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Pala M, Castelein MG, Dewaele C, Roelants SLKW, Soetaert WK, Stevens CV. Tuning the antimicrobial activity of microbial glycolipid biosurfactants through chemical modification. Front Bioeng Biotechnol 2024; 12:1347185. [PMID: 38419728 PMCID: PMC10900251 DOI: 10.3389/fbioe.2024.1347185] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Sophorolipids, glycolipid biosurfactants derived from microorganisms such as Starmerella bombicola, possess distinctive surface-active and bioactive properties, holding potential applications in cosmetics, pharmaceuticals and bioremediation. However, the limited structural variability in wild-type sophorolipids restricts their properties and applications. To address this, metabolic engineering efforts have allowed to create a portfolio of molecules. In this study, we went one step further by chemically modifying microbially produced sophorosides, produced by an engineered S. bombicola. Twenty-four new sophoroside derivatives were synthesized, including sophoroside amines with varying alkyl chain lengths (ethyl to octadecyl) on the nitrogen atom and their corresponding quaternary ammonium salts. Additionally, six different microbially produced glycolipid biosurfactants were hydrogenated to achieve fully saturated lipid tails. These derivatives, along with microbially produced glycolipids and three benchmark biosurfactants (di-rhamnolipids, alkyl polyglucosides, cocamidopropyl betaine), were assessed for antimicrobial activity against bacteria (Bacillus subtilis, Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Pseudomonas aeruginosa) and yeast (Candida albicans). Results indicated that microbially produced glycolipids, such as bola sophorosides, acidic sophorolipids and acidic glucolipids exhibit selective antimicrobial activity against the test organisms. Conversely, lactonic sophorolipids, sophoroside amines and quaternary ammonium salts display a broad antimicrobial activity. N-octyl, N-dodecyl and N-octadecyl derivatives exhibit the lowest minimal inhibitory concentrations, ranging from 0.014 to 20.0 mg mL-1. This study demonstrates the potential synergy of thoughtful biotechnology and targeted chemistry to precisely tailor glycolipid biosurfactants to meet specific requirements across applications.
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Affiliation(s)
- Melike Pala
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Martijn G. Castelein
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Camille Dewaele
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sophie L. K. W. Roelants
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Bio Base Europe Pilot Plant (BBEPP), Ghent, Belgium
| | - Wim K. Soetaert
- Department of Biotechnology, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Bio Base Europe Pilot Plant (BBEPP), Ghent, Belgium
| | - Christian V. Stevens
- SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Chai YC, To SK, Simorgh S, Zaunz S, Zhu Y, Ahuja K, Lemaitre A, Ramezankhani R, van der Veer BK, Wierda K, Verhulst S, van Grunsven LA, Pasque V, Verfaillie C. Spatially Self-Organized Three-Dimensional Neural Concentroid as a Novel Reductionist Humanized Model to Study Neurovascular Development. Adv Sci (Weinh) 2024; 11:e2304421. [PMID: 38037510 PMCID: PMC10837345 DOI: 10.1002/advs.202304421] [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] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/15/2023] [Indexed: 12/02/2023]
Abstract
Although human pluripotent stem cell (PSC)-derived brain organoids have enabled researchers to gain insight into human brain development and disease, these organoids contain solely ectodermal cells and are not vascularized as occurs during brain development. Here it is created less complex and more homogenous large neural constructs starting from PSC-derived neuroprogenitor cells (NPC), by fusing small NPC spheroids into so-called concentroids. Such concentroids consisted of a pro-angiogenic core, containing neuronal and outer radial glia cells, surrounded by an astroglia-dense outer layer. Incorporating PSC-derived endothelial cells (EC) around and/or in the concentroids promoted vascularization, accompanied by differential outgrowth and differentiation of neuronal and astroglia cells, as well as the development of ectodermal-derived pericyte-like mural cells co-localizing with EC networks. Single nucleus transcriptomic analysis revealed an enhanced neural cell subtype maturation and diversity in EC-containing concentroids, which better resemble the fetal human brain compared to classical organoids or NPC-only concentroids. This PSC-derived "vascularized" concentroid brain model will facilitate the study of neurovascular/blood-brain barrier development, neural cell migration, and the development of effective in vitro vascularization strategies of brain mimics.
