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Claes E, Heck T, Coddens K, Sonnaert M, Schrooten J, Verwaeren J. Bayesian cell therapy process optimization. Biotechnol Bioeng 2024; 121:1569-1582. [PMID: 38372656 DOI: 10.1002/bit.28669] [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: 05/31/2023] [Revised: 11/17/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Optimizing complex bioprocesses poses a significant challenge in several fields, particularly in cell therapy manufacturing. The development of customized, closed, and automated processes is crucial for their industrial translation and for addressing large patient populations at a sustainable price. Limited understanding of the underlying biological mechanisms, coupled with highly resource-intensive experimentation, are two contributing factors that make the development of these next-generation processes challenging. Bayesian optimization (BO) is an iterative experimental design methodology that addresses these challenges, but has not been extensively tested in situations that require parallel experimentation with significant experimental variability. In this study, we present an evaluation of noisy, parallel BO for increasing noise levels and parallel batch sizes on two in silico bioprocesses, and compare it to the industry state-of-the-art. As an in vitro showcase, we apply the method to the optimization of a monocyte purification unit operation. The in silico results show that BO significantly outperforms the state-of-the-art, requiring approximately 50% fewer experiments on average. This study highlights the potential of noisy, parallel BO as valuable tool for cell therapy process development and optimization.
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Affiliation(s)
- Evan Claes
- Antleron, Leuven, Belgium
- Biovism, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | | | | | | | - Jan Verwaeren
- Biovism, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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2
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Perneel M, De Smet S, Verwaeren J. Data driven prediction of dairy cattle lifetime production and its use as a guideline to select surplus youngstock. J Dairy Sci 2024:S0022-0302(24)00069-9. [PMID: 38331186 DOI: 10.3168/jds.2023-23660] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
The lifetime production of dairy cows is a complex trait influenced not only by genetics, but also by the environment in which a cow lives and the management practices of the farmer. Moreover, these influential factors show complex interactions with each other, making it difficult to reliably predict the lifetime production of individual animals at birth. However, since well managed dairy farms often have a surplus of youngstock, reliable lifetime production predictions would offer the opportunity to make more substantiated decisions when selecting calves or heifers to sell. Therefore, using data from Dutch herds, we constructed a data set capturing information on genetics, environment and management practices to develop multiple machine learning models capable of predicting the lifetime production of dairy cattle soon after birth. We found that a coupling of trends observed at the country level with farm-specific models largely outperforms off-the-shelf approaches. At birth, our best model could explain up to 47% of the variance in lifetime production, a considerable improvement in comparison with linear regression on the breeding values supplemented with the average lifetime production at farm level, which could only explain 21.7% of the variance in lifetime production. Moreover, we demonstrated surplus youngstock selection according to our model could more than double the surplus animal selection effect in comparison with the benchmark methodology, offering opportunities to increase the average (future) potential lifetime production of the retained heifers significantly. Assuming a static 20% surplus liveborn heifer scenario and random surplus animal selection as the default, our best model for surplus animal selection resulted in a 9.4% greater lifetime production in the retained animals compared with the current Dutch average lifetime production.
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Affiliation(s)
- Maarten Perneel
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Stefaan De Smet
- Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jan Verwaeren
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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3
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Kaya U, Gopireddy S, Urbanetz N, Kreitmayer D, Gutheil E, Nopens I, Verwaeren J. Quantifying the hydrodynamic stress for bioprocesses. Biotechnol Prog 2023; 39:e3367. [PMID: 37293967 DOI: 10.1002/btpr.3367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/10/2023]
Abstract
Hydrodynamic stress is an influential physical parameter for various bioprocesses, affecting the performance and viability of the living organisms. However, different approaches are in use in various computational and experimental studies to calculate this parameter (including its normal and shear subcomponents) from velocity fields without a consensus on which one is the most representative of its effect on living cells. In this letter, we investigate these different methods with clear definitions and provide our suggested approach which relies on the principal stress values providing a maximal distinction between the shear and normal components. Furthermore, a numerical comparison is presented using the computational fluid dynamics simulation of a stirred and sparged bioreactor. It is demonstrated that for this specific bioreactor, some of these methods exhibit quite similar patterns throughout the bioreactor-therefore can be considered equivalent-whereas some of them differ significantly.
