, Thaler E, Jenks C, Walia H, Kominsky A, Kezirian E, Waxman J, Lin H, Boon M. 0637 Comparison of AHI and ESS Outcomes Between Patients with Obstructive Sleep Apnea Undergoing Sleep Surgery versus Upper Airway Stimulation. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Introduction
Single or multi-level soft tissue surgical interventions are common options for CPAP-intolerant patients with OSA. Upper Airway Stimulation (UAS) is an alternative option using an implantable hypoglossal nerve stimulator. We compared patient outcomes between traditional sleep surgery (TSS) and UAS.
Methods
We selected patients who underwent TSS (including palate, oropharynx, tongue, and/or epiglottis-based procedures) for OSA and also met general UAS criteria (BMI≤35, AHI between 15-65, absence of palate concentric collapse during DISE, if available) for chart review. UAS outcomes were collected from the ADHERE international registry. For both groups, post-op AHI was collected, including full-night UAS efficacy studies. Data are presented as mean and standard deviation.
Results
The TSS group (n=284) and UAS group (n=541) were predominantly male and overweight. The TSS group was younger than UAS (47±12 vs 60±11 years, p<0.001). At baseline, both groups had severe OSA with AHI of 34±14 and 36±15 (p=0.23) and excessive daytime sleepiness with ESS of 12±5 and 12±6, (p=0.38), respectively. TSS follow-up was 169±151 days vs 392±181 days for UAS, which was significantly different. UAS had significantly larger decrease in AHI than TSS (-21/h±18 vs -16/h±16, p<0.0001). Both groups had a large decrease in ESS, however, the UAS group had a slightly smaller decrease, (-6±5 vs -5±5, p=0.01). Using the Sher response criteria of 50% AHI reduction and ≤ 20 events/hour, UAS had a 70% response rate vs 51% for TSS.
Conclusion
This study represents largest and first international, multicenter comparison of UAS to traditional surgical interventions for OSA, albeit with limitations of potential differential patient selection. While both TSS and UAS show similar improvement in symptoms, upper airway stimulation has a larger reduction of AHI with higher rates of therapy response than traditional sleep surgery
Support
ADHERE data assistance from Inspire Medical (Minneapolis, MN)
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Affiliation(s)
- C Huntley
- Thomas Jefferson University, Philadelphia, PA
| | - K Doghramji
- Thomas Jefferson University, Philadelphia, PA
| | - K Tschopp
- Kantonsspital Baselland, Liestal, SWITZERLAND
| | - S Tschopp
- Kantonsspital Baselland, Liestal, SWITZERLAND
| | - P B Jardin
- Clinica Universitaria de Navarra, Navarra, SPAIN
| | - C Heiser
- Technical University of Munich, Munich, GERMANY
| | - R Schwab
- University of Pennsylvania, Philadelphia, PA
| | - E Thaler
- University of Pennsylvania, Philadelphia, PA
| | - C Jenks
- University of Pennsylvania, Philadelphia, PA
| | - H Walia
- Cleveland Clinic, Cleveland, OH
| | | | - E Kezirian
- University of Southern California, Los Angeles, CA
| | - J Waxman
- Wayne State University, Detroid, MI
| | - H Lin
- Wayne State University, Detroid, MI
| | - M Boon
- Thomas Jefferson University, Philadelphia, PA
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23
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Boon M, Calvo-Lerma J, Claes I, Havermans T, Asseiceira I, Bulfamante A, Garriga M, Masip E, van Schijndel BAM, Fornes V, Barreto C, Colombo C, Crespo P, Vicente S, Janssens H, Hulst J, Witters P, Nobili R, Pereira L, Ruperto M, Van der Wiel E, Mainz JG, De Boeck K, Ribes-Koninckx C. Use of a mobile application for self-management of pancreatic enzyme replacement therapy is associated with improved gastro-intestinal related quality of life in children with Cystic Fibrosis. J Cyst Fibros 2020; 19:562-568. [PMID: 32335023 DOI: 10.1016/j.jcf.2020.