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Affiliation(s)
- Yoke Chin Chai
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - San Kit To
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Susan Simorgh
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Samantha Zaunz
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - YingLi Zhu
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Karan Ahuja
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Alix Lemaitre
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Roya Ramezankhani
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Bernard K. van der Veer
- Laboratory for Stem Cell and Developmental EpigeneticsDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Keimpe Wierda
- Electrophysiology Expert UnitVIB‐KU Leuven Center for Brain & Disease ResearchLeuven3000Belgium
| | - Stefaan Verhulst
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Leo A. van Grunsven
- Liver Cell Biology Research GroupVrije Universiteit Brussel (VUB)Brussels1090Belgium
| | - Vincent Pasque
- Stem Cell Institute LeuvenDepartment of Development and RegenerationLeuven Institute for Single Cell Omics (LISCO)KU Leuven, O&N4, Herestraat 49Leuven3000Belgium
| | - Catherine Verfaillie
- Stem Cell Institute LeuvenDepartment of Development and RegenerationKU Leuven, O&N4, Herestraat 49Leuven3000Belgium
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Van Gerrewey T, Navarrete O, Vandecruys M, Perneel M, Boon N, Geelen D. Bacterially enhanced plant-growing media for controlled environment agriculture. Microb Biotechnol 2024; 17:e14422. [PMID: 38380980 PMCID: PMC10880579 DOI: 10.1111/1751-7915.14422] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/19/2024] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
Microbe-plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant-growing medium determine the root-associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant-growing media composition and bacterial community inoculation on the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant-growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1-5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root-associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root-associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root-associated bacterial communities independently from the plant-growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant-growing media raw material selection and bacterial community inoculation in shaping root-associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant-growing media to promote plant growth in controlled environment agriculture.
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Affiliation(s)
- Thijs Van Gerrewey
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Urban Crop Solutions BVBAWaregemBelgium
- Agaris Belgium NVGentBelgium
| | | | | | - Maaike Perneel
- Cropfit, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
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Claeys H, Neyrinck E, Dumoulin L, Pharazyn A, Verstichele A, Pauwels L, Nuccio ML, Van Ex F. Coordinated gene upregulation in maize through CRISPR/Cas-mediated enhancer insertion. Plant Biotechnol J 2024; 22:16-18. [PMID: 37861059 PMCID: PMC10753999 DOI: 10.1111/pbi.14191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Affiliation(s)
| | | | | | | | | | - Laurens Pauwels
- Ghent UniversityDepartment of Plant Biotechnology and BioinformaticsGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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Al-Ahmad O, Ourak M, Vlekken J, Lindner E, Vander Poorten E. Three-dimensional catheter tip force sensing using multi-core fiber Bragg gratings. Front Robot AI 2023; 10:1154494. [PMID: 36968129 PMCID: PMC10031093 DOI: 10.3389/frobt.2023.1154494] [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: 01/30/2023] [Accepted: 02/21/2023] [Indexed: 03/11/2023] Open
Abstract
Awareness of catheter tip interaction forces is a crucial aspect during cardiac ablation procedures. The most important contact forces are the ones that originate between the catheter tip and the beating cardiac tissue. Clinical studies have shown that effective ablation occurs when contact forces are in the proximity of 0.2 N. Lower contact forces lead to ineffective ablation, while higher contact forces may result in complications such as cardiac perforation. Accurate and high resolution force sensing is therefore indispensable in such critical situations. Accordingly, this work presents the development of a unique and novel catheter tip force sensor utilizing a multi-core fiber with inscribed fiber Bragg gratings. A customizable helical compression spring is designed to serve as the flexural component relaying external forces to the multi-core fiber. The limited number of components, simple construction, and compact nature of the sensor makes it an appealing solution towards clinical translation. An elaborated approach is proposed for the design and dimensioning of the necessary sensor components. The approach also presents a unique method to decouple longitudinal and lateral force measurements. A force sensor prototype and a dedicated calibration setup are developed to experimentally validate the theoretical performance. Results show that the proposed force sensor exhibits 7.4 mN longitudinal resolution, 0.8 mN lateral resolution, 0.72 mN mean longitudinal error, 0.96 mN mean lateral error, a high repeatability, and excellent decoupling between longitudinal and lateral forces.