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Affiliation(s)
- Umut Kaya
- Supply Chain Operations, Pharmaceutical Development, Daiichi Sankyo Europe GmbH, Pfaffenhofen, Germany
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Srikanth Gopireddy
- Supply Chain Operations, Pharmaceutical Development, Daiichi Sankyo Europe GmbH, Pfaffenhofen, Germany
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Nora Urbanetz
- Supply Chain Operations, Pharmaceutical Development, Daiichi Sankyo Europe GmbH, Pfaffenhofen, Germany
| | - Diana Kreitmayer
- Supply Chain Operations, Pharmaceutical Development, Daiichi Sankyo Europe GmbH, Pfaffenhofen, Germany
| | - Eva Gutheil
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany
| | - Ingmar Nopens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Jan Verwaeren
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
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4
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Ipek N, Van Damme LGW, Tuyttens FAM, Verwaeren J. Quantifying agonistic interactions between group-housed animals to derive social hierarchies using computer vision: a case study with commercially group-housed rabbits. Sci Rep 2023; 13:14138. [PMID: 37644059 PMCID: PMC10465565 DOI: 10.1038/s41598-023-41104-6] [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: 11/18/2022] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
In recent years, computer vision has contributed significantly to the study of farm animal behavior. In complex environments such as commercial farms, however, the automated detection of social behavior and specific interactions between animals can be improved. The present study addresses the automated detection of agonistic interactions between caged animals in a complex environment, relying solely on computer vision. An automated pipeline including group-level temporal action segmentation, object detection, object tracking and rule-based action classification for the detection of agonistic interactions was developed and extensively validated at a level unique in the field. Comparing with observations made by human observers, our pipeline reaches 77% precision and 85% recall using a 5-min tolerance interval for the detection of agonistic interactions. Results obtained using this pipeline allow to construct time-dependent socio-matrices of a group of animals and derive metrics on the dominance hierarchy in a semi-automated manner. Group-housed breeding rabbits (does) with their litters in commercial farms are the main use-case in this work, but the idea is probably also applicable to other social farm animals.
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Affiliation(s)
- Nusret Ipek
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Gent, Belgium.
| | - Liesbeth G W Van Damme
- Animal Sciences Unit, ILVO, Scheldeweg 68, 9090, Melle, Belgium
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Frank A M Tuyttens
- Animal Sciences Unit, ILVO, Scheldeweg 68, 9090, Melle, Belgium
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Jan Verwaeren
- Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000, Gent, Belgium
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De Blaere R, Lievens K, Van Hassel D, Deklerck V, De Mil T, Hubau W, Van Acker J, Bourland N, Verwaeren J, Van den Bulcke J, Beeckman H. SmartWoodID-an image collection of large end-grain surfaces to support wood identification systems. Database (Oxford) 2023; 2023:7161700. [PMID: 37178209 PMCID: PMC10182821 DOI: 10.1093/database/baad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/24/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Wood identification is a key step in the enforcement of laws and regulations aimed at combatting illegal timber trade. Robust wood identification tools, capable of distinguishing a large number of timbers, depend on a solid database of reference material. Reference material for wood identification is typically curated in botanical collections dedicated to wood consisting of samples of secondary xylem of lignified plants. Specimens from the Tervuren Wood Collection, one of the large institutional wood collections around the world, are used as a source of tree species data with potential application as timber. Here, we present SmartWoodID, a database of high-resolution optical scans of the end-grain surfaces enriched with expert wood anatomical descriptions of macroscopic features. These can serve as annotated training data to develop interactive identification keys and artificial intelligence for computer vision-based wood identification. The first edition of the database consists of images of 1190 taxa, with a focus on potential timber species from the Democratic Republic of the Congo with at least four different specimens per species included. Database URL https://hdl.handle.net/20.500.12624/SmartWoodID_first_edition.