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Most patients with cystic fibrosis (CF) suffer from pancreatic insufficiency (PI), leading to fat malabsorption, malnutrition, abdominal discomfort and impaired growth. Pancreatic enzyme replacement therapy (PERT) is effective, but evidence based guidelines for dose adjustment are lacking. A mobile app for self-management of PERT was developed in the context of the HORIZON 2020 project MyCyFAPP. It contains an algorithm to calculate individual PERT-doses for optimal fat digestion, based on in vitro and in vivo studies carried out in the same project. In addition, the app includes a symptoms diary, educational material, and it is linked to a web tool allowing health care professionals to evaluate patient's data and provide feedback. METHODS A 6-month open label prospective multicenter interventional clinical trial was performed to assess effects of using the app on gastro-intestinal related quality of life (GI QOL), measured by the CF-PedsQL-GI (shortened, CF specific version of the Pediatric Quality of Life Inventory, Gastrointestinal Symptoms Module). RESULTS One hundred and seventy-one patients with CF and PI between 2 and 18 years were recruited at 6 European CF centers. Self-reported CF-PedsQL-GI improved significantly from month 0 (M0) (84.3, 76.4-90.3) to month 6 (M6) (89.4, 80.35-93.5) (p< 0.0001). Similar improvements were reported by parents. Lower baseline CF-PedsQL-GI was associated with a greater improvement at M6 (p < 0.001). CONCLUSIONS The results suggest that the MyCyFAPP may improve GI QOL for children with CF. This tool may help patients to improve self-management of PERT, especially those with considerable GI symptoms.
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Affiliation(s)
- M Boon
- Department of Pediatrics, Center for Cystic Fibrosis, University Hospital Leuven, Leuven, Belgium.
| | - J Calvo-Lerma
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - I Claes
- Department of Pediatrics, Center for Cystic Fibrosis, University Hospital Leuven, Leuven, Belgium
| | - T Havermans
- Department of Pediatrics, Center for Cystic Fibrosis, University Hospital Leuven, Leuven, Belgium
| | - I Asseiceira
- Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Lisbon, Portugal
| | - A Bulfamante
- Università degli Studi di Milano, Fondazione IRCCS Ca" Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - M Garriga
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - E Masip
- Gastroenterology and Pediatric cystic Fibrosis Unit, La Fe Hospital, Valencia, Spain
| | - B A M van Schijndel
- Department of Pediatrics, div of Gastro-Enterology, Erasmus MC- Sophia Children's Hospital, University Hospital Rotterdam, the Netherlands
| | - V Fornes
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - C Barreto
- Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Lisbon, Portugal
| | - C Colombo
- Università degli Studi di Milano, Fondazione IRCCS Ca" Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - P Crespo
- Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - S Vicente
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - H Janssens
- Department of Pediatrics, div Respiratory Medicine and Allergology, Erasmus MC-Sophia Children's Hospital, University Hospital Rotterdam, the Netherlands
| | - J Hulst
- Department of Pediatrics, div of Gastro-Enterology, Erasmus MC- Sophia Children's Hospital, University Hospital Rotterdam, the Netherlands
| | - P Witters
- Department of Pediatrics, Center for Cystic Fibrosis, University Hospital Leuven, Leuven, Belgium
| | - R Nobili
- Università degli Studi di Milano, Fondazione IRCCS Ca" Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - L Pereira
- Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Lisbon, Portugal
| | - M Ruperto
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - E Van der Wiel
- Department of Pediatrics, div Respiratory Medicine and Allergology, Erasmus MC-Sophia Children's Hospital, University Hospital Rotterdam, the Netherlands
| | - J G Mainz
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Germany; Cystic Fibrosis Center Brandenburg Medical School (MHB), University, Brandenburg an der Havel, Germany
| | - K De Boeck
- Department of Pediatrics, Center for Cystic Fibrosis, University Hospital Leuven, Leuven, Belgium
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24
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Boon M, De Zitter E, De Smet J, Wagemans J, Voet M, Pennemann FL, Schalck T, Kuznedelov K, Severinov K, Van Meervelt L, De Maeyer M, Lavigne R. 'Drc', a structurally novel ssDNA-binding transcription regulator of N4-related bacterial viruses. Nucleic Acids Res 2020; 48:445-459. [PMID: 31724707 PMCID: PMC7145618 DOI: 10.1093/nar/gkz1048] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.