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Affiliation(s)
- Omar Al-Ahmad
- Robot-Assisted Surgery (RAS) group, Department of Mechanical Engineering, KU Leuven University, Leuven, Belgium
- FBGS International NV, Geel, Belgium
- *Correspondence: Omar Al-Ahmad ,
| | - Mouloud Ourak
- Robot-Assisted Surgery (RAS) group, Department of Mechanical Engineering, KU Leuven University, Leuven, Belgium
| | | | | | - Emmanuel Vander Poorten
- Robot-Assisted Surgery (RAS) group, Department of Mechanical Engineering, KU Leuven University, Leuven, Belgium
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Bharadwaj PS, Sanchez L, Li D, Enyi D, Van de Poel B, Chang C. The plant hormone ethylene promotes abiotic stress tolerance in the liverwort Marchantia polymorpha. Front Plant Sci 2022; 13:998267. [PMID: 36340412 PMCID: PMC9632724 DOI: 10.3389/fpls.2022.998267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/29/2022] [Indexed: 06/13/2023]
Abstract
Plants are often faced with an array of adverse environmental conditions and must respond appropriately to grow and develop. In angiosperms, the plant hormone ethylene is known to play a protective role in responses to abiotic stress. Here we investigated whether ethylene mediates resistance to abiotic stress in the liverwort Marchantia polymorpha, one of the most distant land plant relatives of angiosperms. Using existing M. polymorpha knockout mutants of Mpein3, and Mpctr1, two genes in the ethylene signaling pathway, we examined responses to heat, salinity, nutrient deficiency, and continuous far-red light. The Mpein3 and Mpctr1 mutants were previously shown to confer ethylene insensitivity and constitutive ethylene responses, respectively. Using mild or sub-lethal doses of each stress treatment, we found that Mpctr1 mutants displayed stress resilience similar to or greater than the wild type. In contrast, Mpein3 mutants showed less resilience than the wild type. Consistent with ethylene being a stress hormone, we demonstrated that ethylene production is enhanced by each stress treatment. These results suggest that ethylene plays a role in protecting against abiotic stress in M. polymorpha, and that ethylene has likely been conserved as a stress hormone since before the evolutionary divergence of bryophytes from the land plant lineage approximately 450 Ma.
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Affiliation(s)
- Priyanka S. Bharadwaj
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Lizbeth Sanchez
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Dongdong Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | - Divine Enyi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
- KU Leuven Plant Institute, University of Leuven, Leuven, Belgium
| | - Caren Chang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
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Proesmans VLJ, Vermeir I, de Backer C, Geuens M. Food Media and Dietary Behavior in a Belgian Adult Sample: How Obtaining Information From Food Media Sources Associates With Dietary Behavior. Int J Public Health 2022; 67:1604627. [PMID: 35677192 PMCID: PMC9169530 DOI: 10.3389/ijph.2022.1604627] [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] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: We aim to relate Flemish adults’ main food information sources (e.g., celebrity chefs, experts) with their dietary behavior. Methods: A cross-sectional online survey among 1115 Flemish adults who regularly cook, measured the food information sources the respondents used to obtain recipes, their dietary intake and dietary restrictions. Ordinal and logistic regression were used to investigate the relation between food media, dietary intake and dietary restrictions. Results: Celebrity chefs were mentioned most often (37%) as main food information source, followed by family and acquaintances (21%) and lifestyle gurus (12%). Using lifestyle gurus as a source of dietary information is associated with more dietary restrictions and a higher intake frequency of plant-based food groups, whereas using celebrity chefs or experts is associated with a different (but less unequivocal vegetarian or healthy) dietary intake. Conclusion: Media icons like lifestyle gurus and celebrity chefs appear to be among people’s main sources of food information. There is a significant association between using them as a source of food information and dietary behavior. Further research on the influence of media on diet is required.