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Affiliation(s)
- Ruben De Blaere
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
| | - Kévin Lievens
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
| | - Dieter Van Hassel
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
| | - Victor Deklerck
- Jodrell laboratory, Royal Botanic Gardens, Kew, Richmond, London TW9 3A, UK
| | - Tom De Mil
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech (Université de Liège), Passage des Déportés 2, Gembloux 5030, Belgium
| | - Wannes Hubau
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
- UGent-Woodlab, Laboratory of Wood Technology, Department of Environment, Ghent University, Coupure Links 653, Gent 9000, Belgium
| | - Joris Van Acker
- UGent-Woodlab, Laboratory of Wood Technology, Department of Environment, Ghent University, Coupure Links 653, Gent 9000, Belgium
| | - Nils Bourland
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
| | - Jan Verwaeren
- UGent-KERMIT, Research Unit Knowledge-based, Predictive and Spatio-temporal Modelling, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, Gent 9000, Belgium
| | - Jan Van den Bulcke
- UGent-Woodlab, Laboratory of Wood Technology, Department of Environment, Ghent University, Coupure Links 653, Gent 9000, Belgium
| | - Hans Beeckman
- Service of Wood Biology, Royal Museum for Central Africa, Leuvensesteenweg 13, Tervuren 3080, Belgium
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Deloose A, Gysels G, De Baets B, Verwaeren J. Combining natural language processing and multidimensional classifiers to predict and correct CMMS metadata. COMPUT IND 2023. [DOI: 10.1016/j.compind.2022.103830] [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: 12/25/2022]
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7
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Rondou K, De Witte F, Rimaux T, Dewinter W, Dewettinck K, Verwaeren J, Van Bockstaele F. Multiscale analysis of monoglyceride oleogels during storage. J AM OIL CHEM SOC 2022. [DOI: 10.1002/aocs.12645] [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: 11/07/2022]
Affiliation(s)
- Kato Rondou
- Food Structure and Function (FS&F) Research Group, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering Ghent University Ghent Belgium
- Vandemoortele Centre ‘Lipid Science and Technology’, Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Fien De Witte
- Food Structure and Function (FS&F) Research Group, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Tom Rimaux
- Vandemoortele Centre ‘Lipid Science and Technology’, Faculty of Bioscience Engineering Ghent University Ghent Belgium
- Department of R&D Vandemoortele Izegem Belgium
| | | | - Koen Dewettinck
- Food Structure and Function (FS&F) Research Group, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering Ghent University Ghent Belgium
- Vandemoortele Centre ‘Lipid Science and Technology’, Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Jan Verwaeren
- KERMIT, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering Ghent University Ghent Belgium
| | - Filip Van Bockstaele
- Food Structure and Function (FS&F) Research Group, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering Ghent University Ghent Belgium
- Vandemoortele Centre ‘Lipid Science and Technology’, Faculty of Bioscience Engineering Ghent University Ghent Belgium
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8
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Schouteten JJ, Verwaeren J, Rini L, Almli VL. Comparing a product-specific versus a general emoji list to measure consumers’ emotional associations with chocolate and predict food choice. Food Res Int 2022; 157:111299. [DOI: 10.1016/j.foodres.2022.111299] [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] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 04/22/2022] [Indexed: 11/16/2022]
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9
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Rosa da Silva N, Deklerck V, Baetens JM, Van den Bulcke J, De Ridder M, Rousseau M, Bruno OM, Beeckman H, Van Acker J, De Baets B, Verwaeren J. Improved wood species identification based on multi-view imagery of the three anatomical planes. Plant Methods 2022; 18:79. [PMID: 35690828 PMCID: PMC9188236 DOI: 10.1186/s13007-022-00910-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The identification of tropical African wood species based on microscopic imagery is a challenging problem due to the heterogeneous nature of the composition of wood combined with the vast number of candidate species. Image classification methods that rely on machine learning can facilitate this identification, provided that sufficient training material is available. Despite the fact that the three main anatomical sections contain information that is relevant for species identification, current methods only rely on transverse sections. Additionally, commonly used procedures for evaluating the performance of these methods neglect the fact that multiple images often originate from the same tree, leading to an overly optimistic estimate of the performance. RESULTS We introduce a new image dataset containing microscopic images of the three main anatomical sections of 77 Congolese wood species. A dedicated multi-view image classification method is developed and obtains an accuracy (computed using the naive but common approach) of 95%, outperforming the single-view methods by a large margin. An in-depth analysis shows that naive accuracy estimates can lead to a dramatic over-prediction, of up to 60%, of the accuracy. CONCLUSIONS Additional images from non-transverse sections can boost the performance of machine-learning-based wood species identification methods. Additionally, care should be taken when evaluating the performance of machine-learning-based wood species identification methods to avoid an overestimation of the performance.