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Affiliation(s)
- Maarten Boon
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Elke De Zitter
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Jeroen De Smet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Jeroen Wagemans
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Marleen Voet
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Friederike L Pennemann
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | - Thomas Schalck
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
| | | | | | - Luc Van Meervelt
- Department of Chemistry, Biomolecular Architecture, KU Leuven, Leuven 3001, Belgium
| | - Marc De Maeyer
- Department of Chemistry, Laboratory of Biomolecular Modelling and Design, KU Leuven, Leuven 3001, Belgium
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven 3001, Belgium
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25
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Johnstone DL, Al-Shekaili HH, Tarailo-Graovac M, Wolf NI, Ivy AS, Demarest S, Roussel Y, Ciapaite J, van Roermund CWT, Kernohan KD, Kosuta C, Ban K, Ito Y, McBride S, Al-Thihli K, Abdelrahim RA, Koul R, Al Futaisi A, Haaxma CA, Olson H, Sigurdardottir LY, Arnold GL, Gerkes EH, Boon M, Heiner-Fokkema MR, Noble S, Bosma M, Jans J, Koolen DA, Kamsteeg EJ, Drögemöller B, Ross CJ, Majewski J, Cho MT, Begtrup A, Wasserman WW, Bui T, Brimble E, Violante S, Houten SM, Wevers RA, van Faassen M, Kema IP, Lepage N, Lines MA, Dyment DA, Wanders RJA, Verhoeven-Duif N, Ekker M, Boycott KM, Friedman JM, Pena IA, van Karnebeek CDM. PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights. Brain 2020; 142:542-559. [PMID: 30668673 DOI: 10.1093/brain/awy346] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 10/30/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.
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Affiliation(s)
- Devon L Johnstone
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Hilal H Al-Shekaili
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Maja Tarailo-Graovac
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Institute of Physiology and Biochemistry, Faculty of Biology, The University of Belgrade, Belgrade, Serbia.,Departments of Biochemistry, Molecular Biology, and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Nicole I Wolf
- Department of Child Neurology, Amsterdam University Medical Centres, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Autumn S Ivy
- Division of Child Neurology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, CA, USA
| | - Scott Demarest
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Children's Hospital Colorado, CO, USA
| | - Yann Roussel
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jolita Ciapaite
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Carlo W T van Roermund
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Ceres Kosuta
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kevin Ban
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Skye McBride
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Khalid Al-Thihli
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Rana A Abdelrahim
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Roshan Koul
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Amna Al Futaisi
- Paediatric Neurology Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Charlotte A Haaxma
- Department of Pediatric Neurology, Amalia Children's Hospital and Donders Institute of Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Heather Olson
- Department of Neurology, Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, MA, USA
| | - Laufey Yr Sigurdardottir
- Department of Neurology, University of Central Florida, Nemours Children's Hospital, Orlando, FL, USA
| | - Georgianne L Arnold
- Department of Pediatrics, University of Pittsburgh Medical Center, Pittsburg, PA, USA
| | - Erica H Gerkes
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Boon
- Department of Neurology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M Rebecca Heiner-Fokkema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sandra Noble
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Marjolein Bosma
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands
| | - Judith Jans
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Britt Drögemöller
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada
| | | | | | - Wyeth W Wasserman
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Tuan Bui
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford Medicine, Stanford, CA, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron A Wevers
- United for Metabolic Diseases, The Netherlands.,Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn van Faassen