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Affiliation(s)
- Viktor Lowie Juliaan Proesmans
- Department of Marketing Innovation and Organisation, Ghent University, Ghent, Belgium
- *Correspondence: Viktor Lowie Juliaan Proesmans,
| | - Iris Vermeir
- Department of Marketing Innovation and Organisation, Ghent University, Ghent, Belgium
| | - Charlotte de Backer
- Department of Communication Studies, University of Antwerp, Antwerp, Belgium
| | - Maggie Geuens
- Department of Marketing Innovation and Organisation, Ghent University, Ghent, Belgium
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Locy H, Verhulst S, Cools W, Waelput W, Brock S, Cras L, Schiettecatte A, Jonckheere J, van Grunsven LA, Vanhoeij M, Thielemans K, Breckpot K. Assessing Tumor-Infiltrating Lymphocytes in Breast Cancer: A Proposal for Combining Immunohistochemistry and Gene Expression Analysis to Refine Scoring. Front Immunol 2022; 13:794175. [PMID: 35222378 PMCID: PMC8876933 DOI: 10.3389/fimmu.2022.794175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/13/2021] [Accepted: 01/06/2022] [Indexed: 12/12/2022] Open
Abstract
Scoring of tumor-infiltrating lymphocytes (TILs) in breast cancer specimens has gained increasing attention, as TILs have prognostic and predictive value in HER2+ and triple-negative breast cancer. We evaluated the intra- and interrater variability when scoring TILs by visual inspection of hematoxylin and eosin-stained tissue sections. We further addressed whether immunohistochemical staining of these sections for immune cell surface markers CD45, CD3, CD4, and CD8 and combination with nanoString nCounter® gene expression analysis could refine TIL scoring. Formalin-fixed paraffin-embedded and fresh-frozen core needle biopsies of 12 female and treatment-naive breast cancer patients were included. Scoring of TILs was performed twice by three independent pathologists with a washout period of 3 days. Increasing intra- and interrater variability was observed with higher TIL numbers. The highest reproducibility was observed on tissue sections stained for CD3 and CD8. The latter TIL scores correlated well with the TIL scores obtained through nanoString nCounter® gene expression analysis. Gene expression analysis also revealed 104 and 62 genes that are positively and negatively related to both TIL scores. In conclusion, integration of immunohistochemistry and gene expression analysis is a valuable strategy to refine TIL scoring in breast tumors.