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Affiliation(s)
- Núbia Rosa da Silva
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium.
- Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, Brazil.
- Institute of Biotechnology, Federal University of Catalão, Catalão, Goiás, Brazil.
| | | | - Jan M Baetens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Jan Van den Bulcke
- Laboratory of Wood Technology, Department of Environment, Ghent University, Ghent, Belgium
| | - Maaike De Ridder
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Mélissa Rousseau
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Odemir Martinez Bruno
- Institute of Mathematics and Computer Science, University of São Paulo, São Carlos, Brazil
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Hans Beeckman
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Joris Van Acker
- Laboratory of Wood Technology, Department of Environment, Ghent University, Ghent, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Jan Verwaeren
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
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Kaya U, Gopireddy S, Urbanetz N, Nopens I, Verwaeren J. Predicting the Hydrodynamic Properties of a Bioreactor: Conditional Density Estimation as a Surrogate Model for CFD Simulations. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.03.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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De Zutter N, Ameye M, Bekaert B, Verwaeren J, De Gelder L, Audenaert K. Uncovering New Insights and Misconceptions on the Effectiveness of Phosphate Solubilizing Rhizobacteria in Plants: A Meta-Analysis. Front Plant Sci 2022; 13:858804. [PMID: 35310667 PMCID: PMC8924522 DOI: 10.3389/fpls.2022.858804] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/07/2022] [Indexed: 05/05/2023]
Abstract
As the awareness on the ecological impact of chemical phosphate fertilizers grows, research turns to sustainable alternatives such as the implementation of phosphate solubilizing bacteria (PSB), which make largely immobile phosphorous reserves in soils available for uptake by plants. In this review, we introduce the mechanisms by which plants facilitate P-uptake and illustrate how PSB improve the bioavailability of this nutrient. Next, the effectiveness of PSB on increasing plant biomass and P-uptake is assessed using a meta-analysis approach. Our review demonstrates that improved P-uptake does not always translate in improved plant height and biomass. We show that the effect of PSB on plants does not provide an added benefit when using bacterial consortia compared to single strains. Moreover, the commonly reported species for P-solubilization, Bacillus spp. and Pseudomonas spp., are outperformed by the scarcely implemented Burkholderia spp. Despite the similar responses to PSB in monocots and eudicots, species responsiveness to PSB varies within both clades. Remarkably, the meta-analysis challenges the common belief that PSB are less effective under field conditions compared to greenhouse conditions. This review provides innovative insights and identifies key questions for future research on PSB to promote their implementation in agriculture.
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Affiliation(s)
- Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics (LAMP), Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Laboratory of Environmental Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- *Correspondence: Noémie De Zutter,
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics (LAMP), Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Boris Bekaert
- Laboratory of Applied Mycology and Phenomics (LAMP), Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jan Verwaeren
- Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Leen De Gelder
- Laboratory of Environmental Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics (LAMP), Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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De Zutter N, Ameye M, Debode J, De Tender C, Ommeslag S, Verwaeren J, Vermeir P, Audenaert K, De Gelder L. Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status. Microb Biotechnol 2021; 14:1594-1612. [PMID: 34021699 PMCID: PMC8313256 DOI: 10.1111/1751-7915.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants' P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize's P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.