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nathalie Lepage
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Matthew A Lines
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Division of Metabolics and Newborn Screening, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Ronald J A Wanders
- Department of Pediatrics and Clinical Chemistry, Laboratory Division, Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Nanda Verhoeven-Duif
- Department of Genetics, Center for Molecular Medicine, University Medical Center, Utrecht, The Netherlands.,United for Metabolic Diseases, The Netherlands
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Izabella A Pena
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Clara D M van Karnebeek
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.,United for Metabolic Diseases, The Netherlands.,Departments of Pediatrics and Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, The Netherlands.,Centre for Molecular Medicine and Therapeutics, Department of Pediatrics, University of British Columbia, Vancouver, Canada
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26
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Ribeiro HG, Melo LDR, Oliveira H, Boon M, Lavigne R, Noben JP, Azeredo J, Oliveira A. Characterization of a new podovirus infecting Paenibacillus larvae. Sci Rep 2019; 9:20355. [PMID: 31889094 PMCID: PMC6937236 DOI: 10.1038/s41598-019-56699-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/28/2019] [Indexed: 12/17/2022] Open
Abstract
The Paenibacillus larvae infecting phage API480 (vB_PlaP_API480) is the first reported podovirus for this bacterial species, with an 58 nm icosahedral capsid and a 12 × 8 nm short, non-contractile tail. API480 encodes 77 coding sequences (CDSs) on its 45,026 bp dsDNA genome, of which 47 were confirmed using mass spectrometry. This phage has got very limited genomic and proteomic similarity to any other known ones registered in public databases, including P. larvae phages. Comparative genomics indicates API480 is a new species as it's a singleton with 28 unique proteins. Interestingly, the lysis module is highly conserved among P. larvae phages, containing a predicted endolysin and two putative holins. The well kept overall genomic organisation (from the structural and morphogenetic modules to the host lysis, DNA replication and metabolism related proteins) confirms a common evolutionary ancestor among P. larvae infecting phages. API480 is able to infect 69% of the 61 field strains with an ERIC I genotype, as well as ERIC II strains. Furthermore, this phage is very stable when exposed to high glucose concentrations and to larval gastrointestinal conditions. This highly-specific phage, with its broad lytic activity and stability in hive conditions, might potentially be used in the biocontrol of American Foulbrood (AFB).
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Affiliation(s)
- Henrique G Ribeiro
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Luís D R Melo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Maarten Boon
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Agoralaan D, 3590, Hasselt, Belgium
| | - Joana Azeredo
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal
| | - Ana Oliveira
- CEB - Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057, Braga, Portugal.
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Abstract
Introduction: Sugammadex is a modified cyclodextrin that is able to reverse neuromuscular block induced by aminosteroidal neuromuscular blocking drugs. Compared to reversal with neostigmine, it reverses neuromuscular block quicker and more predictable and without cholinergic side effects. However, there have been concerns about sugammadex ability to bind other drugs and its effects on QT interval and clotting times. In addition, sugammadex might induce hypersensitivity reactions more frequently than initially anticipated. This review summarizes current evidence with regard to these and other safety aspects of sugammadex. Areas covered: This review provides an overview of the efficacy of sugammadex in various patient populations, evaluates potential interactions with other drugs and discusses adverse effects and reactions that have been reported in the literature. Expert opinion: Sugammadex quickly reverses aminosteroid neuromuscular block with less side effects compared to neostigmine. As such, it has the potential to significantly reduce the incidence of residual neuromuscular block and to improve postoperative pulmonary outcome. Current safety concerns mainly focus on hypersensitivity reactions and cardiac arrhythmias. Although the absolute risk for these events is low, ongoing vigilance and research in this area are needed.