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Affiliation(s)
- Hanne Locy
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences (BMWE), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- *Correspondence: Hanne Locy, ; Karine Breckpot,
| | | | - Wilfried Cools
- Interfaculty Center Data processing and Statistics, VUB, Brussels, Belgium
| | - Wim Waelput
- Department of Anatomo-Pathology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Stefanie Brock
- Department of Anatomo-Pathology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Louise Cras
- Department of Anatomo-Pathology, Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | | | | | | | | | - Kris Thielemans
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences (BMWE), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Karine Breckpot
- Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences (BMWE), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- *Correspondence: Hanne Locy, ; Karine Breckpot,
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Nijs M, Smets T, Waelkens E, De Moor B. A mathematical comparison of non-negative matrix factorization related methods with practical implications for the analysis of mass spectrometry imaging data. Rapid Commun Mass Spectrom 2021; 35:e9181. [PMID: 34374141 PMCID: PMC9285509 DOI: 10.1002/rcm.9181] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 05/25/2023]
Abstract
RATIONALE Non-negative matrix factorization (NMF) has been used extensively for the analysis of mass spectrometry imaging (MSI) data, visualizing simultaneously the spatial and spectral distributions present in a slice of tissue. The statistical framework offers two related NMF methods: probabilistic latent semantic analysis (PLSA) and latent Dirichlet allocation (LDA), which is a generative model. This work offers a mathematical comparison between NMF, PLSA, and LDA, and includes a detailed evaluation of Kullback-Leibler NMF (KL-NMF) for MSI for the first time. We will inspect the results for MSI data analysis as these different mathematical approaches impose different characteristics on the data and the resulting decomposition. METHODS The four methods (NMF, KL-NMF, PLSA, and LDA) are compared on seven different samples: three originated from mice pancreas and four from human-lymph-node tissues, all obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). RESULTS Where matrix factorization methods are often used for the analysis of MSI data, we find that each method has different implications on the exactness and interpretability of the results. We have discovered promising results using KL-NMF, which has only rarely been used for MSI so far, improving both NMF and PLSA, and have shown that the hitherto stated equivalent KL-NMF and PLSA algorithms do differ in the case of MSI data analysis. LDA, assumed to be the better method in the field of text mining, is shown to be outperformed by PLSA in the setting of MALDI-MSI. Additionally, the molecular results of the human-lymph-node data have been thoroughly analyzed for better assessment of the methods under investigation. CONCLUSIONS We present an in-depth comparison of multiple NMF-related factorization methods for MSI. We aim to provide fellow researchers in the field of MSI a clear understanding of the mathematical implications using each of these analytical techniques, which might affect the exactness and interpretation of the results.
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Affiliation(s)
- Melanie Nijs
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT)KU LeuvenLeuvenBelgium
| | - Tina Smets
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT)KU LeuvenLeuvenBelgium
| | - Etienne Waelkens
- Department of Cellular and Molecular MedicineKU Leuven Campus Gasthuisberg O&N 2LeuvenBelgium
| | - Bart De Moor
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT)KU LeuvenLeuvenBelgium
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Gibney R, Ferraris E. Bioprinting of Collagen Type I and II via Aerosol Jet Printing for the Replication of Dense Collagenous Tissues. Front Bioeng Biotechnol 2021; 9:786945. [PMID: 34805132 PMCID: PMC8602098 DOI: 10.3389/fbioe.2021.786945] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Collagen has grown increasingly present in bioprinting, however collagen bioprinting has mostly been limited to the extrusion printing of collagen type I to form weak collagen hydrogels. While these weak collagen hydrogels have their applications, synthetic polymers are often required to reinforce gel-laden constructs that aim to replicate dense collagenous tissues found in vivo. In this study, aerosol jet printing (AJP) was used to print and process collagen type I and II into dense constructs with a greater capacity to replicate the dense collagenous ECM found in connective tissues. Collagen type I and II was isolated from animal tissues to form solutions for printing. Collagen type I and II constructs were printed with 576 layers and measured to have average effective elastic moduli of 241.3 ± 94.3 and 196.6 ± 86.0 kPa (±SD), respectively, without any chemical modification. Collagen type II solutions were measured to be less viscous than type I and both collagen type I and II exhibited a drop in viscosity due to AJP. Circular dichroism and SDS-PAGE showed collagen type I to be more vulnerable to structural changes due to the stresses of the aerosol formation step of aerosol jet printing while the collagen type II triple helix was largely unaffected. SEM illustrated that distinct layers remained in the aerosol jet print constructs. The results show that aerosol jet printing should be considered an effective way to process collagen type I and II into stiff dense constructs with suitable mechanical properties for the replication of dense collagenous connective tissues.
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Affiliation(s)
- Rory Gibney
- Department of Mechanical Engineering, KU Leuven Campus De Nayer, Leuven, Belgium
- Department of Materials Engineering, KU Leuven, Leuven, Belgium
| | - Eleonora Ferraris
- Department of Mechanical Engineering, KU Leuven Campus De Nayer, Leuven, Belgium
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