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Affiliation(s)
- Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Jane Debode
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Caroline De Tender
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityKrijgslaan 281 S9GhentB‐9000Belgium
| | - Sarah Ommeslag
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Jan Verwaeren
- Research Unit Knowledge‐based Systems (KERMIT)Department of Data Analysis and Mathematical ModelingGhent UniversityCoupure links 653GhentB‐9000Belgium
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA)Faculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Leen De Gelder
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
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13
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Venneman J, Vandermeersch L, Walgraeve C, Audenaert K, Ameye M, Verwaeren J, Steppe K, Van Langenhove H, Haesaert G, Vereecke D. Respiratory CO 2 Combined With a Blend of Volatiles Emitted by Endophytic Serendipita Strains Strongly Stimulate Growth of Arabidopsis Implicating Auxin and Cytokinin Signaling. Front Plant Sci 2020; 11:544435. [PMID: 32983211 PMCID: PMC7492573 DOI: 10.3389/fpls.2020.544435] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/14/2020] [Indexed: 05/17/2023]
Abstract
Rhizospheric microorganisms can alter plant physiology and morphology in many different ways including through the emission of volatile organic compounds (VOCs). Here we demonstrate that VOCs from beneficial root endophytic Serendipita spp. are able to improve the performance of in vitro grown Arabidopsis seedlings, with an up to 9.3-fold increase in plant biomass. Additional changes in VOC-exposed plants comprised petiole elongation, epidermal cell and leaf area expansion, extension of the lateral root system, enhanced maximum quantum efficiency of photosystem II (Fv/Fm), and accumulation of high levels of anthocyanin. Notwithstanding that the magnitude of the effects was highly dependent on the test system and cultivation medium, the volatile blends of each of the examined strains, including the references S. indica and S. williamsii, exhibited comparable plant growth-promoting activities. By combining different approaches, we provide strong evidence that not only fungal respiratory CO2 accumulating in the headspace, but also other volatile compounds contribute to the observed plant responses. Volatile profiling identified methyl benzoate as the most abundant fungal VOC, released especially by Serendipita cultures that elicit plant growth promotion. However, under our experimental conditions, application of methyl benzoate as a sole volatile did not affect plant performance, suggesting that other compounds are involved or that the mixture of VOCs, rather than single molecules, accounts for the strong plant responses. Using Arabidopsis mutant and reporter lines in some of the major plant hormone signal transduction pathways further revealed the involvement of auxin and cytokinin signaling in Serendipita VOC-induced plant growth modulation. Although we are still far from translating the current knowledge into the implementation of Serendipita VOCs as biofertilizers and phytostimulants, volatile production is a novel mechanism by which sebacinoid fungi can trigger and control biological processes in plants, which might offer opportunities to address agricultural and environmental problems in the future.
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Affiliation(s)
- Jolien Venneman
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Lore Vandermeersch
- Research Group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christophe Walgraeve
- Research Group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jan Verwaeren
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kathy Steppe
- Laboratory of Plant Ecology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Herman Van Langenhove
- Research Group EnVOC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Danny Vereecke
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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De Wever J, Tulkens D, Verwaeren J, Everaert H, Rottiers H, Dewettinck K, Lefever S, Messens K. A Combined RNA Preservation and Extraction Protocol for Gene Expression Studies in Cacao Beans. Front Plant Sci 2020; 11:992. [PMID: 32695136 PMCID: PMC7338848 DOI: 10.3389/fpls.2020.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 06/17/2020] [Indexed: 05/23/2023]
Abstract
Despite the high economic importance of cacao beans, few RNA-based studies have been conducted on this plant material and hence no optimal RNA-extraction has been reported. Moreover, extraction of high-quality RNA from recalcitrant cacao bean tissue has shown many difficulties and requires optimization. Furthermore, cacao beans are mostly found at remote and under-resourced locations, which pressures the outsourcing of such analysis and thereby demands RNA-stable preservation and transportation of cacao beans. This study aims to select an appropriate RNA extraction and preservation/transportation method for cacao beans. For this purpose, three sample homogenization and five extraction protocols on cacao beans were compared. In addition, 13 preservation conditions-differing in tissue crushing degree, preservation method, duration, and temperature-were compared and evaluated. A comparative analysis revealed that CTAB-based homogenization and extraction outcompeted all tested commercial protocols in RNA yield and integrity, respectively. Preservation at -80°C affected RNA quality the least, whereas freeze-drying was most suitable for transportation at room temperature for maximum 1 week. The cacao bean RNA obtained from the selected methods were compatible for downstream applications. The results of this study will facilitate on-field sampling and transportation of genetically sensitive cacao material prior to cacao bean transcriptomic studies. In addition, valuable insights on sample homogenization, extraction, preservation, and transportation have been provided, which is of interest to every plant geneticist.