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Affiliation(s)
- Ghm Honing
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | - C H Martini
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | | | - M van Velzen
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | - M Niesters
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | - Lphj Aarts
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | - A Dahan
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
| | - M Boon
- Department of Anesthesiology, Leiden University Medical Center , Leiden , The Netherlands
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28
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Martinez-Tellez B, Nahon K, Janssen L, Sardjoe-Mishre A, van Weeghel M, Vaz F, Houtkooper R, Burakiewicz J, Dzyubachyk O, Kooijman S, Webb A, Kan H, Berbée J, Jazet I, Boon M, Rensen P. The Effect Of Mirabegron On Energy Expenditure, Brown Adipose Tissue And The Lipidomic Profile In Healthy Lean South Asian And White Caucasian Men. Atherosclerosis 2019. [DOI: 10.1016/j.atherosclerosis.2019.06.864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Custers D, Vermeulen F, De Boeck K, Boon M, Proesmans M. P204 Hypogammaglobulinemia in children with cystic fibrosis. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30498-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Boon M, Calvo-Lermo J, Claes I, Havermans T, Fornes V, Asseiceira I, Bulfamente A, Garriga M, Massip E, Walet S, Barreto C, Colombo C, Crespo P, Janssens H, Ruperto M, Hulst J, Nobili R, Pereira L, Van der Wiel E, Vicente S, De Boeck K, Ribes-Koninckx C. ePS5.08 MyCyFAPP project: use of a mobile application for self-management of PERT improves gastrointestinal related quality of life in children with cystic fibrosis. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30286-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Vermeulen F, Proesmans M, Vermaelen M, Boon M, De Boeck K. P196 Enterobacteriaceae in airway samples of preschool children with cystic fibrosis and worse outcome. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30490-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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De Groof J, Vermeulen F, Proesmans M, Boon M, De Boeck K. P214 Cumulative radiation exposure of radiologic imaging in patients with cystic fibrosis. J Cyst Fibros 2019. [DOI: 10.1016/s1569-1993(19)30507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Krijtenburg P, Honing G, Martini C, Olofsen E, van Elst H, Scheffer G, Dahan A, Keijzer C, Boon M. Comparison of the TOF-Cuff® monitor with electromyography and acceleromyography during recovery from neuromuscular block. Br J Anaesth 2019; 122:e22-e24. [DOI: 10.1016/j.bja.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 11/24/2022] Open
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34
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Attai H, Boon M, Phillips K, Noben JP, Lavigne R, Brown PJB. Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens. Front Microbiol 2018; 9:1861. [PMID: 30154772 PMCID: PMC6102473 DOI: 10.3389/fmicb.2018.01861] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/24/2018] [Indexed: 01/21/2023] Open
Abstract
Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease, leading to the damage of agriculturally-important crops. As part of an effort to discover new phages that can potentially be used as biocontrol agents to prevent crown gall disease, we isolated and characterized phage Atu_ph07 from Sawyer Creek in Springfield, MO, using the virulent Agrobacterium tumefaciens strain C58 as a host. After surveying its host range, we found that Atu_ph07 exclusively infects Agrobacterium tumefaciens. Time-lapse microscopy of A. tumefaciens cells subjected to infection at a multiplicity of infection (MOI) of 10 with Atu_ph07 reveals that lysis occurs within 3 h. Transmission electron microscopy (TEM) of virions shows that Atu_ph07 has a typical Myoviridae morphology with an icosahedral head, long tail, and tail fibers. The sequenced genome of Atu_ph07 is 490 kbp, defining it as a jumbo phage. The Atu_ph07 genome contains 714 open reading frames (ORFs), including 390 ORFs with no discernable homologs in other lineages (ORFans), 214 predicted conserved hypothetical proteins with no assigned function, and 110 predicted proteins with a functional annotation based on similarity to conserved proteins. The proteins with predicted functional annotations share sequence similarity with proteins from bacteriophages and bacteria. The functionally annotated genes are predicted to encode DNA replication proteins, structural proteins, lysis proteins, proteins involved in nucleotide metabolism, and tRNAs. Characterization of the gene products reveals that Atu_ph07 encodes homologs of 16 T4 core proteins and is closely related to Rak2-like phages. Using ESI-MS/MS, the majority of predicted structural proteins could be experimentally confirmed and 112 additional virion-associated proteins were identified. The genomic characterization of Atu_ph07 suggests that this phage is lytic and the dynamics of Atu_ph07 interaction with its host indicate that this phage may be suitable for inclusion in a phage cocktail to be used as a biocontrol agent.