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Affiliation(s)
- Jocelyn De Wever
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Dieter Tulkens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
| | - Jan Verwaeren
- Research Unit Knowledge-based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Helena Everaert
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hayley Rottiers
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Koen Dewettinck
- Food Structure & Function Research Group (FSF), Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Steve Lefever
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent (BIG), Ghent University, Ghent, Belgium
| | - Kathy Messens
- Research Unit Molecular Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Debonne E, Van Schoors F, Maene P, Van Bockstaele F, Vermeir P, Verwaeren J, Eeckhout M, Devlieghere F. Comparison of the antifungal effect of undissociated lactic and acetic acid in sourdough bread and in chemically acidified wheat bread. Int J Food Microbiol 2020; 321:108551. [DOI: 10.1016/j.ijfoodmicro.2020.108551] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 11/16/2022]
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16
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Van den Hove A, Verwaeren J, Van den Bossche J, Theunis J, De Baets B. Development of a land use regression model for black carbon using mobile monitoring data and its application to pollution-avoiding routing. Environ Res 2020; 183:108619. [PMID: 31836206 DOI: 10.1016/j.envres.2019.108619] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 05/02/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Black carbon is often used as an indicator for combustion-related air pollution. In urban environments, on-road black carbon concentrations have a large spatial variability, suggesting that the personal exposure of a cyclist to black carbon can heavily depend on the route that is chosen to reach a destination. In this paper, we describe the development of a cyclist routing procedure that minimizes personal exposure to black carbon. Firstly, a land use regression model for predicting black carbon concentrations in an urban environment is developed using mobile monitoring data, collected by cyclists. The optimal model is selected and validated using a spatially stratified cross-validation scheme. The resulting model is integrated in a dedicated routing procedure that minimizes personal exposure to black carbon during cycling. The best model obtains a coefficient of multiple correlation of R=0.520. Simulations with the black carbon exposure minimizing routing procedure indicate that the inhaled amount of black carbon is reduced by 1.58% on average as compared to the shortest-path route, with extreme cases where a reduction of up to 13.35% is obtained. Moreover, we observed that the average exposure to black carbon and the exposure to local peak concentrations on a route are competing objectives, and propose a parametrized cost function for the routing problem that allows for a gradual transition from routes that minimize average exposure to routes that minimize peak exposure.
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Affiliation(s)
- Annelies Van den Hove
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, Ghent, Belgium.
| | - Jan Verwaeren
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, Ghent, Belgium.
| | - Joris Van den Bossche
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, Ghent, Belgium; Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, Belgium.
| | - Jan Theunis
- Flemish Institute for Technological Research (VITO), Boeretang 200, Mol, Belgium.
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, Ghent, Belgium.
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Schouteten JJ, Verwaeren J, Gellynck X, Almli VL. Comparing a standardized to a product-specific emoji list for evaluating food products by children. Food Qual Prefer 2019. [DOI: 10.1016/j.foodqual.2018.09.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Ameye M, Allmann S, Verwaeren J, Smagghe G, Haesaert G, Schuurink RC, Audenaert K. Green leaf volatile production by plants: a meta-analysis. New Phytol 2018; 220:666-683. [PMID: 28665020 DOI: 10.1111/nph.14671] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/02/2017] [Indexed: 05/19/2023]
Abstract
666 I. Introduction 667 II. Biosynthesis 667 III. Meta-analysis 669 IV. The type of stress influences the total amount of GLVs released 669 V. Herbivores can modulate the wound-induced release of GLVs 669 VI. Fungal infection greatly induces GLV production 672 VII. Monocots and eudicots respond differentially to different types of stress 673 VIII. The type of stress does not influence the proportion of GLVs per chemical class 673 IX. The type of stress does influence the isomeric ratio within each chemical class 674 X. GLVs: from signal perception to signal transduction 676 XI. GLVs influence the C/N metabolism 677 XII. Interaction with plant hormones 678 XIII. General conclusions and unanswered questions 678 Acknowledgements 679 References 679 SUMMARY: Plants respond to stress by releasing biogenic volatile organic compounds (BVOCs). Green leaf volatiles (GLVs), which are abundantly produced across the plant kingdom, comprise an important group within the BVOCs. They can repel or attract herbivores and their natural enemies; and they can induce plant defences or prime plants for enhanced defence against herbivores and pathogens and can have direct toxic effects on bacteria and fungi. Unlike other volatiles, GLVs are released almost instantly upon mechanical damage and (a)biotic stress and could thus function as an immediate and informative signal for many organisms in the plant's environment. We used a meta-analysis approach in which data from the literature on GLV production during biotic stress responses were compiled and interpreted. We identified that different types of attackers and feeding styles add a degree of complexity to the amount of emitted GLVs, compared with wounding alone. This meta-analysis illustrates that there is less variation in the GLV profile than we presumed, that pathogens induce more GLVs than insects and wounding, and that there are clear differences in GLV emission between monocots and dicots. Besides the meta-analysis, this review provides an update on recent insights into the perception and signalling of GLVs in plants.
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Affiliation(s)
- Maarten Ameye
- Department of Applied Bioscience, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Silke Allmann
- Department of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94215, 1090 GE, Amsterdam, the Netherlands
| | - Jan Verwaeren
- Department of Applied Bioscience, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Bioscience, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
| | - Robert C Schuurink
- Department of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94215, 1090 GE, Amsterdam, the Netherlands
| | - Kris Audenaert
- Department of Applied Bioscience, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
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Affiliation(s)
- Jan Verwaeren
- Department of Data Analysis and Mathematical Modeling; Ghent University; Gent Belgium
| | - Xavier Gellynck
- Department of Agricultural Economics; Ghent University; Gent Belgium
| | - Sofie Lagast
- Department of Agricultural Economics; Ghent University; Gent Belgium
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Debonne E, De Leyn I, Verwaeren J, Moens S, Devlieghere F, Eeckhout M, Van Bockstaele F. The influence of natural oils of blackcurrant, black cumin seed, thyme and wheat germ on dough and bread technological and microbiological quality. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.03.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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21
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Vanderroost M, Ragaert P, Verwaeren J, De Meulenaer B, De Baets B, Devlieghere F. The digitization of a food package’s life cycle: Existing and emerging computer systems in the pre-logistics phase. COMPUT IND 2017. [DOI: 10.1016/j.compind.2017.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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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22
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Venneman J, Audenaert K, Verwaeren J, Baert G, Boeckx P, Moango AM, Dhed’a BD, Vereecke D, Haesaert G. Congolese Rhizospheric Soils as a Rich Source of New Plant Growth-Promoting Endophytic Piriformospora Isolates. Front Microbiol 2017; 8:212. [PMID: 28261171 PMCID: PMC5306995 DOI: 10.3389/fmicb.2017.00212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 09/23/2016] [Accepted: 01/30/2017] [Indexed: 12/26/2022] Open
Abstract
In the last decade, there has been an increasing focus on the implementation of plant growth-promoting (PGP) organisms as a sustainable option to compensate for poor soil fertility conditions in developing countries. Trap systems were used in an effort to isolate PGP fungi from rhizospheric soil samples collected in the region around Kisangani in the Democratic Republic of Congo. With sudangrass as a host, a highly conducive environment was created for sebacinalean chlamydospore formation inside the plant roots resulting in a collection of 51 axenically cultured isolates of the elusive genus Piriformospora (recently transferred to the genus Serendipita). Based on morphological data, ISSR fingerprinting profiles and marker gene sequences, we propose that these isolates together with Piriformospora williamsii constitute a species complex designated Piriformospora (= Serendipita) 'williamsii.' A selection of isolates strongly promoted plant growth of in vitro inoculated Arabidopsis seedlings, which was evidenced by an increase in shoot fresh weight and a strong stimulation of lateral root formation. This isolate collection provides unprecedented opportunities for fundamental as well as translational research on the Serendipitaceae, a family of fungal endophytes in full expansion.