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Affiliation(s)
- Hedieh Attai
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Maarten Boon
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Kenya Phillips
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, Hasselt, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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35
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de Mol CL, Wong YYM, van Pelt ED, Ketelslegers IA, Bakker DP, Boon M, Braun KPJ, van Dijk KGJ, Eikelenboom MJ, Engelen M, Geleijns K, Haaxma CA, Niermeijer JMF, Niks EH, Peeters EAJ, Peeters-Scholte CMPCD, Poll-The BT, Portier RP, de Rijk-van Andel JF, Samijn JPA, Schippers HM, Snoeck IN, Stroink H, Vermeulen RJ, Verrips A, Visscher F, Vles JSH, Willemsen MAAP, Catsman-Berrevoets CE, Hintzen RQ, Neuteboom RF. Incidence and outcome of acquired demyelinating syndromes in Dutch children: update of a nationwide and prospective study. J Neurol 2018; 265:1310-1319. [PMID: 29569176 PMCID: PMC5990581 DOI: 10.1007/s00415-018-8835-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/14/2018] [Accepted: 03/15/2018] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Acquired demyelinating syndromes (ADS) are immune-mediated demyelinating disorders of the central nervous system in children. A nationwide, multicentre and prospective cohort study was initiated in the Netherlands in 2006, with a reported ADS incidence of 0.66/100,000 per year and MS incidence of 0.15/100,000 per year in the period between 2007 and 2010. In this study, we provide an update on the incidence and the long-term follow-up of ADS in the Netherlands. METHODS Children < 18 years with a first attack of demyelination were included consecutively from January 2006 to December 2016. Diagnoses were based on the International Paediatric MS study group consensus criteria. Outcome data were collected by neurological and neuropsychological assessments, and telephone call assessments. RESULTS Between 2011 and 2016, 55/165 of the ADS patients were diagnosed with MS (33%). This resulted in an increased ADS and MS incidence of 0.80/100,000 per year and 0.26/100,000 per year, respectively. Since 2006 a total of 243 ADS patients have been included. During follow-up (median 55 months, IQR 28-84), 137 patients were diagnosed with monophasic disease (56%), 89 with MS (37%) and 17 with multiphasic disease other than MS (7%). At least one form of residual deficit including cognitive impairment was observed in 69% of all ADS patients, even in monophasic ADS. An Expanded Disability Status Scale score of ≥ 5.5 was reached in 3/89 MS patients (3%). CONCLUSION The reported incidence of ADS in Dutch children has increased since 2010. Residual deficits are common in this group, even in monophasic patients. Therefore, long-term follow-up in ADS patients is warranted.