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Affiliation(s)
- Jolien Venneman
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Kris Audenaert
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Jan Verwaeren
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Geert Baert
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Pascal Boeckx
- Isotope Bioscience Laboratory-ISOFYS, Ghent UniversityGhent, Belgium
| | - Adrien M. Moango
- Faculty of Science and Agriculture, Kisangani UniversityKisangani, Congo
| | - Benoît D. Dhed’a
- Faculty of Science and Agriculture, Kisangani UniversityKisangani, Congo
| | - Danny Vereecke
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Ghent UniversityGhent, Belgium
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Jorjong S, van Knegsel ATM, Verwaeren J, Bruckmaier RM, De Baets B, Kemp B, Fievez V. Milk fatty acids as possible biomarkers to diagnose hyperketonemia in early lactation. J Dairy Sci 2015; 98:5211-21. [PMID: 26094221 DOI: 10.3168/jds.2014-8728] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 08/11/2014] [Accepted: 04/27/2015] [Indexed: 11/19/2022]
Abstract
The aim of this study was to assess the potential of milk fatty acids as diagnostic tool for hyperketonemia of 93 dairy cows in a 3×2 factorial arrangement. Cows were fed a glucogenic or lipogenic diet and originally were intended to be subjected to a 0-, 30-, or 60-d dry period. Nevertheless, some of the cows, which were intended for inclusion in the 0-d dry period group, dried off spontaneously. Milk was collected in wk 2, 3, 4, and 8 of lactation for milk fat analysis. Blood was sampled from wk 2 to 8 after parturition for β-hydroxybutyrate (BHBA) analysis. Cases were classified into 2 groups: hyperketonemia (BHBA ≥1.2mmol/L) and nonhyperketonemia (BHBA <1.2mmol/L). Concentrations of 45 milk fatty acids and ratios of anteiso C15:0-to-anteiso C17:0 and C18:1 cis-9-to-C15:0 were subjected to a logistic regression analysis (stepwise forward method). The milk fat C18:1 cis-9-to-C15:0 ratio revealed the most discriminating factor for diagnosis of hyperketonemia. Ninety percent of nonhyperketonemia cases showed a milk fat C18:1 cis-9-to-C15:0 ratio of 40 or lower, whereas 70% of cows suffering from hyperketonemia showed milk fat C18:1 cis-9-to-C15:0 ratios exceeding 40. Additionally, cows with a milk fat ratio C18:1 cis-9-to-C15:0 of at least 45 in wk 2 after parturition had about 50% chance to encounter blood plasma BHBA values of 1.2mmol/L or more during the first 8 wk of lactation. Of the cows not suffering from hyperketonemia during the first 2 mo of lactation, only 9% exceeded this wk 2 threshold. Practical implementation requires routine analysis of both milk fatty acids, which currently is lacking for C15:0. The inclusion of other variables, such as test-day information and a more frequent sampling protocol should be considered to further improve diagnostic performance of this biomarker.
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Affiliation(s)
- S Jorjong
- Laboratory for Animal Nutrition and Animal Product Quality, Ghent University, Proefhoevestraat 10, 9090 Melle, Belgium
| | - A T M van Knegsel
- Adaptation Physiology Group, Department of Animal Science, Wageningen University, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - J Verwaeren
- KERMIT, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - R M Bruckmaier
- Veterinary Physiology, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109ª, CH-3001 Bern, Switzerland
| | - B De Baets
- KERMIT, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - B Kemp
- Adaptation Physiology Group, Department of Animal Science, Wageningen University, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - V Fievez
- Laboratory for Animal Nutrition and Animal Product Quality, Ghent University, Proefhoevestraat 10, 9090 Melle, Belgium.
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Gonnelli G, Stock M, Verwaeren J, Maddelein D, De Baets B, Martens L, Degroeve S. A Decoy-Free Approach to the Identification of Peptides. J Proteome Res 2015; 14:1792-8. [DOI: 10.1021/pr501164r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giulia Gonnelli
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Michiel Stock
- Department
of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jan Verwaeren
- Department
of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Davy Maddelein
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Bernard De Baets
- Department
of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Sven Degroeve
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
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Sader M, Verwaeren J, Ioannidis AG, Vanderroost M, Devlieghere F, De Baets B. PREDICTING CONSUMER ACCEPTANCE OF PACKAGED MEAT USING L1-REGULARIZED ORDINAL REGRESSION. Commun Agric Appl Biol Sci 2015; 80:123-127. [PMID: 26630766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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26
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Jorjong S, van Knegsel A, Verwaeren J, Lahoz M, Bruckmaier R, De Baets B, Kemp B, Fievez V. Milk fatty acids as possible biomarkers to early diagnose elevated concentrations of blood plasma nonesterified fatty acids in dairy cows. J Dairy Sci 2014; 97:7054-64. [DOI: 10.3168/jds.2014-8039] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/05/2014] [Indexed: 01/23/2023]
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27
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