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Affiliation(s)
- C L de Mol
- Department of Neurology, MS Centre ErasMS, Erasmus MC, Rotterdam, The Netherlands
| | - Y Y M Wong
- Department of Neurology, MS Centre ErasMS, Erasmus MC, Rotterdam, The Netherlands
| | - E D van Pelt
- Department of Neurology, MS Centre ErasMS, Erasmus MC, Rotterdam, The Netherlands
| | - I A Ketelslegers
- Department of Neurology, MS Centre ErasMS, Erasmus MC, Rotterdam, The Netherlands
| | - D P Bakker
- Department of Paediatric Neurology, VU Medical Centre, Amsterdam, The Netherlands
| | - M Boon
- Department of Paediatric Neurology, UMCG, Groningen, The Netherlands
| | - K P J Braun
- Department of Paediatric Neurology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - K G J van Dijk
- Department of Paediatrics, Rijnstate Hospital, Arnhem, The Netherlands
| | - M J Eikelenboom
- Department of Neurology, Westfriesgasthuis, Hoorn, The Netherlands
| | - M Engelen
- Department of Paediatric Neurology, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands
| | - K Geleijns
- Department of Paediatric Neurology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - C A Haaxma
- Department of Paediatric Neurology, Radboud UMC, Nijmegen, The Netherlands
| | - J M F Niermeijer
- Department of Neurology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - E H Niks
- Department of Neurology, Leiden University Medical Centre, Leiden, The Netherlands
| | - E A J Peeters
- Department of Paediatric Neurology, Juliana Children Hospital/Haga Hospital, The Hague, The Netherlands
| | | | - B T Poll-The
- Department of Paediatric Neurology, Academic Medical Centre Amsterdam, Amsterdam, The Netherlands
| | - R P Portier
- Department of Neurology, Medical Spectrum Twente, Enschede, The Netherlands
| | | | - J P A Samijn
- Department of Neurology, Maasstad Hospital, Rotterdam, The Netherlands
| | - H M Schippers
- Department of Neurology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - I N Snoeck
- Department of Paediatric Neurology, Juliana Children Hospital/Haga Hospital, The Hague, The Netherlands
| | - H Stroink
- Department of Neurology, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - R J Vermeulen
- Department of Neurology, Maastricht UMC, Maastricht, The Netherlands
| | - A Verrips
- Department of Neurology, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - F Visscher
- Department of Paediatric Neurology, Admiraal de Ruyter Hospital, Goes, The Netherlands
| | - J S H Vles
- Department of Neurology, Maastricht UMC, Maastricht, The Netherlands
| | - M A A P Willemsen
- Department of Paediatric Neurology, Radboud UMC, Nijmegen, The Netherlands
| | - C E Catsman-Berrevoets
- Paediatric Neurology, Erasmus MC-Sophia, P.O. Box 2060, 3000 CB, Rotterdam, The Netherlands
| | - R Q Hintzen
- Department of Neurology, MS Centre ErasMS, Erasmus MC, Rotterdam, The Netherlands
| | - R F Neuteboom
- Paediatric Neurology, Erasmus MC-Sophia, P.O. Box 2060, 3000 CB, Rotterdam, The Netherlands.
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Calvo-Lerma J, Hulst J, Boon M, Masip E, Fornés-Ferrer V, Garriga M, Colombo C, Crespo P, Roca M, Woodcock S, Van der Wiel E, Claes I, de Boeck K, Ribes-Koninckx C, MyCyFAPP. WS03.6 A first approach for an evidence-based method to adjust PERT: in vivo validation of the in vitro model. J Cyst Fibros 2018. [DOI: 10.1016/s1569-1993(18)30136-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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37
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Proesmans M, Dings A, Van Meerbeek S, Boon M, De Boeck K, Vermeulen F. P178 Sodium status in children with CF: evaluation of fractional sodium excretion in a paediatric cohort. J Cyst Fibros 2018. [DOI: 10.1016/s1569-1993(18)30473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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38
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Huntley C, Doghramji K, Boon M. 0539 Outcomes Of Upper Airway Stimulation At A High Volume Academic Center. Sleep 2018. [DOI: 10.1093/sleep/zsy061.538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- C Huntley
- Thomas Jefferson University, Philadelphia, PA
| | - K Doghramji
- Thomas Jefferson University, Philadelphia, PA
| | - M Boon
- Thomas Jefferson University, Philadelphia, PA
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Maurer JT, Boon M, Steffen A, Strollo P, Heiser C. Internationale Registerstudie zur selektiven oberen Atemwegsstimulation. Pneumologie 2018. [DOI: 10.1055/s-0037-1619294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- JT Maurer
- Schlafmedizinisches Zentrum, Universitäts-HNO-Klinik Mannheim
| | - M Boon
- Thomas Jefferson University Hospital, Philadelphia
| | | | - P Strollo
- University of Pittsburgh, VAHS Pittsburgh, University of Pittsburgh
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40
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Dahan A, Boon M, Martini C. Postoperative conditions after antagonism of neuromuscular blocking agent and extubation without use of a neuromuscular monitor. Br J Anaesth 2017; 119:1061-1062. [DOI: 10.1093/bja/aex372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Peeters E, Boon M, Rollie C, Willaert RG, Voet M, White MF, Prangishvili D, Lavigne R, Quax TEF. DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1. Viruses 2017; 9:v9070190. [PMID: 28718834 PMCID: PMC5537682 DOI: 10.3390/v9070190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.
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Affiliation(s)
- Eveline Peeters
- Research Group of Microbiology, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Clare Rollie
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | - Ronnie G Willaert
- Alliance Research Group VUB-UGhent NanoMicrobiology, IJRG VUB-EPFL, BioNanotechnology & NanoMedicine, Research Group Structural Biology Brussels, Department of Bio-Engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife, North Haugh, St. Andrews KY16 9AJ, UK.
| | | | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
| | - Tessa E F Quax
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, 3001 Leuven, Belgium.
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42
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Boon M, Vermeulen F, Proesmans M, De Boeck K. 227 CFCT, LCI and FEV1 in children with PCD compared to CF. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30572-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Boon M, Claes I, Havermans T, Asseiceira I, Bulfamante A, Garriga M, Martinez-Barona S, Woodcock S, Verhoeven K, Barreto C, Calvo-Lerma J, Colombo C, Crespo P, Hulst J, Masip E, Nobili R, Pereira L, Ruperto M, De Boeck K, Ribes-Koninckx C. 341 MyCyFAPP project: assessment and validation of the PEDsQL GI symptom scale in children with CF. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30679-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Vermeulen F, Boon M, Proesmans M, De Boeck K. WS19.4 Predictors of long term changes in lung clearance index in children with CF. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Doghramji K, Huntley C, Boon M. 0581 OUTCOMES FOR A LARGE COHORT OF PATIENTS UNDERGOING UPPER AIRWAY STIMULATION THERAPY: THE JEFFERSON EXPERIENCE. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Huntley C, Grewal R, Boon M. 0585 DRUG INDUCED SLEEP ENDOSCOPY; PREDICTIVE OF SUCCESS FOR ORAL APPLIANCE THERAPY IN TREATING OBSTRUCTIVE SLEEP APNEA. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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47
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Boon M, Huntley C, Doghramji K. 0580 COMPLIANCE TO UPPER AIRWAY STIMULATION THERAPY: A SINGLE UNIVERSITY-BASED CENTER EXPERIENCE. Sleep 2017. [DOI: 10.1093/sleepj/zsx050.579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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48
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Boon M, Martini C, Broens S, van Rijnsoever E, van der Zwan T, Aarts L, Dahan A. Improved postoperative oxygenation after antagonism of moderate neuromuscular block with sugammadex versus neostigmine after extubation in ‘blinded’ conditions. Br J Anaesth 2016; 117:410-1. [DOI: 10.1093/bja/aew246] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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van Dam A, Bekkering S, Crasborn M, van Beek L, van den Berg S, Vrieling F, Joosten S, van Harmelen V, de Winther M, Lutgens E, Boon M, Riksen N, Rensen P, Berbée J. Bacille-calmette-guÉrin lowers plasma cholesterol and delays atherosclerotic lesion progression in mice. Atherosclerosis 2016. [DOI: 10.1016/j.atherosclerosis.2016.07.841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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50
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Nahon K, Hoeke G, Bakker L, Drettwan D, Pagel P, Jazet I, Berbée J, Boon M, Rensen P. Short-term cold exposure modulates human VLDL and HDL metabolism. Atherosclerosis 2016. [DOI: 10.1016/j.atherosclerosis.2016.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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